Gen5 User Guide
Gen5™ & Gen5 Secure
User's Guide
Microplate Data Collection & Analysis Software
BioTek® Instruments, Inc.
July 2007
© 2006-2007
PN 5321001
Revision D
Contents | i
Contents
Notices ................................................................................ vii
About this Guide ................................................................... viii
Chapter 1: Initial Setup............................................................. 1
Set up Gen5......................................................................... 2
Set up Gen5 Secure .............................................................. 8
Set up Gen5 Reader Control................................................... 20
Connecting a Reader ............................................................. 21
Setting up the Clarity Luminometer......................................... 23
Setting up Preferences .......................................................... 24
Chapter 2: Getting Started ........................................................ 27
Getting Started..................................................................... 28
Gen5's Workspace ................................................................ 30
About the Plate Workspace .................................................... 32
Introducing the Protocol Workspace ........................................ 33
Gen5's Wizard ...................................................................... 35
Buttons and Icons Guide........................................................ 36
About the Menu Tree............................................................. 38
Tips for KC4 Users ................................................................ 39
Getting Technical Assistance .................................................. 41
Chapter 3: Essential Concepts ................................................... 43
Essential Concepts ................................................................ 44
Experiment vs. Protocol ......................................................... 45
About File Storage ................................................................ 47
Best Practices....................................................................... 48
Chapter 4: Assay Examples ....................................................... 51
Sample Protocols and Experiments ......................................... 52
How do I set up my assay? .................................................... 54
Quantitative ELISA Example ................................................... 55
Subtracting Blank Plate Reads ................................................ 58
Gen5 User Guide
ii|
Pathlength Correction Example ............................................... 60
Dual Wavelength Absorbance Endpoint .................................... 62
Basic Spectrum Analysis ........................................................ 64
Protein Quantification: Endpoint Absorbance ............................ 66
Basic Fluorescence Assay Example .......................................... 69
Kinetic Fluorescence Assay Example........................................ 71
Fluorescence Assay with Injection........................................... 74
Fluorescence Area Scan Example ............................................ 77
Fluorescence Polarization Example .......................................... 79
Basic Luminescence Glow Assay Example ................................ 81
Luminescence Flash Assay with Injection ................................. 82
Max Binding Determination/Competitive Assay ......................... 83
Toxicity/Cytotoxicity Assay .................................................... 86
Endotoxin Test ..................................................................... 89
ß-Galactosidase .................................................................... 92
Dispensing Reagent .............................................................. 94
Fast Kinetics with Injection for Absorbance .............................. 97
Chapter 5: Basic Tasks .............................................................. 99
Quick Read .......................................................................... 100
How to Create a Standard Curve............................................. 101
Viewing Results .................................................................... 102
Printing Results .................................................................... 104
Quick Export ........................................................................ 105
Quick Output Options ............................................................ 106
Reader System Test .............................................................. 108
Setting up an Experiment ...................................................... 109
Read a Plate......................................................................... 110
Acquiring Data ..................................................................... 110
Chapter 6: Designing a Protocol................................................ 111
Design a Protocol.................................................................. 112
Defining the Reading Procedure .............................................. 113
Modify a Protocol .................................................................. 114
Defining the Plate Layout ....................................................... 115
BioTek Instruments, Inc.
Contents | iii
Setting up Data Reduction ..................................................... 116
Customizing Data Views, Reports, and Exports ......................... 117
Reporting Results ................................................................. 118
Using the Default Protocol...................................................... 119
Default Protocol Setup........................................................... 120
Chapter 7: Defining the Procedure ............................................ 121
Defining the Reading Parameters ............................................ 122
Validate the Procedure .......................................................... 125
Read Step............................................................................ 127
Procedure Steps: Reading-Related Activities ............................ 138
Chapter 8 : Fluorescence and Luminescence ............................. 149
Fluorescence Analysis............................................................ 150
Luminescence Analysis .......................................................... 153
Time-Resolved Fluorescence Analysis ...................................... 154
Fluorescence Polarization ....................................................... 155
Filter Set Options.................................................................. 156
PMT Sensitivity ..................................................................... 158
Measurement Options ........................................................... 162
Synchronized Modes ............................................................. 164
Troubleshooting Fluorescence/Luminescence............................ 169
Filters and Mirrors................................................................. 173
Multi-Detection/Multi-Mode Protocols ...................................... 182
Features and Restrictions of Kinetic Multi-Detection Protocols..... 183
Chapter 9: Kinetic Analysis ....................................................... 185
How to set up a Kinetic Analysis ............................................. 186
Kinetic Minimum Interval ....................................................... 188
Discontinuous Kinetic Procedure ............................................. 189
Well Zoom ........................................................................... 191
Well Analysis Calculation Types .............................................. 196
Chapter 10: Scanning Analysis Options ..................................... 199
Area Scan ............................................................................ 200
Linear Scan.......................................................................... 202
Gen5 User Guide
iv|
Spectrum Scan ..................................................................... 203
Chapter 11: Multi-Plate Protocols ............................................. 205
Designing a Multi-Plate Protocol.............................................. 206
About Multi-Plate Protocols .................................................... 207
Running a Multi-Plate Protocol ................................................ 209
Calibrator-Plate Protocols....................................................... 212
Multi-Plate Assay Protocols .................................................... 215
Processing a Batch of Samples ............................................... 218
Chapter 12: Preparing Plates .................................................... 219
Defining the Plate Layout ....................................................... 221
Assigning Well IDs ................................................................ 223
Custom Plate Layout ............................................................. 229
Plate Information.................................................................. 230
Runtime Prompts .................................................................. 231
Assigning Sample IDs............................................................ 235
Chapter 13: Data Reduction Options ......................................... 245
Setting up Data Reduction ..................................................... 246
Define Transformations ......................................................... 249
Plotting a Curve.................................................................... 261
Curve Fit ............................................................................. 264
Multiple Curves..................................................................... 282
Troubleshooting Curve Fits..................................................... 288
Kinetic Analysis Options......................................................... 289
Define Cutoffs ...................................................................... 296
Validation ............................................................................ 301
Fluorescence Polarization ....................................................... 307
Chapter 14: Viewing Results ..................................................... 309
Viewing Results .................................................................... 310
Data Views .......................................................................... 315
Data Set Naming Convention ................................................. 316
Symbols and Special Notations ............................................... 317
Data Points Reference ........................................................... 319
BioTek Instruments, Inc.
Contents | v
Gen5's Tables....................................................................... 320
Modify/Customize Views/Data ................................................ 323
Chapter 15: Reporting Results .................................................. 333
Building Reports ................................................................... 334
How to create and customize a report ..................................... 336
Customizing Reports ............................................................. 338
Reporting Well Analysis Results .............................................. 340
Edit Report Items ................................................................. 344
Fields and Field Groups.......................................................... 346
Chapter 16: Exporting Results .................................................. 351
Exporting Results.................................................................. 352
Quick Export ........................................................................ 354
Right-Click Menu Options ....................................................... 356
Export to File (File Export Builder) .......................................... 358
Power Export........................................................................ 362
Chapter 17: Managing Files ....................................................... 369
Managing Files ..................................................................... 370
File Storage ......................................................................... 371
Database Management .......................................................... 372
Database Errors.................................................................... 379
Chapter 18: Security ................................................................. 383
Security............................................................................... 384
Changing Your Password........................................................ 385
Login/Password Controls........................................................ 386
FDA's 21 CFR Part 11 ............................................................ 388
Signing Protocols .................................................................. 389
Audit Trail............................................................................ 391
User Accounts ...................................................................... 398
Chapter 19: Reader Control....................................................... 405
When you have Two Readers ................................................. 406
Reader Configuration ............................................................ 408
Controlling the Clarity ........................................................... 409
Gen5 User Guide
vi|
Reader Settings .................................................................... 413
Reader Control Panel............................................................. 417
Testing the Reader................................................................ 423
Chapter 20: System Management.............................................. 425
System Requirements ........................................................... 426
Gen5's System Administrator ................................................. 427
Changing Your Password........................................................ 428
Changing Your Startup Preferences ......................................... 429
Customize the Toolbar........................................................... 430
Plate Types Database ............................................................ 431
Chapter 21: Troubleshooting..................................................... 435
Troubleshooting.................................................................... 436
Communication Errors: Reader to Computer ............................ 437
Error Messages..................................................................... 438
Calculation Warnings............................................................. 439
Restoring Optimal Performance .............................................. 442
System Administrator's Password ........................................... 442
Index ........................................................................................ 443
BioTek Instruments, Inc.
Notices | vii
Notices
BioTek Instruments, Inc.
Highland Park, P.O. Box 998
Winooski, Vermont 05404-0998 USA
All Rights Reserved
© 2007, BioTek® Instruments, Incorporated. No part of this publication may be
reproduced, transcribed, or transmitted in any form, or by any means electronic
or mechanical, including photocopying and recording, for any purpose other
than the purchaser’s use without written permission of BioTek Instruments,
Inc.
Trademarks
BioTek® is a registered trademark, and Gen5™, Synergy™ 4, Synergy™ 2,
Synergy™ HT, and other instrument logos are trademarks of BioTek
Instruments, Inc. Microsoft®, Windows®, and the Windows logo are registered
trademarks of Microsoft Corporation in the United States and other countries.
All other trademarks are the property of their respective holders.
Restrictions and Liabilities
Information in this document is subject to change and does not represent a
commitment by BioTek Instruments, Inc. Changes made to the information in
this document will be incorporated in new editions of the publication. No
responsibility is assumed by BioTek for the use or reliability of software or
equipment that is not supplied by BioTek or its affiliated dealers.
Gen5 User Guide
viii|
About this Guide
This user guide is intended for licensed users of Gen5™ and Gen5™ Secure, BioTek’s
microplate data collection and analysis software.
Document Conventions
Special or important information uses this format to call your attention
to it.
Tips or suggestions, for example, to improve performance, are shown in this
manner, following a light bulb graphic.
Navigation instructions for the current topic are presented in this format
Document History
Revision
Date
Changes
A
May 2006
Initial Release
C
March 2007
D
June 2007
Added description of new features and
enhancements released in Gen5 version 1.02
B
Sept 2006
New features related to the Synergy™ 2 reader and
Filter Wheel Library
New features related to the Synergy™ 4 reader and
enhancements released in Gen5 version 1.04
BioTek Instruments, Inc.
Chapter 1
Initial Setup
This section provides instructions and suggestions for setting up
Gen5 to perform most efficiently and effectively in your lab.
Setting up Gen5 ...................................................................... 2
Setting up Gen5 Secure ............................................................ 8
Setting up Gen5 Reader Control................................................. 20
Connecting a Reader ................................................................ 21
Setting up Preferences.............................................................. 24
2| Chapter 1: Initial Setup
Set up Gen5
For Gen5™ Only
Gen5™ fulfills the reader control and analytical needs for a wide range of laboratory
settings. The degree to which you follow the recommendations provided here depends
on the needs of your organization.
Recommended tasks to perform:
1.
2.
Designate a System Administrator
Install Gen5 on the Administrator's computer
Installation instructions are included in the Getting Started Guide
shipped with the CD.
3.
4.
5.
6.
7.
8.
Change the System Administrator's Password (see below)
Determine the optimal way to store Gen5's protocol and experiment files:
File Storage (page 4)
 Organize the Database (page 10) or your Windows® file structure
Install Gen5 for other users and Connect a Reader (page 21) to each
computer
If applicable, direct each user's Database Configuration (page 12) to point to
the correct shared database
Set User Preferences (page 24)
Learn how to use Gen5:0.
 Check out the tutorials (animated demos) in the Help system: Select
Help>Tutorials
 Alternatively, begin by performing the Learning Exercises in the Getting
Started Guide.
BioTek Instruments, Inc.
Set up Gen5 | 3
Gen5's System Administrator
For all levels of Gen5 except Gen5 Secure
It is necessary to login as the System Administrator to change User Permissions and
Database Configuration, and to access any features which are denied as Users
Permissions
How to change the System Administrator's password:
This function is only available to the System Administrator. You
must login, System> Administrator LogIn, as the Administrator to
access these controls
1.
Select System> User Setup, and select the Administrator tab
3.
Enter the new password in both the New and Confirm password fields
2.
4.
Enter the current password in the Current Password field. Gen5 ships with
the password set to "admin."
Click OK.0
How to maintain Users Permissions
Except in Gen5 Secure, access to Gen5's functions, like reading a plate, modifying a
protocol, and masking values, is defined equally for all users except the System
Administrator, who has all "permissions." Learn more on page 5.
Learn about Gen5's Databases
You can opt to save Gen5's protocol and experiment files in Gen5 SharedDB:
 About Gen5 Databases (refer to the Managing Files chapter)
 Organize Your Database Files (page 10)
Gen5 User Guide
4| Chapter 1: Initial Setup
File Storage
System> Preferences> File Storage Mode
Use this control to select a method for storing protocol and experiment files.
Attention Gen5 Secure users: To ensure 21 CFR Part 11 compliance
use the Gen5 Database for file storage
About File Storage
Gen5 provides two methods for storing protocol and experiment files. You can use the
secure, shared-access database provided with Gen5, which is required for compliance
with the FDA's 21 CFR Part 11 regulation on electronic records submission.
Alternatively, you can use the file system provided with the Windows® operating
system on a local PC or network (LAN). If your organization is unconcerned with FDA
regulations, the choice is a matter of preference. However, one advantage to using the
Gen5 Database is its ability to recover from a system crash. New and modified files are
saved as Temporary Files in the database and can be used to recover information that
wasn't saved before a system failure.
Clarity™ Luminometer protocol files, with a .bpf extension, cannot be
stored in Gen5’s shared database. They are typically stored in the
C:\Program Files\BioTek\Clarity\protocols folder.
How to
Select an option for storing Experiment and Protocol files:
 Gen5 Database: all actions related to managing and maintaining files, like
File>Open, File>Save, Browse..., and so on, will occur in Gen5's SharedDB.
 Windows File System: Gen5 will not control the management of files. Actions
related to managing and manipulating files will be determined by the
Windows operating system, e.g. you can use Windows® Explorer. Generally
during file management activities like File>Open, Windows begins at the last
directory and folder used.
AutoSave Feature: Gen5 offers this feature to give you additional
control over the storage of saved files.
BioTek Instruments, Inc.
Set up Gen5 | 5
User Setup
For all levels of Gen5 except Gen5 Secure
System> User Setup
Gen5 User Permissions
Only the Gen5 Secure product level offers the multiple-user login and password
controls required to comply with the FDA's electronic-records submission directive.
This page describes the more limited security options provided in other Gen5
products.
About Gen5 User Accounts
There are only two types of Users in Gen5: Administrator and User, i.e. System
Administrator and non-administrator. Neither account be deleted
You Can:
Change the
Administrator's password
Change the Permissions
for User
Maintain/store Gen5 files
in a secure database
Select a Startup option
and Protocol and
Experiment Folders for
users
Gen5 User Guide
You Cannot:
Login as a User; only the System
Administrator requires login
Change the Permissions for
Administrator: all rights and privileges
are already given
Keep track of which user is responsible
for Gen5 activities
Turn on/off Audit Trail notification.
Events for which users are invited to add
comments to the change log/audit trail
are fixed by Gen5
6| Chapter 1: Initial Setup
Permissions
Prerequisite:
To change the User Permissions, you must login, System>Administrator LogIn, as
the System Administrator
Function
Add a New Plate: Access to menu options and toolbar buttons for Adding
one or multiple plates to an experiment
Delete a plate: Access to Plate menu option to Delete, i.e. remove the
plate information and all data associated with the plate (if any) from an
experiment
Mask/Unmask values: Access to Mask button in the Plate View to mask
the values for selected wells. Masked wells are ignored in data reduction and
curve plotting
Edit values: Access to Edit button in the Plate View to change the values of
selected wells
Re-read plate: Access to Read button after plate has been read to
overwrite the current measurement results with newly acquired
measurements
Simulate Read: Access to Simulate option of the Plate Read dialog to let
Gen5 simulate a reading instead of actually reading the plate. (Useful for
Gen5 training/tutorials.)
Read from File (import): Access to Read From File option of the Plate
Reading dialog to acquire/import reading data from a text file
Enter Manually (raw data): Access to Enter Manually option of the Plate
Reading dialog to manually enter (type in) reading data instead of actually
reading a plate
System Controls
This table describes the capability each Permission gives users.
Function
Manage and Maintain Systems: This switch gives or denies access to the
next five items. You can override it by individually assigning access to the
permissions
Edit Default Protocol: Access to define or modify the Default Protocol
Settings
Edit file storage mode: Access to menu option System>Preferences>File
Storage to alter the option: database or Windows® file system
BioTek Instruments, Inc.
Set up Gen5 | 7
Function
Edit Read from File options:
Manage and Maintain Devices: This switch gives or denies access to the
next four related permissions. You can override it by individually assigning
access to them
Define Test Plates: Access to Diagnostics options to set up and modify the
Universal Test Plate records used to conduct testing
Delete Diagnostic Test History: Ability to delete test records. All users
can view the test history, only users with this permission can delete the
records
Manage and Maintain File Storage: This switch gives or denies access to
the next seven related permissions. You can override it by individually
assigning access to them. They are only applicable when File Storage "uses
the SharedDB"
Create folder in Database: Ability to create a new folder while maintaining
database files and when saving protocol and experiment files. Users denied
this function are limited to saving files in existing database folders
Delete/Overwrite folder in Database: Ability to delete or overwrite
(Save As) folders and files from/in the database
Export file from Database: When maintaining database files, ability to use
the right-click menu to Export to Disk
Rename folder/file in Database: Ability to rename database files and
folders in the database
Move folder/file in Database: Ability to relocate folders and files within
the database
Import file to Database: Ability to import, paste from clipboard, or drag
and drop files from another location
View hidden files and folders in Database: Ability to hide files, to see
hidden files, and to reveal hidden files
Gen5 User Guide
8| Chapter 1: Initial Setup
Set up Gen5 Secure
For Gen5™ Secure Only
Follow these procedures to set up Gen5 Secure:
1.
Designate a System Administrator
3.
Organize the Database (page 10)
2.
4.
5.
6.
7.
8.
9.
Complete the System Administrator's To Do List (see below)
Review/modify Signature Reasons and other security controls (see Gen5’s
Help)
Define certain Preferences by using Gen5's Default Protocol. Each shared
database has one Default Protocol which defines the initial settings for all
newly-created protocols. (page 24)
Set up each user's Database Configuration to point to the correct shared
database, if applicable. (page 13)
Connect a reader to each user's computer (page 21)
Advise users to change their passwords (see Gen5’s Help)
Encourage users to watch the Help>Tutorials and run through the Learning
Exercises provided in the Getting Started Guide.0
System Administrator's To Do List
Also see information about the FDA’s Requirements on the next page.
Initial Setup Tasks
1.
2.
Make sure all designated computers (PCs) and BioTek readers meet the
System Requirements
Install Gen5 Secure on one computer (PC)
Installation instructions are included in the Getting Started Guide
shipped with the CD.
3.
Start Gen5 and log in as the System Administrator
5.
Copy the database: Shared.mdb to a secure network location (page 13)
4.
6.
7.
8.
Change the System Administrator’s password (page 14)
Test Database Configuration of the Shared.mdb on the network (page 13)
Create/modify User Groups, as needed, and assign User Permissions to the
Groups (page 15)
Create new user accounts and assign the users to a Group
BioTek Instruments, Inc.
Set up Gen5 Secure | 9
9.
Connect reader(s) to the PC and establish communication (page 21)
10. Repeat steps 2, 3, 6, and 8 for the remaining PCs0
Periodic/As Needed Tasks
 Customize the security features to accommodate your organization's needs
 Organize your database files
 Educate users on regulatory requirements and Gen5 best practices
 Establish and implement a procedure and schedule for record retention and
archival
 Review records, including any training/user-qualification records
Before modifying a user's account, make sure he/she is not logged into
the system. You can check the System Audit Trail to determine who is
currently logged in.
FDA's System Administrator Requirements
The FDA’s Electronic Signatures Rule (21 CFR Part 11) contains requirements that sites
must meet in order to be in compliance. The System Administrator should be
cognizant of the following:
 Administrator: The site shall select an “Administrator” who will be the person
responsible for all high-level administration of the program. This person will
control access to the program by adding new users, structuring the individual
users authority levels, and reporting to management, as appropriate, on any
unauthorized use of the program.
 Personnel Qualifications: Personnel who develop, maintain, or use electronic
records/electronic signatures shall have the education, training and experience
necessary to perform their assigned tasks.
 Written Policies: There shall be written policies which hold individuals
accountable and responsible for action initiated under their electronic
signatures, in order to deter record and signature falsification. There shall be
written revision and change control procedures to ensure that the program is
administered in compliance with the FDA’s requirements.
 Record Archiving and Deletion: The site is responsible to ensure that
archiving or other file management techniques are suitable such that electronic
records generated by the system shall be accurate and readily retrievable.
Records may be removed by deleting the entire shared database or individual
files within the database. This action may be conducted by the Administrator
or by any Power User.
 User Identity: Any person who will be authorized to use an electronic
signature will have their identity confirmed by the Administrator prior to
granting them program access. Only the genuine owner of the electronic
Gen5 User Guide
10| Chapter 1: Initial Setup
signature is allowed to access the program through their ID/password
combination. System users should be informed that accessing the program
using someone else’s login is a violation of the FDA rule.
 Password Expiration/Recall: All passwords must be checked, recalled, or
revised at an interval appropriate with the security needs of the organization.
Personnel who no longer work at the establishment shall have their program
access capabilities deactivated in a timely manner.
 Certification to FDA: The site must certify to FDA that the electronic
signatures utilized on records are intended to be as legally binding as
handwritten signatures, prior to or at the time of record submission to FDA.
The FDA rule should be consulted for details and method to be used.
 Notification of Attempted Security Breaches: The software utilizes an error
log system to notify the Administrator of log-in failure incidents that exceed
the limits they have established. The administrator is responsible to
“immediately and urgently” notify the appropriate personnel at the site if the
activity appears to be an attempt to breach security.
 Signature Representations: The administrator should be made aware that
while electronic signatures representations cannot be excised or added they can
be copied by screen copy techniques and pasted into other documents. These
modified documents cannot be re-saved in the secure program but may be
printed out as is.
Organize Your Database Files
During regular installation, Gen5 Secure installs and enables the
shared database to store experiment and protocol files. All other
levels of Gen5 must elect to use the database at System>
Preferences> File Storage
All of your file management requirements can be fulfilled using Gen5's secure
databases. You'll be most satisfied with the final structure if you spend some time
planning it up-front. In a multiple-user environment, you can set up Gen5's database
on a shared-network drive (LAN) so multiple users can access the same protocol and
experiment files, including the Default Protocol.
Multiple Databases: You can create multiple copies of the clean, installed SharedDB,
renaming them with meaningful titles for use by various projects or teams or
researchers. Within each database you can set up a consistent file structure, e.g. specific
folders for specific types of Protocols and Experiments, or a different folder for each
user. The possibilities are endless.
Backups: Performing backups on a regular schedule is highly recommended to
preserve your data. And, Gen5 provides a tool to schedule backups to occur
periodically. See below.
BioTek Instruments, Inc.
Set up Gen5 Secure | 11
 File Management Recommendations
 Put a copy of the SharedDB on a shared-network drive where all your Gen5
users can access it. Be sure to set each user's Database Configuration to point to
the correct location.
 Before moving the SharedDB to a network location, make a copy of it to use as
a template for future use:
1.
2.
3.
4.
In the default SharedDB folder, highlight the original, right-click and
select Copy
De-select the original (click elsewhere in the dialog), right-click and
select Paste
Highlight the copy, right-click and select Rename
Give the copy a unique name, like SharedDB_original.mdb.0
 Consider setting up shared databases for different projects or teams within
your organization. You can follow the steps defined above to create multiple
databases in the same folder (or directory), or you can move the unique
databases to a different network location/folder. Use Database Configuration
to point user's Gen5 sessions to the correct database.
 Regularly archive and backup the database to preserve your records. There are
numerous ways to do this, so BioTek recommends following your
organization's existing policy for securing data. For example, if you put the
shared database on the network and your network is backed up every night,
this may be sufficient. You can use Gen5's Optimize and Backup Settings to
facilitate your data-protection policy.
 Consider using Gen5's automatic Save feature to create a new, date-stamped
folder for storing experiment records. This is an especially good practice for
large labs with multiple users who run hundreds of plates per day. Gen5 will
keep all that data organized by date. Define this kind of file management
setting in the Default Protocol so it will apply to all newly-created protocols.
 Gen5 handles multiple, simultaneous users performing database management
tasks by giving precedence to the user with the greater administrative rights.
Gen5 User Guide
12| Chapter 1: Initial Setup
File Storage
System> Preferences> File Storage Mode
Use this control to select a method for storing protocol and experiment files.
Attention Gen5 Secure users: To ensure 21 CFR Part 11 compliance
use the Gen5 Database for file storage
About File Storage
Gen5 provides two methods for storing protocol and experiment files. You can use the
secure, shared-access database provided with Gen5, which is required for compliance
with the FDA's 21 CFR Part 11 regulation on electronic records submission.
Alternatively, you can use the file system provided with the Windows® operating
system on a local PC or network (LAN). If your organization is unconcerned with FDA
regulations, the choice is a matter of preference. However, one advantage to using the
Gen5 Database is its ability to recover from a system crash. New and modified files are
saved as Temporary Files in the database and can be used to recover information that
wasn't saved before a system failure.
Clarity™ Luminometer protocol files, with a .bpf extension, cannot be
stored in Gen5’s shared database. They are typically stored in the
C:\Program Files\BioTek\Clarity\protocols folder.
How to
Select an option for storing Experiment and Protocol files:
 Gen5 Database: all actions related to managing and maintaining files, like
File>Open, File>Save, Browse..., and so on, will occur in Gen5's SharedDB.
Learn About Gen5's Databases
 Windows File System: Gen5 will not control the management of files. Actions
related to managing and manipulating files will be determined by the
Windows operating system, e.g. you can use Windows® Explorer. Generally
during file management activities like File>Open, Windows begins at the last
directory and folder used.
AutoSave Feature: Gen5 offers this feature to give you additional
control over the storage of saved files.
BioTek Instruments, Inc.
Set up Gen5 Secure | 13
Database Configuration
System> Database Configuration
Prerequisite
Some features of this dialog require System Administrator privileges.
When Gen5 is installed, there are two primary databases, a shared and a local
database. They are named SharedDB.mdb and LocalDB.mdb respectively. The
LocalDB cannot be moved or renamed. The SharedDB can be moved and renamed. All
operations affecting them take place using their respective tabs, except the upgrade
utility. Learn more: About Gen5's Databases
Source
Gen5 displays the current location of the database.
 LocalDB: You cannot move or rename the LocalDB database, thus the 3-dot
button is disabled. If necessary to see the full pathname of its location, you can
click inside the text field and scroll to the right.
 SharedDB: Click the 3-dot button to view the current location of the database.
You can move, rename or copy the SharedDB database.
Test
Use the Test button to check the connection to the Gen5 database.
 Potential error messages are referenced in the Troubleshooting section above.
Move/Copy Database to Network
System> Database Configuration
Gen5 Secure installs and enables the databases during regular
installation. All other levels of Gen5 must elect to use the database to
store protocol and experiment files at System>Preferences>File
Storage
In a multiple-user environment, you can set up Gen5's database on a shared network
drive so multiple users can access the same protocol and experiment files. This is a
recommended step for Gen5 Secure System Administrators. You can also set up
multiple databases, one for each user, for example. During a Gen5 session, access is
provided to only one database at a time.
Gen5 User Guide
14| Chapter 1: Initial Setup
How to:
1.
2.
3.
4.
5.
6.
7.
8.
Select System> Database Management> Database Configuration
Select the SharedDB tab
Next to the Source field, click the 3-dot button
In the Open dialog, highlight and right-click the file
SharedDB.mdb, and select Copy or Cut: use cut to move and copy to copy
(see File Management Recommendations below)
Note: SharedDB is the installed/original name for the shared database.
Since you can change the name, it's possible it has already been changed.
Use the browse tools to navigate to the desired location in the Look in field
When the correct location is selected, right-click in the window and select
Paste
Click the Open button to save and close the window and return to the Gen5
Database Configuration dialog
Shut down and restart Gen5 to make the changes take effect.0
Important: if you're moving the Shared DB to a network drive you
may want to consider Disabling Write Caching. Consult your IT
department or Microsoft’s knowledge base.
Changing the System Administrator's Password
For Gen5™ Secure Only
System> Security> Users
BioTek recommends changing the System Administrator's password immediately
following Gen5 installation to ensure a secure operating environment.
To change the password:
1.
Login as the System Administrator, if you haven't already done so:
3.
Set the User to Administrator
2.
4.
5.
6.
7.
Select System> Login/Logout
Enter the default password: admin
Select System> Security> Users
Double click the System Administrator user (to Edit the record)
Define and confirm the new password.0
Important: Do not forget the Administrator's password. If you do,
you'll have to reinstall Gen5.
BioTek Instruments, Inc.
Set up Gen5 Secure | 15
About User Accounts
For Gen5™ Secure Only
System> Security> Users
Prerequisite
This function is only available to the System Administrator.
How to Create, Modify or Delete User Accounts
Only an Administrator can add, modify, or delete users. Except for the Administrator,
any user account can be changed or deleted:
Click New to set up a new user

(Double-click or) Highlight a user and click Edit to modify its
name, password, or Group assignment

 Highlight a user and click Delete to remove the user account
Creating/Maintaining User Accounts
For Gen5™ Secure Only
System> Security> Users
Prerequisite
Most options for user accounts are only available to the System Administrator. Nonadministrators are limited to changing their own password and selecting a Startup
Action and Protocol Folder.
User ID
Enter a unique ID using 1 to 16 alphanumeric characters. The user will enter or select
this ID when logging into Gen5 and when signing files.
Full Name
Enter the user’s name. This name will be associated with events logged by this user’s
actions and with the digital signature applied by this user.
Group
Choose a Group membership to assign access rights and permissions to the user. Users
receive the rights assigned to the Group.
Gen5 User Guide
16| Chapter 1: Initial Setup
Status
The checkbox shows whether or not the user’s account is currently locked. The System
Administrator can lock or unlock the account. When a user’s account is locked, the
user cannot log into Gen5 and cannot sign files. A user’s account may become locked
due to one of three events:
 Intentional lock by the Administrator through this dialog
 Automatic lock if the user exceeded the number of successive failed login
attempts
 Automatic lock if the user’s password expired
Important: Unlocking a user's account following an automatic lock
resets its counter or clock. The reset is specific to the reason for the
lockout: when it is caused by password expiration, the password
expiration clock is reset and when it is caused by failed logins, the
user's history of "successive failed login attempts" is reset to 0.
When lock out occurs due to an expired password, unlocking the account allows the
user to login to Gen5 with the same password, giving them a chance to change it.
Alternatively, as system administrator, you can simply change the password yourself
(which will by default unlock the account) and tell the user to login with the password
you have assigned him/her.
Startup Action
Use the drop-down to select the preferred method for starting Gen5:
 Startup Window is the default setting, it offers several options including
creating a new item or opening a recently used item
 Create new experiment opens Gen5 with the Protocol selection dialog
open, as if the user had selected File>New Experiment
 Start at main menu opens Gen5 showing the File, System and Help menus
only. Since neither a protocol nor experiment is open, the workspace is
blank.
Protocol and Experiment Folders
Browse to or enter the full path and directory to define the folder in which the current
user will typically store protocol and experiment files. If a folder is not specified, Gen5
will default to the most recently accessed folder.
Password
Assign a password for the user to enter the first time he/she logs in to Gen5. Instruct
users to change their password after the first login using the Password you've
assigned. Users can only change their own password. System Administrators can
change any user's password.
BioTek Instruments, Inc.
Set up Gen5 Secure | 17
Login/Password Controls
For Gen5™ Secure Only
System> Security> Login
Prerequisite
Only the System Administrator can access these controls. You must login:
System>Login/Logout, as the Administrator to change the settings.
Important: The default settings shipped with Gen5 Secure, and
shown in the screenshot below, comply with the FDA's 21 CFR Part 11
requirements for controls for identification codes/passwords.
Login
 Lock user account after: Specify the number of successive failed login attempts
a user may make before being locked out of Gen5. This feature does not apply
to System Administrator accounts and only a System Administrator can
reinstate a locked out account. Valid entry range: 2-10. When this feature is
unchecked, users login attempts are unlimited. Compliance with 21 CFR Part
11 requires setting a limit for failed login attempts.
 Lock session after: Specify the number of minutes that a Gen5 session can be
idle before it is locked and requires successful user login to reactivate. A
session is considered idle when there is no keyboard or mouse activity and
Gen5 is not controlling a reader activity. Valid entry range: 1-1440 minutes.
Compliance with 21 CFR Part 11 requires setting an idle-time limit.
 Force user to type ID: apply this control if your security rules require users to
enter their ID at login and to apply their Signature. When this feature is
unchecked, the last user's ID is displayed in the login and signature screens and
users can select an ID from a drop-down list of users. This is not a requirement
for compliance with 21 CFR Part 11.
Password
 Minimum password length: Specify the minimum number of alphanumeric
characters required for a valid password. Valid entry range: 2-10 characters.
 Password expiration: Specify the number of days a password can be used
before users are required to change it. When users let their password expire
without changing it, their accounts are locked out and only a System
Administrator can reinstate a locked out account. Valid entry range: 1-10000
days. If this feature is unchecked passwords do not expire. Compliance with 21
CFR Part 11 requires an expiration period.
Gen5 User Guide
18| Chapter 1: Initial Setup
Lock out: when a user's password has expired, the system administrator has two
choices:
 manually remove the Locked out flag: this resets the password
expiration period allowing the user to login using his/her current
password.
 enter a new password for the user (which unlocks the account) and tell
the user to login with the password you have assigned him/her. Advise
the user to change the password after logging in.
 Advise user: If password expiration is set, specify the number of days before
their password expires to alert users to change their password. Valid entry
range: 1-30 days, but cannot exceed the number of days to Password
Expiration.
 Password reuse: Specify the number of passwords Gen5 will remember for
each user's account to prevent a recently used password from being reused.
Valid entry range: 2-20.
About User Groups
For Gen5™ Secure Only
System> Security> Groups
Prerequisite
This function is only available to the System Administrator.
Gen5 Secure uses Groups to manage the rights or permissions granted to users. When
creating (or maintaining) a group, you define the level of access and the controls
available to certain types of users, and then assign actual users to the groups. Gen5
ships with three groups: Administrator, Power User, and Standard User.
The System Administrator and Power User groups are given access rights to all
functions. The Administrator's rights cannot be changed, and include additional rights
to manage user accounts that are not extended to Power Users. When Gen5 Secure is
installed, the Standard User is limited to the following permissions. The System
Administrator can change these controls as needed:
 Quick Read/Use Default Protocol
 Add a New Plate
 Create/Edit Sample IDs
 Edit Plate Information
 Edit Report Builder
 Create folder in database
BioTek Instruments, Inc.
Set up Gen5 Secure | 19
How to create new and modify existing groups:
Only a System Administrator can add, modify, or delete groups. Except for the
Administrator group, any group can be changed or deleted, and any group can be
renamed.
Click New to set up a new group



permissions
Highlight a group and click Edit to modify its name and
Highlight a group and click Delete to remove it as an option. First
you must reassign any users to another group. You cannot delete a group with
users assigned to it.
Gen5 User Guide
20| Chapter 1: Initial Setup
Set up Gen5 Reader Control
For Gen5™ Reader Control Only
Recommended tasks to perform:
1.
Install Gen5 on the computer
Installation instructions are included in the Getting Started Guide
shipped with the CD.
2.
3.
4.
5.
Determine the optimal way to store Gen5's protocol and experiment files:
File Storage (page 4)
Connect a Reader to the computer (page 21)
Set User Preferences (page 24)
Learn how to use Gen5: 0
 Watch the online demos, select Help>Tutorials
 Alternatively, begin by performing the Learning Exercises in the Getting
Started Guide.
BioTek Instruments, Inc.
Connecting a Reader | 21
Connecting a Reader
System> Reader Configuration
After following the Operator's Manual instructions for attaching the reader to the
computer, you must tell Gen5 what type of reader it is and which communications port
(Com Port) it is plugged into. Gen5 and Gen5 Secure allow up to two readers to be
assigned at a time.
Special note for Clarity users: Configuration parameters and port
settings can only be defined through the Clarity PC software: Follow
instructions on page 23.
1.
2.
3.
4.
5.
6.
7.
8.
Turn on the reader
From the menu, select System> Reader Configuration
Click the Add button to define the Reader Settings
Use the drop-down list to select the Reader Type
Except for the Clarity (see page 23), in the Com Port text field, enter the
number of the communications port.
Retain the default Baud Rate.
Click Test Comm. Gen5 will attempt to communicate with the reader.
After you receive a passing message, "The reader is communicating," click
OK and then click Close at Reader Configuration. If you receive any other
message look for a remedy in the Troubleshooting section of this guide.0
That's it! Gen5 captures the information it needs from the reader itself, including probe
size, wavelength and bandwidth capability, and any other applicable information.
Instrument-Specific Information
 Synergy™ HT: For this multi-detection reader, Gen5 must obtain the
fluorescence/luminescence filter sets. BioTek sets the reader's on-board
software with the ordered configuration before shipping the reader. Gen5 will
capture the stored information when it initiates communication with the
reader.
 Synergy™ 2: For this multiple-module, multiple-detection reader, Gen5 must
obtain both the fluorescence/luminescence filter sets and the mirror-holder
configuration. BioTek sets the reader's on-board software with the ordered
configuration before shipping the reader. Gen5 will capture the stored
information when it initiates communication with the reader.
 Synergy™ 4: For this multiple-module, multiple-detection reader, Gen5 must
obtain both the fluorescence/luminescence filter sets and the mirror-holder
configuration. BioTek sets the reader's on-board software with the ordered
Gen5 User Guide
22| Chapter 1: Initial Setup
configuration before shipping the reader. Gen5 will capture the stored
information when it initiates communication with the reader.
 Clarity™: A Clarity luminometer can be added or deleted in the instrument
configuration dialog. But, unlike other readers, the COM port that is used to
attach to the Clarity cannot be set or modified in Gen5's Reader Configuration
dialog. You must use the Clarity software to define the connection settings. Use
the Clarity Control Panel.
 FLx800™: Gen5 must obtain the fluorescence/luminescence filter wheel
configuration. BioTek sets the reader's on-board software with the ordered
configuration before shipping the reader. Gen5 will capture the stored
information when it initiates communication with the reader.
 PowerWave™: This 8-channel monochromator does not need special set up.
When Gen5 communicates with the reader the Absorbance Wavelength table
currently stored in the reader's memory is displayed. When defining a Read
Step select from the stored wavelengths or enter a different one.
 PowerWave™ XS: This single-channel monochromator does not need special
set up. When Gen5 communicates with the reader the Absorbance Wavelength
table currently stored in the reader's memory is displayed. When defining a
Read Step select from the stored wavelengths or enter a different one.
Two models of PowerWave XS are listed in the Gen5: PowerWave XS
and PowerWave XS2. If you are connecting a PowerWave XS reader
that has a USB port and an MQX200R2 product number (take note of
the 2), you must select the PowerWave XS2. Our changes to the
PowerWave XS hardware to incorporate a USB/RS-232 com port
requires unique reader identification in Gen5. There is no difference in
the optical performance characteristics of the reader.
 ELx800™ and ELx808™: BioTek configures the on-board software of these
filter-wheel-based readers with the installed filters. Gen5 will capture the filter
configuration when it initiates communication with the reader.
 µQuant™: This single-channel monochromator does not need special set up.
When Gen5 communicates with the reader the Absorbance Wavelength table
currently stored in the reader's memory is displayed. When defining a Read
Step select from the stored wavelengths or enter a different one.
Learn about the Absorbance Wavelengths tables in the Reader Control
and Configuration chapter.
BioTek Instruments, Inc.
Setting up the Clarity Luminometer | 23
Setting up the Clarity Luminometer
Clarity users must follow a slightly different sequence of steps to establish
communication between the Clarity and Gen5. First, follow the installation instructions
provided with the Clarity, including installing the Clarity PC software. After
installation, when you're running assays, Gen5 uses the Clarity PC software in place of
its StepWise™ Procedure. But, you define the other elements of the Protocol and run
the Experiment with Gen5.
Important: Install the Clarity PC software before proceeding.
1.
2.
3.
4.
5.
6.
7.
Connect the luminometer to the computer (if not already connected) and
turn it on.
Start the Clarity software and set up the communications port (Options>
Com Port Settings).
Then, select Options> Instrument Info to test communication. Details
about the current instrument should be displayed on-screen. If not, repeat
Step 2, making sure the correct port is selected.
Important: Close the Clarity software.
Start Gen5 and log in (if required).
Select System> Reader Configuration and set the Reader Type to
Clarity
Select System> Reader Control> Clarity to make sure Gen5 is
communicating with the Clarity. If the control panel does not open, repeat
Step 6 and retry. Contact BioTek TAC if problems persist.0
If the control panel does not open:
 on Windows® XP and 2000 systems, repeat Step 6 and retry.
 on Windows® Vista systems:
1
2
3
4
Locate and right-click the Clarity desktop icon, and select Run as
administrator. If prompted, enter the password,
At the User Account Control dialog, click Allow,
The Clarity software will launch and communicate with the reader.
Close the Clarity software.
Return to Gen5 and test communication with the Clarity by
performing Step 7 above.
 Contact BioTek TAC if problems persist.
Gen5 User Guide
24| Chapter 1: Initial Setup
Setting up Preferences
Gen5™ offers tools for defining certain preferences. Take advantage of them to save
time and enforce consistency of use. They can be overridden, as needed, during normal
use of the software.
Set up the Default Protocol
The Default Protocol can be used to define numerous settings that you're likely to
apply to all experiments. Consider using the Default Protocol to:
 Customize Well IDs in the Plate Layout
 Set up Protocol Options to automatically save files and to automatically execute
your preferred method of results output immediately after reading a plate.
Define File Naming Conventions and File Locations for your export files under
Export Options
Set Startup Preferences
Set user's Startup Preference and Protocol and Experiment Folders:
 Gen5 Secure: Creating/Maintaining User Accounts (page 15)
 All other Gen5 levels select System>User Setup
Define Startup Preferences
1.
Use the drop-down to select the preferred method for Startup Action:
 Display Welcome dialog is the default setting, it opens Gen5 with a
screen that offers links to several common tasks including creating a
new item or opening a recently used item. Note: the only way to access
the Welcom page is to launch Gen5.
 Create new experiment opens Gen5 with the Protocol selection dialog
open, as if the user had selected File>New Experiment
 Start at main menu opens Gen5 showing the File, System and Help
menus only. Since neither a protocol nor experiment is open, the
workspace is blank.
2.
3.
Use the 3-dot button to change your Protocol and Experiment Folders:
browse to the full path and directory to define the folder where you will
typically store protocol and experiment files. Gen5 will point to these
folders when you save and open a protocol or experiment.
Click OK.0
The changes will take effect the next time you log into Gen5.
BioTek Instruments, Inc.
Setting up Preferences | 25
Customize the Toolbar
Gen5 has two toolbars, one for each mode: Protocol or Experiment. You can change
their configuration to facilitate your work. Find instructions in the System
Management chapter.
Select a List Separator for Import Files
If you regularly import data files, rather than obtaining measurements from the reader,
take a moment to identify for Gen5 your normal list separator. Select
System>Preferences> Read from File Settings
Gen5 User Guide
26| Chapter 1: Initial Setup
BioTek Instruments, Inc.
Chapter 2
Getting Started
This section provides a basic introduction to Gen5. It also includes
contact information for obtaining technical support and tips for
users of BioTek’s KC4 software.
Getting Started........................................................................ 28
Gen5’s Workspace.................................................................... 30
Introducing the Protocol Workspace ........................................... 33
Gen5’s Wizard ......................................................................... 35
Buttons and Icons Guide ........................................................... 36
About the Menu Tree ................................................................ 38
Tips for KC4 Users ................................................................... 39
Getting Technical Assistance ..................................................... 41
28| Chapter 2: Getting Started
Getting Started
Welcome to Gen5™! To make you feel comfortable with this very capable reader
control and data analysis software, we've provided several learning tools. Tackle them
progressively and you'll be a pro in no time. You'll find these tools in Gen5’s Help.
Important: these topics do not describe the Initial Setup
requirements, like connecting a reader. Unless your System
Administrator has already done so, complete the initial setup
requirements before trying the lessons described here.
 Watch an Online Demonstration: select Help> Tutorials
 Basic #1: Intro to Gen5
 Basic #2: Setting up the Procedure
 Basic #3: Defining the Plate Layout (not for Gen5 Reader Control)
 Basic #4: Creating Data Reduction Steps (not for Gen5 Reader Control)
 Basic #5: Runtime Prompts
 Basic #6: Building Reports
 Data Views: Create a New View
 Intro to Power Export (to use Microsoft® Excel for reporting) (not for Gen5
ELISA or Reader Control)
 How to create multiple standard curves
 Intro to Calibrator-Plate Protocols (not for Gen5 Reader Control)
 How to select the optimal PMT Sensitivity (for fluorescence and luminescence)
 Synergy 2 and Synergy 4: Filter-based FL Detection Methods
 Practice using Gen5 with the Learning Exercises:
 Refer to the Getting Started Guide shipped with the product CD or Gen5’s Help
system for step-by-step learning exercises
BioTek Instruments, Inc.
Getting Started | 29
 Open a Sample Protocol:
Gen5 ships with numerous protocols so you can load one up, customize it to fit your
particular requirements, and run an experiment.
1.
2.
Select File>Open Protocol
At the top of the Open dialog, click the "Up One Level" button
3.
In the Gen5 folder or the DB (shared database), select the Samples folder
5.
Open the Protocol (or Synergy 2_Synergy 4) folder and select one. 0.
4.
Select the folder for the desired detection method: Absorbance,
Fluorescence or Luminescence
Recommendation: Before making any modifications to the sample
protocols, we recommend selecting File>Save As after opening them
and assigning a unique name to the protocol. This will preserve the
original sample protocol for future use. Also recommended when
saving a copy of the original protocol is selecting the most convenient
location for it. You may want to use the Up One Level button a few
times to get back to the Gen5/Protocol folder, a more likely location
for your "in use" protocols. Note: the step-by-step instructions for
opening a sample protocol are based on the default filenames and
path.
Important: The sample protocols must be considered as examples
provided for demonstration and guidance purposes. If you plan to use
these protocols or similar ones in a real application, it is your
responsibility to validate the protocol parameters, including the report
and export content (if applicable), before using them.
One more thing: your reader may not support all of the sample
protocols provided. Review the descriptions in the Sample Protocols
and Experiments Guide to see if your reader is compatible with the
defined steps. If you can read PDF files: click the Windows® Start
button, select All Programs>Gen5>Sample Protocols and
Experiments Guide
Gen5 User Guide
30| Chapter 2: Getting Started
Gen5's Workspace
Gen5 offers several controls and workspaces for developing protocols, running
experiments, and viewing and reporting results:
Gen5's Welcome screen is only available when Gen5 is initially
launched. You restart Gen5 to get to the Welcome screen.
1 Protocol
Every experiment is based on a protocol. The differences between a Protocol and an
Experiment in Gen5 are described in the Essential Concepts chapter.
2 Plate View
Gen5 provides a view or workspace for each plate processed (or to be processed) in an
Experiment. You must have an Experiment, rather than a Protocol, open to have a Plate
View:
Opening the Plate View/Workspace
In an Experiment, if it is not already open in the main view of Gen5™:
 from the menu tree: Double-click the desired
 Or, select Plate> View
item
BioTek Instruments, Inc.
Gen5's Workspace | 31
Gen5 offers several ways to modify and customize the Plate View for on-screen display
and reporting/outputting results, see the Viewing Results chapter to learn more.
3 Menu Tree
The menu tree, docked at the left side of the workspace, provides a quick and easy way to
open all the tools needed to create and run experiments.
 About the Menu Tree (page 38)
4 Toolbars and Menus
Here is a reference guide to learn about Gen5's buttons and icons:
 Buttons and Icon Guide (page 36)
5 Running an Experiment
All of the views and components come into play when running an experiment (File>New
Experiment). The Protocol menu tree is the primary engine for an experiment and Plates
(one for each plate processed or to be processed) are added to the menu tree. The Plate
View and other plate components are made available:
Information contains the text input at the Runtime Prompts when the plate is read
and Bio-Cell™ results when this pathlength-correction option is used
Sample IDs are user-defined sample names or bar codes
Calculation Log keeps track of and displays any data reduction errors
Audit Trail logs changes (masking and editing) of data points for all levels of Gen5,
and numerous other events for Gen5 Secure. Audit trail events can be included in reports
and export files.
Gen5 User Guide
32| Chapter 2: Getting Started
About the Plate Workspace
The Plate View represents the microplates processed (or to be processed) in an
Experiment. The following tabs are available depending on the Protocol definition:
 Matrix: a representation of the microplate layout. Each cell in the grid
shows the data-set results for the well it represents in the plate. The Layout
data set shows the current Plate Layout. You can use this view for masking
or editing results.
 Statistics: a standard set of statistical values are determined for you and
displayed in a table
 Graphs: when a standard curve is defined it is shown in the Graphs tab
 Cutoff Values: when a Cutoff Data Reduction step has been defined, this
tab displays the values or results of the cutoff formulas
 Validation Results: when a Validation Data Reduction step has been
defined, this tab displays the results of any calculations
BioTek Instruments, Inc.
Introducing the Protocol Workspace | 33
Introducing the Protocol Workspace
When you create a new protocol, Gen5 opens a special workspace limited to the protocol's
components:
The workspace is made up of the menu tree with a branch for each of the protocol's
elements. The order of the protocol elements reflects the order to follow when defining
most protocols:
Defining the Procedure or reading parameters, like detection method, wavelength,
and other factors, is the most important step to Gen5. The Procedure describes the data
sets which are used in most subsequent steps to generate results output. The Plate Layout
is the only other protocol element that is not affected by the Procedure.
For most protocols, it's best to define the Plate Layout in your second step. Gen5
automatically performs a blank-subtraction calculation when Blanks are defined in the
plate layout. (You'll see this Transformation in the Data Reduction workspace.) Defining
the standards and their concentrations in the plate layout is a prerequisite to generating a
standard curve.
Data Reduction is one of Gen5's most powerful features, and it requires the
information provided by the two previous steps to logically offer you its capabilities.
Automatically-generated transformations, like pathlength correction, and the ability to
conduct well analysis, for example, depend on the Procedure. To plot a standard or titer
curve, and to validate Transformation formulas requires knowing the Plate Layout.
Gen5 User Guide
34| Chapter 2: Getting Started
Runtime Prompts are user-defined text fields that are presented to users when they
read a plate. The information obtained is stored in the Plate Information component of the
experiment and can be included in reports and export files.
Viewing and Reporting Results: the next four options (or three options if you're running
Gen5 ELISA or Reader Control, which do not offer Power Export) are tools for selecting
and customizing the appearance of data sets: raw data measurements and data reduction
results. Data Views controls the on-screen appearance of data. Data Views also stores and
makes available for reporting and exporting any customizations made to the data sets. For
example, you can build your own matrix, table, or curve view of a data set by combining
and formatting data elements. When you do this in Data Views, that user-defined data set
is available for printing or exporting using the Report Builder, File Export Builder and
Power Export Builder.
Protocol Options provide several special features and preferences. Many of the
options may be rarely used by your organization. Review the options provided and if your
preferences vary from the default settings, use the Default Protocol to set them for all
newly-created protocols. The exception to this rule occurs with multi-plate protocols:
Calibrator-Plate Protocols and, for Gen5 and Gen5 Secure users, multi-plate assay
protocols. These types of protocols begin by selecting the Protocol Type defined in the
Protocol Options.
BioTek Instruments, Inc.
Gen5's Wizard | 35
Gen5's Wizard
Use Gen5's Wizard to create a new protocol. Then, you can run an unlimited number
of experiments based on that protocol. Learn the difference between a Protocol and
Experiment in Gen5, in the Essential Concepts chapter to make the most of Gen5.
How to use the wizard:
1.
On each screen of the wizard, click the button to define that protocol
element (each function is described in a subsequent chapter):
Defining the Reading Procedure
Defining the Plate Layout
Setting up Data Reduction
Building Reports
Using the File Export Builder
How to use Power Export
2.
3.
4.
5.
Gen5 User Guide
After defining a protocol element, click Next to proceed to the next one.
Gen5 displays a checkmark for an element that has been defined.
Click Finish to generate the protocol based on your selections.
Select File>Save and give the protocol a unique name.
Now you're ready to run an experiment.
Select File>New Experiment. The just-created protocol will be
highlighted, click OK to select it. 0
36| Chapter 2: Getting Started
Buttons and Icons Guide
Buttons Descriptions
The 3-dot (three-dot) button is a tool for customizing or modifying the item's
contents. In some report options, you must click in a field to activate its 3-dot
button
Open an existing Experiment
Create a new Experiment or Protocol
Add another plate to the current Experiment
Read the plate (or Simulate, Manually Enter, or Import data)
Save the Experiment
Gen5's Wizard to help you create an Experiment
Print the results, but first use Report Builder to select what to include
Print Preview
Reader Control: check the status, open the control panel
Duplicate View: click the button in the upper-right corner of the Plate View
to open a coincident display of the plate's results
Gen5 Secure Only: Sign a protocol or experiment
384- and 1536-well Plate View Toggle: zoom in to view the top-left
section of the plate, zoom out to view the whole plate
Menu Tree Icons
Plate - Not read. Put the plate in the reader and click the Read button
Plate read successful
Plate read paused by Stop/Resume step. When you're ready, put the plate
in the reader, click the Read button and select Resume to continue
Plate read aborted. To begin again, put the plate in the reader, click the
Read button and select Re-Read
Plate read in progress
BioTek Instruments, Inc.
Buttons and Icons Guide | 37
Plate read error, which is always preceded by an error message
Protocol
Procedure: define the reading parameters
Plate Layout: assign location of samples
Data Reduction: set up calculations
Runtime Prompts: define the information requested when a plate is read
Report Builder: select the content to print
File Export Builder: select the content to export
Power Export Builder: select the content to export to Excel®
Data Views: customize the appearance of data for online viewing and
reporting
Protocol Options: miscellaneous options for saving, naming, exporting and
calculating results
Plate Information: information obtained at runtime
Sample IDs: user-defined names or IDs assigned to samples
Calculation Warning Log: Data Reduction-related errors issued by
unexpected curve or calculation results
Multi-Plate plate view of data reduction statistics and curves
Audit Trail displays any logged events
3-dot (Edit) Button
The 3-dot button leads to editing features for the field or data point it is associated
with. Click the button when it is next to or in a field to change the selection list or
format of the field's items.
Note: In Field Groups and in Headers and Footers you must click
inside a field in the table to enable a 3-dot button.
Gen5 User Guide
38| Chapter 2: Getting Started
About the Menu Tree
 In an experiment, the menu tree is docked at the left side of the workspace,
unless its position has been previously altered. When you're working with a
protocol file, the menu tree, like the toolbar, is limited to related operations.
Learn the difference between Gen5's Protocols and Experiments in the next
chapter
 The menu tree provides a visual cue of the steps to follow when creating a
protocol
 All of the controls available from the menu tree can alternatively be accessed
using toolbar buttons or the drop-down menus

and
icons next to an item expand or close it to reveal or hide its
components
 Highlight an item in the menu tree and right click for a context-sensitive menu
of options, including Read when a plate is selected, for example.
 * asterisks are displayed next to plate icons (and in the title bar) of an
experiment when a change is made or an action is taken but the file has not yet
been saved

You can move the menu tree to another corner of the workspace or let it float
undocked like the Plate workspace: click the undock button, drag the title bar
and drop it in the desired location
 When you Add multiple plates to an experiment, highlight a plate and rightclick for menu options to delete and renumber plates.
BioTek Instruments, Inc.
Tips for KC4 Users | 39
Tips for KC4 Users
BioTek relied on input from KC4 users to develop this improved next-generation
product. It may take a bit of practice to learn how to use them, but we think you'll find
the new features worth it.
1.
2.
In Gen5, reading parameters are not defined in one dialog (screen), but set up
as steps in the StepWise™ Procedure. This gives you far more flexibility in
defining an experiment. Depending on the level of Gen5 you're running, this
includes multiple read steps and reading-related functions, like shaking and
dispensing.
The filename extensions are slightly different and file formats are simpler.
Gen5 replaces the .pla and .glb formats with one experiment file: .xpt. Gen5
keeps the .prt filename for protocol files. The experiment file (.xpt) like its
predecessor the .glb or global data file, contains the .prt or protocol as it was
defined at runtime
KC4
Gen5
.pla
.glb
.xpt
.prt
3.
4.
.prt
Gen5 does not offer Power Reports for Microsoft® Word. Power Export to Excel
is available and a full-featured, user-customizable Report Builder eliminates
the need for Word for most users. In addition, a new Quick Export to Excel
feature and a user-customizable File Export tool are offered, which can be used
to port files to Word. Learn more: Reporting Results
Append to Kinetic File, a KC4 feature, has been replaced in Gen5 with new
features:
 multiple read steps can be performed in one experiment, and Gen5 offers to
Append to previous Kinetic data when multiple kinetic loops are defined
in a Procedure
 a long, discontinuous-interval Kinetic analysis can be performed using the
Discontinuous Kinetic option
5.
6.
 multiple plates can be used to run a single assay, review Multi-Plate
Protocols
Eject Between Filter Sets, a KC4 option, is omitted from Gen5 because it is not
needed. Instead, you can set up multiple read steps interspersed with a Plate
In/Out or Stop/Resume step
Lag time defined in Reading Parameters in KC4 is accomplished with a Delay
step in the Procedures in Gen5
Gen5 User Guide
40| Chapter 2: Getting Started
7.
8.
9.
In Gen5, add a Kinetic loop to the Procedure rather than ticking a checkbox in
KC4. See Setting up a Kinetic Analysis. Also note that the Data Reduction
options for kinetic analysis do not include KC4's "Formula" and individual
reading point identifier "R." These calculations can be replicated using Gen5's
Transformation dialog.
In Gen5, to "Pre-Read Blank Plate" you'll set up two Read Steps with a
Stop/Resume step between them: for instructions see Subtracting a Blank
Plate (This is not available for Gen5 ELISA)
Gen5 does not automatically generate dual-wavelength subtraction or Delta
OD data reductions, for instructions see: How to perform Dual-Wavelength
Subtraction
10. Set up a Dispense step in the Procedures, rather than ticking a checkbox in
KC4. Here are instructions for setting up Dispensing Protocols
11. Luminescence reading parameters in Gen5 require definition of Integration
Time rather than the number of samples per well and delay time before and
after sampling. When selecting the Emission filter setting, Lum/E has been
replaced with Hole.
12. Don't confuse what was called "Multi-Plate Transformations" in KC4 with
multi-plate protocols or multiple-plate experiments in Gen5. Multi-plate
transformations have been replaced with the StepWise™ Data Reduction
steps, where an almost unlimited number of calculations can be performed
13. Multi-Detection was called Multi-Mode in KC4
14. Raw Data Correction options in KC4 are engaged differently in Gen5:
 Blank Plate Subtraction is described above
 Blank Wells Subtraction occurs automatically when there are Blanks
assigned to the Plate Layout. You'll find these automatically-generated
Transformations in the Data Reduction dialog
 Pathlength Correction can be enabled when defining an Absorbance Read
Step
15. When viewing Well Analysis results in the Well Zoom view:
 Gen5 uses brackets [ ] to show the revised Calculation Zone, instead of
showing the data points in different colors as in KC4
 Setting "Scales for Kinetic Reads" and "Individual Well Auto Scaling" for
scanning reads is replaced with more feature-rich tools for editing the
results output, see Modify a Graph. When you combine these features with
the ability to define the calculation zone (select Calculation Options when
defining the Well Analysis step), you have enormous control over the
appearance of the results
16. Monitoring Wells is more flexible in Gen5 because it is defined as a separate
step in the Procedure. The read parameters are specific to the monitoring
process and can be different than those defined to obtain measurements0.
BioTek Instruments, Inc.
Getting Technical Assistance | 41
Getting Technical Assistance
Gen5™ is backed by a superior support staff. If the software fails to work perfectly, please
contact BioTek’s Technical Assistance Center (TAC). You can call, write, fax, or email your
questions and concerns to BioTek:
Email Support: [email protected]
Fax Support
Send a fax with your questions or requests for help 24 hours a day:
 Technical Assistance Center (TAC): 802.655.3399
 European Coordination Center: +49 (0) 7136.968.111
Phone Support:
You can telephone the Technical Assistance Center between 8:30 AM and 5:30 PM
Eastern Standard Time (EST), Monday through Friday, excluding holidays.
Customer Service:
(802) 655-4040
Technical Assistance Center:
 In the US call: (800) 242.4685
 Outside the U.S. call: (802) 655.4740
European Coordination Center: +49 (0) 7136.9680
Whichever method of contact you choose, please be prepared to provide the
following information:
 The software version and revision numbers displayed at Help>About Gen5...
 The license type or software level: Gen5, Gen5 Secure, Gen5 ELISA, or Reader
Control
 The specific steps that produce your problem
 Any error codes displayed
 A daytime phone number
 Your name and company information
 An email address and/or a fax number, if available.
Gen5 User Guide
42| Chapter 2: Getting Started
BioTek Instruments, Inc.
Chapter 3
Essential Concepts
This section reveals the basic concepts upon which Gen5 was built.
Learning them will enhance your experience using Gen5.
Experiment vs. Protocol ............................................................ 45
File Storage............................................................................. 47
Best Practices.......................................................................... 48
44 | Chapter 3: Essential Concepts
Essential Concepts
Understanding the basic concepts behind Gen5's structure and behavior will help you
make the most of it. A few topics are covered here, on the next few pages, more
information is provided in Gen5’s Help.
 Experiment vs. Protocol on page 45
 File Formats:
Gen5's files are identified by their filename extension:
 .prt = Protocol file
 .xpt = Experiment file (contains the protocol and any data acquired or
generated within the experiment)
 File Storage on page 47
 Best Practices on page 48
In Gen5, select Help>Help Topics to find:
 Multiple-Plate Experiments
 Security and FDA Electronic Records Compliance
Only the Gen5 Secure level of software offers all the capability
required to meet the FDA's electronic records requirements: §21 CFR
Part 11.
Experiment vs. Protocol | 45
Experiment vs. Protocol
Gen5™ uses two common terms to define distinct elements of its toolkit. The
distinction is subtle and understanding it will improve your Gen5 experience.
Protocol
(*.prt)
Experiment
(*.xpt)
A protocol is a "recipe" or set of
instructions designed to capture,
transform and report and/or export
data
An experiment has a copy of the
protocol and at least one plate. It
executes the instructions provided by
the protocol to produce results
Protocols are created and saved as
standalone files. They function as a
template; an unlimited number of
experiments can be based on one
While an experiment is created using an
existing protocol, the experiment’s copy
of the protocol can be modified within
the experiment
A protocol consists of reading
requirements, like detection method
and wavelength, and reading-related
actions, like shaking and incubation
(Procedure), plate layout, data
reduction, and data viewing, reporting
and exporting definitions
Running an experiment is the only way
to process a protocol. Gen5’s Quick
Read function may at first appear to
skip the protocol development stage,
but it uses the default protocol, and
generally requires reading parameters
to be defined
A protocol can be used repeatedly (asis or modified) within experiments. By
itself, a protocol does not produce
results. Protocols do not have plates
associated with them
Multiple plates can be processed in an
experiment; each one considered a
unique assay with independently
reported or exported results. The
exception is multi-plate protocols,
described later
.prt is the protocol's filename extension
.xpt is the experiment's filename
extension
A copy of the protocol is saved within
an experiment, or as a standalone .prt
file. Since protocols do not have plates,
they cannot generate data outside of an
experiment
An experiment is saved as the full
collection of procedures, formulas,
reporting definitions, and other details,
i.e., the protocol, and the plate data
from readings and calculation results
The Gen5™ Secure level of software
maintains an audit trail of all activity
and changes related to a protocol. All
other Gen5™ software levels do not
support this feature
Data acquired and transformed in an
experiment is protected by an audit trail
in both Gen5 Secure and other Gen5
software editions. The Reader Control
edition does not support this feature
46 | Chapter 3: Essential Concepts
Protocol
(*.prt)
Changes made to a standalone protocol
are not reflected in any previously
created experiments based on that
protocol. A new experiment must be
created to apply the revised protocol
Experiment
(*.xpt)
Within an experiment, you can select
Save Protocol As to capture the current
details of the protocol and save them as
either a new protocol or as an overwrite
of the original protocol
All newly created protocols and (unless another protocol is selected)
experiments are based upon the Default Protocol
Gen5™ also supports more complex multi-plate protocols that are not
covered in this introductory material. Check out: Designing a MultiPlate Protocol in a subsequent chapter.
About File Storage | 47
About File Storage
File Types
Gen5™ creates two file types: Protocol = .prt and Experiment = .xpt
 The Gen5 executable file (.exe) and numerous other types of supporting files,
like an Excel® template, are also installed on the computer.
 In addition, Clarity™ Microplate Luminometer users will work with Clarity
protocol files, which use a .BPF extension. Gen5 references the Clarity files as
they contain the reading parameters required to control the luminometer.
Databases
Gen5 installs two databases on your system called LocalDB and SharedDB. While the
databases are always used for critical, internally-used files, Gen5 offers you the choice
of using the Windows® File System or the Gen5 (SharedDB) database for storing Gen5's
Protocol (.prt) and Experiment (.xpt) files. This option, combined with the ability to
create multiple databases, allows you to structure file storage according to your
organization's requirements.
 Files may be stored on the computer’s hard drive, on a network, or on a CD or
other portable medium. Windows Explorer or a similar application can be used
to view the file names and locations, and to move, copy, rename, and delete
files.
 Alternatively, protocol and experiment files may be stored in a secure, sharedaccess database. This database, initially named SharedDB.mdb, can be stored
on a user’s computer or on a shared-access network/computer (LAN). Gen5
provides a special file maintenance utility for viewing the file names and their
locations, and for moving, copying, renaming, deleting, importing, and
exporting files.
 Select the preferred method of storing protocol and experiment files at
System>Preferences>File Storage
File Location
During a conventional installation:
 the program files are stored in this default location: C:\Program
Files\BioTek\Gen5 (software edition)
 the databases are stored in these default locations:
Windows XP and 2000 systems: C:\Documents and Settings\All
Users\Application Data\BioTek Instruments\Gen5 (software
edition)\(version #)\SharedDB or LocalDB
Windows Vista: Windows XP and 2000 operating systems: C:\Program
Data\BioTek \Gen5 (software edition)\(version #)\SharedDB or LocalDB
 Gen5 installs Protocol and Experiment folders in the respective File Storage
locations, e.g. C:\Program Files\BioTek\Gen5 (software edition)\Protocol
48 | Chapter 3: Essential Concepts
Best Practices
Like most software tools, Gen5™ is flexible, it offers several ways to accomplish a task.
Here are some recommendations for saving time and using it most efficiently:
Efficiencies
 For an assay or experiment that you will run numerous times, develop a
Protocol to define the Procedure, Data Reduction, Data Views and Reports
required. Then you can run an Experiment (File>New Experiment) based on
the Protocol whenever necessary. You can fine-tune the protocol within an
experiment, but remember to select File>Save Protocol As to update the
original protocol with your improvements.
 Just like word processing documents, when you run similar types of
experiments, you can use File>Save As to give you a head start creating a new
protocol based an existing protocol that contains the same plate layout, reading
parameters, or other elements that will be repeated in your new protocol.
 Define and customize Data Views before selecting what to include in reports or
export files. All the on-screen data (i.e. data views) can be reported or exported.
If you use on-screen views and paper reports equally, it is most efficient to first
fine-tune the Data Views, and then include them in reports/exports.
 Always assign Blanks to the plate. Blanks can be deionized (DI) water, buffer,
reagent without analyte, substrate and so on. When running fluorescence
cellular assays, a DI-water blank illustrates the background contributed by the
instrument and labware as separate from the cells and media. Identify the
location of the Blanks in the Plate Layout and Gen5 will automatically create
the blank-subtraction data reductions.
 Backup your database regularly, BioTek recommends once per week for most
organizations. If you're using Gen5's Database for protocol and experiment file
storage, use the built-in Periodic Optimization feature.
 Take action if you get a warning message about the remaining size of your
databases, see Maintaining Files for instructions on reducing the database size.
 Consider using Gen5's automatic Save feature to create a new, date-stamped
folder for storing experiment records. This is an especially good practice for
large labs with multiple users who run hundreds of plates per day. Gen5 will
keep all that data organized by date. Define this kind of file management
setting in the Default Protocol so it will apply to all newly created protocols.
 Turn off the Multi-Read Calculation option to improve Gen5's performance.
Calculation results will be the same, but your PC's resources will not be
diverted for performing interim calculations.
Best Practices | 49
Time Savers
 Partial Plate: for assays using strips or partially-filled plates, especially if the
read steps are long or complicated, you can save time by telling the reader
exactly which wells or portion of the plate to read
 Default Protocol: all newly created protocols and Quick Reads are based on the
Default Protocol. If some protocol elements, like plate layout, runtime prompts,
report headers and footers, etc., are largely the same for most of your projects,
you'll save significant time by defining these elements before creating the next
protocol/experiment
 Print Preview: save time and paper by viewing reports on-screen before
sending them to the printer
50 | Chapter 3: Essential Concepts
Chapter 4
Assay Examples
This section contains step-by-step instructions for programming
commonly known assays using Gen5. Gen5 also ships with Sample
Protocols for most of these assays. Both the Sample Protocols and
the assay descriptions are learning tools. It is your responsibility to
customize and validate them to meet your needs. Find a list of the
assays described in this chapter in the “How do I set up my assay”
section.
Sample Protocols and Experiments............................................. 52
How do I set up my assay? ....................................................... 54
52 | Chapter 4: Assay Examples
Sample Protocols and Experiments
Numerous sample protocols are shipped with Gen5. You can use the protocols to learn
more about Gen5 and as a timesaver, customizing them to meet your needs and then
running them in an experiment to obtain results.
Recommendation: Before making any modifications to the sample
protocols, we recommend selecting File>Save As after opening them
and assigning a unique name to the protocol. This will preserve the
original sample protocol for future use.
A matching experiment file is also shipped with Gen5 for use as a learning tool. Many
of the experiment files contain actual data so you can see how Gen5 presents the
results on-screen and in reports.
Find the sample protocols and experiments shipped with Gen5 in the default file
storage locations. A folder for each detection method is available: Absorbance,
Fluorescence, Luminescence and and for Synergy 2 and Synergy 4 users, there is a Synergy
2_Synergy 4 folder within each detection method folder:
 Gen5 Secure (and database users): Select File>Open Protocol, in the DB
directory select the Samples folder.
 All other levels of Gen5: Select File>Open Protocol and browse to C:/Program
Files/BioTek/Gen5/Samples.
Tip: Select File>Open Protocol and use
(the Up One Level button).
 Gen5’s Welcome screen also offers the option to open a Sample File.
Important: The sample protocols must be considered as examples
provided for demonstration and guidance purposes. If you plan to use
these protocols or similar ones in a real application, it is your
responsibility to validate the protocol parameters, including the report
and export content (if applicable), before using them.
Notes: Your system administrator can change the path and filenames
described above. If you cannot find the Samples folder, contact your
system administrator. Also note, your reader may not support all of
the sample protocols provided. Review the descriptions in the Samples
Protocol Listing to see if your reader is compatible with the defined
steps.
Sample Protocols and Experiments Guide
You can review a complete description of samples in the Sample Protocols and
Experiments Guide.PDF shipped with Gen5: click the Windows® Start, select All
Programs>Gen5>Sample Protocols and Experiments Guide
Sample Protocols and Experiments | 53
Gen5 installs a copy of the Sample Protocols and Experiments Guide in
the Samples folder of the main Gen5 directory. (By default this is
C:\Program Files\BioTek\Gen5\Samples)
You can also find a summary listing and brief description of the sample protocols in
Gen5’s Help. Review the description of the sample protocol to make sure it is
compatible with your reader.
54 | Chapter 4: Assay Examples
How do I set up my assay?
Here are step-by-step instructions for creating Gen5 Protocols to run common assays.
(More Assay Examples can be found in Gen5’s Help.) We hope that by following the
instructions, making some changes to names and other details, you can adapt them for
use in your lab. Also see the Kinetic Analysis chapter.
Absorbance
 Quantitative ELISA Example on page 55
 Subtracting Blank Plate Reads on page 58
 Pathlength Correction Example on page 60
 Dual Wavelength Absorbance Endpoint on page 62
 Basic Spectrum Analysis on page 64
 Protein Quantification Assay on page 66
 Max Binding Determination on page 83
 Toxicity/Cytotoxicity Assay on page 86
 Endotoxin Test on page 89
 ß-Galactosidase Kinetic Assay on page 92
Fluorescence
 Basic Fluorescence Assay on page 69
 Kinetic Fluorescence Assay on page 71
 Fluorescence Assay with Injection on page 74
 Fluorescence Area Scan Example on page 77
 Fluorescence Polarization on page 79
Luminescence
 Basic Luminescence Glow Assay on page 81
 Luminescence Flash Assay with Injection on page 82
Dispensing Reagent
 Dispensing Reagent in a Kinetic Analysis on page 94
 Dispensing Reagent in an Endpoint Analysis on page 95
 Fast Kinetics with Injection for Absorbance on page
Quantitative ELISA Example | 55
Quantitative ELISA Example
To help you set up your own assay here is an example of the steps required to run a
quantitative ELISA assay. In this example we set up an endpoint Absorbance read,
subtract Blank wells from all others, plot a standard curve, and define a Control to
express the samples as a percentage of the control.
It may be easier to follow these instructions if you have already watched the Gen5
Basic series of online tutorials: select Help>Tutorials or if you've completed the
learning exercises described in the Getting Started Guide.
To set up the protocol, we'll define the:
1.
Reading Procedure
3.
Data Reductions0.
2.
Plate Layout
Reporting Results is the same process for all types of experiments
1. Defining the reading Procedure
This assay example has the simplest read Procedure: a single-wavelength Absorbance
endpoint read:
1.
Select File>New Protocol
3.
Click the Read button and select the wavelength. Use the drop-down list or
type the wavelength in the text field (overwrite the current value).
2.
4.
Select Protocol>Procedure
Click OK twice to save the Procedure0.
56 | Chapter 4: Assay Examples
2. Defining the Plate Layout
This step is critical for the data reduction steps to be defined later. Here's the plate
layout we need:
The critical factor is using the Well IDs, not their location on the plate. We did not need
to customize the Well IDs for this example. We simply selected the Type, defined the
known concentration of the standards and assigned them to the plate:
Well ID
Type
Description
BLK
Blank
DI water only
STD
Standard
Known concentrations
CTL1
Assay Control
Known Control
SPL
Sample
Unknown samples
Find specific instructions in the Preparing Plates chapter.
3. Defining the Data Reduction Steps
Now that we've defined the reading parameters and plate layout, we can define the
data reduction steps: blank-well subtraction, standard curve, and expressing samples
as a percentage of the control. Gen5 creates the blank-subtraction step for you
automatically.
1.
2.
Select Protocol> Data Reduction
Notice that one Transformation, named "Blank nnn" where nnn is the
wavelength, has already been created. We'll use the results of this calculation to
plot the standard curve.
Click Curve Analysis
Quantitative ELISA Example | 57
3.
4.
5.
Notice on the Data In tab, the Well ID is set to STD and X Axis Data to <Plate
Layout Settings>. The known concentrations entered for Standards are plotted
on the X Axis. Use the drop-down list for the Y Axis Data to select Blank nnn
(wavelength)
Click the Curve Fit tab: depending on your assay, you may want to change the
curve fit method to 4 Parameters or another option, or use Log values on the X
or Y axis. For now, retain the defaults and click the Data Out tab. Take note
that the Data Set Name produced from the standard curve is called Conc (by
default. You can change it.). Click OK to save and close the curve.
Click Transformation
1.
For the Data In use the drop-down list to select Conc.
3.
In the Formula field enter: (X/CTL1)*100
Retain the default setting to Use single formula for all wells. X represents
the value of the current well. CTL1 is the well ID for the control we
assigned in Plate Layout.
2.
Enter a New Data Set Name for the results of this calculation, e.g.
%Control
After the plate is read, you can return to the Data Reduction dialog to make any
needed changes, like the Curve Fit Method. Do not change the Data Out or Data Set
Names, this would invalidate the data reduction steps that use those data sets.
6.
Save the protocol.0.
Now you're ready to define your reporting requirements, and run the protocol in an
experiment.
58 | Chapter 4: Assay Examples
Subtracting Blank Plate Reads
To perform a blank-plate subtraction in your experiment, set up an additional Read
Step for the blank plate, and then, create a Data Reduction Transformation to subtract
the measurements of the blank plate from the samples plate.
You can insert a Plate in/Out step in the Procedure sequence to first read the blank
plate, pause the experiment to pipette samples to the plate, and then, read the samples
plate.
Step-by-step procedure:
1.
2.
Select File>New Protocol
Double click Procedures to set the reading parameters:
1
First, create a Read Step for the blank plate: enter Blank for the Step
Label to easily identify the raw data.
2
Add a Plate In/Out step to eject the plate to pipette samples, standards,
etc. Optionally, enter "Load Samples" in the comment field.
3
Finally, create a Read Step for the samples plate. 0
Other steps can be included in the sequence, like Set Temperature and
Shake, if required.
3.
4.
Set up the Plate Layout to match the distribution of samples and standards or
controls.
Double click Data Reduction to define a transformation: Blank Plate Data
Reduction
1
The dialog will contain any automatically generated data reductions.
Highlight the top-most one and click Transformation, to position the
blank subtraction as the first calculation.
2
Click
3
In the Multiple Data Sets screen, use the drop-down lists to select the
Blank plate read data for DS1 and the samples plate data for DS2.
In multiple wavelength protocols there may be several data sets to
choose from. If you've used the Step Labels for each Read Step, it's
easy to match up the blank plate with the samples plate.
Subtracting Blank Plate Reads | 59
4
Enter a New Data Set Name for the resulting data set, e.g. Blanked 390
6
Repeat steps 2-4 to create as many blank-plate subtraction
Transformations as needed, e.g. one per wavelength.
5
7
5.
Enter DS2-DS1 in the Plate Formula field and click OK.
Now you're ready to create other Data Reduction steps using the
blanked data sets. For example, select Curve Analysis to generate a
standard curve based on the blank-subtracted test plate.0
Customize the Data Views and fine-tune the Report Builder as needed before
saving and closing this protocol. File>Save0.
Now you're ready to run the protocol in an experiment: File> New
Experiment
Running the experiment:
After reading the blank plate, Gen5 ejects the carrier so you can load the samples
If you entered a comment, e.g. Load Samples in the Plate
In/Out step, it is displayed on screen. Here's how to proceed:
 Click OK after loading the samples, when you're ready to continue reading the
plate
60 | Chapter 4: Assay Examples
Pathlength Correction Example
Here is an example of the steps required to perform pathlength correction in an ELISA
assay. In this example we set up an endpoint Absorbance read, subtract Blank wells
from all others, and transform the data to determine the concentrations of the
unknown samples. This is the process used to create the Direct Oligo Quantification
assay shipped as a sample protocol with Gen5.
It may be easier to follow these instructions if you have already watched the Gen5
Basic series of online tutorials: select Help>Tutorials or if you've completed the
learning exercises described in the Getting Started Guide.
To set up this protocol, we'll define the:
1.
Reading Procedure
3.
Data Reductions0.
2.
Plate Layout
Reporting Results is the same process for all types of experiments
1. Defining the reading Procedure
This assay example has the simplest read Procedure: a single-wavelength Absorbance
endpoint read:
1.
Select File>New Protocol
3.
Click the Read button and keep the default settings for Detection Method,
Read Type and Read Speed
2.
4.
5.
6.
Select Protocol>Procedure
Fill in the checkbox next to Pathlength Correction. [Optionally, click the 3dot button to view (and modify if desired) the test and reference wavelengths
used in the process.]
Set the Wavelength. Use the drop-down list or type the wavelength in the text
field (overwrite the current value). For this example, enter 260.
Click OK twice to save the Read step and the Procedure0.
2. Defining the Plate Layout
For this assay example, the plate layout is very simple, comprising two blank wells and
94 unknown samples:
1.
Select Protocol> Plate Layout
Pathlength Correction Example | 61
2.
3.
4.
In the Well Settings box, select the Type of specimen, first Blanks, then
Samples
Assign the blanks to cells A1 and B1
Change the Type to Sample, make sure Next ID is enabled, click and drag over
the remaining wells to assign the unknown samples0.
3. Defining the Data Reduction Steps
After defining the reading parameters and plate layout, we can define the data
reduction steps. Gen5 creates the blank subtraction and the pathlength correction for
you automatically.
1.
2.
3.
4.
5.
6.
Select Protocol> Data Reduction
Notice the two Transformations, "Blank 260" and "Corrected [Blank 260]", Gen5
first subtracts the blanks and then applies the Pathlength Correction
Calculation.
Click Transformation to add anther Data Reduction step
For the Data In use the drop-down list to select Corrected [Blank 260] data set
Enter a New Data Set Name for the results of this calculation, e.g.
Concentration
In the Plate Formula field enter: X*32.5
Retain the default setting to Use single formula for all wells. X represents the
value of the current well. The extinction coefficient for ssDNA oligonucleotides
(1 mg/ml) at 260 nm is 13 ODs for a 1 cm pathlength; this can be recalculated to
mean 1.0 OD has a concentration of 32.5 µg/ml.
Save the protocol.0.
Now you're ready to define your reporting requirements, and run the protocol in an
experiment.
62 | Chapter 4: Assay Examples
Dual Wavelength Absorbance Endpoint
Here are step-by-step instructions for setting up a dual-wavelength absorbance read with
known concentrations of standards against which a linear regression curve is plotted.
Create the protocol:
1.
2.
Select File>New Protocol
Double-click Procedure in the menu tree:
 Click Read to set the reading parameters: Keep the default settings for
Detection Method and Read Type: Absorbance Endpoint
 For Wavelengths, click the button for 2 and use the drop-down list to
select (or enter) the test and reference wavelengths: 410 and 630 for this
example.
 Click OK twice to close the Read Step, and then, the Procedure dialogs.
3.
Double-click Plate Layout to define the location of standards, samples,
and blanks on the microplate. For this example, the standards are placed in the
center of the plate, modify the instructions to match the distribution of samples
and standards on your plate:
 Set the Well Settings Type to Standard and click the 3-dot button next to the
Conc. field to enter the expected concentrations. For this example, leave 0 in
the STD1 cell at the top of the table. Select Incr. with a tick mark, and enter
10 in the field, then click in the STD1 cell, then in the STD2 cell, and each
subsequent cell in the table until STD8. Click OK to save and close the
concentrations.
 At the grid, set the Number of Replicates to 2, and select Next Conc. under
Auto Select. Click and hold as you roll the mouse over the 5 and 6 columns,
(the cursor changes to a black, down-facing arrow) to fill the entire
columns.
 Set the Well Settings Type to Blank, keep the Number of Replicates at 2,
and click and drag over wells A1 and A2.
 Set the Well Settings Type to Sample, keep the Number of Replicates at 2,
and select Next ID under Auto Select. Click and drag the cursor over the
remaining wells in columns 1 and 2, and then 3-4, and then 7-12, to assign
samples to all the other wells of the plate.
4.
Double-click Data Reduction
Gen5 automatically creates the Blank-Subtraction transformations.
 Click Transformation to set up the calculation:
5.
Click
Dual Wavelength Absorbance Endpoint | 63
6.
For DS1 (selected by default) use the drop-down list to select Blank 410
8.
Click OK to close the Multiple Data Set dialog
7.
9.
Select DS2 and use the drop-down list to select Blank 630
For this example, we'll call the New Data Set Name: Dual Wavelength. Enter
the name in the text box. Dual wavelength is also known as Delta OD, you may
want to use this name instead .
10. In the Plate Formula field enter: DS1-DS2 to subtract the reference
wavelength (630) measurements from the test (410) measurements. Retain the
default: Use single formula for entire plate.
11. Click OK to save and close the Transformation
 Click Curve Analysis. In the Data In tab, use the drop-down list to select Y
Data: Dual Wavelength and click OK.
For this simple protocol, the remaining default settings are acceptable.
More options are available, like customizing the names of data sets,
plotting interpolations in the generated curve, and so on. See Plotting
a Curve in the Data Reduction Options chapter.
 Click OK to close the Data Reduction dialog.
12.
Set the Report parameters and Data Views as desired. For instructions, see
Viewing Results.
13. Save the protocol: select File>Save and name it DualWave1 for this example.
0.
Run the protocol:
Now, you're ready to run the DualWave1 protocol in an experiment.
1.
2.
Select File>New Experiment. By default, Gen5 highlights the DualWave1
protocol in the dialog, making selection quick and easy.
If the reader is all set up, you're ready to go: Click Read and follow the online
prompts.
64 | Chapter 4: Assay Examples
Basic Absorbance Spectrum Analysis
Numerous applications can profit by a preliminary spectral screening. Here are
instructions for setting up a basic spectrum protocol in Gen5.
It may be easier to follow these instructions if you have already watched the Gen5
Basic series of online tutorials: select Help>Tutorials, or if you've completed the
learning exercises described in the Getting Started Guide.
1. Defining the reading Procedure
This assay example uses a kinetic read for analysis.
1.
Select File>New Protocol
3.
Click Read and change the Read Type to Spectrum
2.
4.
5.
6.
Open the Procedure (double click Procedure in the menu tree)
Set the Wavelength range: for this exercise set Start to 200 and Stop to 550
Set the Step to 3, and close the Read step
Click OK to save and close it.0.
2. Defining the Plate Layout
Define the plate layout in the usual way to reflect the arrangement of unknown
samples, standards and blanks on the microplate.
3. Defining the Data Reduction Steps
Now that you've defined the reading parameters and plate layout, you can define the
data reduction steps:
1.
2.
3.
4.
5.
6.
Select Protocol> Data Reduction
Gen5 automatically sets up the a Well Analysis for Min/Max OD. If Blanks
have been assigned to the plate, it will be preceded by and based on a blanksubtraction Transformation step.
Click Well Analysis to add another step
Enter a unique name for this step in the Label field
Select one of the offered Calculation Types: Integral or Formula
Click OK to save and close the step
Click OK to save and close Data Reduction0.
Basic Absorbance Spectrum Analysis | 65
4. Save the Protocol
1.
2.
Define the Reporting Requirements using the Report Builder or export options
Save the protocol0.
Now you can run it in an experiment: select File>New Experiment
5. Viewing the Results
After you read the plate, you can take advantage of Gen5's Well Zoom to examine the
results. This feature is described in the Kinetic Analysis chapter.
66 | Chapter 4: Assay Examples
Protein Quantification: Endpoint Absorbance
Here are instructions for the Gen5 portion of running this type of assay — the easy
part. Correctly mixing and dispensing the standards, and pipetting reagents to the
plate is the tricky part. Follow the assay instructions closely and modify these steps, as
needed. Click the links for instructions at each step.
1.
2.
Select File>New Protocol
Define the Procedure
1.
2.
3.
4.
5.
Select Protocol>Procedure
Click Read to add one read step
Keep the default settings:
 Detection Method = Absorbance
 Read Type = Endpoint
Set the Wavelength using the drop-down or enter 650 in the nm field
Click OK twice to close and save the Read step and the Procedure0
Protein Quantification: Endpoint Absorbance | 67
3.
Define the Plate Layout
Set up Gen5's plate layout to match your placement of samples and standards on the
plate, for example:
1.
2.
3.
4.
5.
4.
Select Protocol> Plate Layout
In the Well Settings box, select the Type of specimen, first Standards,
then Blanks, then Samples
Define the Concentration of the Standards:
Set the Replicates to 4
Assign the well IDs to their corresponding locations in the plate matrix
by clicking in the respective wells in the matrix. Use the Auto Select
options to speed up your work. 0
Define the Data Reduction:
Gen5 creates a Blank Subtraction data set when you put blanks on the plate, as defined
above. Click in the white space below the Transformation step:
 Click Curve Analysis to create a standard curve:
 Data In: Well ID is set to STD. Set the Y Axis = Blank [650]
68 | Chapter 4: Assay Examples
 Curve Fit: Method is set to Linear Regression
5.
Define the Reporting Requirements 0.
Save the Protocol
Select File> Save when you're finished setting up the protocol. You'll be able to use
this protocol repeatedly to run this assay in an experiment.
Select File> New Experiment and select the protocol when you're ready to run it, i.e.
reagents are reconstituted, the plate is prepared, etc.
Basic Fluorescence Assay Example | 69
Basic Fluorescence Assay Example
To help you set up your own assay in Gen5 here is an example of the steps required for
nucleic acids quantitation using a fluorescent stain, such as the dsDNA specific
PicoGreen™.
1. Defining the reading Procedure
This assay example defines a single-filter-set Fluorescent endpoint read:
1.
Select File>New Protocol
3.
Click the Read button and change the Detection Method to Fluorescence
2.
4.
6.
7.
8.
Select Protocol>Procedure
To set the Filter Set: filter-based reads use the drop-down list to select the
filter for Excitation and Emission, for this exercise 485/20 and 528/20,
respectively; monochromator-based reads enter 485 and 528 in the text fields.
Keep the Optics Position set to Top and if applicable select a mirror, e.g. Top
510, that corresponds to the selected filters. Top 50% works with any filter.
Enter 65 for the Sensitivity setting when using filters or enter 100 for the
setting when using the monochromator
Click OK twice to save and close the Procedure0.
2. Defining the Plate Layout
Define the plate layout in the usual way to reflect the arrangement of unknown
samples, standards and blanks, if any, on the microplate. For the sample protocol
shipped with Gen5, we set up the plate this way:
70 | Chapter 4: Assay Examples
Defining the expected concentration of the standards is the required to plot a curve.
Find specific instructions in the Preparing Plates chapter.
3. Defining the Data Reduction Steps
With the reading parameters and plate layout defined, Data Reduction steps can be
created: a standard curve for determining the concentrations of the unknown samples:
1.
Select Protocol> Data Reduction
3.
Notice on the Data In tab, the Well ID is set to STD and X Axis Data to <Plate
Layout Settings>. The known concentrations entered for Standards are plotted
on the X Axis. Use the drop-down list for the Y Axis Data to select
485/20,528/20 (or 485,528).
2.
4.
5.
Click Curve Analysis
Retain the default settings for Curve Fit and the Data Out tab. Take note that
the Data Set Name produced from the standard curve is called Conc (by
default. You can change it.). Click OK to save and close the curve.
Click OK twice to save and close Data Reduction0.
After the plate is read, you can return to the Data Reduction dialog to make any
needed changes, like the Curve Fit Method. Do not change the Data Out or Data Set
Names, this would invalidate the data reduction steps that use those data sets.
4. Save the Protocol
1.
2.
Define the Reporting Requirements using the Report Builder or export options
Save the protocol
Now you can run it in an experiment: select File>New Experiment
Kinetic Fluorescence Assay Example | 71
Kinetic Fluorescence Assay Example
To help you set up your own assay in Gen5 here is an example of the steps required to
measure antioxidant capacity based on the free radical damage to a fluorescent probe,
as in the Oxygen Radical Absorbance Capacity (ORAC) Assays. This protocol deploys
Gen5's Synchronized Plate Mode for precise timing of the measurements.
1. Defining the reading Procedure
This assay example defines a single-filter-set Fluorescent endpoint read:
1.
Select File>New Protocol
3.
Click Set Temperature and enter 37 for the temperature
2.
4.
5.
6.
7.
8.
9.
Select Protocol>Procedure
Click Plate Out/In and select Move plate in
Click Delay and enter 0:30:00 minutes to let the reader warm up
Click Plate Out/In and select Move plate out
Under Synchronized Modes, click Plate for a synchronized-plate mode block
Click Shake and change the Intensity to Fast and the Duration to 0:15 seconds
Click Kinetic and set the Run Time to 1:00:00 hour and the Interval to 0:01:00
minute
10. Click the Read button, change the Detection Method to Fluorescence and set
the Filter Set: filter-based reads use the drop-down list to select the filter for
Excitation and Emission, for this exercise 485/20 and 528/20, respectively;
monochromator-based reads enter 485 and 528 in the text fields.
11. Keep the Optics Position set to Top and if applicable select a mirror, e.g. Top
510, that corresponds to the selected filters. Top 50% works with any filter.
12. Enter 65 for the Sensitivity setting when using filters or enter 100 for the
setting when using the monochromator
13. Click OK twice to close and save the Read step and the Procedure0.
72 | Chapter 4: Assay Examples
2. Defining the Plate Layout
Define the plate layout in the usual way to reflect the arrangement of unknown
samples, standards, controls and blanks on the microplate. For the sample protocol
shipped with Gen5, we set up the plate this way:
Defining the expected concentration of the standards is required to plot a curve. Find
instructions in the Preparing Plates chapter.
3. Defining the Data Reduction Steps
Now that we've defined the reading parameters and plate layout, we can define the
data reduction steps: two well analysis steps and a standard curve.
1.
2.
Select Protocol> Data Reduction
Gen5 automatically creates two steps: the Blank Subtraction Transformation
and Well Analysis for Max V
Click Well Analysis to add another step to perform a calculation on the results
of individual read intervals:
6.
Enter a unique Label for this step, e.g. AUC
8.
Click OK
7.
3.
Select Formula and enter it in the text field:
(R1/R1)+(R2/R1)+(R3/R1)+(R4/R1)+(R5/R1)+(R6/R1)+(R7/R1)+(R8/
R1)+...(R61/R1). This formula normalizes the AUC (area under the
curve), the results are used to plot the standard curve to determine
unknown concentrations
Click Curve Analysis to plot a standard curve:0.
1
On the Data In tab, select the Y-Axis Data. In this example, choose the
Well Analysis "AUC: Formula Result [Blank 485/20, 528/20]" or [Blank
485,528]"
Kinetic Fluorescence Assay Example | 73
2
Click OK twice to save and close the Curve and the Data Reduction
dialog
After the plate is read, you can return to the Data Reduction dialog to make any
needed changes, like the Curve Fit Method. Do not change the Data Out or Data Set
Names, this would invalidate the data reduction steps that use those data sets.
4. Save the Protocol
1.
2.
Define the Reporting Requirements using the Report Builder or export options
Save the protocol
Now you can run it in an experiment: select File>New Experiment
74 | Chapter 4: Assay Examples
Fluorescence Assay with Injection
To help you set up your own assay in Gen5 here is an example of the steps required to
develop an ion channel assay and similar FRET assays which are well suited for
sodium, potassium, calcium and ligand-gated ion channel research. This protocol
deploys Gen5's Synchronized Well Mode to quickly switch between two emission
filters in well kinetic mode.
1. Defining the reading Procedure
This assay defines a kinetic dual-filter-set Fluorescent read:
1.
Select File>New Protocol
3.
Under Synchronized Modes, click Well for a synchronized-well mode block
2.
4.
5.
Select Protocol>Procedure
Click Kinetic and set the Run Time to 0:40.00 and the Interval to 00.15 second
Click the Read button and change the Detection Method to Fluorescence
1
2
6.
7.
8.
9.
3
Define the Filter Set using the filter wheels, for this exercise set the first
filter set to 360/40 and 460/40, and the second filter set to 360/40 and
590/35
Set the Optics Position set to Bottom and enter 65 for the Sensitivity
setting
Click OK to close and save the Read step
In the Procedure workspace, highlight the End Mode step and click Dispense.
Define the parameters for injecting the wells with 100 µl of a High K+ solution
to initiate depolarization. Select Tip priming
Click Kinetic and again set the Run Time to 0:40.00 and the Interval to 00.15
second
Click the Read button. Gen5 offers the limited-form read step because the
parameters must match the first read step. De-select Append to previous
Kinetic data and click OK (We're going to compare the before and after
injection data sets, so we do not want them combined into one.)
Click OK to save and close the Procedure0.
Fluorescence Assay with Injection | 75
2. Defining the Plate Layout
Define the plate layout in the usual way to reflect the arrangement of the cells and
blanks on the microplate. For this assay we set it up the plate this way:
Find instructions in the Preparing Plates chapter.
3. Defining the Data Reduction Steps
Now that we've defined the reading parameters and plate layout, we can define the
data reduction steps. This type of FRET assay supports a direct comparison between
the 590-nm and 460-nm fluorescence results via a ratiometric data reduction.
1.
2.
Select Protocol> Data Reduction
Gen5 automatically creates four Blank Subtraction Transformation steps and
four Well Analysis for Max V (one for each data set)
Click Transformation to add another step to determine the ratio of the preinjection (polarized) reads:
1
2
3
3.
4.
4
Click the Select multiple data sets button: click the button for DS2,
use the drop-down lists to select DS1: Blank Read 1:360/40,460/40 and
for DS2: Blank Read 1: 360/40,590/35
Enter a New Data Set Name, e.g. Polarized Em Ratio
In the Plate Formula field enter DS1/DS2
Click OK
Repeat Step 2 selecting Read 2 data sets to calculate the post-injection
(depolarized) ratio: DS1: Blank Read 2:360/40,460/40 and for DS2: Blank Read
2: 360/40,590/35. For this assay we called the New Data Set: Depolarized Em
Ratio
Create one more Transformation to calculate the response ratio:
76 | Chapter 4: Assay Examples
1
2
3
5.
6.
7.
4
Click the Select multiple data sets button: click the button for DS2,
use the drop-down lists to select the previously calculated ratios, we
named them DS1: Depolarized Em Ratio and for DS2: Polarized Em
Ratio
Enter a New Data Set Name, e.g. Response Ratio
In the Plate Formula field enter DS1/DS2
Click OK
Perform additional Data Reduction steps, as needed, for further analysis
outputs.
Define the Reporting Requirements using the Report Builder or export options
Save the protocol0.
Now you can run it in an experiment: select File>New Experiment
Fluorescence Area Scan Example | 77
Fluorescence Area Scan Example
To help you set up your own assay in Gen5 here is an example of the steps required to
perform a fluorescent area scan.
The Synergy 2's and Synergy 4's probe size limits its ability to
perform Fluorescence area scan in plates with a small well diameter.
Generally, this means you must use a plate with fewer than 96 wells.
1. Defining the reading Procedure
This assay example defines a single-filter-set Fluorescent area scan read on four wells:
1.
2.
Select File>New Protocol
Select Protocol>Procedure
 Synergy 2/4 users must change the Plate Type
3.
Click the Read button and change the Detection Method to Fluorescence
5.
Click the Full Plate button in the upper right corner of the screen
4.
6.
7.
8.
9.
Set the Read Type to Area Scan
Turn off the Use all wells by clicking the checkbox
Click and drag over the matrix to select four adjacent wells to read
Define the Filter Set
Keep the Optics Position set to Top and if applicable select a mirror, e.g. Top
510, that corresponds to the selected filters. Top 50% works with any filter.
10. Enter 65 for the Sensitivity setting when using filters or enter 100 for the
setting when using the monochromator
11. Click OK twice to save and close the Procedure0.
2. Defining the Plate Layout
Define the plate layout to reflect the arrangement of unknown samples, standards and
blanks, if any, on the microplate. Find instructions in the Preparing Plates chapter.
3. Defining the Data Reduction Steps
Gen5 automatically creates a Well Analysis Data Reduction step to determine the
Mean, Standard Deviation and CV% of the scanned wells. You can additional
calculations as needed: Protocol> Data Reduction
78 | Chapter 4: Assay Examples
4. Viewing the Results
1.
2.
To view the results on-screen:
Open the Plate View, and select the Scans data set in the Data field.
For a Well Zoom click on a well
Area scans can be used to determine the optimal settings for an assay.
Fluorescence Polarization Example | 79
Fluorescence Polarization Example
To help you set up your own assay in Gen5 here is an example of the steps required to
perform a fluorescent polarization experiment.
It may be easier to follow these instructions if you have already watched the Gen5
Basic series of online tutorials: select Help>Tutorials or if you've completed the learning
exercises described earlier. Learn more about Fluorescence Polarization in Gen5's Help.
To set up the protocol, we'll define the:
1.
Reading Procedure
3.
Data Reductions 0.
2.
Plate Layout
Reporting Results is the same process for all types of experiments
1. Defining the reading Procedure
This assay example defines a single-filter-set Fluorescent area scan read on four wells:
1.
Select File>New Protocol
3.
Click the Read button and change the Detection Method to Fluorescence
2.
4.
Select Protocol>Procedure
Select Polarization by clicking the checkbox
5.
Optionally, you can change the default settings for Light Source and Read
6.
To set the Filter Set, use the drop-down list to select the filter for Excitation
and Emission, for this exercise 485/20 and 528/20, respectively
7.
8.
9.
Speed
Gen5 automatically sets the Optics Position to Top and selects the mirror in
position 3 because the polarizers are located above this mirror in the mirror
holder. Since the mirror position is fixed for FP analysis, you must select a filter
set that corresponds to the mirror in position 3.
Enter 65 for the Sensitivity setting
Click OK twice to save and close the Procedure0.
2. Defining the Plate Layout
Define the plate layout to reflect the arrangement of unknown samples, standards and
blanks, if any, on the microplate.
80 | Chapter 4: Assay Examples
3. Defining the Data Reduction Steps
Gen5 automatically creates the Fluorescence Polarization steps, preceded by the blanksubtraction transformations if Blanks were assigned to the plate layout. You can add other
Data Reduction steps as needed: Protocol> Data Reduction
4. Save the Protocol
1.
2.
Define the reporting requirements using the Report Builder or export options
Save the protocol. 0.
Now you can run it in an experiment: select File>New Experiment
Basic Luminescence Glow Assay Example | 81
Basic Luminescence Glow Assay Example
To help you set up your own assay in Gen5 here is an example of the steps required to
use reporter genes, such as luciferase, for studying gene expression. The step-by-step
instructions provided here mirror the sample protocol shipped with Gen5 for Glow
Luciferase Assay.
1. Defining the reading Procedure
This assay example defines a single-filter-set Luminescent endpoint read:
1.
Select File>New Protocol
3.
Click the Read button and change the Detection Method to Luminescence
2.
4.
5.
6.
7.
Select Protocol>Procedure
Set the Integration Time to 1.0 SS.ss
To set the Filter Set, use the drop-down list to select the Hole for Emission
Keep the Optics Position set to Top and enter 200 for the Sensitivity setting
Click OK twice to save and close the Procedure
2. Defining the Plate Layout
Define the plate layout in the usual way to reflect the arrangement of unknown
samples, standards and blanks on the microplate. For the sample protocol shipped
with Gen5, a Blank well and 47 unknown Sample wells in duplicate were defined.
Find instructions in the Preparing Plates chapter.
3. Defining the Data Reduction Steps
With the reading parameters and plate layout defined, Data Reduction steps can be
created. Gen5 automatically creates the Blank Subtraction transformation. You can add
additional calculations as needed.
4. Save the Protocol
1.
2.
Define the Reporting Requirements using the Report Builder or export options
Save the protocol
Now you can run it in an experiment: select File>New Experiment
82 | Chapter 4: Assay Examples
Luminescence Flash Assay with Injection
To help you set up your own assay in Gen5 here is an example of the steps required to
use automated injection and luminescence detection for studying gene expression. The
step-by-step instructions provided here mirror the sample protocol shipped with Gen5
for Flash Luciferase Assay.
1. Defining the reading Procedure
This assay example defines a single-filter-set Fluorescent endpoint read:
1.
Select File>New Protocol
3.
Click Well to set up a Synchronized Well Mode block
2.
4.
5.
6.
Select Protocol>Procedure
Click Dispense and set the Volume to 100 and the Rate to 300
Click Delay to define a Delay Time of 0:02.00 (two seconds)
Click the Read button and change the Detection Method to Luminescence
1
2
3
4
Set the Integration Time to 5.0 SS.ss
To set the Filter Set, use the drop-down list to select the Hole for
Emission
Keep the Optics Position set to Top and enter 180 for the Sensitivity
setting
Click OK twice to save and close the Procedure
2. Defining the Plate Layout
Define the plate layout in the usual way to reflect the arrangement of unknown
samples, standards and blanks on the microplate. For the sample protocol shipped
with Gen5, 48 unknown Sample wells in duplicate were defined.
3. Defining the Data Reduction Steps
With the reading parameters and plate layout defined, Data Reduction steps can be
created. Gen5 automatically creates the Blank Subtraction transformation. You can add
additional calculations as needed.
4. Save the Protocol
1.
2.
Define the Reporting Requirements using the Report Builder or export options
Save the protocol
Now you can run it in an experiment: select File>New Experiment
Max Binding Determination/Competitive Assay | 83
Max Binding Determination/Competitive Assay
To help you set up your own assay in Gen5 here is an example of the steps required to
run a competitive ELISA assay to determine maximum binding. In this example we set
up an endpoint Absorbance read, subtract Blank wells from all others, subtract NSB
(non-specific binding) wells from all others, plot a standard curve, and define B/B0 as a
percentage of bound sample and identify the Total Activity (TA) wells.
1. Defining the reading Procedure
This assay example has a simple read Procedure: a single-wavelength Absorbance
endpoint read:
1.
Select File>New Protocol
3.
Click the Read button and select the wavelength. Use the drop-down list or
type the wavelength in the text field (overwrite the current value).
2.
4.
Select Protocol>Procedure
Click OK twice to save the Procedure
2. Defining the Plate Layout
This step is critical for the data reduction steps to be defined later. Here's the plate
layout we need:
The critical factor is using the Well IDs, not their location on the plate. We customized
the Well IDs for this example, changing the first three Assay Control IDs to NSB, Bo,
and TA. Then, defined the known concentration of the standards and assigned all of
them to the plate:
84 | Chapter 4: Assay Examples
Well ID Type
Description
BLK
Blank
DI water only
NSB
Assay Control Assay-specific
Bo
Assay Control Assay-specific
TA
Assay Control Assay-specific
STD
Standard
Known concentrations
SPL
Sample
Unknown samples
3. Defining the Data Reduction Steps
Now that we've defined the reading parameters and plate layout, we can define the
data reduction steps: blank-well subtraction, NSB subtraction, determine the percentage
bound and plot a standard curve. Gen5 creates the blank-subtraction step for you
automatically.
1.
2.
Select Protocol> Data Reduction
Notice that one Transformation, named "Blank nnn" where nnn is the
wavelength, has already been created. We'll use the results of this calculation to
build the next step.
Click Transformation
1
For the Data In use the drop-down list to select Blank nnn.
3
In the Formula field enter: (X-NSB)/(Bo-NSB)*100
2
3.
Click Curve Analysis
1
2
4.
Enter a New Data Set Name for the results of this calculation, e.g.
B/Bo
3
Notice on the Data In tab, the Well ID is set to STD and X Axis Data to
<Plate Layout Settings>. The known concentrations entered for
Standards are plotted on the X Axis. Use the drop-down list for the Y
Axis Data to select B/Bo (or whatever you named the New Data Set
Name in the previous step.)
Click the Curve Fit tab: depending on your assay, you may want to
change the curve fit method to 4 Parameters or another option, or use
Log values on the X or Y axis. For now, retain the defaults and click the
Data Out tab. Take note that the Data Set Name produced from the
standard curve is called Conc (by default. You can change it.).
Click OK to save and close the curve.
Save the protocol.
Now you're ready to define your reporting requirements, and run the protocol in an
experiment.
Max Binding Determination/Competitive Assay | 85
More Advanced Options
 Monitor Wells: Sometimes it is necessary/desirable to wait until a certain
amount of activity has occurred in the plate before reading it. Gen5 will
periodically check designated wells until they've reached a certain
measurement when the Monitor Wells option is used. When the criterion is
met, Gen5 continues the Procedure, i.e. the regular plate reading is performed.
86 | Chapter 4: Assay Examples
Toxicity/Cytotoxicity Assay
To help you set up your own assay in Gen5 here is an example of the steps required to
run a Toxicity or Cytotoxicity assay to determine LD50 (lethal dose). In this example
the Read step is straightforward, but the Plate Layout takes full advantage of Gen5's
ability to customize Well IDs. We'll create two samples with six dilutions each, and a
control and blank for each sample. Then, we'll plot a standard curve based on blanksubtraction and toxicity percentage. We'll use Gen5's Curve Interpolation to identify
LD50. toxicology
1. Defining the reading Procedure
This assay example has a simple read Procedure: a single-wavelength Absorbance
endpoint read:
1.
Select File>New Protocol
3.
Click the Read button and select the wavelength. Use the drop-down list or
type the wavelength in the text field (overwrite the current value).
Alternatively, you may want to perform a kinetic analysis.
2.
4.
Select Protocol>Procedure
Click OK twice to save the Procedure
2. Defining the Plate Layout
This step is critical for the data reduction steps to be defined later. Here's the plate layout we
need:
Toxicity/Cytotoxicity Assay | 87
The critical factor is setting up the Well IDs and dilution values. For the Samples,
(notice there are only two samples on the plate) we defined the known dilution values
and assigned them to the plate using the Auto Select features Next ID and Next Dil for
3 Replicates. We customized the Well IDs for the Sample Control IDs to BLK to have
sample-specific blanks and assigned them to plate without using the Auto Select
features. Assay Controls were assigned to the plate in the same way as the BLK1 and
BLK2.
Well ID Type
Description
SPL
Sample
Unknown samples with dilution values
CTL
Assay Control
Sample-specific
BLK
Sample Control Customized to be sample specific
3. Defining the Data Reduction Steps
Now that we've defined the reading parameters and plate layout, we can define the
data reduction steps: blank-well subtraction, toxicity percentage determination and a
standard curve.
1.
2.
Select Protocol> Data Reduction
Click Transformation
1
2
3
Enter a New Data Set Name for the results of this calculation, e.g.
%Toxicity
De-select the Use single formula for all wells
4
In the Current Formula field enter: (X-BLK1)/(CTL1-BLK1)*100
6
Change the Current Formula for SPL2 wells: (X-BLK2)/(CTL2BLK2)*100 and assign the formula to them
5
3.
For the Data In only one data set, the raw data from the Read step is
available.
7
Click and drag over the SPL1 wells to assign the formula to them
Click OK to save and close the Transformation
Click Curve Analysis
1
2
On the Data In tab, the Well ID is set to SPL- All IDs and X Axis Data
to <Plate Layout Settings>. The known dilutions entered for Samples
are plotted on the X Axis. Use the drop-down list for the Y Axis Data to
select % Toxicity (or whatever you named the New Data Set Name in
the previous step.)
Click the Curve Fit tab and change the curve fit method to 4 Parameters
(unless you prefer another method).
88 | Chapter 4: Assay Examples
3
4.
5.
Click the Data Out tab, in the Interpolations table enter 50 (and 90, if
desired). 50 represents 50% toxicity and it will be plotted on the curve.
Click OK to save and close the curve.
Save the Data Reduction steps (click OK)
Save the protocol
Now you're ready to define your reporting requirements, and run the protocol in an
experiment.
Endotoxin Test | 89
Endotoxin Test
Here are some guidelines for setting up a protocol to detect endotoxins in test samples
using a Limulus Amebocyte Lysate assay kit.
There are numerous variables when running this type of experiment.
This example uses a kinetic analysis rather than an endpoint, for
instance. Modify these procedures to comply with your assay kit
instructions.
First, create a new Protocol: Select File>New Protocol
Set up the Procedure
1.
Begin with Set Temperature
3.
Add a Shake step to mix the ingredients in the well
2.
4.
Add a Delay step to incubate the plate
Add a Monitor Well step to delay the start time for collecting actual
measurements until selected wells reach an OD of 0.05.
Gen5 sets up well monitoring as a loop in the Procedure.
1
Click Monitor Well to add the loop to the Procedure.
3
With the End Monitoring step highlighted, click Read to define the
reading parameters for well monitoring.
2
4
5.
6.
7.
Define the criteria that must be met before the reader moves onto the
next step
Select the wells to monitor and define the same reading parameters as
the actual read step: Absorbance read at 405 nm.
Add Kinetic and set the Run Time to 50 minutes and the Interval to 15
seconds
Set the Read step to Absorbance at 405 nm.
Click OK twice to save and close the Procedure.
90 | Chapter 4: Assay Examples
Define the Plate Layout
Take note of some of the conditions particular to this type of assay: Standards with
decreasing concentration values, and only one Sample, with known dilution values, is
assigned to the plate using the Auto Select features Next ID and Next Dil, in duplicate.
For the "Spiked Samples" we customized the Well ID of Sample Controls (SPLC),
changing it to Spike and assigned a concentration value. The Assay Control IDs were
customized to Pos and Neg.
Well Type
ID
Standard
STD
Sample
SPL
Sample Control
Spike
Assay Control
Pos & Neg
Blanks
BLK
Set up Data Reduction
Data reduction, in this endotoxin example, requires a blank-subtraction, an onset OD
well analysis, a standard curve and a transformation for % Recovery determination.
Gen5 creates the blank-subtraction data set and a Max V Well Analysis step
automatically.
1.
Select Protocol>Data Reduction
Gen5 created the Blank 405 data set (if you defined this wavelength for the
Read step) and used Blank 405 as the Data In for the Well Analysis step. (You
can retain or replace the Max V step.)
Endotoxin Test | 91
2.
Click Well Analysis to determine the Onset OD (if this is the second Well
Analysis step, give it an unique Label):
1
Set the Data In to Blank 405
3
Enter 0.03 for the value.
2
3.
Click Curve Analysis to create a standard curve:
1
2
3
2.
1
3
On the Curve Fit tab: select Linear Regression for the method and
change the X Axis Data and Y Axis Data Transformation to Log
On the Data Out tab: select both Calculate Concentrations options.
Enter a Data Set Name for the Concentration X Dilution results: Conc
X Dil.
For the Data In select Conc X Dil
Enter a New Data Set Name: % Recovery
De-select the Use single formula for all wells
4
In the Current Formula field enter: (Spike1-SPL1:1)/(.125)*100
6
Change the Current Formula for SPL1:2 wells: (Spike2SPL1:2)/(.125)*100 and assign the formula to the Spike2 wells
5
7
4.
On the Data In tab: set the Well ID to STD and the Y Axis Data to t at
Total OD [405]
Click Transformation to calculate the percentage recovery:
2
3.
Select the button for Onset OD
Click in the Spike1 wells to assign the formula to them
Change the Current Formula for SPL1:3 wells: (Spike3SPL1:3)/(.125)*100 and assign the formula to the Spike3 wells
Repeat the process for all the spiked samples
Create two Validation steps:
1
Click Validation and set the Data In = t at Total OD [Blank 405]
2
Click Validation and set the Data In = % Recovery
 enter
the Formula = Neg>STD5*1.1
 enter
the Formula = 50%<Spike#<200%
Set up the Report
Define your reporting requirements as with all other types of experiments.
Save the Protocol
Select File>Save when you're finished setting up the protocol. You'll be able to use
this protocol repeatedly to run this endotoxin assay in an experiment. Select
File>New Experiment and select the endotoxin protocol when you're ready to run it,
i.e. reagents are reconstituted, the plate is prepared, etc.
92 | Chapter 4: Assay Examples
ß-Galactosidase
Quantitation of ß-galactosidase (ß-gal) enzymatic activity is a commonly used
determination in cellular and molecular biology. A colorimetric assay using onitrophenol-B-D-galactoside (ONPG) as the substrate for ß-gal is described in an
Application Note on BioTek's website. Here are instructions for setting up this type of
assay in Gen5.
1. Defining the reading Procedure
This assay example uses a kinetic read for analysis.
1.
Select File>New Protocol
3.
Click Kinetic. Gen5 opens the Kinetic Step controls. Define the timelines:
2.
4.
5.
Open the StepWise Procedure
 Enter 0:30:00 minutes for the Run Time
 Set the Interval to 0:00:30 seconds
With the End Kinetic step highlighted, click Read and set the Wavelength to
420
At the Procedure dialog, click OK to save and close it.
2. Defining the Plate Layout
This assay requires 12 standards are decreasing concentration. The plate layout is
critical to the data reduction steps defined later:
The Standard concentrations can be defined in Gen5 using the Auto entry tools:
ß-Galactosidase | 93
1.
2.
3.
4.
5.
6.
Set the Well Type to Standard
and click the 3-dot button next to
the Conc. field
Enter 10 in the table for STD1
Fill the checkbox next to Fact. and
enter .5 in the text field
Click in the STD2 cell in the table
to apply the factor
Click in or use the down arrow
key to move to each next cell
until STD12
Change STD12 to 0
Assign the location of the standards and unknown samples to the plate.
3. Defining the Data Reduction Steps
Now that we've defined the reading parameters and plate layout, we can define the
data reduction steps: two well analysis steps and a standard curve.
1.
2.
Select Protocol> Data Reduction
Gen5 automatically sets up the first Well Analysis for MaxV
Click Well Analysis to add another step
1
2
3.
3
Select the Mean V Calculation Type
Click OK to save and close the step
Click Curve Analysis to define a standard curve
1
On the Data In tab set the Y-Axis Data to Mv: Mean V[420]
3
Click OK to save and close the curve step
2
4.
Enter a unique name for this step in the Label field, e.g. Mv for this
exercise
On the Curve Fit tab select 4 Parameters
Click OK to save and close Data Reduction0.
4. Save the Protocol
1.
2.
Define the reporting requirements using the Report Builder or export options
Save the protocol0.
Now you can run it in an experiment: select File>New Experiment
94 | Chapter 4: Assay Examples
Dispensing Reagent
Dispensing reagent during an experiment is affected by the type of analysis. Select the
option that most closely fits your requirements:
 Dispensing Reagent in a Kinetic Analysis
 Dispensing Reagent in an Endpoint (non-kinetic) Analysis
Dispensing Reagent in Kinetic Analysis Protocols
If dispensing is required during a kinetic read, here are two options:
Manually Dispensing Reagent:
Create a protocol with an extended kinetic interval; add enough time to dispense
reagent to the plate between readings. During an interval, when the reader is idle:
1.
Push the carrier eject button on the front of the reader to eject the plate
3.
Push the carrier eject button to draw the plate back in
2.
4.
Perform the dispense using a pipette
The read will continue as scheduled0.
Readers with Injectors:
Standard Mode:
Define two kinetic read steps around a dispense step in the Procedures:
1.
Set the Kinetic timelines, define the Reading parameters, and End the loop.
3.
Add a second Kinetic loop, kinetic settings can differ. Add a Read step to the
loop, and check Append to Previous Kinetic Data. Selecting this option copies
the previous defined reading parameters, e.g. wavelength/filter set, to this
step. 0.
2.
After the loop, add a Dispense step to dispense the reagent. (You can add a
Delay and/or Shake step after dispensing and before the next kinetic loop.)
Dispensing Reagent | 95
Synchronized Mode:
For Fluorescence or Luminescence analysis select Plate or Well Mode to most precisely
control the timing of your experiment. Learn About Synchronized Modes in Gen5’s
Help.
1.
Add a Plate or Well mode block to the Procedure
3.
Add a Read step to the block, defining the reading parameters as needed.
2.
4.
Create a Dispense step to dispense the reagent. (You can add a Delay, and in
Plate mode a Shake step, after dispensing and before reading.)
Within the block you can repeat any or all of the options: Dispense, Delay,
Shake in Plate mode, and Read, again. Note: the first Read step in the block sets
the parameters0.
Dispensing Reagent in Endpoint Analysis
Manually Dispensing Reagent:
Add a Plate In/Out step to the Procedure:
1.
2.
3.
You might want to incubate the plate before adding the reagent. If so, and your
reader is capable, add a Set Temperature step.
Add a Plate In/Out step. Enter "Add Reagent" in the Comment field.
Add a Read Step.0.
Readers with Injectors:
Define a dispense step in the Procedure:
1.
Create a Dispense step to dispense the reagent.
3.
Add a Read step.0.
2.
Add a Delay and/or Shake step after dispensing, if desired.
96 | Chapter 4: Assay Examples
 Other Options
Multi-Detection Methods
For readers capable of performing multiple detection methods, like BioTek's Synergy
models, Gen5 supports multi-detection kinetic protocols.
Discontinuous Kinetic Procedure
A Discontinuous Kinetic Procedure can be defined to execute a sequence of readings
over an extended time period. Use the Procedure's Advanced Options to conduct an
experiment that requires long periods of downtime (for rest or incubation) between
reads. Learn more in the Gen5 Help.
Fast Kinetics with Injection for Absorbance | 97
Fast Kinetics with Injection for Absorbance
for Synergy HT with Injectors, Synergy 2, and Synergy 4
multi-detection readers Synergy 2 and Synergy 4 can perform
 BioTek's
absorbance reads in Synchronized Mode, providing more ways to perform fast
kinetics. You may need to experiment with the various options to determine the
best method for your assays. Generally, for the shortest kinetic intervals, < 2
seconds, use Well Mode. For intervals > 15 seconds, use Synchronized Plate
Mode. Alternatively, copy the procedure described here, it is a work-around for
Synergy HT.
Gen5 lets you dispense fluid to wells when performing a kinetic absorbance analysis, but
the Synergy HT cannot perform Absorbance reads in Synchronized Mode. Here is a way to
mimic this fast kinetic behavior: define the Procedure to dispense and read one row at a
time, like this:
3.
Add a Dispense step
1.
Click the Full Plate button and change it to read the first row, A1-A12
3.
Set the Dispense Volume
2.
4.
4.
Select Priming and set the Volume to 20 µl
Click OK0.
Click Kinetic, set the Run Time and click Minimum Interval
98 | Chapter 4: Assay Examples
5.
Add the Read step
5.
Click the Full Plate button and change it to read the first row, A1-A12
7.
Select the wavelength
6.
6.
7.
8.
Set the Read Speed to Sweep
Click OK0.
Now, repeat steps 3-5 selecting the next row (e.g., B1-B12, then, C1-C12 ...) for
each series of steps. Note: Highlight the empty space beneath the End Kinetic
step before adding the next Dispense step. When defining the subsequent Read
steps, de-select Append to previous Kinetic data to enable the reading
parameters controls.
When you've defined a Dispense step and Kinetic read for each row of the
plate, click Validate to obtain the minimum kinetic interval for each read and to
make sure the reader can perform the Procedure. 0.
Chapter 5
Basic Tasks
This section provides instructions for performing basic tasks in
Gen5. It also describes the process for creating an Experiment
(based on a protocol).
Quick Read ............................................................................. 100
Create a Standard Curve........................................................... 101
View Results............................................................................ 102
Print Results............................................................................ 104
Quick Export ........................................................................... 105
Quick Output Options ............................................................... 106
Test the Reader ....................................................................... 108
Setting up an Experiment ......................................................... 109
Read a Plate ............................................................................ 110
100 | Chapter 5: Basic Tasks
Quick Read
In Gen5, a Quick Read is using the microplate reader connected to the PC to read a
plate and report the results. It's called quick because it is accomplished without taking
the time to set up a protocol.
To perform a Quick Read:
1.
2.
Click Read a Plate from the Welcome page (and skip down to Step 4)
or Click
or select File>New Experiment
Select Default Protocol
3.
Click
(the Read button)
The Procedures dialog opens.
4.
Click
and enter the desired reading parameters, and any other
needed steps. When you click OK to save and close the Procedure, the Plate
Reading dialog opens.
5.
Click Read0.
When the reading is done you can report the results or select a view and click the
Quick Export button to use Excel® to manipulate the data.
How to Create a Standard Curve | 101
How to Create a Standard Curve
Gen5 lets you create one or more standard or calibration curves for determining the
concentration of test samples:
1.
Select File> New Protocol
3.
Select Plate Layout:
2.
4.
5.
6.
7.
Select Procedure and define the Read step (and any other required steps)
 Define the Concentrations of the Standards
 Assign the location of the standards, samples, and blanks (if any) on the
plate
Select Data Reduction> Curve Analysis
 Gen5 may have generated a "corrected" data set: if you assigned blanks to
the plate or selected Pathlength Correction in the Read step, you'll want to
select these data sets for Data In for the Y-Axis Data when plotting the
curve
On the Data In tab, use the drop-down to select the Y-Axis Data
On the Curve Fit tab, choose a curve fit method
Other options and requirements when defining multiple curves:
 Curve Name: replace the default "Curve" with a more meaningful or unique
name
 On the Data Out tab, replace the default "Conc" for the Data Set Name with
a more meaningful or unique name
8.
 On the Data Out tab, define interpolations to plot on the curve
Define the reporting or export requirements and Save the protocol. Now,
you're ready to run an experiment: select File> New Experiment to read the
plate and generate the curve.0.
102 | Chapter 5: Basic Tasks
Viewing Results
Learn more in the Viewing Results chapter.
You can instantly view the results of an experiment in Gen5's main workspace using
the Plate View:
 After reading the plate (or otherwise acquiring data), in the Plate View use the
drop-down list for Data to display the raw data and any data reduction results

Click the 3-dot button next to a data set to customize the view's
appearance, including changing the numeric Format, e.g. number of decimal
places, and the Font. (This feature is also available in the Data Views dialog.)
 ** Asterisks are used to signal a change: in Gen5's title bar an asterisk
indicates the current file has been changed but not-yet saved. When asterisks
enclose a data set it has been become invalid. Generally this is because a Read
step or Data Reduction step has been altered. Edit custom-made data views to
select valid data sets

384- and 1536-well plates require resizing to effectively see the data. Gen5
adds a button to the Plate View to zoom in on the top-left quadrant of the plate
and zoom out to view the entire plate. After zooming in, use the scroll bars to
bring the other quadrants into focus. Find more on resizing the views in Gen5’s
Help

Click the Quick Export button to instantly open the current view in Excel®.
Learn more about Gen5's Export Options
 Multi-index readings offer another viewing option. Kinetic and scanning reads
generate views based on the number of read intervals, wavelengths, or
Viewing Results | 103
positions defined. Use the spin buttons or enter the desired read index and
click Show to display it. Gen5 displays the time, wavelength, or position of the
selected read number.

Kinetic and Scanning protocols can generate Well Analysis data sets
labeled Curves in the Matrix drop-down list, open the Curves data set and click
on a well for a Well Zoom
Starting at the Curves data set, you can display multiple well zooms
simultaneously by holding down the Ctrl key while selecting (up to 8) wells
 You can also select Create new Matrix to define a new view
 Select the Statistics tab to view a table of data reduction results
 Select the Graphs tab (when available) to view any Curves, except kinetic
analysis curves, which Gen5 calls Well Analysis and is described above
 Select the Cutoffs tab (when available) to view the values or results of the
cutoff formulas
 Select the Validation tab (when available) to view the values and results of the
validation formulas
 Review this description of Gen5's naming convention for the raw data/results:
Data Set Naming on page 316
 Important Notes:
 Gen5 may not display some data points by default; to see them you must
create your own Data Views. If you expected to see certain results that are
not currently displayed, try creating your own views.
 All data views are also available for Reporting and/or Exporting
 Gen5 always uses your computer's Regional Settings to display and input
data.
 Modify a data view to change the way results are reported, including the
number of decimal places and significant digits. Learn more in the Viewing
Results chapter, including the meaning of the Symbols and Notations
displayed
104 | Chapter 5: Basic Tasks
Printing Results
Gen5 offers numerous options for results output. It's report engine offers two primary
outputs:

Click the Print button to print the results of an experiment AFTER you
have created a report.
 QuickPrint instantly generates a print out of the current view or selection.
After selecting the current view or specific content, right-click and select
QuickPrint. Click and drag to select contiguous cells or hold down the Ctrl key
and click to select non-contiguos cells.
Create a Report:
Before you can print a report, you must select the report content using Gen5's Report
Builder.
Reporting in an experiment is done on a per plate basis:
 Highlight a
in the menu tree and select Print/Print Preview.
 In a multi-plate experiment: You can select multiple plates by holding the
Ctrl key while highlighting them, or to select contiguously-ordered plates,
highlight the first plate, hold down the Shift key and select the last plate.
Then, click the Print button.
Gen5 offers enormous flexibility in report output. After defining the report
elements, use the Print Preview option to view the report on-screen before printing it
to paper. Unneeded columns and other individual report elements can be removed or
modified to improve the appearance and usefulness of the report.
More Information:
Find step-by-step instructions for creating and customizing reports in the Reporting
Results chapter.
Quick Export | 105
Quick Export
Click the Quick Export button to instantly create a copy of the current screen in
Excel®.
Where it works:
Wherever you see the Quick Export button, you can export the view. Almost every
Data View has a Quick Export button. For example, the Matrix, Statistics, Cutoff and
Validation tabs offer it and the Graph tab has two, one for the curve and another for
the Curve Results Table.
Adjust the Quick Export Settings to select the target spreadsheet for the Quick
Export. You can add items to the bottom of an existing Excel worksheet, for example.
Select Protocol>Protocol Options>Quick Export Settings.
If you don't have MS Excel:
Use one of these options (described in the Exporting Results chapter) to select content
and export it for use in another software application:
 File Export Builder: to export selected data to a text file
 Right-Click Menu Options - Copy to Clipboard and Save As: to copy or save
the current selection for use in another software application
106 | Chapter 5: Basic Tasks
Quick Output Options
In addition to the
Quick Export option, Gen5 offers several ways to output data,
results and current views. Use the right-mouse-click menu that is available in most views
for instant printing or exporting content for use in other software applications.
Simply right-click to select the entire current view for a quick output. Or, to limit the
output: click and drag to select contiguous cells or hold down the Ctrl key and drag to
select noncontiguous cells, then right-click for an option.
Copy to Clipboard
1.
2.
3.
After selecting specific content or a current view, right-click and select the
Copy to Clipboard feature
Open another software application, e.g. Microsoft® Word, WordPad, Paint,
Outlook and similar products offered by other manufacturers, where you want
to use the Gen5 content
Paste the selected content. Try:0.
 Ctrl-V
 Right-click and select Paste
 From the menu, select Edit> Paste
Quick Print
You can print the whole view or click and drag an area to select specific content for the
QuickPrint.
 After selecting specific content or a current view, right-click and select the
QuickPrint feature.
Quick Output Options | 107
It is similar to printing from the Report Builder, you can select a local printer. The
current view or selected content is printed in formatted text with row and column
headers.
Save As
In any graph, i.e. Curve or Well Zoom, you can:
1.
Right-click and select the Save As feature
3.
Use the drop-down list to select the Save as type: 0.
2.
Gen5 opens the standard Save As dialog so you can browse to any
file/directory available to your PC to choose the Save In location
 Portable Network Graphic (.png)
 24-bit Bitmap (.bmp)
 CompuServe Graphics Interchange Format (.gif)
 JPEG Format (.jpg)
 Windows Enhanced Meta File (.emf)
Export Multiple Plates to One File
When you run multiple plates in an experiment you can export all the data to one text
file:
1.
2.
In the menu tree, select/highlight multiple plates (by holding down the Ctrl
key)
Right-click and select File Export0.
Make sure the File Export Settings are defined to automatically append
the data.
108 | Chapter 5: Basic Tasks
Reader System Test
System> Diagnostics> Run System Test
The System Test for the Clarity™ Microplate Luminometer must be
performed using the Clarity PC software. Refer to the Clarity
Operator’s Manual for instructions.
Run the Test
Most BioTek readers perform a self-test every time they're turned on, but when you want
to view and/or print the results of a system (aka optics) test:
1.
Select System> Diagnostics>Run System Test
3.
When the test is completed:0.
2.
When there is more than one reader attached to the PC, select the desired
reader and click OK
1.
2.
3.
Test History
Fill in the text fields, User, Company, Comments, to be included in the
report of the test results. Then, click OK.
Print the report to retain a hard copy for your records
Save As to convert the results to a text file. This is especially useful when
troubleshooting a reader. You can email the text file to BioTek TAC.0.
Gen5 keeps the results of System Tests when they are performed using the menu
controls. To review or print them, select System> Diagnostics> Test History...
Setting up an Experiment | 109
Setting up an Experiment
File> New Experiment
About Experiments
In Gen5, all plates are processed in an Experiment, which is based on a protocol. The
Experiment holds all the information: the Protocol as it was executed, the plate layout,
the raw data, and the transformed data and calculation results from Data Reductions.
An experiment is stored in a file with an .xpt extension.
How to:
1.
2.
3.
Click the
button or select File>New Experiment
This opens the Protocol selection dialog with the most recently
opened/modified protocol selected
Select a protocol:
 You can select an existing one: double-click the desired protocol, or
 Select Default Protocol
Review (and modify as needed) the elements of the selected protocol, and
when you're ready click the Read button
4.
Select File>Save or click
 In an experiment, you can:
and give the experiment file a unique name.0.

Add Plates: to process additional plates using the same protocol

Read multiple plates: when multiple plates have been defined in an
experiment, highlight one and hold the Ctrl key to select others, then right
 Delete and Renumber Plates: When multiple plates have been added to an
experiment, highlight a plate in the menu tree, right click and select Delete.
After removing a plate, right click and select Renumber All, if needed
click for options: Read or Print

Use the Quick Export feature to instantly export the current view to
Excel®
You can make changes to the Protocol when running it in an Experiment. Select
File>Save Protocol As to save the changes for a future experiment. Otherwise, the
Experiment's protocol and the original Protocol will be different.
110 | Chapter 5: Basic Tasks
Read a Plate
Highlight the plate in the menu tree and click the Read button on the toolbar or
right-click and select Read to read the plate.
Prerequisites and other issues:
 Minimally, you must define some reading directions, like wavelength. In Gen5
this is a Quick Read
 If the reading is part of an experiment or assay that you'll perform numerous
times, create a new protocol
 Click the Read button when an experiment is stopped and you want to begin
again:
 you can Resume a reading procedure: continue from the stopping point, if
a Stop/Resume step has been defined
 or Re-Read the plate, starting from scratch, i.e. overwriting any previously
obtained measurements
 Define the Runtime Prompts: You can customize the "prompts" or text fields
users see when they read a plate
Immediately before a read:
 Runtime Prompts: Fill in the fields defined in the Protocol as Runtime Prompts
 Set Temperature: Gen5 displays a warning message telling users to wait until
the defined temperature is reached before proceeding with the read
 Load Plate: Gen5 displays the current reading-chamber temperature (if the
reader has an incubator). If the temperature is too high, you can Cancel the
read to wait until it cools down
Acquiring Data
There are three ways for Gen5™ to acquire the data used in calculations and analysis:
 Reading a plate
 Manual entry
 Import a text file
In Gen5 select Help>Help Topics to learn about the latter two options.
Chapter 6
Designing a Protocol
This chapter covers the steps required to create a protocol. It also
provides instructions for using the Default Protocol.
Define the Procedure ................................................................ 113
Define the Plate Layout............................................................. 111
Define the Data Reduction ........................................................ 116
Define the Reporting Requirements ............................................ 118
Using the Default Protocol......................................................... 119
112 | Chapter 6: Designing a Protocol
Design a Protocol
The menu tree provides a visual clue to the steps involved in creating most protocols
(File>New Protocol... opens only the Protocol section of the menu tree):
1.
Define the Procedure (or Reading Parameters)
3.
Define the Data Reduction Requirements (for all except Gen5 Reader Control)
2.
4.
5.
6.
Define the Plate Layout (for all except Gen5 Reader Control software)
Define the Runtime Prompts to collect user input at runtime (plate reading)
Define the Reporting Requirements
Save the Protocol0.
Important: follow this sequence of tasks, when developing a protocol
to take advantage of Gen5's automatically created data reduction
events. For example, when you add Blanks to the Plate Layout, Gen5
automatically creates a Blank-Subtraction data set.
You can find specific, step-by-step instructions for numerous types of protocols in
Gen5's Help system.
Protocols are run or executed within an Experiment. Learn more about the differences
between Experiments and Protocols in the Essential Concepts chapter
Alternatively, you may want to begin with one of Gen5's Sample
Protocols described in Chapter 4. They can give you a head start.
Defining the Reading Procedure | 113
Defining the Reading Procedure
Protocol> Procedure
Set up the Procedure to control the reader: define the
parameters and related activities of the Protocol/Experiment.
reading
Grayed out? Once a reading has been done in an experiment, the
Procedure cannot be changed for the current experiment. If this isn't
the case, your System Administrator may have restricted your ability
to modify the protocol elements.
Grayed out buttons mean the action cannot be performed by the
current reader or because previously defined steps, e.g. kinetic loop,
limit the function.
How to:
1.
2.
3.
Click a button to add that step to the procedure. Most buttons open a screen for
defining the parameters of that step, e.g. Read lets you define wavelengths, etc.
When defining a kinetic or synchronized well/plate mode analysis, add the
Kinetic or Synchronized Mode steps first. Kinetic and Synchronized Mode
steps form a loop or block. Put the Read and other valid steps to be performed
inside the loop, between the Start and End. Monitor Well is similar, first add
the Monitor Well step and then, add a Read step inside the monitor-well loop.
Define the details of the step and click OK
Click Validate to check the selection and sequence of the steps
Your reader must be communicating with Gen5 for it to fully validate
the Procedure: make sure your reader is turned on, not busy, and
properly connected to the PC.
More details and a Validation Checklist are provided in the Defining a Procedure
chapter beginning on page 121.
114 | Chapter 6: Designing a Protocol
Modify a Protocol
Gen5 does not restrict your ability to change a protocol, but other factors may:
 the Procedure cannot be changed in an Experiment after more than one plate
has been read. Other protocol elements, like Data Reduction and reporting
parameters can be changed at any time.
 Gen5 Secure's System Administrator can prohibit a user's ability to modify a
protocol.
 All Gen5 System Administrators can limit users' ability to modify the Default
Protocol.
To change the Procedure, you can:
 When only one plate has been read in an Experiment, you can modify the
Procedure and then re-read the plate, but this requires deleting the data
originally obtained from the reader,
 Alternatively, create a new Experiment based on the Protocol, then change
the Procedure and re-read the plate,
 Or, open the original Protocol, revise and save it, then create a new
Experiment based upon it.
Gen5 tracks plate deletions in the Audit Trail
Changing the protocol is easy:
7.
8.
9.
Open the protocol element you want to modify. For example, double-click
Procedure in the menu tree.
Make the required changes:
 In the Procedure and Data Reduction dialogs, double-click an alreadydefined step to open it for editing
 For other protocol elements, use the controls to make the needed changes.
When you're happy with the changes, save the file (File>Save or File>Save
Protocol As). 0.
Defining the Plate Layout | 115
Defining the Plate Layout
Protocol> Plate Layout
It's easy to define the plate layout with Gen5's tools for identifying samples, standards,
controls and blanks. Follow these steps:
In the Well Settings box in the top-left corner, select the Type of specimen
1.
2.
Customize the ID or Well Identifiers, if necessary, by clicking the 3-dot
button.
3.
Define the Concentration or Dilution, if applicable, by clicking the 3-dot
button.
4.
Assign the well IDs to their corresponding locations in the plate grid by
clicking in the wells in the matrix.0.

When you select a corresponding starting # the ID changes
accordingly for assignment to the plate.
 Use the Auto Select and Replicates options to speed up your work: set the
options and click and drag to fill multiple wells at once. Click a column or
row header to fill it.
The type of plate, e.g., 96-well, is defined in the Procedure and
displayed in a representative matrix or grid format in the Layout and
Transformation screens.
More details are provided in the Plate Preparation chapter beginning
on page 219, and Gen5’s Help offers an instructive animated demo of
the process: Select Help>Tutorials.
116 | Chapter 6: Designing a Protocol
Setting up Data Reduction
Protocol> Data Reduction
There are several options available for interpreting the results of your experiment.
Gen5™ automatically creates the most commonly applied data reduction steps (based
on previously-defined Protocol parameters). You can design your own or modify the
calculations.
Find more details and the Top 6 Things You Should Know about
Data Reduction in the chapter beginning on page 245.
Data Reduction Options
Find details about each option in the Data Reduction Options chapter.

Define a Transformation

Define a Curve Analysis

Define a Well Analysis

Define Cutoffs

Define Validation criteria

Fluorescence Polarization

Gen5 shows an invalid data reduction step by blocking out its icon.
Changing the Procedure, e.g. reading parameters or sequence of
events, renaming a Read step or data set, or making other Protocol
changes can invalidate a data reduction step. Generally, it is easiest to
delete the invalid step and recreate it, selecting valid options.
Customizing Data Views, Reports, and Exports | 117
Customizing Data Views, Reports, and Exports
Gen5™ provides several tools for changing the appearance of views and reports. All
selections and customizations to views and to report and export elements can be saved
with the protocol, (File>Save Protocol As) so they are retained for all future
experiments based on that protocol.
Check out the tips and rules for customizing the views and output format of data
elements:
 Best Practice:
 A good habit to develop when setting up a Protocol is customizing the content
and format of the Data Views: the on-screen presentation of data. The settings
defined in Data Views become available for selection in the Report Builder and
Export definition screens, so it is most efficient to begin with Data Views (after
defining the Procedures, Plate Layout, and Data Reduction details)
 Important: Attributes applied to data items and field groups in the Data Views
dialog take effect going forward. They do not replace, update, or overwrite an
item that has previously been assigned to a Report or Export output. You must
refresh the Report/Export contents after making any changes to a data element,
to capture them in the report. Any previously saved Experiment will not reflect the
content or formatting changes.
 Gen5 limits the ability to customize system-provided views, but creating new
ones offers enormous flexibility. For example, if you do not use Sample IDs,
you'll always have an empty Name column in the system-provided Statistics
tables. But, you can create your own view that excludes the Name/Sample ID
data point.
 You can choose the way Gen5 formats data/text that is too long to fit
completely in a field or column by Changing the Font settings for a data
elements.
 Protocol Summary report sections can be added to the Default Protocol so that
all future protocols will include them. These are the only Data Views you
cannot view on-screen, so they are only available in the reporting tools: Report
and Export Builders. Unlike most of the other data views, these report elements
are always available, even before you have defined the Protocol.
 Field Groups (for use in reports) can only be created in the Data Views dialog,
but they can be modified in the Report Builder and Export dialogs
118 | Chapter 6: Designing a Protocol
Reporting Results
Gen5 offers several tools for reporting results from experiments.
You can use:
 Gen5's full-featured report engine: begin with the Report Builder described
in the Reporting Results chapter beginning on page 333.
 or Export the results and use Excel® or another software application to
generate a report; its described in the Exporting Results chapter.
Using the Default Protocol | 119
Using the Default Protocol
Use the default protocol to work more efficiently in Gen5.
About the Default Protocol
System> Preferences> Default Protocol...
Gen5 provides a mirror-image of the Protocol menu tree to create a Default Protocol, a
template, to help you save time when creating new Protocols. If some protocol elements
remain the same from experiment to experiment in your lab, you can make them default
settings that are applied to all new protocols. Any aspect of the Default Protocol can be
overridden in a newly-created protocol or experiment using the regular menu options.
There is a limiting factor controlling the use of the Default Protocol for most users,
defining the Procedure or read parameters is a prerequisite to defining Data Reduction
and selecting Report and Export content. Since reading parameters generally vary from
experiment to experiment, the role of the Default Protocol is somewhat limited. However,
it can still be used to define numerous settings that you're likely to apply to all
experiments.
The Default Protocol is stored in Gen5's database: SharedDB. When this is stored on a
network drive that all your Gen5 users can access, they can also share the Default Protocol.
Unless the reading parameters, like wavelengths, remain the same for
all experiments in your lab, it is best to NOT define a Procedure for the
Default Protocol. Users can alter the Procedure when they define a
new protocol, but this action will invalidate any Data Reduction steps
and report content, which may go unobserved by the user.
Customize Well IDs
A major advantage of the Default Protocol is to customize the Well IDs (see next page)
used in the Plate Layout. You may also be able to define the concentration values and
location of Standards, and Blanks on the plate. Similarly, for Sample Identification
fields. The customized IDs become available for selection in new protocols. Find
instructions for defining customized Well IDs and Sample Identification fields in the
Plate Preparation chapter beginning on page 219.
Common Default Settings
You may want to define Runtime Prompts, Report Headers and Footers, and Export
Options, which are commonly static elements in an organization's protocol design. The
pre-built Protocol Summary data views, Procedure Summary and Data Reduction
Summary, can be added to the Report and/or Export Builder in the Default Protocol so
they are automatically included in reports for every experiment.
Important: Defining the default protocol settings takes effect going
forward, i.e. they are only applied to newly created protocols and have
no effect on existing protocols or experiments.
120 | Chapter 6: Designing a Protocol
Default Protocol Setup
System> Preferences> Default Protocol...
Use these controls to define the default settings for newly created protocols.
How To
Define the Default Protocol as you would a standard protocol, keeping in mind that
your selections will be applied to all newly created protocols.
As with standard protocols, you cannot define Data Reduction steps until the
reading Procedure has been defined. Conversely, altering the Procedure can
invalidate any previously defined Data Reduction steps.
Reset
Use the Reset button to clear the Default Protocol settings, erasing any selections or
customizations. Reset returns the Default Protocol to its out-of-the-box definition.
Customizing IDs in the Default Protocol
Gen5 ships with certain abbreviations for the various well types, but they may not
match your organization's naming convention. Customizing the Well IDs in the
Default Protocol's Plate Layout makes them available for all newly created protocols.
This can be a real timesaver for your users.
Common Changes
Well Type
Default ID
New Default ID
Sample
SPL
SMP
Assay
Control
CTL1
PC (Positive Control)
CTL2
NC (Negative Control)
CTL3
HPC (High Pos)
Chapter 7
Defining the Procedure
This chapter provides instructions for setting up Gen5’s Procedure,
the reading parameters.
Defining the Reading Parameters ............................................... 122
About Gen5’s StepWise™ Procedure ........................................... 123
Validate the Procedure.............................................................. 125
Read Step ............................................................................... 127
Procedure Steps (Reading Related) ............................................ 137
122 | Chapter 7: Defining the Procedure
Defining the Reading Parameters
Protocol> Procedure
Set up the Procedure to control the reader: define the
parameters and related activities of the Protocol/Experiment.
reading
Grayed out? When more than one plate has been read in an
experiment, the Procedure cannot be changed for the current
experiment. If this isn't the case, your System Administrator may have
restricted your ability to modify the protocol elements.
Grayed out buttons mean the action cannot be performed by the
current reader or because previously defined steps, e.g. kinetic loop,
limit the function.
How to:
1.
Use the drop-down list to define the Plate Type
3.
Define the details of the step and click OK
2.
4.
Click a button to add that step to the procedure. Most buttons open a screen for
defining the parameters of that step, e.g. Read lets you define wavelengths, etc.
When defining a kinetic or synchronized well/plate mode analysis, add the
Kinetic or Synchronized Mode steps first. Kinetic and Synchronized Mode
steps form a loop or block. Put the Read and other valid steps to be performed
inside the loop, between the Start and End. Monitor Well is similar, first add
the Monitor Well step and then, add a Read step inside the monitor-well loop.
Click Validate to check the selection and sequence of the steps0.
Gen5 must be communicating with the reader to fully validate the
Procedure. Make sure the reader is correctly attached, turned on, and
not busy reading a plate or performing a test.
Features:
 You can Drag and Drop steps in the Procedure to change their sequence order
 Highlight a step in the Procedure, and then click an action button to add a step
before it
 Double click a step to open it for editing
 Select a step in the sequence and right click for additional options
 Click Validate at any time to verify the reader's ability to perform the current
sequence of steps
 Highlight a step and press Delete to remove it from the procedure
Defining the Reading Parameters | 123
Drag and Drop is limited in Synchronized Modes, for example, you
cannot drag and drop a step into or out of a Well Mode block
Review the Validation Checklist on page 125
Learn about: Synchronized Modes (for Synergy 2, Synergy 4; Synergy HT and FLx800
with Injectors) in the Fluorescence and Luminescence chapter.
About Gen5's StepWise Procedure
Gen5™ offers lots of flexibility in defining a Procedure: the read steps and related
activities, like incubation, shaking (or mixing), dispensing reagent, and so on. Each
activity or requirement is defined chronologically or StepWise.
The StepWise Procedure can be simple, performing only one reading at one
wavelength. It can also be complex, a series of events that includes multiple readings,
incubation, shaking, and ejecting plates between reads to add reagent. The sequence of
steps in the StepWise Procedure workspace defines the order of events performed by
the reader.
After a plate has been read based on the Procedure, it cannot be changed unless the
data obtained is discarded. Gen5 offers several ways to modify the Procedure, as
described on page 114.
The current reader determines the availability of options:
 Readers are set up under System>Reader Configuration.
 When more than one reader is connected to the PC, Gen5 opens the Instrument
Selection dialog to let you select the desired reader before offering the
Procedures dialog.
Depending on your reader, the possible combination of steps in a Procedure is
numerous. For example, you can:
 Set the Temperature followed by a Delay to reach the correct setting,
before adding a multiple-wavelength Read step
 Give the plates a long time to react in an experiment by adding a
Stop/Resume step between readings. This frees up the reader for use in
other experiments during the down time
 Perform multiple Read steps, each interspersed with a Plate In/Out to add
reagent, followed by a Shake step to mix the contents before performing the
next read
 Define a kinetic analysis: Click Kinetic, followed by a Read step. Gen5 adds
an End Kinetic event to close the kinetic loop
 Apply different read methods within a Procedure, performing a Scanning
step, followed by a multi-read Endpoint step, and finish with a kinetic loop
124 | Chapter 7: Defining the Procedure
 Define one Read step for half the plate, and another Read step (with
different parameters) for the other half of the plate
 Perform a multi-mode or multi-detection experiment by defining
Absorbance and Fluorescence Read steps in the same Procedure
 and so on ...
Along with the reader's capabilities, the sequence of a step in the
Procedure, especially the steps immediately before and after it, determines its validity.
Click Validate to test the sequence of steps.
Validate the Procedure | 125
Validate the Procedure
About Procedure Validation
Gen5™ supports your effort to design a protocol by validating the Procedure
based on the capabilities of the current microplate reader and the sequence of
steps to be performed. Validation is also helpful at runtime, when a protocol may
have been designed without a specific reader attached to Gen5, and the actual
reader's capabilities are more limited than expected by the protocol. Gen5's
validation feature will display an error message alerting you of the need to fix the
Procedure.
Important: Gen5 must be communicating with the reader to fully
validate the Procedure.
Click the Validate button in the Procedure dialog to validate the reading
events. Certain activities in the Procedure sequence, like Shake, cannot be standalone
events, but must be related to a read or other activity. Here are the rules:
Device Step
Valid Combination/Limitations
Read
May be a standalone event. At least one read step is
required.
Set Temperature
May be a standalone event
Cannot be inside a Kinetic loop
Cannot be in a synchronous block
Shake
Shake » Read
Shake » Start Kinetic » Read » End Kinetic
Start Kinetic » Shake » Read » End Kinetic
These restrictions
apply to all readers
except the Synergy
4, which supports a
shake step anywhere
in the Procedure.
Shake cannot:
 precede a Spectral or Area Scan


be included in a Well Mode block
be the first step in a multi-detection
kinetic loop if the first read is
Luminescence
Dispense
May be a standalone event
Delay
May be a standalone event
Cannot be in a kinetic loop
Cannot be between Shake and Read
Kinetic
Requires at least one read step
Start Kinetic » Read » End Kinetic
Shake » Start Kinetic » Read » End Kinetic
Start Kinetic » Shake » Read » End Kinetic
126 | Chapter 7: Defining the Procedure
Device Step
Valid Combination/Limitations
Cannot include Scanning and Spectral reads
Only one read step allowed in Synchronized Well
Mode
Only one read and one shake step allowed in
Synchronized Plate Mode
Monitor Well
Monitor Well » Read » End Monitoring
Monitor Well » Shake » Read » End Monitoring
Shake » Monitor Well » Read » End Monitoring
Plate In/Out
May be a standalone event
Cannot be inside a Kinetic loop
Cannot be in a synchronous block
Stop/Resume
May be
Cannot
Cannot
Cannot
Well Mode
Requires at least one read step
Excluding a Delay step:
Synergy HT: can have up to 9 steps
Synergy 2/4: can have up to 20 steps
FLx800: can have up to 3 steps;
Kinetic loop is limited to one read, except Synergy
2/4 allows a Shake
Multi-Detection kinetic loop is not allowed
Plate Mode
Requires at least one read step
Synergy HT: can have up to 9 steps (excluding
Delay)
Synergy 2/4: can have up to 20 steps (excluding
Delay)
FLx800: can have up to 3 steps (excluding Delay)
Kinetic loop is limited to one read and one shake
Multi-Detection kinetic loop is not allowed
a standalone event
be inside a Kinetic loop
be in a synchronous block
be the final event in a sequence
Read Step | 127
Read Step
Protocol> Procedure> Read
Define the reading parameters based on the capability of the current reader:
1.
2.
3.
4.
5.
6.
(Optional) Enter a Step Label or unique name for this step. Data sets based on
the reading results will use the label in online views, reports, and export files.
Keep the Full Plate or set a portion of the plate to process.
(The Plate Type is set for all steps in the Procedure.)
Select the Detection Method. Options are controlled by the current reader.
Select the Read Type. Options are controlled by the current reader and the
detection method selected above.
Select the Read Speed from the list offered for the current reader
Set the Wavelengths or Filter Sets:
1
2
7.
Use the numbered buttons to set the number of wavelengths/filter sets
to obtain measurements with. Kinetic, Spectrum, Area and Linear Scans
limit this option.
Click the down arrow or type in the text field to set the wavelengths.
If applicable, define:0.
 Pathlength Correction
 Optics Position
 Sensitivity and Filter Set Options
 Top Probe Vertical Offset
Read Types
Depending on the reader, detection method, Gen5 product level, and the type of analysis
you're conducting, one of several read types can be selected:
 Endpoint
The most commonly used Read Type, Endpoint, performs one read in the
center of the well for each wavelength. It is the only read type that
supports Pathlength Correction.
Check your assay kit instructions to determine if this type of reading is
required. Endpoint reads are generally conducted after a Stopping
Solution is applied to the samples or when the effects of the chemistry
occur at an expected time point.
128 | Chapter 7: Defining the Procedure
 Area Scan
When performing an Area Scan, the reader takes multiple measurements
down and across each well, in a “matrix” format. This method is more
effective for cellular assays than reading once in the center of the well.

Learn more in the Scanning Analysis Options and Features chapter
Readers that support Area Scanning include the ELx800, µQuant, FLx800,
SynergyHT, Synergy 2, and Synergy 4.
Note: If the Scanning options are inaccessible, well scanning cannot
be performed with the currently defined plate type. This may be due to
a hardware limitation or an unacceptable combination of optic probe
size and well diameter.
Read Matrix Size represents the number of measurements taken across
and down each well. If, for example, the Read Matrix Size is 5 x 5 a total
of 25 measurements are taken. The potential Read Matrix Size is a
function of the well size of the current plate.
 Linear Scan
When performing a Linear Scan, the reader takes multiple measurements
in a line across the center of each well. Linear scanning allows you to
observe a pattern that may be present in the well bottom, such as an
agglutination pattern.

Learn more in the Scanning Analysis Options and Features chapter
Readers that support linear scanning include the ELx808 and all
PowerWave models. Note for PowerWave X Select: Linear scanning is
supported for the 96-well plate type only.
Horizontal Reading Points setting represents the total number of points
to be read across the center of each well. Valid entries are odd integers
from 1 to 39.
Note: If the Scanning options are inaccessible, well scanning
cannot be performed with the currently defined plate type. This
may be due to a hardware limitation or an unacceptable
combination of optic probe size and well diameter.
 Spectrum
During a Spectrum Read, multiple readings are taken across a wavelength
range. The objective is to plot a graph with absorbance versus wavelength.


Learn more in the Scanning Analysis Options and Features chapter
The Stop wavelength must be greater than or equal to the Start
wavelength + the Step
Readers that support spectrum reads are µQuant, and all models of the
PowerWave, Synergy HT, Synergy 2, and Synergy 4.
Read Step | 129
Fluorescence Read Step for FLx800 and Synergy HT
Synergy 2/4 users find instructions beginning on page 131
Protocol> Procedure> Read
When defining reading parameters for
Fluorescence analysis, setting the PMT Sensitivity (for the Filter Sets) is important for
obtaining useful measurements. The valid range is 25 to 255, but too low a setting, like
25, can result in insufficient readings, and too high a setting, >120, can damage the
PMT. BioTek recommends a setting between 40 -120 for Fluorescence assays and
between 150 - 255 for Time Resolved Fluorescence.
1.
2.
3.
(Optional) Enter a Step Label or unique name for this step. Data sets based on
the reading results will use the label in online views, reports, and export files.
Keep the Full Plate or set a portion of the plate to process.
(The Plate Type is set for all steps in the Procedure.)
Click the down arrow at Detection Method to select Fluorescence
4.
Select Time Resolved to perform this type of fluorescence analysis (learn more
in the Florescence and Luminescence chapter)
5.
In Synchronized mode, you can select Close Light Shutter to turn off the light
between reads. Optionally, to protect the fluorescent nature of your samples,
use this feature to block the light between measurements to prevent photobleaching effects. Gen5 blocks the light with a Plug in the filter wheel.
5.
Important:
A plug or blocking filter in the excitation filter wheel must be adjacent to the filter used
in the reading. Two plugs must be placed next to each other (which ensures they are
adjacent to the two filters used) in a dual-filter-set read step. Define the Reader
Settings
For the Read Type select:
 Endpoint
6.
The most common read type, Endpoint, performs one reading per
well for each filter set defined.
 Area Scan (not available in Synchronized mode)
When performing an Area Scan, the reader takes multiple
measurements down and across each well, in a “matrix” format.
This method is more effective for cellular assays than reading once
in the center of the well.
Set the Filter Sets:0.
1
Use the numbered buttons to set the number of wavelengths.
130 | Chapter 7: Defining the Procedure
2
3
Click the down arrow to select the filter
If applicable, define:0
 Optics Position
 Sensitivity or click Options to let Gen5 determine the optimal
setting
 Filter Switching: reading each well with both filters before moving
to the next well, is offered when only two filters are selected.
In Synchronized Mode, the read step settings for the first read in a
Plate or Well mode block are applied to any subsequent read steps in
the block.
Learn more in the Florescence and Luminescence chapter
Read Step | 131
Filter-based Fluorescence Read for Synergy 2 and Synergy 4 readers
Protocol> Procedure> Read
When defining reading parameters for Fluorescence analysis, setting the PMT
Sensitivity (for the Filter Sets) is important for obtaining useful measurements.
1.
2.
3.
4.
5.
6.
7.
(Optional) Enter a Step Label or unique name for this step. Data sets based on
the reading results will use the label in online views, reports, and export files.
Keep the Full Plate or set a portion of the plate to process.
(The Plate Type is set for all steps in the Procedure.)
Click the down arrow at Detection Method to select Fluorescence
Optionally, select Time Resolved or Polarization to perform this type of
fluorescence analysis. Your choice enables or disables related options as
appropriate for the process.
Read Speed: Use the drop-down list to make a selection and/or click the 3-dot
button to change the default settings for Measurement Options
For the Read Type select:
 Endpoint: The most common read type, Endpoint, performs one reading
per well for each filter set defined.
 Area Scan: (not available in Kinetic or Synchronized mode): When
performing an Area Scan, the reader takes multiple measurements down
and across each well, in a “matrix” format. This method is more effective
for cellular assays than reading once in the center of the well. But, The
Synergy 2's and Synergy 4’s probe size limits its ability to perform
Fluorescence area scan in plates with a small well diameter. Generally, this
means you must use a plate with fewer than 96 wells.
Light Source: except for TRF, you can select the lamp to use for this read step:
Xenon Flash (Xe) or Tungsten (Tg)
Using the Xenon Flash (Xe)
Advantages
Disadvantages
Very high energy, slightly more
sensitive than Tg bulb
It is expensive compared to the Tg
High light output below 300 nm (UV
Fluorescence)
Noise
Enables Sweep mode as a Read Speed
Prohibits use of the Extended Range
132 | Chapter 7: Defining the Procedure
Performs direct protein and amino
acid quantification assays
Using the Tungsten Lamp (Tg)
Advantages
Disadvantages
Enables Extended Dynamic Range
Cannot perform TRF
Strong and stable light output in
visible range
Slightly less sensitivity than Xe Flash
Inexpensive, with high sensitivity for
Fluorescence Intensity (FI) and
Fluorescence Polarization (FP)
Sweep read speed is prohibited
No light output below 300 nm
8.
9.
10.
In Synchronized (non-kinetic) mode, you can select Close Light Shutter to turn
off the light between reads. To protect the fluorescent nature of your samples,
use this feature to block the light between measurements to prevent photobleaching effects. Gen5 blocks the light with a Plug in the filter wheel.
Set the Filter Sets:
Use the numbered buttons to set the number of wavelengths
11. Click the down arrow to select the filter
12. If applicable, define:
 Optics Position: for top reading select the mirror
 Sensitivity or click
to let Gen5 determine the optimal setting
 Filter Switching: reading each well with both filters before moving to the
next well, is offered when only two filters are selected.
 Top Probe Vertical Offset
In Synchronized mode, the read step settings for the first read in a
Plate or Well mode block are applied to any subsequent read steps in
the block.
The Filters offered for selection are defined by the Filter Wheel Library
or Reader Configuration
Read Step | 133
Monochromator-based Fluorescence Read for Synergy 4
Protocol> Procedure> Read
Prerequisites
 Filter wheel: to perform monochromator reads, the reader’s excitation filter
wheel must contain a Hole and a Mono LP filter.
 PMT Sensitivity: a setting between 50-150 for monochromator-based reads is
required for obtaining useful measurements.
 Well volume: a minimum volume of 200 µl is needed for regular 96-well plates,
100 µl for 384-well plates. Consider using 96-well half-area plates for smaller
volumes.
Procedure
1.
2.
(Optional) Enter a Step Label or unique name for this step. Data sets based on
the reading results will use the label in online views, reports, and export files.
Keep the Full Plate or set a portion of the plate to process.
(The Plate Type is set for all steps in the Procedure.)
3.
Click the down arrow at Detection Method to select Fluorescence
4.
Optionally, click the Read Type down arrow to select a different option
5.
6.
7.
8.
For endpoint reads you can select Time Resolved to perform this type of
fluorescence analysis. Your choice enables or disables related options
Read Speed: Use the drop-down list to make a selection and/or click the 3-dot
button to change the default settings for Measurement Options
Light Source: except for TRF, you can select the lamp to use for this read step:
Xenon Flash (Xe) or Tungsten (Tg)
In Synchronized (non-kinetic) mode, you can select Close Light Shutter to turn
off the light between reads.
De-select Use Filter Wheel to use the monochromator
9.
10. Set the Filter Sets:
1.
2.
Use the numbered buttons to set the number of wavelengths
Enter wavelengths for the monochromator. Valid values for Excitation
wavelengths depend on the Light Source selected above: Xe supports 250700 nm, while Tg supports 340-700 nm; for Emission wavelengths the range
is 300-800 nm.
11. If applicable, define:0.
 Sensitivity or click

Top Probe Vertical Offset
to let Gen5 determine the optimal setting
134 | Chapter 7: Defining the Procedure
 Column Offset
Valid Range: 0.0 - 3.0
Due to the angled approach of the probe, lowering it may also require a
small adjustment to the plate position beneath it.
In Synchronized Mode, the read step settings for the first read in a
Plate or Well mode block are applied to any subsequent read steps in
the block.
Read Step | 135
Read Step for Luminescence
Protocol> Procedure> Read
When defining reading parameters for
Luminescence analysis, setting the PMT Sensitivity is important for obtaining useful
measurements. The valid range is 25 to 255, but BioTek recommends a setting between
100 - 160 for Luminescence assays.
1.
2.
3.
4.
(Optional) Enter a Step Label or unique name for this step. Data sets based on
the reading results will use the label in online views, reports, and export files.
Keep the Full Plate or set a portion of the plate to process.
(The Plate Type is set for all steps in the Procedure.)
Click the down arrow at Detection Method to select Luminescence
The Read Type must be set to Endpoint
Enter the Integration Time: to set the read duration for each well in seconds or
milliseconds. Click in the field and enter the Sec.Msec or use the spin buttons to
set the duration.
Valid values:
 Synergy HT: 0.1 - 19.9 seconds;
 Synergy 2/4: 0.1 - 99.9 seconds, in 20 ms intervals
 FLx800: 0.1 - 6.0 seconds
5.
Synergy 2/4: Click the 3-dot button to change the default settings for
6.
Set the Filter Sets:0.
Measurement Options
1
2
3
Use the numbered buttons to set the number of wavelengths.
Click the down arrow to select the filter or Hole (to not filter the light)
If applicable, define: (Learn more in the Florescence and Luminescence
chapter)0
 Optics Position
 Sensitivity or click
setting
to let Gen5 determine the optimal
In Synchronized Mode, the read step settings for the first read in a
Plate or Well mode block are applied to any subsequent read steps in
the block.
136 | Chapter 7: Defining the Procedure
Read Step for Spectrum Analysis
Protocol> Procedure> Read
Define the reading parameters based on the capability of the current reader:
1.
(Optional) Enter a Step Label or unique name for this step.
3.
Set the Detection Method to Absorbance (except for Synergy 4, Absorbance is
the only option.)
2.
4.
Keep the Full Plate or set a portion of the plate to process.
Click the down arrow to set the Read Type to Spectrum.
Certain parameters specific to the detection method and reader's capability must
be defined:
 Read Speed: Use the drop-down list to make a selection and/or click the 3dot button to change the default settings for Measurement Options
 Calibrate Before Read: When selected, the reader will always perform
calibration at the wavelengths specified in the protocol, just prior to plate
reading. If Calibrate is not selected, the reader will calibrate at only those
wavelengths specified in the protocol that have not yet been calibrated since
the reader was turned on.
 Spectrum Type (for Fluorescence Only): Fluorescence spectrum analysis
can be performed on either the Excitation or Emission wavelength, with the
opposite wavelength set to a fixed value. And the range of wavelengths
scanned can either be lower or higher than the fixed wavelength (including
bandwidth). See the description of Acceptable Values below.
 Light Source (for Fluorescence Only)
5.
 Integration Time (for Luminescence Only): Enter the Integration Time: to
set the read duration for each well in seconds or milliseconds. Click in the
field to enter the Min:Sec:Msec (MM.SS.ss) or use the spin buttons to set the
duration. Valid values.
Set the range of Wavelengths:
Acceptable Values:
 The acceptable range for the Start wavelength is from the lowest
wavelength the reader supports to one less than the Stop wavelength
selected.
 The acceptable range for the Stop wavelength is any wavelength greater
than the Start wavelength to the highest wavelength allowed by the reader.
 The acceptable range for the Step value is any number equal to or less than
the difference between the Start and Stop values.
6.
 The only read speeds available for Spectrum reads are Normal and Sweep.
Enter the Start and Stop wavelengths to define the spectral range.
Read Step | 137
7.
 For Fluorescence reads: select a Spectrum Type, enter a fixed wavelength
for the opposite type, and enter a wavelength range that does not overlap
the fixed wavelength.
Enter the number of Steps to define the number of measurements to take.
 Fluorescence and Luminescence readers let you adjust the Top Probe
Vertical Offset and the Column Offset.
Read Step for Clarity
Protocol> Procedure
Gen5 communicates with the Clarity™ software to define the Procedure.
Learn about the relationship between Gen5 and the Clarity PC
software, if you haven't already done so.
When creating a new protocol or experiment for the Clarity, Gen5 replaces its StepWise™
Procedure dialog with a gateway to the Clarity PC software, which you must use to define
the read command. Select:
 Create New... to create a new procedure (.bpf file)
 Browse... to select/run an existing Clarity protocol (.bpf file)
 Edit... after using Browse to select a file, to modify an existing Clarity protocol
(.bpf file)
After the read step (Procedure) is defined/selected, you can set up the rest of the Protocol
elements, like Plate Layout and Data Reduction, and so on.
Double-click Procedure in the menu tree to modify it (select Edit). This is possible before
the plate is read. After the plate is read, like all Gen5 protocols, the Procedure can not be
modified.
Specific instructions for defining the Clarity read parameters are provided in the
Clarity Operator's Manual.
138 | Chapter 7: Defining the Procedure
Procedure Steps: Reading-Related Activities
Protocol > Procedure
The following features may or may not be available for creating a protocol depending on
the attached reader, and your level of software.
 Set Temperature (Incubation): page 138
 Shake the plate: page 139
 Dispensing Reagent: page 140
 Kinetic Analysis: page 142
 Delay Step: page 143
 Monitor Wells: page 144
 Plate In/Out: page 145
 Stop/Resume the experiment: page 146
 Synchronized Modes: refer to the Fluorescence and Luminescence chapter
Set Temperature
Use these controls to set the desired temperature for the reading chamber or incubator.
Most BioTek readers allow a temperature range of 20-50°C. Add a Delay step to the
Procedure to incubate the plate. Learn more below. turn off the incubator
1.
2.
Enter the desired temperature in the Temperature field.
Select (or de-select) the option to Preheat before continuing with next step
to wait for the temperature to reach the set point before proceeding with the
next step in the Procedure. Selecting this option activates the Pre-Heating
function available from the Control Panel: System>Control Panel.0.
Stop/Resume: Gen5 considers a Stop/Resume step the end point of
the series of steps that precede it. It frees up the reader for running
other experiments. If you want the steps following a Stop/Resume to
be performed at a certain temperature you must add a Set
Temperature step after the Stop/Resume step.
You cannot put a Temperature Step inside a kinetic loop
When the experiment is started (the Read button is pressed) before
the reader has reached the defined temperature, Gen5 offers the
option to override the Set Temperature step.
Procedure Steps: Reading-Related Activities | 139
Reporting the temperature: you can include the temperature of a read step in a
report or export file. Add the Fields to your report: from the Plate Information
category, select the desired Temperature field.
How to incubate the plate:
The Set Temperature step in Gen5's StepWise Procedure does not by itself incubate the
plate. It heats up or cools down the reader to the defined setting. To use your reader to
incubate the plate define the Procedure this way:
1.
2.
3.
4.
Set Temperature with preheating
Plate Out/In step, enter Incubate Plate in the Comments field
Delay for the incubation duration
Read
Shake the Plate
Use these controls to set the Intensity and Duration of a Shake step to mix the plate contents:
 Intensity - use the drop-down list to select a level. The reader's operator's
manual may define the specifications of each level.
 Duration - enter a time period (minutes:seconds) to shake the plate. The
potential range is 1 second to 60 minutes.
 Continuous Shake - within a kinetic loop, if the reader is capable of
performing it, you can select this option to shake the plate whenever it is not
being read during the kinetic time interval
As part of a Kinetic Analysis:
 To shake the plate only before the first reading in a kinetic analysis define
the sequence of activities: Shake » Start Kinetic » Read » End Kinetic
 To shake the plate before every reading in a kinetic loop define the
sequence of activities: Start Kinetic » Shake » Read » End Kinetic
 To continually shake the plate whenever it is not being read, select
Continuous Shake instead of a time interval
In multi-mode kinetic analysis a Shake step cannot precede the kinetic
loop, but can be the first step in the loop: Start Kinetic » Shake » Read
» Read » End Kinetic
140 | Chapter 7: Defining the Procedure
Dispensing
This option is only available for Readers with Injectors.
The Dispense dialog fields are described here and information to help you choose the
optimal Dispense Rate begins on page 141.
Dispenser
Select the number of the Dispenser to be used for this step. The numbers correspond to
the numbers on the dispense module.
Partial or Full Plate?
The button to define a full or partial plate is dynamic, it changes from Full Plate to a platemap description of the area to be dispensed to/read, e.g. A1..H5. Click the button to define
the specific wells for dispensing, and if this step is in a loop, for reading in the subsequent
Read Step(s).
In Synchronized Mode the first step in a block controls the full or
partial plate for the entire block. For example, if the steps in a Well
Mode block are Dispense>Delay>Read, when the Dispense step is
defined to dispense to the first two columns of the plate, the Read step
is also limited to the first two columns. Likewise, if the steps in a Plate
Mode block are Read>Dispense>Read, and the first Read step is a
partial plate read E5...H12, the Dispense and Read steps to follow will
automatically be set to the same portion of the plate
Tip Prime
Priming: select an option:
 none: Do not prime the tip
 before the dispense step: Prime the tip with fluid before injection of fluid
to the plate
 once before the Well/Plate Mode block: In Synchronized mode, you can
prime the tip one-time-only before the process begins
 before this dispense step: In Synchronized Plate Mode, you can prime the
tip before each dispense step in the block
 More About Tip Priming: Priming is performed in a small, removable priming trough
located in the rear of the carrier. The purpose of tip priming is to compensate for
any fluid loss at the dispense tip due to evaporation since the last dispense. Each
trough holds up to 1500 µl of liquid and must be periodically emptied and cleaned.
Gen5 warns you to empty the trough before the first Dispense event and keeps
track of the amount of fluid primed into the trough during the Procedure. Selecting
Yes at one of Gen5's messages to empty the trough resets the trough volume
record to zero.
Procedure Steps: Reading-Related Activities | 141
Do not perform Tip Priming when using tall plates. Generally, plates with fewer
than 96 wells are too tall for error-free tip priming, and it is rarely required for
these larger-volume plates.
Volume: enter the amount of fluid in microliters. The valid range is 5 to 20.
Important: For optimal dispense accuracy and precision when
dispensing volumes less than or equal to 20 µl/well, BioTek
recommends priming the tip: use a tip prime volume equal to the
dispense volume. For dispense volumes greater than 20 µl/well, we
recommend a tip prime volume of 20 µl.
Dispense
Volume: Enter the dispense volume in microliters. The valid range is 5 to 1000
Rate: Select the dispense rate (microliters per second) based on the volume.
Keep the fluid path clean: You'll get the best results from your BioTek reader with
Injectors if you keep the fluid path clean. Minimally, you should Purge the reagent and
flush the lines with DI water when the experiment is finished. Follow instructions for
daily maintenance in your Operator's Manual.
When the Dispense step is the last step in the Procedure, add a Plate
Out step to eject the plate carrier when the Procedure is finished.
Dispense Rate
Gen5's options are:
Rate (ul/sec) Volume Range (ul)
225
5-1000
250
15-1000
275
25-1000
300
30-1000
The maximum volume for a dispense operation is 1000ul. The minimum volume
depends on the dispense rate. For example, when dispensing <= 10µl you must use a
rate of 225.
Here are some factors to consider when selecting the dispense rate or injection speed:
 Use the fastest rate for the best mixing affect in the wells
 Use the slowest rate (225) when a cell layer is involved; especially if the level of
liquid in the well is low (<100µl) before injection
142 | Chapter 7: Defining the Procedure
 Lower the rate if you notice some spills on the plate after injection. (This may
be caused by a high (>200µl) or low (<50µl) pre-injection volume, or to a
specific plate type, like round-bottom wells.)
 Assay kits generally provide guidelines, review the kit insert to determine its
recommendation for a slow or high dispense speed
 High-viscosity fluids perform better with a slow rate
Kinetic
Learn more in the Kinetic Analysis chapter beginning on page 185.
To set up a kinetic (or time-course) analysis, put one or more Read steps within the
Start Kinetic and End Kinetic loop. The steps are conducted within the specified
timelines:
Run Time: Enter the full duration of the kinetic analysis, i.e. the length of time
required to perform all the steps within the kinetic loop:
 Time Format: Hours (HH): Minutes (MM): Seconds (SS) in standard mode
and Minutes (MM): Seconds (SS): Milliseconds (ss) in synchronized mode.
 Maximum time period is 168 hours except in Synchronized Modes. Well
Mode kinetic run time is limited to 60 minutes and the block must be
completed in 2.78 hours. Plate Mode kinetic run time is limited to 24 hours
and the block must be completed in 27.8 hours.
Interval: Enter the desired time interval between readings or select Minimum Interval.
Gen5 will read the plate at every interval, e.g. every 00:10:30 = 10 minutes and 30
seconds, for the duration of the Run Time
Minimum Interval: Select this option to let Gen5 determine the fastest possible
processing time. Follow the instructions in the Kinetic Analysis chapter.
Reads: Gen5 calculates the number of reads from your input of Run Time and Interval.
The maximum number of reads depends on your reader and detection method.
Important: Numerous factors affect the acceptable kinetic run time.
To make sure your reader can process the steps in the kinetic loop
within the defined timelines, click Validate (with the reader attached
and communicating with Gen5) when all the Procedure steps have
been defined. If the interval is too short for the parameters chosen, an
error will be displayed.
Discontinuous Kinetic Interval: Gen5 let's you perform a
discontinuous-interval analysis that requires long periods of downtime
(for rest, manipulation, or incubation) between reads. Engage this
feature with the Procedure's Advanced Options.
Note: The actual runtime of a kinetic loop may exceed the defined
Run Time by +1 Interval. Gen5 does this to ensure that the number
of Reads displayed are actually captured.
Procedure Steps: Reading-Related Activities | 143
Delay the Procedure
Use this command to add a Delay event to the series of steps defined, telling the reader
to halt processing for the defined duration. You cannot put a Delay step in a kinetic
loop, nor can you have a Delay between Shake and Read steps.
Delay Time: Enter a time period for the duration: HH:MM:SS
You may want to use a Stop/Resume step or Plate In/Out instead
Delay in Synchronized Mode
Use these controls to add a Delay event to the steps in a Synchronized Mode block,
telling the reader to halt processing for the defined duration.
Delay Time: Enter a time period for the duration
 In Plate mode: HH:MM:SS (hours:minutes:seconds)
 In Well mode: Min:Sec.Msec (minutes:seconds:milliseconds)
Start Delay From: Select an option
 Beginning of Previous Step: to define the delay time to include the time it
takes to perform the previous step, as well as the delay time
 End of Previous Step: to set the delay time to begin when the previous step
is finished. This is the default and most typical setting
Example: You may want to use the Start Delay from Beginning of Previous Step
option in a Dispense>Wait>Read protocol when the precise timing of every step is
critical to your experiment.
FLx800: In Well Mode it is necessary to include a Delay step set to "Start delay
from Beginning of previous step" to precisely control the reader to process each
well within the same timeline. Set the Delay Time sufficient to perform the
previous step with a little padding: this is usually 0:00.10 milliseconds or more.
When you click the Validate button, Gen5 communicates with the FLx800 to
determine if the Procedure is doable. If not, it provides instructions for adding a
Delay step or increasing the Delay Time.
144 | Chapter 7: Defining the Procedure
Monitor Wells
Use these controls to define well-monitoring criteria that must be met before the reader
begins to capture the actual measurement values used in the experiment.
About Monitoring Wells
Gen5's Monitor Wells feature can be used to detect a certain level of activity in the
plate before capturing regular, saved measurements. You define measurement criteria
that must be met in one or more specific wells before the complete plate read can
begin. Gen5 directs the reader to continuously read the wells at the defined time
interval until the criteria are met. This feature sets up a loop, like a Kinetic loop, with a
start step and an end step in the Procedure. A Monitor Read step must be defined
within the loop. A Shake step is also permitted either before the read or before the
entire Monitor Well loop.
Example: you can specify that the average of the measurements in wells A1, A2, B1
and B2 must be greater than or equal to 0.500 OD before initiating the plate read. When
the Monitor Wells step is executed, the following information will be displayed: wells
being monitored, current value of the wells, the required measurement value, and the
elapsed time since the last well was read. At any point the user can choose to bypass
the monitoring process and continue forward with the read or cancel the operation,
aborting the entire Procedure.
How To:
1.
Click Monitor Well to start the loop
 Interval: enter the time interval between readings for the duration of the
well monitoring. Alternatively, check the Minimum Interval option (if you
have a reader attached) to let Gen5 determine the shortest possible interval
for monitoring
 Stop Monitoring When: tells the reader when to conclude the monitoring
process. Use the drop-down list to select a conditional option and an
operator, and enter a measurement value to be met:
Condition
Operator
Measurement Value
At least one well
> greater than,
>= or equal to
Absorbance valid range: –
1.000 to 5.000
Average of wells
< less than,
<= or equal to
Fluorescence/ Luminescence
valid range: 0 – 99998
All wells
2.
Define a read and shake step, if desired, for the Monitor Well loop:
 Read: with End Monitoring highlighted in the Procedure, click Read and
define the Wells to Monitor:
Click
to select the wells to monitor for the "Stop Monitoring
Procedure Steps: Reading-Related Activities | 145
When" criteria. Single or multiple wells can be selected by clicking in the
grid. Multiple wells must be contiguous.
 Define the reading parameters using the modified Read step dialog. .
3.
 Add a Shake step, if desired, as normal.
Add the regular Procedure steps to follow the Monitor Well loop, i.e. an
endpoint or kinetic reading and any associated activities. Gen5 always requires
at least one actual read step. The "Monitor Read Step" does not fill this
requirement.0.
Important: Gen5 does not save the reading results (measurements) obtained during
the Monitor Well step. Only measurements collected during a regular read step are
retained for analysis and data reduction.
Plate In/Out
Add a Plate In/Out step to a Procedure to pause the run and change the position of the
plate carrier. This command can be used to perform a manual task, like adding reagent
to the plate between reads steps, for example. You can also use this step to change the
behavior of the plate carrier, for example, if you want to move the carrier back into the
reader at the end of a run.
Unlike the Stop/Resume step, this command does not completely
interrupt or end the run.
Select one:
 Move carrier out, Display dialog, Move carrier in
Enter text in the Comment field. When the plate is ejected Gen5 will display
the comment.
 Move carrier out (no dialog)
 Move carrier in (no dialog)
Results:
Move carrier out, Display dialog, Move carrier in:
146 | Chapter 7: Defining the Procedure
When the first option is selected, Gen5 displays
the comment in a dialog like this when the plate
carrier is moved out:
When the user clicks OK, the plate carrier is
moved back in. The plate can be handled in the
interim.
The other two options open or close the plate carrier without displaying a message.
Stop/Resume
Use this command to stop the experiment where it is inserted in the Procedure. It is
typically used for long interruptions (such as incubation periods), and allows the
reader to be used for other experiments. Gen5 will stop the experiment until you
resume it. See how to resume below. Only then will it continue to perform the
Procedure steps that follow the Stop/Resume step. You can close the experiment when
it is stopped and reopen it when you're ready to resume.
Set Temperature: Gen5 considers a Stop/Resume step the end point
of the series of steps that precede it. If you want the steps following a
Stop/Resume to be performed at a certain temperature you must add
a Set Temperature step after the Stop/Resume step.
Set up:
Eject Plate Before Stop: Gen5 will open the plate carrier to eject the plate before
stopping the experiment, unless you de-select this option. When this option is not
selected, Gen5 lets the previous Procedure step determine the position of the plate
carrier. Since most Procedure steps do eject the plate upon completion, to keep the
plate inside the reader during the downtime, you may need to add a Plate In step
before the Stop/Resume step.
Comment: Enter a comment to be displayed on-screen
Results:
The Comment you enter, "Add reagent" in this example, is
displayed in a message like this when the experiment is
stopped. Users must click OK to acknowledge the message.
The experiment is stopped, until it is resumed.
Gen5 signals the experiment has been stopped using the
plate-paused icon in the menu tree.
Procedure Steps: Reading-Related Activities | 147
To Resume:
1.
Open the experiment, if it was closed.
2.
Click the Read button when you're ready to resume the experiment. The
standard read screen changes, offering Resume instead of Read.
3.
Click the Resume button to continue with the
Procedure. Note: If Re-Read is selected, Gen5 restarts the Procedure from its
beginning (first step), reading the plate again and discarding the initial data.0.
148 | Chapter 7: Defining the Procedure
Chapter 8
Fluorescence and
Luminescence
This chapter provides useful information for conducting
Fluorescence and Luminescence analysis, including Time-Resolved
Fluorescence. For Synergy HT, Synergy 2 and Synergy 4 readers,
there is also a section on Multi-Mode assays. You’ll find details
about how to set the PMT Sensitivity and use Gen5’s Synchronized
Modes in this chapter.
Fluorescence Analysis ............................................................... 150
Luminescence Analysis ............................................................. 153
Time-Resolved Fluorescence...................................................... 154
Fluorescence Polarization .......................................................... 155
Filter Set Options ..................................................................... 156
PMT Sensitivity ........................................................................ 158
Measurement Options............................................................... 162
Synchronized Modes................................................................. 164
Troubleshooting ....................................................................... 169
Multi-Mode Detection................................................................ 182
150 | Chapter 8: Fluorescence and Luminescence
Fluorescence Analysis
Your choice of fluorescent detection method depends on the reader's capability. All
BioTek readers are capable of performing filter-based reads, only the Synergy 4 also
offers monochromator-based reads, as well. When Fluorescence is the chosen detection
method, Gen5 presents the filters installed in the reader or defined in the Filter Wheels
Library. When you're running a Synergy 4, Synergy 2, or a Synergy HT or FLx800 with
Injectors, you can perform fluorescence analysis in Synchronized Mode.
Read Type options for fluorescence analysis (depending on the reader) are:
 Endpoint (FI)
 Area Scan
 Time Resolved (TRF or TR-FRET)
 Polarization (FP)
 Spectrum
Read Parameters
Read Speed is a Synergy 2 and Synergy 4 option: Click the 3-dot button to change
the default settings for Measurement Options
The Filter Set buttons (up to 6) determine the number of reads to perform. Only
two filter sets are permitted in a Kinetic loop.
 Filter-based Fluorescence: Excitation and Emission filters can be selected
using the drop-down list of filters available for the current reader. The list is
defined from one or two sources: the Filter Wheels Library or the Reader
Setup
 Monochromator-based Fluorescence: Excitation and Emission wavelengths
can be set to any value supported by the reader. Synergy 4's range is
dependent on the light source for Excitation wavelengths: the Xenon Flash
supports 250-700 nm, the Tungsten Lamp supports 340-700 nm; for
Emission wavelengths the range is 300-800 nm.
Filter Switching is offered when only two filter sets are defined (described below). It
is similar to Synchronized Well Mode.
Optics Position can be set to Top or Bottom for each selected filter set, depending on
the reader's capability. Readers are equipped with one or two optical probes,
positioned above (Top) and/or below (Bottom) the assay plate. Synergy 2/4 offers
mirror selection for the Top probe.
Sensitivity of the PMT can be set by entering the desired value (valid settings range
between 25-255) or by letting Gen5 determine the optimal sensitivity setting using the
Filter Set Options (described below).
Fluorescence Analysis | 151
Filter Set Options: Each filter set has a corresponding set of measurement
options which can be defined by clicking the Options button. See page 156.
Filter Switching: When two filter sets are selected Gen5 offers this option to read
every well with each filter set before moving onto read the next well. When this option
is not selected the reader reads the whole plate with one filter set, then reads it again
with the second filter set.
The advantage of this option is closely timed well measurements. The disadvantage is
a longer runtime. It is useful when working with two, possibly unstable, fluorescent
labels. Learn more in Gen5’s Help.
Top Probe Vertical Offset: parameter is available when at least one of the filter sets
uses the "top" optics position. It allows you to define how far the top probe is
positioned from the top surface of the plate during the read. The valid range is
determined on a plate-by-plate basis. The calculation is based on the plate height and
the maximum travel of the top probe. Learn more in Gen5’s Help.
Column Offset (for Monochromator-based reads only): Valid Range: 0.0 - 3.0
Due to the angled approach of the probe, lowering it may also require a small
adjustment to the plate position beneath it.
Troubleshooting
If you're not getting expected results review these suggestions:
Troubleshooting Fluorescence/Luminescence Measurements on page 169.
About Fluorescence Monochromator Reads
Synergy 4's monochromator has a quadruple-grating design for maximum spectral
control. Background noise is significantly reduced by the angled approach of the probe to
the well and the use of an order-sorting filter. And, the mono uses a red-shifted PMT that
can read up to 900 nm. Here are some essential facts to keep in mind when using the
monochromator for fluorescent measurements:
 It requires a special configuration of the Excitation filter wheel. Two positions
are needed for the monochromator, one for the order-sorting filter called Mono
LP that is shipped with the reader, the other position is empty, defined as a
Hole. The reader tests for this configuration and will not perform a mono read
without it.
 The Xenon Flash lamp is more sensitive and thus the best choice for most
assays. The Xenon also offers a choice of Lamp Energy, to give you more
control. However, the Tungsten lamp offers stronger output in the red range,
and a choice of Dynamic range: Extended or Standard, which may be better for
some assays.
 Time Resolved Fluorescence (TRF) can be performed with the monochromator,
but it is much less sensitive than filter-based processing.
152 | Chapter 8: Fluorescence and Luminescence
 Sufficient well volume is an important factor for this system. 384-well plates
show optimal performance. A minimum volume of 200 µl is required for
regular 96-well plates; half-area 96-well or 384-well plates should be used for
lower volumes. When well volumes cannot be increased, Gen5's Top Probe
Vertical Offset and Column Offset controls can be used to improve
performance.
Perform multiple read steps with slightly varied settings to determine the optimal
combination of settings for a mono read. Multiple experiments may be needed because all
read steps must use the same light source in one experiment.
Luminescence Analysis | 153
Luminescence Analysis
When Luminescence is the chosen detection method, the Read Step presents the emission
filters for the current reader or you can select Hole for no filtering. The excitation filters are
not available for selection, because the reader will automatically use a Plug in the
excitation filter wheel. Also see Luminescence Best Practices in Gen5’s Help.
Read Type is limited to Endpoint , except with Synergy 4 which offers spectrum scans.
Integration Time is set as minutes:seconds.milliseconds (MM:SS.ss).
 Synergy HT and FLx800: Gen5 reports the measurement results as RLU
(Relative Luminescence Units) per Second, except in Well Mode Kinetic
experiments, which are reported as RLU, and integration time is replaced with
the kinetic timelines. Gen5 collects data in each well for the duration of the
integration time, then sums the data points and displays the result as
RLU/second.
 Synergy 2 and Synery 4: Gen5 reports the measurement results as RLU
(Relative Luminescence Units). The reader collects data in each well for the
duration of the integration time, then averages the data points and displays the
result as RLU.
You should know: in Luminescence Reading Mode there is a tight link between
CV's and integration time. This correlation is independent of the instrument (type,
brand) and of the reagents. If you increase your measurement time by a factor of 2, you
will decrease your CV's by the square root of 2. If you increase your measurement time
by a factor of X, you will decrease your CV's by the square root of X.
Reading Parameters

The Filter Set buttons (up to 6) determine the number of reads to perform.
Only two filter sets are permitted in a Kinetic loop. Emission Filters can be
selected using the drop down list of filters available for the current reader.
 The recommended Optics Position for Luminescence readings is Top.
 Sensitivity of the PMT can be set by entering the desired value (valid settings
range between 25-255), or by letting Gen5 determine the optimal sensitivity
setting using the Measurement Options (learn more on page 158). BioTek
recommends a setting between 100-160 for Luminescence

Filter Set Options - For each filter set you can use Gen5's tool to
automatically determine the optimal Sensitivity of the PMT. See page 156.
 Top Probe Vertical Offset parameter is available when at least one of the
filter sets uses the "top" optics position. Generally, you do not have to change
the default value. For all Luminescence assays Gen5 sets the probe as close to
the well as possible.
154 | Chapter 8: Fluorescence and Luminescence
Time-Resolved Fluorescence Analysis
Measuring fluorescence using a delay after the cessation of excitatory light is called timeresolved fluorescence (TRF). Auto-fluorescence in a sample or microplate is a common
source of background fluorescence. Lanthanide ions, for example, have extremely long
fluorescent decay times, several hundred microseconds instead of several nanoseconds.
The rapid on/off nature of a xenon flash lamp allows for fluorescence analysis of the these
compounds with a delay after the excitation flash. The delay lets virtually all of the
background fluorescence diminish before measuring lanthanide’s long-lived fluorescence,
resulting in superior detection limits. The TRF option is available if the selected detection
method is Fluorescence and the current reader supports it.
1.
For each Excitation filter set:
 Synergy HTTR: enter a wavelength value between 200 and 999 nm. The
bandpass is not variable; it is pre-defined to be 10 nm.
 Synergy 2: select the filter, as usual. The light source is fixed to Xenon.
2.
3.
4.
 Synergy 4: opt to "Use Filter Wheels" or the monochromator (but filterbased is more sensitive). The light source is fixed to Xenon Flash (at High
intensity). Spectrum and Area Scan read types, in addition to Endpoint, are
available when other constraints are met, e.g. well size of the plate.
For each Emission filter, use the drop-down lists to select the wavelengths.
Sensitivity: BioTek recommends a setting between 150-200 for TRF.
click the Options button when using the Synergy HTTR
or click the 3-dot button next to the Time Resolved checkbox when using the
Synergy 2/4: Specify the length of time to delay before data collection and the
data collection duration and define the other related measurement options.0.
Fluorescence Polarization | 155
Fluorescence Polarization
For each Fluorescence Polarization (FP) read step, Gen5 actually performs two reads. It
takes a measurement through a parallel polarizer, and then, through a perpendicular
polarizer. Two raw data sets are generated. Gen5 automatically transforms the data in
an FP-dedicated data reduction step.
When applicable, Gen5 also performs the other automated data reductions, blank
subtraction and kinetic well analysis on the FP data sets. Anisotropy is also offered as a
data reduction option for FP analysis. You can choose to transform the data to produce
Polarization results, Anisotropy results or both. Results are reported as mP (millipees),
with an expected range between 0 - 500 mP with precision of ± 2 mP.
When the reader is equipped with the polarizers and mirrors required to excite the
sample and capture the polarized emission, the polarizing lenses reside in position 3 of
the mirror holder. Thus, when FP is the selected read type, the Optics Position choice
of mirrors is fixed to position 3.
Top 5 Things to Know about Fluorescence Polarization
 Mirror selection is fixed by Gen5 to use position 3. If you have a dichroic mirror
in position 3 (which is the default configuration), you must select filters that
correspond to its Min-Max range
 When Gen5's Auto-Sensitivity adjustment is used to determine the optimal
PMT sensitivity, it is performed on the parallel read/measurement
 Either light source can be used for FP: Tungsten or Xenon Flash
 Read Speed can be set to sweep when the Xenon Flash is used
 Synchronized Well and Plate Modes are available for time-sensitive FP assays
BioTek’s FP Process
For each sample in an FP experiment, the Excitation light travels from the light source
through the EX polarizer and then is reflected by the mirror to excite the sample. The
sample’s emitted light travels through the mirror and parallel Emission (EM) polarizer
and then through the emission filter into the PMT. The mirror holder then shifts so that
the emitted light travels through the perpendicular EM polarizer, through the emission
filter, and into the PMT. Gen5 corrects for the optical variations between the parallel and
perpendicular emission paths during the FP data reduction step. Learn more in the Data
Reduction chapter, page 307.
156 | Chapter 8: Fluorescence and Luminescence
Filter Set Options
In Fluorescence and Luminescence assays, you can set the sensitivity level of
the PMT or let Gen5 determine the optimal setting. You may need to experiment with
the settings to find the combination of options that works best for your assay. In
Fluorescence analysis, you can also set the Measurement Options.
Automatic Sensitivity Adjustment
Click in the checkbox to use this option to determine the optimum Sensitivity
setting for the plate:
1.
First, select one:
 Scale to High Wells - to evaluate optimal sensitivity based on the strongest
signal
 Scale to Low Wells - to evaluate optimal sensitivity based on the weakest
signal
 Use First Filter Set Sensitivity:
 of This read step when there is more than one filter set;
2.
 of First read step when there is more than one read step of the same
detection method, i.e., Fluorescence or Luminescence.
Then, define:0.
 Scale Wells - a range of microplate wells with the highest or lowest
expected signals, click in the field to select one or a range of adjacent wells,
e.g., A1-B12
 Scale Value - the highest or lowest expected value for the entire plate.
For input recommendations review the valid value ranges in the PMT Sensitivity
section on page 158.
Luminescence
Synergy HT and FLx800: Gen5 performs the Automatic Sensitivity Adjustment based
on an integration time of 1 second (0:01:0) regardless of the Integration Time defined
for the Read step .
Synergy 2 and Synergy 4: Gen5 uses the read step's integration time to peform the
Automatic Sensitivity Adjustment. It may be unable to determine the optimal
sensitivity, especially when scaling to low wells, if the determination takes longer than
3 minutes, which generally translates into integration times > 1 second.
Filter Set Options | 157
Fluorescence Measurement Options
The values for each measurement option depend on whether the assay is defined as
Standard (Non-Synchronized Mode), Synchronized Plate Mode or Well Mode. This table
displays the recommended values and Allowable Range for these modes for each option.
Note: For Kinetic analysis in Well mode these options are unavailable, they are determined
by the kinetic interval.
Option
Standard &
Time
Resolved
Plate
Mode
Well
Mode
Allowable
Range
Delay after plate
movement
100 msec
250 msec
10 msec
10-2550
msec
Measurements per
well
10
10
1
1-255
Delay between
measurements
1 msec
24 msec
0
0-255 msec
Time-Resolved Fluorescence Parameters
Delay before data collection: is time delay between the flash and the beginning of data
collection or the delay before integration. Valid values are 0 µsec and 20 - 16000 µsec.
The default value is 20 µsec.
A delay of 0 µsec is not the same as a fluorescence read with the time-resolved
option turned off. They differ in two ways: (1) the excitation wavelength is
generated by the monochromator; and (2) the user can specify the data collection
time, which is not an available parameter for normal fluorescence reads.
Data collection duration: is the amount of time for which readings are collected after
the delay before integration time has expired. The valid range is from 20 - 16000 µsec.
The default value is 100 µsec.
158 | Chapter 8: Fluorescence and Luminescence
PMT Sensitivity
In fluorescence and luminescence assays, the signal can be very weak, very strong, or
anywhere in between. For each assay, the Sensitivity of the photomultiplier tube (PMT)
should be adjusted to ensure that the signals from all wells fall within the appropriate
dynamic range of 0 to 99998 relative fluorescence or luminescence units (RFU or RLU).
Automatic Sensitivity Adjustment
You can let Gen5 determine the optimal sensitivity setting: click Options and
provide some criteria on which a determination can be made.
 Guidelines:
 Typical fluorescent assays using 96- (or fewer) well plates require sensitivities
between 35 and 130. Assays using 384-well or other higher-density plates will
likely require higher sensitivities due to narrower optical probes. Luminescent
reactions may require sensitivities up to 200. BioTek recommends selecting a
PMT Sensitivity setting between these ranges:
Detection
Type
Low
High
Fluorescence
Filter wheel
35
120
Fluorescence
Monochromator
50
150
Luminescence
Filter wheel
100
255
Luminescence
Monochromator
100
255
Time-Resolved FL
Filter wheel
100
255
Time-Resolved FL: Synergy HT
Filter wheel
150
255
Time-Resolved FL
Monochromator
100
255
Fluorescence Polarization
Filter wheel
35
120
 As the sensitivity setting increases, so will the fluorescence values. If many
wells result in “OVRFLW,” the sensitivity setting is probably too high:
 OVRFLW indicates RFU or RLU values greater than 99998 in Standard
Range (e.g. with Xenon Flash)
 OVRFLW indicates RFU or RLU values greater than 5.8 million in Extended
Range.
 Recommendation: one way to determine the optimal Sensitivity setting is to set
up one Read Step to perform 6 filter-set reads each applying a different
Sensitivity. Review the results to determine the best setting.
PMT Sensitivity | 159
 When the wells contain more than one fluorophore, one of which might give
brighter or weaker results, assign each filter set its own sensitivity.
 When the field shows ‘Auto’, the Automatic Sensitivity Adjustment feature is
enabled to determine optimum sensitivity. See Filter Set Options above.
Automatic Sensitivity Adjustment for PMT
Gen5™ can determine the optimum PMT Sensitivity setting for the plate based on one
of three methods: Scale to High Wells, Scale to Low Wells, or when multiple filter sets
are used: Use First Filter Set Sensitivity. The best method depends on your
application (some experimentation may be necessary).
Scale to High Wells
High Wells are wells with the highest expected signal (measurement value) on the
plate, such as the highest standard wells.
Scale to High Wells searches for two consecutive gain values where the measured
values are lower and higher than the defined high well values.
Scale to Low Wells
Low Wells are wells with the lowest expected signal (measurement value) on the plate,
such as blank wells, negative controls, or the zero standard wells.
Scale to Low Wells searches for two consecutive gain values where the measured
values are lower and higher than the defined low value wells. Scale to Low Wells is
recommended for weakly luminescent reactions.
When you let Gen5 determine the optimal sensitivity setting for your assay, the valid
values for Scale to High or Low Wells is dependent on the reader, detection method,
and light source:
Dynamic
Range
Synergy HT/FLx800
Synergy 2/Synergy 4
Xe
Tg
Lum
Standard
0-99,999
RFU
0-99,999
RFU
0-99,999
RFU
0-99,999
RLU
05,800,000
RFU
05,800,000
RLU
Extended
FI
Lum
05,000,000
RLU/sec
BioTek recommends retaining Gen5's default values when the expected measurements
are unknown.
Use First Filter Set Sensitivity of This or the First read step
This option is available when multiple filter sets and/or multiple read steps of the
same detection method have been defined. It applies the same sensitivity setting
to the current filter set read.
160 | Chapter 8: Fluorescence and Luminescence
Use first filter set from First read step: Notice that both the first filter set and first
read step are referenced: it applies either the manually input or automatically
determined Sensitivity setting of the first read step's first filter set. This only
applies to the same detection method. In a multi-mode Procedure, Gen5 selects
the first read step of the same detection method (e.g. FI or Lum).
Use first filter set from This read step is offered when there are multiple filter
sets in the current read step. It applies either the manually input or automatically
determined Sensitivity setting of the first filter set to the current read.
In Dispense protocols, if two filter sets are defined, the Sensitivity
field for the second filter set always shows Auto and it will use the first
filter set’s sensitivity.
In multiple-plate experiments, when the Automatic Sensitivity
option is used, Gen5 applies the sensitivity setting determined for the
first plate, to all other plates processed in the experiment.
How to let Gen5 determine the Sensitivity setting:
1.
2.
3.
In the Fluorescence or Luminescence read step, click the Options
button for the Filter Set
Turn on Automatic Sensitivity Adjustment: click the box to insert a
checkmark
Select a button for one of the options described above:0.
 Scale Wells: click in the field to select one or a range of adjacent wells that
you expect to produce the highest or lowest measurements
 Scale Value: Enter a value that represents the upper limit when scaling to
High Wells and the lowest limit when scaling to Low Wells of the expected
range of values for the entire microplate. The recommended high value is
50,000 to 70,000 RFU/RLU. The recommended low value is 100 to 200
RFU/RLU.
Reviewing results
After using the AutoSensitivity feature in an experiment, you can view on-screen and
include in reports the applied Sensitivity value. When the read step is completed:
 to Report the Sensitivity Value in reports (see below)
 to Display the AutoSensitivity Value on-screen described on page 161
The sensitivity value applied during the experiment is retained in the
Experiment file, but not in the protocol (.prt) the experiment was
based on. Unless it is updated, the protocol will continue to be defined
as using the AutoSensitivity option.
PMT Sensitivity | 161
Report the Sensitivity Value
Fixed Value: use the pre-built Procedure Summary in the Report and Export Builders and
set it to Detailed report to include the defined Sensitivity value in a report.
AutoSensitivity: when you let Gen5 determine the optimal sensitivity, follow these
instructions to include the Sensitivity value in a report. You must use a field group. After
you have defined a fluorescence or luminescence Read Step using Gen5's AutoSensitivty
determination:
1.
Select Protocol> Data Views
3.
Name the new Field Group
2.
4.
5.
Locate the Field Group element at the bottom of the tree, highlight Field Group
and click New
Click in the first cell in the first column to enable the 3-dot button, and click
the 3-dot button to open the Fields dialog
Set the Category to Procedure
6.
Set the Field to Sensitivity # (there is one value for each read/filter set)
8.
Save or Save As the Protocol to make sure this field group is available
whenever you run the experiment.0.
7.
Now, you can add this field group to Reports or Export files
Display the AutoSensitivity Value
When the Procedure is completed in an experiment:

Highlight Procedure in the menu tree and right click, select
AutoSensitivity Results
or
 Open the Procedure dialog (double click the menu tree item), the sensitivity
value applied during the first read step is displayed.
162 | Chapter 8: Fluorescence and Luminescence
Measurement Options
Procedure> Read> Fluorescence> click Options
Synergy 2/4: Procedure> Read> click 3-dot button next to Read Speed
This section describes all the possible measurement options available
in Gen5. You will be offered more or fewer of them depending on your
reader and the context of the Read step.
You may need to experiment with various combinations of settings to determine the
optimal value for each. Generally it is a trade off between speed and precision. Increase
the number of measurements per well for better precision; decrease them to increase
speed.
Define the measurement parameters for read speed:
 Delay after plate movement is the time between the end of the movement
of the plate carrier (plate is in the read position) and the beginning of the
acquisition of the data. The valid range is from 10 to 2550 milliseconds. The
recommended setting to ensure that the fluid has settled in a 96-well plate is
100 milliseconds. This parameter is especially important in absorbance mode,
where the vibration of the liquid's surface meniscus just after a plate movement
can lead to variations in OD measurements.
 Measurements per data point are the number of measurements the reader
takes per well per read. The data point reported for each well represents the
average of its measurements. The valid range is from 1 to 255 measurements.
Usually, the more measurements per well the better the CVs, although selecting
a large number of measurements typically results in only marginal
improvement. Consider a setting that represents the optimal combination of
precision and speed. The recommended setting to achieve a balance between
speed and precision is 10 measurements per well. This is not adjustable in
Absorbance reads.
Note: The reader takes approximately 10 milliseconds to perform each
measurement.
 Delay between measurements is the time delay between measurements
taken in each well. The valid range is from 0 to 255 milliseconds. The
recommended setting is 1 millisecond. Longer delays between samples may
result in better CVs between replicates.
 Dynamic Range: offers two ways to express the measurements taken by the
reader:
 Standard Range: reports measurements between 0 - 99,999, higher values
are reported as "OVRFLW." This is the only setting available for Synergy
Measurement Options | 163
HT, FLx800. Synergy 4 and Synergy 2 are limited to this option when the
Xenon Flash is used, e.g. for TRF.
 Extended Range: reports measurements between 0 - 5,800,000, higher
values are reported as "OVRFLW."
Some of the benefits of Extended Range, you can:
 take measurements with a high Sensitivity setting without fear of overranging the wells,
 measure samples with very low and very high outputs in the same Read
step,
 reduce the risk of over-ranging in kinetic mode (when the signal grows
over time).
164 | Chapter 8: Fluorescence and Luminescence
Synchronized Modes
Synergy 2/4, Synergy HT/FLx800 with Injectors: Protocol> Procedure>
Synchronized Modes
Gen5 supports three modes of processing plates. All readers can process plates in the
standard mode, we'll call Non-Synchronized Plate Mode to distinguish it from the
other options. If you're running a Synergy 4, Synergy 2, or a Synergy HT or FLx800
with Injectors, you have two more processing mode options: Synchronized Plate
Mode and Well Mode. These options give you more control in time-sensitive
procedures.
Tip: When defining a Synchronized Plate Mode and Well Mode procedure, in the
Procedure dialog the first step is adding the Well or Plate mode block. Then, put the
Read and other steps inside the block.
Non-Synchronized Plate Mode
Non-Synchronized Plate Mode is the standard mode for processing and is supported
by all BioTek readers. Each step in a Procedure is processed for the entire plate (or
partial plate) before the next step is processed. No attempt is made to maintain
consistent well-to-well timing from one step to the next.
Multi-Detection Kinetics
For readers that support multiple detection methods (absorbance, fluorescence,
luminescence), the Non-Synchronized Plate Mode supports the ability to include
multiple read steps in a single kinetic block. This capability is called MultiDetection Kinetics.
With a Synergy HT, for example, in Non-Synchronized Plate Mode, you can
perform a four-wavelength absorbance read, followed by a kinetic loop that
includes a dual-wavelength fluorescence read.
Synchronized Plate Mode
In Synchronized Plate Mode each step is processed for the entire plate (or partial plate)
before the next step is processed, but the time spent at each well is identical. Steps
within a Synchronized Plate Mode block maintain consistent well-to-well timing, such
that the time required to process two successive steps is the same for each well on the
plate. The Synergy HT and FLx800 readers can only perform Fluorescence in Plate
Mode; the Synergy 2 and Synergy 4 can perform all detection methods.
When timing is critical to your research, Synchronized Plate Mode gives you the ability
to perform a precisely timed sequence of steps on each well. For example, you can
define the timeline for a Dispense>Wait>Read block of steps that encompasses the time
to complete all three steps from beginning to end, so you know precisely when reagent
was dispensed to each well and when it was read.
Synchronized Modes | 165
Synchronized Well Mode
In Synchronized Well Mode, all steps within a block are performed on a single well,
before proceeding to the next well. Like Synchronized Plate Mode, the time spent at
each well is exactly the same. The Synergy HT and FLx800 readers can only perform
Luminescence and Fluorescence in Well Mode; the Synergy 2 and Synergy 4 can
perform all detection methods.
How to choose which option to use?
You may want to test the different options to see which works best for your
experiments, but here are some general guidelines to help narrow the choice:
 When you expect the well signal to vary over time, select Synchronized Plate
Mode or Well Mode (Synergy HT and FLx800 do not support a Shake step
following reagent dispensing in Well Mode)
 Non-Synchronized Plate Mode is efficient when using a Stop solution and the
well signal is stable over time
 In kinetic analysis, use Synchronized Plate Mode or Well Mode when it is
important to have the same exact timing for each well
 In kinetic analysis, use Non-Synchronized Plate Mode when it is important to
obtain as many data points as possible
 When conducting long-time-span kinetic reads (hours), Non-Synchronized
Plate Mode is sufficient
 In Synchronized Mode you can define the duration of a Delay step to include
the time it takes to perform the previous step
 Multi-Detection (multi-mode) Kinetic Reads can only be performed in NonSynchronized Plate Mode
166 | Chapter 8: Fluorescence and Luminescence
Processing Modes Comparison
Here's a tabular breakdown of the differences between Non-Synchronized Plate
Mode, Synchronized Plate Mode, and Well Mode.
Process
Detection
Supported
Steps
Kinetic
Loop
Steps
Read
Settings
Partial
Plate
Processing
NonSynchronized
Plate Mode
Absorbance
Fluorescence
Luminescence
All
Procedure
steps
supported
by Reader
Shake
Read
Can define
unique
settings for
each read
step
Can define
unique
setting for
each step
Synchronized
Plate Mode
Synergy 2/4:
all methods
Synergy HT &
FLx800:
Fluorescence
Read
Dispense
Shake
Delay
Kinetic
Shake
Read
Defined in
first step
for all
subsequent
steps
Defined in
first step for
all
subsequent
steps
Well Mode
Synergy HT &
FLx800:
Fluorescence
Luminescence
Synergy 2/4:
all methods
Read
Dispense
Delay
Kinetic
Synergy
2/4: Shake
Read
Synergy
2/4:
Shake
Defined in
first step
for all
subsequent
steps
Defined in
first step for
all
subsequent
steps
Synchronized Mode Performance Chart
Reader
Max #
of
Steps
Max #
Kinetic
Reads
Max Kinetic
Interval (sec)
Synergy HT
9
999
Plate = 9999
Well = 99.99
Plate = 1 sec
Well = 20 ms
FLx800
3
300
Plate = 9999
Well = 12
Plate = 1 sec
Well = 20 ms
Synergy 2
Synergy 4
20
999
Plate = 9999
Well = 99.99
Plate = 1 sec
Well = 20 ms
Time Increment
Synchronized Modes | 167
Synchronized Plate Mode Limitations
Here is a listing of the Plate Mode limitations:
 Synergy 2/4 support all detection methods, but Synergy HT and FLx800
only support Fluorescence
 All parameters set in the first read step of the block are automatically
applied to subsequent read steps, with the exception of Step Label and
Light Shuttering
 Partial plate settings are automatically applied to all read and dispense
steps using the settings in the first step
 The only available steps in a plate mode block are: Read, Dispense, Shake,
Delay, and Kinetic
 When two filter sets are used in the read step, the second filter set
automatically uses the sensitivity of the first, except Synergy 2/4 allow
different sensitivity values for each step
 A Shake step must immediately precede a Read step or a Kinetic Start step
 The maximum duration of a plate-mode block is approximately 27 hours 47
minutes for Synergy HT an FLx800 and approximately 277 hours 47
minutes for the Synergy 2/4
 The only available steps within a plate mode kinetic loop are Shake and
Read and the maximum runtime duration for a loop is 24 hours
 A maximum of one read step and one shake step is supported in a plate
mode kinetic block
 384- and 1536-well plates are not supported
 In the FLx800, a plate mode block must contain at least one kinetic loop to
be valid. If two kinetic loops are present in the plate mode block, they must
have the same kinetic interval
 In the FLx800, a plate mode block can contain only one dispense step, and a
dispense step cannot be the last step in the plate mode block
 Light Shuttering is available
168 | Chapter 8: Fluorescence and Luminescence
Synchronized Well Mode Limitations
Here is a listing of the limitations that apply to Well Mode blocks:
 Synergy 2/4 support all detection methods, but Synergy HT and FLx800
only support Fluorescence and Luminescence
 All parameters set in the first read step of the block are automatically
applied to subsequent read steps, with the exception of Step Label and
Light Shuttering
 Partial plate settings are automatically applied to all read and dispense
steps using the settings in the first step
 The only available steps in a well mode block are: Read, Dispense, Delay,
and Kinetic, except Synergy 2/4 also support a Shake step before a Read or
Kinetic loop
 The maximum duration of a well-mode block is approximately 16 minutes
40 seconds
 The only available step within a well mode kinetic loop is a Read step,
except Synergy 2/4 also support a Shake step
 When two filter sets are used in the read step, the second filter set
automatically uses the sensitivity of the first, except Synergy 2/4 allow
different sensitivity values for each step
 A maximum of one read step is supported within a well mode kinetic block
 Luminescence read steps within a well mode kinetic loop do not support
the entry of an Integration Time. It is replaced by the kinetic run time
 384- and 1536-well plates are not supported
 Light Shuttering is available
 Important: FLx800 readers require adding a Delay step (beginning at the
start of the previous step) to the Procedure to avoid potential loss of data.
You must determine the correct duration of the delays
Troubleshooting Fluorescence/Luminescence | 169
Troubleshooting Fluorescence/Luminescence
Here's a list of potential problems, the possible cause and a remedy:
Fluorescence / Luminescence Readings Too Low
 Possible cause: The Sensitivity in the Read Step dialog is currently set too low
Raise the Sensitivity to an appropriate level. For fluorescence, the Sensitivity is
usually set between 45 and 130. For luminescence it is usually set between 100 and
200.
If using Automatic Sensitivity Adjustment, use the Scale to High Well option and
set the target value to be between 20,000 and 80,000 for standard range; or
1,000,000-3,500,000 for extended range.
 Possible cause: The wrong filters are selected in the Read Step dialog
Examine the current filter settings and make any corrections. If the filter settings
appear to be correct, check the locations of the actual filters in the instrument.
 Possible cause: Top probe is too high
 Synergy HT: If a plate cover is not being used, lower the top probe to 1 mm
above the selected plate using the Top Probe Vertical Offset option in the
Read Step dialog
 Synergy 2/4: Gen5 generally positions the top probe at the optimal height
for fluorescence reads: it focuses the beam above the well. Refer to Gen5’s
Help and use the Top Probe Vertical Offset option in the Read Step dialog
to make adjustments
 FLx800: Refer to the Operator’s Manual for instructions to manually lower
the Top Optical Probe
Fluorescence Background Too High
 Possible cause: Using incorrect microplates
Solid black plates and top probe reading lower the background. Black plates with
clear bottoms lower the background if bottom reading is necessary. Corning 3615
or 3614 (for cell culture) are appropriate.
 Possible cause: The wrong filters are selected in the Read Step dialog
Examine the current filter settings and make any corrections. If the filter settings
appear to be correct, check the locations of the actual filters in the instrument.
 Possible cause: Phenol red is used in the media when exciting at 485 nm and
reading at 528-530 nm
Eliminate or replace the phenol red
 Possible cause: Cells, media and other contents fluoresce
170 | Chapter 8: Fluorescence and Luminescence
Use deionized-water blank wells as a diagnostic tool. The blank-well reading will
help you determine the background value contributed by the instrument, labware
and media.
 Possible cause: The top and/or bottom probe needs cleaning
Refer to the Operator’s Manual for instructions to open and clean the reader’s
internal components.
 Possible cause: The instrument has fluorescing material spilled inside
Refer to the Operator’s Manual for instructions to open and clean the reader’s
internal components.
 Possible cause: The Sensitivity in the Reading parameters dialog is currently set
too high
Lower the Sensitivity setting. The background should still read higher than zero.
200 is a recommended minimum and a value of 1000 takes advantage of the
system’s 5-digit resolution.
Reader Not Achieving Desired Fluorescence Detection Limit
 Possible cause: The wrong filters are selected in the Read Step dialog
Examine the current filter settings and make any corrections. If the filter settings
appear to be correct, check the locations of the actual filters in the instrument.
 Possible cause: Using incorrect microplates
Solid black plates and top probe reading lower the background. Black plates with
clear bottoms lower the background if bottom reading is necessary. Corning 3615
or 3614 (for cell culture) are appropriate.
 Possible cause: The Sensitivity is currently set too low
Raise the Sensitivity setting until the background wells read at least 200 RFU, (1000
RFU is preferred) in the Read Step dialog
 Possible cause: Readings are taken using the bottom probe
Switch to the top probe (Optics Position in the Read Step dialog)
 Possible cause: The solution volume is 50 ul or less
Increase the solution volume to 150 - 200 ul, if possible.
 Possible cause: Wrong pH
Fluorescence is very pH dependent. Use the appropriate pH.
 Possible cause: Phenol red is used in the media when exciting at 485 nm and
reading at 528-530 nm
Eliminate or replace the phenol red.
 Possible cause: Top probe is too high
Troubleshooting Fluorescence/Luminescence | 171

Synergy HT: If a plate cover is not being used, lower the top probe to 1 mm
above the selected plate using the Top Probe Vertical Offset option in the
Read Step dialog
 Synergy 2/4 filter-based reads: Gen5 generally positions the top probe
at the optimal height for fluorescence reads: it focuses the beam above the
well. Refer to Gen5’s Help and use the Top Probe Vertical Offset option in
the Read Step dialog to make adjustments
 Synergy 4 mono-based reads: Gen5 positions the top probe at 4 mm for
96-well plates and at 6 mm for 384-well plates because these settings were
determined to be the optimal height. You may be able to lower the probe,
but lowering it may require a small adjustment to the Column Offset, as
well.
 FLx800: Refer to the Operator’s Manual for instructions to manually lower
the Top Optical Probe
 Possible cause: Transfection efficiency in gene expression is too low
Use more cells, or improve the transfection efficiency.
 Possible cause: DNA is old or of poor quality
Use high quality, new DNA.
 Possible cause: Not using nuclease-free buffer in DNA quantitation
Use nuclease-free buffer.
 Possible cause: Poor dilution methods
Use appropriate dilution method in tubes.
Reader Over-ranging in Fluorescence
 Possible cause: The Sensitivity in the Read Step dialog is currently set too high
Lower the Sensitivity setting. Refer to the Sensitivity table on page 157 for valid
values.
If using Automatic Sensitivity Adjustment, try the Scale to High Well option and
set the High Value in the range of 50,000 to 70,000 for standard range.
Bandwidth Verification Failed
 Error or warning messages are issued when Gen5 detects overlapping
wavelengths or bandwidth
Select/enter Filter Set wavelengths that do not overlap. Learn more about Gen5's
bandwidth verification in Gen5’s Help.
Error during Auto-Sensitivity Determination
 Reader cannot fulfill request to determine optimal Sensitivity
Gen5 displays an error message when the reader cannot determine the optimal
sensitivity based on the defined reading parameters.
172 | Chapter 8: Fluorescence and Luminescence
 Luminescence integration time should be <= 1 sec and > 1 ms, especially when
scaling to low wells.
 Manually enter a Sensitivity value or use an alternative method to determine the
optimal sensitivity, if the error persists. Learn more in Gen5’s Help.
Filters and Mirrors | 173
Filters and Mirrors
Changing Filter Wheels
Important! It is essential to conform to the specific BioTek instrument procedures for
altering the filter wheel configuration. The reader does not automatically detect which
filters are installed. Before the instrument is shipped from the factory, BioTek updates the
reader's internal software with the current filter wheel settings. When you make changes
to a filter wheel, it is your responsibility to ensure that Gen5’s wavelength table exactly
matches the new contents of each filter wheel. For specific instructions on changing filters,
see the reader's operator’s manual. In order to obtain accurate results and prevent damage
to the PMT, they must match exactly.
To exchange wavelength information between Gen5 and the
instrument, the two must be communicating: the reader must be
turned on and properly configured in Gen5.
In Gen5, there are two ways to update the reader with filter wheel configuration:
 use the Fluorescence/Luminescence tab of the Reader Setup (System>Reader
Configuration>View/Modify>Setup) to ensure the wavelengths table matches
the filters installed in the attached reader
 use the Filter Wheels Library (System>Optics Library>Filter Wheels) to select a
pre-defined wheel and send its values to the reader.
Filter Wheels Library
System> Filter Wheels
Only for Fluorescence- and Luminescence-equipped readers
Refer to the reader's Operator's Manual for instructions for physically
changing the filter wheel
About the Filter Wheels Library
Gen5 provides these controls to create a catalog of your Fluorescence and
Luminescence excitation and emission filter wheels. If you regularly change filter
wheels, this feature provides significant time savings: define the filters in each wheel
once, and with one click, update the reader's internal software to match the
configuration of the selected wheel.
When you add new filters to the catalog, Gen5 offers them for selection when you're
defining a Read step. This feature lets you create protocols, i.e. define reading
parameters, using filters that are not currently installed in the reader. The Read Plate
Prompt Option will ensure that users are alerted when they try to run a Procedure that
calls for filters not currently installed.
174 | Chapter 8: Fluorescence and Luminescence
Gen5 considers filter wheels to have distinct uses, they are either Excitation or
Emission wheels. BioTek ships wheels labeled either EX for excitation or EM for
emission. The Time-Resolved Fluorescence, TR cartridge for the Synergy HTTR is NOT
eligible for this catalog.
Some Read-step parameters, e.g. Light Shuttering, require a special filter-wheel
configuration. This feature provides a short-cut for setting up this type of experiment.
After creating a record for the special wheel in the library, you can simply exchange
the wheels and with one click, update the reader's settings.
How to use the Filter Wheels Library
Select System>Filter Wheels to perform these functions:
1.
First, the library records (descriptions of your filter wheels), must be created
(page 175)
2.
When records have been added to the library, select the Type of wheel you
want to view or modify using the drop-down list. The list box shows all
previously defined wheels of that type.
3.
4.
Highlight a record and click View/Modify to see or change the details of a
record or Delete, as needed.
Select a Read Plate Prompt Option:
 Select the Always prompt option to tell Gen5 to always open the Filter
Wheel Selection dialog whenever the Procedure is Validated and when a
plate is read
 Select the Only prompt option to tell Gen5 to only open the dialog when
the Read step calls for a filter that is not in a currently installed wheel
5.
After you have physically exchanged a filter wheel, when you
want to update the reader's internal software to match a selected wheel, click
Set Reader. This performs the same function as the Reader Setting's Setup
option.0.
Updating the reader with a filter-wheel configuration from the Filter Wheel Library
also updates the Reader Configuration> Reader Settings> Fluorescence/
Luminescence Filters table
Filters and Mirrors | 175
Creating and Modifying Filter Wheels
System> Optics Library> Filter Wheels> Add or View/Modify
Creating new filter wheel records
To add a new filter wheel to your library:
1.
Select System> Optics Library> Filter Wheels
3.
Name the new filter wheel
2.
4.
5.
6.
Click Add...
Select the Wheel Type: Excitation or Emission
Select the filter Type using the drop-down list for each Filter position in the
Excitation and Emission filter wheels.
When applicable for the filter Type, enter Wavelength and Bandwidth values
in the fields.
The Wavelength value and its accompanying Bandwidth, in
nanometers, are etched into the filters. For example, the
Wavelength/Bandwidth combination of 485/20 will transmit light from
475 to 495 nm (10 nm on either side of the center). See the reader's
operator’s manual for details.
7.
When the filter wheel is fully defined, click OK. 0.
Special filter position requirements for the Synchronized Modes:
For Dispensing Protocols and certain other procedures, Gen5 offers an option: Close Light
Shutter, to block the light between measurements to inhibit photo bleaching:
 Single filter-set protocols: When light blocking is enabled, a blocking filter
(Plug) must be placed in the excitation filter wheel in one of the two positions
next to the excitation filter that is specified in the protocol.
 Dual filter-set protocols: When light blocking is enabled, two blocking filters
(Plugs) must be placed next to each other in the excitation filter wheel, except
for Synergy 2 and Synergy 4, which need only one plug anywhere in the filter
wheel.
Gen5 issues an error message when the configuration of the filter
wheel does not match the requirements of the Procedure/Read step.
Filter Wheel Configurations
The valid combination of filters, plugs, and holes in a filter wheel depends on the reader
model.
Band Pass - standard interference filter with a defined central wavelength and bandwidth.
176 | Chapter 8: Fluorescence and Luminescence
Plug - light blocker or solid plug in the filter wheel. A plug in the Excitation filter wheel is
typical for luminescence assays, to prevent ambient light from entering the measurement
chamber.
Hole - empty space in the filter wheel to allow unfiltered light to pass through. An empty
location in the Emission filter wheel is typical for luminescence assays.
Synergy 4 Readers Only support:
Long Pass - an "edge pass filter" with a cut-on Wavelength where the filter stops reflecting
and starts transmitting light. It can be used in the Emission filter wheel.
Short Pass - an "edge pass filter" with a cut-off Wavelength where the filter stops
transmitting and starts reflecting light. It can be used in the Emission filter wheel.
Mono LP - positioned in the Excitation wheel for use as an order-sorting filter by the dual
monochromator.
Important filter wheel requirement: to perform monochromator
reads, the reader’s excitation filter wheel must contain a Hole and a
Mono LP filter. And, when light shuttering is required, there must be a
Plug between the Hole and the Mono LP filter.
Mirrors and Mirror Holders
Before shipping the reader, BioTek configures the reader's internal basecode to match the
mirrors installed in the reader. Unless you are changing the current configuration do not
alter the settings.
Your reader's Operator's Manual provides detailed instructions for maintaining and
changing mirrors and mirror holders.
About Mirrors
For all top-reading filter-based fluorescent reads, Fluorescence Intensity (FI),
Fluorescence Polarization (FP), and Time-Resolved Fluorescence (TRF), the Synergy 2
and Synergy 4 use mirrors to direct light to the sample and obtain measurements from
it. Up to three mirrors, either 50%, Dichroic, or custom, can be installed in the reader.
Mirrors reside in a mirror holder with three possible reading positions. Any mirror can
be used for any type of experiment, except FP (Fluorescence Polarization), which
Filters and Mirrors | 177
requires using the mirror in position 3, because it holds the polarizing lenses. Keep in
mind when using dichroic mirrors that the filter sets must match the wavelength
range.
The mirror holder (pictured above) is a rectangular box located inside the reader.
(Additional mirror holders can be purchased as an accessory and kept track of in the
Mirror Holder Library.) The mirror holder and the mirrors are user-changeable. You
can replace the entire holder with a different one; this is the recommended option. Or,
alternatively, you can install different mirrors in the mirror holder. Contact BioTek for
more information on purchasing additional mirrors and holders. Refer to the reader's
Operator's Manual for replacement instructions.
The reader cannot detect which mirrors are installed in it. Whenever you change a
mirror holder or the mirrors in the holder, use Gen5 to update the reader's internal
basecode to match the new hardware.
Gen5 provides two ways to download information about your mirrors to the reader:
 Update the Mirror Configuration table when you have only one mirror
holder
 or use the Mirror Holder Library when you have multiple holders
Dichroic Mirrors
Dichroic mirrors have to match the Excitation and Emission filters. If the excitation
filter and dichroic do not match, the excitation light goes through the mirror, instead of
reflected to the sample and the sample does not get excited. If the emission filter and
dichroic don't match, even when the excitation light is reflected to excite the sample,
the emission light is also reflected by the mirror and goes back to the light source
instead of the detector (PMT).
Mirrors and filters are defined under Reader Configuration and then, offered for
selection when the Procedure is being defined. Filters can also be defined in the Filter
Wheel Library.
178 | Chapter 8: Fluorescence and Luminescence
When defining and performing a Read step, the filter set must be compatible with the
mirror. 50% mirrors do not have wavelength requirements; they can be used with any
filter sets. But Dichroic mirrors require the filter's central wavelength to fall within the
mirror's EX and EM Min-Max range.
In the Read Step dialog, hover your mouse
over the Optics Position to see a tool-tip
that lists the Excitation and Emission range
for the selected dichroic mirror. Either select
filters that fall within the Ex and Em ranges
(respectively) or change the selected mirror.
Mirrors Configuration
System> Reader Configuration> View/Modify button> Setup button
Normally, these controls are only needed when you are changing a mirror or mirror
holder
To change the current settings and download them to the instrument:
When you exchange a mirror or mirror holder, follow these steps to update the reader:
1.
Select System> Reader Configuration
3.
Click
5.
For each Mirror position, 1, 2, 3, use the drop-down list to select the Type of
mirror. Gen5 assigns a Label based on your selection. For details about the
valid values see Define a Mirror Holder on page .
2.
4.
6.
7.
8.
Double-click the reader to be updated. This opens the Reader Settings dialog.
Select the Mirrors tab
For a Dichroic mirror, you must enter its wavelength range. Refer to the fact
sheet provided with the mirror to enter the values for the Excitation Minimum
and Maximum and the Emission Minimum and Maximum. Gen5 creates the
Label for the mirror based on your input.
with Polarizers: if the mirror holder is equipped with polarizing lenses,
enable this option in Gen5.
When the actual mirrors in the mirror holder are described correctly in the
table, click Send Values to download the data to the reader.0.
Filters and Mirrors | 179
Define a Mirror Holder
Gen5 provides two ways to manage information about your mirror holders:
 Use the Mirror Holder Library when you have multiple holders
 Otherwise, you can simply update the Mirrors table
To define the mirrors in a Mirror Holder:
1.
2.
Either update the library or the mirror table:
 Select System> Optics Library> Mirror Holders> Add or Modify
 Select System> Reader Configuration> Reader Settings> Setup >
Select the Mirrors tab
For each Mirror position, 1, 2, 3, use the drop-down list to select the Type of
mirror. Gen5 assigns a Label based on your selection:
 50% = works with any wavelength. It is a glass slide with small, reflective
silver dots; 50% of the surface reflects light, 50% of the surface transmits
light. It's Label is Top 50%.
 Dichroic = works with a specific wavelength range; they are transparent to
one part of the spectrum and block the other part. You must know the
mirror's specific excitation and emission wavelength range to properly
configure the reader.
 Custom = select this option when your mirror is neither a 50% nor a
dichroic. Gen5 lets you select any combination of filters when defining a
Read step using a custom mirror. Assign it a Custom Name to distinguish it
from other mirrors. You can use up to 8 characters.
3.
4.
 None = select this option when there is an empty position in the mirror
holder. It is not given a label and this position cannot be selected when
defining a Read step.
For a Dichroic mirror, you must enter its wavelength range. Refer to the fact
sheet provided with the mirror to enter the values for the Excitation Minimum
and Maximum and the Emission Minimum and Maximum. Gen5 creates the
Label for the mirror based on your input. Learn more...
with Polarizers: if the mirror holder is equipped with polarizing lenses,
enable this option in Gen5.0.
Mirror Labels
Gen5 assigns each mirror a Label as you define or modify them. Mirrors are only used
when top reading (rather than bottom reading) is performed on the plate, thus all labels
(except Custom) begin with Top:
 50% mirrors are always labeled Top 50%.
180 | Chapter 8: Fluorescence and Luminescence
 For dichroic mirrors Gen5 calculates the average of the Excitation Max and
Emission Min and assigns this value as the label. For example, Top 400
becomes the label when the EX Max = 390 and the EM Min = 410.
 Labels for custom mirrors are the user-defined Custom Name.
Mirror Holder Library
System> Optics Library> Mirror Holders...
Refer to the reader's Operator's Manual for instructions for physically
changing the mirror holder
About the Mirror Holder Library
Gen5 provides these controls to create a catalog of your Mirror Holders. If you regularly
change mirror holders, this feature provides significant time savings: define the mirrors in
each holder once, and with one click, update the reader's internal software to match the
configuration of the installed holder.
First you must create a library record for each mirror holder. Then, after you physically
change a mirror holder, you can select its record and instantly update the reader's internal
mirror table.
When you add new mirrors to the catalog, Gen5 offers them for selection when you're
defining a Read step. This feature lets you create protocols, i.e. define reading parameters,
using mirrors that are not currently installed in the reader. The Read Plate Prompt Option
will ensure that users are alerted when they try to run a Procedure that calls for mirrors
not currently installed.
Changing mirrors in a mirror holder: the library is intended to
keep track of multiple mirror holders. When you are limited to
changing individual mirrors in a single mirror holder, it is quicker and
easier to simply update the reader's internal mirror table using the
Reader Setup controls.
How to use the Mirror Holder Library
Select System>Optics Library>Mirror Holders to perform these functions:
1.
2.
First, the library records (descriptions of your mirror holders) must be created.
See Define a Mirror Holder on page 179.
When records have been added to the library the list box displays them.
Highlight a record and click View/Modify to review or change its details or to
Delete it, as needed.
Filters and Mirrors | 181
3.
Select a Read Plate Prompt Option:
 Select the Always prompt option to tell Gen5 to always open the Filter
Wheel Selection dialog whenever the Procedure is validated and when a
plate is read
 Select the Only prompt option to tell Gen5 to only open the dialog when
the Read step calls for a filter that is not in a currently installed wheel
4.
When you want to update the reader's internal software to match
a selected mirror holder, click Set Reader. This performs the same function
as the Reader Setting's Setup option.
Select a Mirror Holder
System> Optics Library> Mirror Holders...
These controls are presented during Procedure Validation and plate processing when Gen5
is instructed to "Always prompt before a procedure" or when the Read step calls for
mirrors that are not currently installed in the reader.
When validating a Procedure
Gen5 opens the Mirror Holder Selection dialog when validating a Procedure to offer any
mirror holder that meets the requirements of the read step:
1.
2.
Highlight a holder in the Available Mirror Holders box
Click Continue to validate the Procedure using the selected filter wheel.0.
When executing a Procedure
Gen5 displays an error message and, if a valid mirror holder is available, opens the Mirror
Holder Selection dialog when the Procedure calls for a mirror that is not currently
installed in the reader. Only holders that meet the requirements of the read step are
offered for selection in this scenario.
1.
Highlight a holder in the Available Mirror Holders box
3.
Physically change the mirror holder in the reader. Follow instructions provided
in the Operator's Manual. After it is changed and the reader is turned on and
has completed its self test, return to Gen5 and click Send Values. The reader's
mirror table is not updated until this final step is completed.0.
2.
Click Update Reader to select the mirror holder you will install.
When using the Mirror Holder Library
From the Mirror Holder Library, click Set Reader... when you want to
update the reader's internal software to match the configuration of a selected holder
182 | Chapter 8: Fluorescence and Luminescence
Multi-Detection/Multi-Mode Protocols
Synergy™ HT and Synergy™ 2/4 Only
Prerequisite
only BioTek's multi-detection readers Synergy HT, Synergy 4 and
 Currently
Synergy 2 are capable of running multi-mode protocols.
Gen5™ lets you perform multiple detection methods on a plate within one protocol.
Examples
 Stand-Alone Multi-Detection Protocol - You can define independent read
steps, performing each read with a different detection method. Other
Procedure steps (e.g. Shake) can be included in the sequence, following the
rules for all types of protocols.
 Kinetic Multi-Detection Protocol - You can perform a multi-detection kinetic
analysis, conducting the reads within a kinetic loop, reading each plate with a
different method in sequence. Reads must be done in Standard Plate Mode (not
in Synchronized Mode).
Read the permissions and restrictions for conducting multi-detection within a
kinetic loop on the next page and view examples on page 184.
Features and Restrictions of Kinetic Multi-Detection Protocols | 183
Features and Restrictions of Kinetic Multi-Detection
Protocols
Supported features:
 Up to 6 wavelengths for Absorbance reads
 Up to 2 filter sets for Fluorescence and Luminescence reads
 Time-Resolved Fluorescence (TRF)
 Automatic Sensitivity Adjustment
 All other valid combinations of Procedures can precede or follow the
kinetic loop
Limitations:
 Only Standard (non-synchronous) plate mode reads are supported
 Up to 3 read steps can be performed in a multi-detection kinetic loop
 A Shake step is the only reading-related activity that can be inside a multidetection kinetic loop
 Synergy HT cannot perform a time-resolved fluorescence and standard
fluorescence read in the same kinetic loop (nor in the same protocol).
Synergy 2/4 can perform TRF and other types of fluorescence analysis (FI
and FP) within a kinetic loop when every read within the loop uses the
same light source. TRF requires use of the Xenon Flash, so you must select
this light source for any other fluorescence read within the kinetic loop
 A continuous shake event must be the first step in the sequence
 When more than one kinetic loop is defined you cannot "Append to
previous Kinetic data" as is possible in a mono-detection kinetic Procedure
Features that are not supported:
 Spectrum and Scanning read types
 Pathlength correction
 Dispense steps (Readers with Injectors)
 (but you can work around this limitation, see Dispensing Reagent in a
Kinetic Analysis Protocol in Gen5’s Help)
184 | Chapter 8: Fluorescence and Luminescence
Examples of Kinetic and Stand-Alone Multi-Detection Procedures
In a Kinetic Multi-Detection Protocol readings are performed sequentially in a kinetic
loop
In a Stand-Alone Multi-Detection Protocol readings are performed independently
Chapter 9
Kinetic Analysis
This chapter focuses on the tools and techniques available for
creating a kinetic analysis assay.
How to set up a Kinetic Analysis ................................................ 186
Kinetic timelines ...................................................................... 186
Kinetic Minimum Interval .......................................................... 188
Discontinuous (Long) Kinetic Procedure ...................................... 189
Well Zoom .............................................................................. 191
Well Analysis Calculation Types.................................................. 196
186 | Chapter 9: Kinetic Analysis
How to set up a Kinetic Analysis
Begin with Protocol> Procedure
In the Procedure, for kinetic analysis, you set up the timelines and intervals to define
the number of reads per wavelength and any other required activities. If you're
performing time-sensitive studies review the Synchronized Mode options in the
Fluorescence and Luminescence chapter.
To set up a kinetic analysis protocol or time course work:
1.
2.
Open Procedures (Protocol> Procedure)
Click Kinetic. Gen5 opens the Kinetic Step controls. Define the timelines (see
the next page for more information):
 Use the spin buttons or click in the Run Time and Interval fields and enter
the desired time settings. Alternatively, let your reader determine the
Minimum Interval for the desired Run Time. Follow these instructions for
applying the Minimum Interval on page 188.
3.
4.
5.
 Gen5 adds a kinetic loop to the Procedure.
With the End Kinetic step of the kinetic loop highlighted, click Read to add at
least one read step to the loop. If desired, include a Shake step before the read.
(Scanning and Spectrum reads are not supported.)
Add other steps, including other kinetic loops, to the Procedure, as needed.
Click Validate to make sure the current reader is capable of processing the
sequence.
Next, go to Data Reduction. At least one Well Analysis calculation is
automatically created for you. Double-click the Well Analysis step to view or
modify it. Add more Well Analysis or other calculations, as needed. 0.
Dispensing Reagent in a Kinetic Analysis
Select Help>Help Topics in Gen5 to review suggestions for including a dispense step
in your Kinetic Procedure.
Kinetic timelines
Numerous factors affect the runtime parameters for a kinetic loop. The minimum
interval for readings can be increased or decreased by the defined reading parameters.
Here are some facts to consider and some limitations of the BioTek readers:
How to set up a Kinetic Analysis | 187
Reading parameters that can affect kinetic timelines:
 Plate size: a 96-well plate can have a shorter minimum interval and obtain more
reads than a 384-well plate in the same runtime duration. Similarly, reading a
partial plate generates more reads during the same time period.
 Read Speed in Absorbance reads: more reads can be obtained in Rapid mode than
at Normal speed
 Measurement Options in Fluorescent reads: you can control the read speed (and
affect the kinetic timelines) by adjusting the number of measurements per data
point, and the delay after plate movement
 Integration Time in Luminescent reads: you can control the read speed (and affect
the kinetic timelines) by adjusting the read duration for each well
 Number of steps in the kinetic loop: adding steps, a Shake and one or more Read
steps, to the kinetic loop effects the timelines
 Duration of a Shake step in the kinetic loop is added to the Run Time
Reader limitations:
All readers are limited to obtaining 9999 reads in Absorbance mode within the 168
hour timeline. The longest interval between reads is 2.5 hours. Fluorescence and
Luminescence kinetic reads and intervals are reader dependent:
Reader
Total #
Reads
Max
Interval
Synergy HT: Standard mode
300
9999 sec
Synergy 2/4: Standard mode
9999
9999 sec
Synergy HT/Synergy 2/4:
Synchronized Plate
999
9999 sec
Synergy HT/Synergy 2/4:
Synchronized Well
999
99.99 sec
Flx800: Standard mode
300
9999 sec
FLx800: Synchronized Plate
300
9999 sec
FLx800: Synchronized Well
300
12.00 sec
188 | Chapter 9: Kinetic Analysis
Kinetic Minimum Interval
Here are instructions for letting Gen5 determine the shortest valid kinetic interval:
Prerequisite: Your reader must be connected and turned on, i.e.
communicating with Gen5, to determine the minimum interval
Gen5 communicates with the reader to determine how quickly the Kinetic loop can be
processed. You must click the Validate button to trigger this communication. Follow
these steps:
1.
2.
3.
4.
In the StepWise Procedure, click Kinetic to add a loop
Define the Run Time for the Kinetic loop and select
click OK
Minimum Interval,
Add a Shake step if desired and define one or more Read steps with the
required wavelengths/filter sets and other conditions. For an Absorbance read
you can increase the Read Speed, for faster processing. For a Fluorescence
analysis, you can modify the Filter Set Options to speed up processing.
Click the Validate button. Gen5 will display a confirmation
message and the Interval will be defined.
What you'll see
You'll notice that the description of the Start Kinetic step will change from "generate
minimum interval" before you hit the Validate button to a specific time setting for
Interval:
Important: Gen5 replaces the "minimum interval" setting with an
actual interval time. If you subsequently make changes to the
Procedure that have an effect on the kinetic interval, e.g. increase the
plate size or add another read step, the minimum interval must be
recalculated.
Discontinuous Kinetic Procedure | 189
Discontinuous Kinetic Procedure
Procedure> Kinetic> Read
About Discontinuous Kinetics
For cell growth assays and similar types of studies, Gen5 provides a way to take
readings over a long time period without tying up the reader, so it can be used in other
experiments during the rest or incubation periods. Gen5 calls this type of analysis:
Discontinuous Kinetic, because the measurements obtained from the multiple readings
are combined, resulting in a multi-read data set. There is virtually no time limit to this
type of procedure.
Limitations of Discontinuous Kinetics:
 Endpoint and Kinetic reads are supported, but Area Scan, Linear Scan, and
Spectral Scans are prohibited
 Synchronous Mode is not supported, i.e. you cannot perform readings in
Synchronized Plate or Well Mode
 Stop/Resume steps are prohibited, i.e. you cannot include a Stop/Resume step
in the Procedure
Gen5's Data Reduction Well Analysis Options are available for this type
of experiment
How to set up a Discontinuous Kinetic Experiment:
1.
Create a new Protocol in the usual way
2.
When defining the Procedure, select Advanced Options,
and select the Discontinuous Kinetic Procedure option
3.
4.
5.
6.
7.
8.
Enter "estimated" time points in Days:Hours:Minutes: for the Estimated total
time and Estimated interval
This is just an estimate, and will not interfere with actual experiment activity.
Gen5 uses your estimated time lines to set up the data views and formulas with
placeholders until the actual data is captured. When in doubt about the
required time period and intervals, it is best to over-estimate them. See the
example on the next page.
Define the Read step(s) as usual, and save the Protocol
Create an Experiment based on the Protocol, and conduct the first Read on the
plate
Close and save the Experiment
Remove the plate and process (e.g. add reagent) or store it (e.g. incubate), until
it is time for the next reading
Open the Experiment, put the plate on the carrier, click the Read button, and
select Next Read
190 | Chapter 9: Kinetic Analysis
9.
Repeat steps 5-7 until all the required reads are completed0.
Gen5 compiles all the reads into a kinetic data set, and performs Data Reduction, e.g.
Well Analysis, as defined in the Protocol.
Example of Discontinuous Kinetic Estimated Time Points
If you expect to read the plate twice a day for 3 days, but an extended time period
may be needed, enter 5 days for the Estimated total time, and 12 hours for the
Estimated interval:
Well Zoom | 191
Well Zoom
Performing a multiple-read Read Step generates the Well Zoom feature, which lets you
zero-in on each well of the microplate to view the reading results for individual wells.
Multiple wells can be selected for simultaneous viewing. Setting up Well Analysis as a
Data Reduction step enhances the view, displaying the calculation results for each
well.
Gen5 automatically creates one Well Analysis step when you define a
kinetic loop
How to:
Tip: To use this feature to monitor kinetic readings in real time, perform these
steps before you start the reading. However...see the note below.
1.
2.
After reading the plate, open the Plate View that represents the plate
In the Matrix view, use the drop-down list of available Data sets to display the
set labeled Curves. (The raw data set upon which a Well Analysis data
reduction has been performed offers the most useful display, for example: When
you assign blanks to the plate, Gen5 first creates a blank-subtraction data set, and
then performs well analysis on that data set. Gen5 creates a Curves data set based on
192 | Chapter 9: Kinetic Analysis
3.
this well analysis, e.g. Curves [Blank 450] where 450 is the wavelength of the reading.
Select this data set for the best well zoom.)
Click any well in the matrix to see its Well Zoom view.0.
Do not display Gen5's "Curves" data in the Plate View while
performing a kinetic analysis. Wait until the read step is finished
before viewing the "Curves" data set. Displaying the Curves data set
during a Kinetic read can consume excessive resources resulting in
performance degradation. You can drill down to a Well Zoom to
monitor the progress of one well, then, leaving the Well Zoom open,
change the Matrix Data to a numeric view.
Open the Well Zoom View
Set the Data set in the Matrix view to Curves, and click in a well for the Well Zoom
Hold the Ctrl key, while selecting up to 8 wells in the Curves data set of the Plate
View, to see all the well results simultaneously (except for Area Scans)
Use the View data/View chart toggle button to show the
data in either a table or graph. See examples beginning on page 198.
View Multiple Wells Simultaneously
Click the 3-dot button next to the Wells field to select multiple wells to view in one
graph. This is dynamic, so you can select and de-select the wells you want to see. Up to
8 wells can be selected at one time.
Well Zoom | 193
Zoom Zoom
Within a well zoom you can further zoom in on selected data points:
1.
2.
Click and drag your mouse over an area of the well zoom. The pointer changes
to a cross as Gen5 maps the selected area. Gen5 presents a pop-up menu when
you release the click
Select an option from the menu:0.
 Zoom In or Zoom Out
 Mask or UnMask Points
Well Zoom Plotting
When Gen5 plots the well zoom curves, the X axis represents the individual reads for
the well, and the Y axis represents the measurements:
Y Axis X Axis
ODs
Kinetic read times
RLUs
Linear horizontal positions
RFUs
Spectrum wavelengths
Well Analysis Results Table
When a Well Analysis Data Reduction step is defined, Gen5 shows the calculation
results in a table beneath the curve. The "Curves" or "Scan" data set that leads to a well
zoom, must be the subject of a Well Analysis step; raw data well zoom views do not
include a Well Analysis Results table.
194 | Chapter 9: Kinetic Analysis
Calculation Zone
The range of reads considered for analysis is determined by the Calculation Zone
setting of the Well Analysis. When the original range is reduced, Gen5 plots the
revised Calculation Zone with brackets: [ ]
Viewing Appended Kinetic Results
When one or more kinetic reads are appended, Gen5 combines them into one data set.
When a Dispense step occurs between the kinetic loops, Gen5 represents the event as a
blue diamond on the X-Axis timeline.
FLx800 with Injectors may show the "Dispensing" event occurring
in the same interval as a Read. This is a limitation of the reader's
basecode or on-board software.
Customizing the Well Zoom View
After launching the Well Zoom dialog, you can:
 Select a different Curve to display (if available)
At the Curve field, click the
for the selected well
drop-down list to select another data set
 Mask or exclude a data point and Recalculate
1.
2.
Click on a data point to temporarily exclude or mask it from the
calculation, then click Recalculate
Click on the data point again to restore it 0
Important: modifying data may adversely effect or possibly invalidate
results!
 Overlay up to 8 other kinetic curves on top of the current one
Click the
3-dot button next to the Wells field to select curves from
other wells to overlay onto the current one.
 Modify or Create a new table (to select the data displayed beneath
the graph)
 Click
the
3-dot button next to the Results field to modify the
 Click
the
drop-down list and select Create a New Table
table.
 Learn
more at Customizing Data Views, Reports, and Exports in the
Reporting Results chapter
Well Zoom | 195
 Display or hide a legend for the graph
Click
next to the Curve field. On the Layout tab, click in the checkbox
to Show the Legend or remove the checkmark to hide it.
 Modify the text and line formatting of the graph
Click
next to the Curve field.
 Create a new graph (curve)
Click
at the Curve field and select Create New Graph. You can combine
multiple curves, if available, with this option, to simultaneously view the well
results of each curve.
196 | Chapter 9: Kinetic Analysis
Well Analysis Calculation Types
Also see the Data Reduction chapter for useful information
Protocol> Data Reduction> Well Analysis
Gen5™ offers the following calculation types when a multiple-index read step is
defined. Each option has its own specific parameters, which you define by selecting the
Calculation Options button.
 Mean V is the calculated value of the mean slope. It is calculated by a linear
regression on points in the Calculation Zone. Define the Calculation Zone with
the Calculation Options button. For Mean V, the zone is typically adjusted to
ignore misleading data points generated at the beginning of a kinetic assay due
to "noise."
 Max V is the calculated value of the maximum slope:
1. Starting at the first point in the calculation zone, Gen5 evaluates n points
and calculates the slope among these n points.
2. Gen5 repeats the operation, starting at the second point in the calculation
zone, and repeats it again, starting at the third point, and so on.
3. Finally, Gen5 compares all calculated slopes to determine the maximum
slope.
Gen5 registers the Delta t time in the middle of the point where the Vmax is
calculated. By default, the calculation zone starts at 2 points and at time zero.
Well Analysis Calculation Types | 197
Select the Calculation Options button to modify the calculation zone.
Gen5 also calculates the kinetic Lag Time, which is the time interval between
the line of maximum slope of the propagation phase and the absorbance
baseline at time = 0. Also calculated: Y Intercept, R and R2, delta time at Max
V, and Max V minus minimum and maximum time.
 Mean Min/Max Mean Min is the mean minimum OD* based on n points. Mean
Max OD is the mean maximum OD based on n points. Gen5 calculates the
Mean Min and Mean Max ODs as follows:
1. Starting at the first point in the calculation zone, Gen5 evaluates n points
and calculates the mean among these n points.
2. Gen5 repeats the operation, starting at the second point in the calculation
zone, and repeats it again, starting at the third point, and so on.
3. Finally, Gen5 compares all of the calculated means to determine the
minimum and maximum of these values.
Gen5 registers the Delta t time at Min/Max OD. Select the Calculation Options
button to modify the calculation zone.
*: For fluorescence and luminescence reads, Gen5 performs calculations based
on fluorescence units (RFU) and luminescence units (RLU), respectively.
 Mean, Std, CV This option calculates and reports the Mean, Standard Deviation,
and Coefficient of Variation for all points in the calculation zone. By default,
the calculation zone includes all of the Reading Points defined in the protocol.
To change the calculation zone, click the Calculation Options button.
 Onset OD Gen5™ reports:
Onset Time: the time it takes to reach Onset OD*
Onset OD: the user-specified value. It can be defined as an absolute value or a
relative value based on the Basis OD
Basis OD: is an optional value used to adjust all wells to a baseline. It is defined
under Calculation Options as a fixed value or the "Mean of first n points"
Basis Time: the time it takes to reach Basis OD,when defined
*: For fluorescence and luminescence reads, Gen5 performs calculations based
on fluorescence units (RFU) and luminescence units (RLU/sec), respectively.
 Integral calculates the area under the curve according to the trapezoidal
method, shown here:
Where y = measurement value and x = read point value.
The area under the curve is displayed in the Well Zoom when this option is
selected.
By default, the calculation zone spans the full Run Time and includes all of the
reading points defined in the protocol. Click Calculation Options to change
the calculation zone.
198 | Chapter 9: Kinetic Analysis
 Formula allows you to calculate a value using data from individual reading
points. Reading points are designated Rn, where n is the reading number. Use
Wn for spectrum reads.
The Formula is calculated for each well and results in one new data set named
"Formula Result [nm]", where nm is the wavelength or filter set defined in the
read step. When a Label is defined it precedes the naming convention: "Label:
Formula Result [nm]".
For example: (R1+R2)/2 + R10 is read point 1 + read point 2 divided by 2 plus
read point 10.
Well Zoom: View Chart/View Data
Gen5 lets you toggle the Well Zoom view between a chart and a table. Click the View
Data button to see the table, click the View Chart button to view the kinetic curve.
Chapter 10
Scanning Analysis Options
Gen5, depending on the capabilities of the current reader, makes it
easy to conduct an area or linear scan of wells in a plate, or a
multi-wavelength spectrum scan. Selecting one of these methods
also enables Well Analysis data reduction features. This chapter
provides details about these capabilities.
Area Scan ............................................................................... 200
Linear Scan ............................................................................. 202
Spectrum Scan ........................................................................ 203
200 | Chapter 10: Scanning Analysis Options
Area Scan
When the reader is capable of performing an area scan, Gen5 provides three ways to
control the output of the captured measurements:
 Scan Options, defined in the Read Step of the Procedures, determine the Read
Matrix Size. The potential Read Matrix Size is a function of the well size of the
current plate.
 Calculation Zone, defined in the Well Analysis Data Reduction step, lets you
limit the values reported, ignoring the lowest OD/RFU measurements for
example, for meaningful results
 Display Options provide more control over the appearance of the results,
letting you limit the results displayed based on their measurement values and
changing the color scale applied to the values for a better presentation of the
results.
The Synergy 2's and Synergy 4’s probe size limits its ability to perform
Fluorescence area scan in plates with a small well diameter. Generally,
this means you must use a plate with fewer than 96 wells.
While you can control the temperature (and incubate the plate) for
these types of reads, due to a reader limitation, area and spectral
scans do not report the temperature on-screen or in reports or export
files.
Calculation Types
 Gen5 calculates and reports the Mean OD/RFU, Standard Deviation and
Coefficient of Variation of samples
Viewing and Reporting Results
When a Well Analysis data reduction step has been defined, Gen5 displays a graphical
representation of the measurements taken across the well:
1.
2.
In the Matrix tab of the Plate workspace, use the drop-down list of available
Data sets to display the set labeled Scans
Click in a cell to show its Well Zoom
As described in Display Options above, Gen5 offers extra controls for
adjusting the view of Area Scans. Perform the next step, Step 3, to
access the controls, which are especially useful for customizing reports
of the scan results.
3.
Click the 3-dot button next to the Curve field to open the controls for
adjusting the view.0.
Area Scan | 201
In Gen5’s Help you can find detailed instructions to:
 Assign a different Title for the graph displayed
 Hide or show the Color Scale legend
 Change the online view to Gray Scale to match the output from non-color
printers
 Change the Data Range and Color Range applied to the results
202 | Chapter 10: Scanning Analysis Options
Linear Scan
When the reader is capable of performing a linear scan, Gen5 plots a curve for each
well using the reading points in the scan.
 Scan Options: You define the number of reading points in the Read Step of the
Procedure
PowerWave-series readers require updating the Filter Table with the
wavelength you want to scan before reading the plate. Enter the
desired wavelength in the table and click Send Wavelengths, then
define the Read step.
Calculation Types
Gen5™ offers the following types of well analysis for linear scan:
 Mean, Std Dev, CV: Gen5 calculates and reports the Mean OD, Standard Deviation
and Coefficient of Variation of samples when this calculation type is selected.
You can define the Calculation Zone, which is based on the number of Horizontal
Reading Points, which you define as Scan Options in the Read Step of the
Procedures
 Mean Min/Max
 Integral
For each of these calculation types, you can adjust the Calculation Zone as desired.
Click on the type to review your options and Gen5's default settings.
Viewing Results
1.
2.
After reading the plate, in the Plate workspace use the drop-down list for Data
to select the data set labeled Curves
Click in a well to see the Well Zoom. When a Well Analysis data reduction step
has been defined, a table beneath the curve shows the results. 0.
Spectrum Scan | 203
Spectrum Scan
Absorbance Spectral Scan
During a Spectrum Read, multiple readings are taken across a wavelength range. The
objective is to plot a graph with absorbance/RFU/RLU versus wavelength. Gen5
automatically generates the spectrum data views:
 one multi-index raw data set: measurements taken at each wavelength
one "Curves" data set (Well Zoom): plot of OD/RFU/RLU per wavelength for
each well
Readers that support Absorbance spectrum reads are µQuant, all models of the
PowerWave and Synergy HT, Synergy 2, and Synergy 4. Only the Synergy 4 supports
spectral scans for Fluorescence and Luminescence detection.

Fluorescence Spectral Scan
Fluorescence spectrum analysis can be performed on either the Excitation or Emission
wavelength, with the opposite wavelength set to a fixed value. And the range of
wavelengths scanned can either be lower or higher than the fixed wavelength (with no
overlap).
Since it is recommended that each individual spectrum read limits the range of
wavelengths to above or below the fixed wavelength, you can define multiple read steps in
one procedure that straddle the fixed wavelength and/or alternate between EX and EM
scans.
For example, to determine the peak response at both an EX and EM wavelengths you
could define a procedure like this:
After reading the plate and reviewing the results, you may want to modify the fixed
wavelengths to match the peak responses.
Gaps in a spectral curve: over-range or immeasurable values, in
combination with Gen5's automatic spectral raw data correction, can
cause unexpected gaps in a curve. Lower the Sensitivity setting and
reread the plate to obtain reliable data.
204 | Chapter 10: Scanning Analysis Options
Calculation Types
 Min/Max is the Well Analysis option Gen5 offers for spectrum scans. It
generates the data sets: Mean Minimum OD and Wavelength at Mean
Minimum OD, Mean Maximum OD and Wavelength at Mean Maximum
OD
Define the Calculation Zone:
You can refine the results output of the well analysis:
 Reduce the range of wavelengths upon which to perform the calculations.
The default zone corresponds to the Start (beginning) wavelength and the
Stop (ending) wavelength defined in the Procedures.
 Reduce the number of spectrum reads upon which to perform the
calculations. The default zone is the total number of wavelengths to be read
based on the Procedure settings: from read 1 to the total number of reads
calculated from the Start, Stop and Step values. Limiting the number of
reads is another way to effectively reduce the wavelength range (nm)
considered in the calculation.
 Set the number of points on which to average/calculate the minimum and
maximum values. The default number of points is 1 (each read stands alone
to determine the min and max). The valid entry range is from 1 to the total
number of reads calculated from the Start, Stop and Step values.
When you increase the number of points, Gen5 first identifies the mean
value for the specified number of consecutive reads, and then determines
which of them is the min and max. For example, if you define 2 as the
number of points, Gen5 determines the mean of the first two reads, the
second two reads, the third two reads, etc., to perform the calculation. This
option is most useful when there are numerous reads to work with.
Viewing the Spectrum Scan
1.
2.
3.
After reading the plate, in the Plate workspace use the drop-down list for Data
to select the data set labeled Spectrum Curves
Click in a well to see the Well Zoom. When a Well Analysis data reduction step
has been defined, a table beneath the curve shows the Well Analysis Results
and you can use the View Data and View Chart toggle button to see the basis
for the curve.
Click the 3-dot button next to the Curve field to change the appearance of
the well zoom. 0.
You can display multiple well zooms simultaneously by holding down the Ctrl key
while selecting (up to 8) wells.
Chapter 11
Multi-Plate Protocols
An overview and specific instructions for creating multi-plate
protocols is provided in this chapter.
Designing a Multi-Plate Protocol ................................................. 206
About Multi-Plate Protocols........................................................ 207
Running a Multi-Plate Protocol ................................................... 209
Calibrator-Plate Protocols .......................................................... 212
Multi-Plate Assay Protocols........................................................ 215
206 | Chapter 11: Multi-Plate Protocols
Designing a Multi-Plate Protocol
There are numerous applications for multi-plate protocols, not to be confused with
multiple-plate experiments described on page 208.
Select the option that best meets your needs:
 Calibration Plate Protocols: Define a calibration or standards plate to
determine concentrations of test samples on other plates
 Multi-Plate Assay Protocol: Use multiple plates to accommodate one assay.
During processing and data reduction, Gen5 treats the multiple plates as if all
samples and controls were on one plate
 Batch Processing: Process a batch of samples, using a limited number of
standards, and incrementing continuous sample numbers across multiple
plates.
Important: All multi-plate protocols begin the same way, by first
defining the number of plates required: Select File>New Protocol
and set the Protocol Type as the first step.
About Multi-Plate Protocols | 207
About Multi-Plate Protocols
For the numerous applications requiring multiple-plate processing, Gen5™ helps you
conduct multi-plate assays or to process multiple plates in an experiment. The method
you choose depends on the requirements of your protocol. This information is
intended to help you select the most efficient method.
The considerations include Plate Layout, Read Type, and data and kinetic analysis
requirements:
 Do you need more than one plate layout to distribute samples,
standards, controls, and blanks? If yes, then a multi-plate protocol is
required. Otherwise, you can process multiple plates in any experiment, each
containing unique Sample IDs to distinguish and track samples, but with the
same plate layout (Well IDs).
 Do you need to perform calculations on the data across multiple
plates that have the same plate layout? Multiple plates with the same
layout can be processed in any experiment, but the results of each plate stand
alone. Results are viewed, reported, exported and transformed individually per
plate. If your assay requires determining means, ratios, or other factors across
the multiple plates being processed, then you need a Multi-Plate Assay
Protocol.
Note: By default, Gen5 averages replicates when performing
calculations. Blanks, controls, and any other identical Well ID that
occurs across the multiple plates will be averaged in automaticallygenerated data sets. You can override this feature by creating your
own transformations for individual plates.
 Can you set up a standards or calibration plate that can be used to
determine the concentration of samples that will be processed on a
different plate? If yes, the best option is the Calibration Plate Protocol, which
lets you define (at least) two plate layouts, one for the calibration plate and one
for all the other plates to be processed. The other plates can contain test
samples, blanks, controls, etc. and like regular experiments, the results of each
plate are viewed, reported, exported and transformed separately. Up to 10
calibrator plates are supported.
 Does your assay require kinetic (or time course) analysis of the plate?
If so, your options are more limited. Gen5 does not support kinetic reads for
Multi-Plate Assay Protocols
Step-by-Step Instructions:
 Setting up a Calibration Plate Protocol on page 212
 Setting up a Multi-Plate Assay on page 215
208 | Chapter 11: Multi-Plate Protocols
Multi-Plate Protocol vs. Experiment
For this explanation you should already know the difference between
an Experiment and a Protocol in Gen5™. If you haven't already done
so, read Experiment vs. Protocol in the Essential Concepts chapter.
Important: This feature is limited by the level of Gen5 you're running:
 Gen5 Reader Control cannot run multi-plate protocols, but can process up to
1000 plates in an experiment. However, since Reader Control does not support
Plate Layout or Sample IDs, the following explanation of Gen5's potential may
not be applicable
 Gen5 and Gen5 Secure are full-featured software levels supporting both types
of multi-plate protocols and up to 1000 plates in an experiment
 In an Experiment you can process a huge number of plates (up to 1000 plates) «
use the Add a Plate feature ». Naturally, an experiment that processes more
than one plate can be called "multiple plate." Regardless of the number of
plates, running this kind of experiment means applying the protocol to each
plate in the same manner, and transforming, reporting, and exporting data
individually, on a per plate basis. Generally, every plate in a multiple-plate
experiment has the same plate layout. But, you can distinguish one plate from
another by assigning unique Sample IDs to each plate.
 A Multi-Plate Protocol allows the definition of up to 10 plates as distinct
entities. Each plate in a multi-plate protocol may serve a different function,
and/or have a different plate layout. It can be as simple as incrementing
continuous sample numbers across multiple plates, or much more complex.
Here are examples:
 Multiple plates are required to run one assay - for quality control or other
purposes it is necessary to distribute test samples, standards, and controls
across a series of plates
 Calibrator plates containing only the standards, not the test samples, are
used to determine the concentration of samples on other plates. This allows
for a one-time setup and processing of the calibrator plate(s), followed by
the processing of up to 1000 test-sample plates in an Experiment
 Processing a batch of samples spread over 10 plates, with incremented or
user-defined sample numbers or IDs
Running a Multi-Plate Protocol | 209
Running a Multi-Plate Protocol
When you run a multi-plate protocol in an experiment (File>New Experiment), the
menu tree, data views and reports are slightly different than a standard experiment.
Calibrator-Plate Protocols:
 Calibrator-Plate experiments add an additional set of Protocol elements to the
menu tree for each calibrator plate and one set for all the Other Plates. In an
Experiment, Gen5 sets up the standard Plate View for every plate, one for each
calibrator and test/sample plate (Other Plates).
When you Add a Plate to the experiment, it takes on the attributes of the Other
Plates.
Reporting is the same as any multiple-plate experiment. After building the
report, highlight a
in the menu tree and click Print/Print Preview.
You can select multiple plates by holding the Ctrl key while highlighting them.
Multi-Plate Assay Protocols:
 Multi-Plate Assay experiments have one set of Protocol elements and a unique
Data View called InterPlates to display the Statistics, Graphs, Cutoff Values
and Validation tabs (if applicable). The Matrix for each plate is still displayed in
the standard Plate View for viewing results in this format.
Unlike other types of protocols, Gen5 does not let you "Add Plates" to this type
of experiment. The total number of plates required to set up the assay must be
defined in the first step of creating the protocol.
210 | Chapter 11: Multi-Plate Protocols
InterPlates

Reporting results for a multi-plate assay is different from standard
experiments in a couple of ways. When you wan to include the Matrix view in
a report or export, each Plate must be added to the Content individually. And,
unlike other multiple-plate experiments, all the plates are reported together in
one output (instead of a separate report for each plate). Just as the InterPlates
view (described above) displays the Statistics, curves, and other data for all the
plates in one view, this data is reported/exported simultaneously for all the
plates.
Plate Layout for Multi-Plate Protocols
Defining the layout of test specimens for a multi-plate protocol is identical to singleplate protocol layouts, only more so, i.e., there are more plates to define.
 Calibration plate protocols have a unique set of protocol elements for each
calibrator plate and one set of protocol elements for the test plates, called Other
Plates in Gen5. So, there are additional Plate Layout options in the menu tree:
one for each calibrator plate, and one for all the Other Plates
 Multi-Plate Assay protocols retain one Plate Layout option but provide a grid
or matrix for each plate within the dialog:
Running a Multi-Plate Protocol | 211
Select each Plate # tab individually to define its layout.
Data Reduction for Multi-Plate Protocols
Special formula syntax is available for performing Transformations across multiple
plates:
<well>.<plate>
When referencing a well
coordinate in a multi-plate
experiment, identify the
specific well and plate using a
period
B3.3 = well B3 on Plate 3
DS1.H6.2 = well H6 of data
set 1 on Plate 2
Review the Formula Syntax tables in the Data Reduction Options chapter for more
information.
212 | Chapter 11: Multi-Plate Protocols
Calibrator-Plate Protocols
Creating a Calibration-Plate Protocol
This procedure defines a multi-plate protocol using a calibrator or standards plate to
generate a standard curve that is used to determine the concentration of samples
processed on other microplates.
Create the Protocol:
1.
Begin by creating a new protocol: File>New Protocol
3.
Highlight Protocol Type and select the Calibration Protocol button. Enter the
number of Calibrator plates, maximum 10. Enter the expected number of
Other Plates: the number of plates with samples to be processed, maximum
1000. Click OK to save and close the dialog
2.
4.
Select Protocol> Protocol Options
The menu tree changes to correspond to your input. Each calibrator plate is
identified as "Plate #", the samples plates are identified as Other Plates. In this
example (click the binoculars), Plate 1, the calibrator plate, is moved to the top
of the tree with its own Procedure and other protocol elements. The Other
Plates represent the test-sample plates and have their own Procedure, Plate
Layout and so on. Generally for calibrator-plate protocols, only the Procedure
for reading the plates are the same. The Plate Layout and Data Reduction steps
are different. When multiple calibration plates are defined, each calibration
plate has its own protocol elements.
Define the Plate Layout for Plate 1 and the Other Plates in the normal manner:
assigning Standards with their respective concentrations to the calibrator plate
(Plate 1) and assigning unknown samples with the required number of
replicates to the Other Plates
Calibrator-Plate Protocols | 213
5.
6.
Set up Data Reduction for Plate 1 and the Other Plates: define a Standard
Curve for Plate 1 in the normal way. Then, for the Other Plates define Curve
Analysis using the option to Use Curve from Calibrator Plate
Define the Report output individually for Plate 1 and the Other Plates. This
can be a real time saver when running the protocol in an experiment

Like single-plate protocols, Calibration Protocols allow additional
plates to be added for processing when you run the experiment. Each
plate is processed and its results reported separately. In Calibration
Protocols, newly added plates are always Other Plates, rather than
calibrator plates.
7.
Save the protocol with a unique name.0.
Run the Calibration Protocol in an Experiment
When the protocol has been created, it is ready to run in an Experiment.
1.
2.
Select File>New Experiment.
Select the calibration protocol.

Plate 1, in the menu tree, is always the first calibration plate
in this type of protocol. After Plate 1, Gen5 adds one plate icon in the
experiment for each calibration plate, and, one plate icon for (all) the
Other Plates.
3.
Highlight one of the plates, click Read and follow the online prompts.
Continue this pattern, until all the plates are read.0.
Each plate generates its own report (based on the user-defined report parameters).
To simultaneously generate a report of all the plates, highlight the first plate in the
menu tree, hold the Shift key and highlight the last plate, then click Print
214 | Chapter 11: Multi-Plate Protocols
Using Curve from Calibrator Plate
For Calibration Protocols, Gen5 makes available a standard curve generated from a
calibration plate, to plot the concentrations of test samples on the current plate.
Prerequisite: You must first define the Procedure, Plate Layout, and
Curve Analysis for the Calibrator or standards plate. Secondly, define
the Procedures and Plate Layout for the sample plate (Other Plates).
1.
Select Data Reduction>Curve Analysis
3.
On the Data In tab, select Use Curve from Calibrator Plate and select the
previously defined calibration-plate curve
2.
4.
5.
Enter a unique Curve Name
On the Data Out tab, select the Y Data. You can also apply Interpolations, if
applicable
Also on the Data Out tab, enter a unique name for the Concentration data set.
If applicable, select the Concentration x Dilutions calculation and give this
resulting data set a unique name.0.
Options on the Curve Fit tab are disabled (grayed out) because they
are owned by the "Curve from the Other Plate."
Multi-Plate Assay Protocols | 215
Multi-Plate Assay Protocols
Creating a Multi-Plate Assay Protocol
This procedure creates a multi-plate protocol for an assay that requires the samples,
standards and controls to be distributed to multiple plates. This method does not
support kinetic analysis.
Create the Protocol:
1.
Begin by creating a new protocol: File> New Protocol
3.
Select Multi-Plate Assay Protocol, and enter the number of plates required
to layout the assay in the Number of Plates field (up to 10).
2.
4.
5.
Select Protocol> Protocol Options, highlight Protocol Type (at the top of
the tree) for the multiple-plate options.
Accept or alter the default setting for identical plate layout. Selecting All plates
have identical layout provides only one Plate Layout grid. Leaving it
unselected provides one grid for each plate.
Define the Plate Layout as you would for any protocol, using the platenumbered tabs to bring each grid into focus. Learn more on page 210.
Keep in mind Gen5's default behavior is to determine and use the mean of likenamed samples in data reductions. This applies to multi-plate protocols that distribute
like-named items across the plates.
6.
Define the Procedure: Read Steps and any other necessary activities.
8.
Now you're ready to define your Report and/or Export requirements.
7.
Define the Data Reduction steps: the calculations will be performed for all the
plates at once. Gen5 will automatically create data sets for Blank subtractions if
the Plate Layout and Procedures suggest them.
Note: In this type of multi-plate assay, Gen5 treats the samples from
all the plates as if they were on one plate, and reports the results from
all the plates together in one report. To report results in the Matrix
format in reports and exports, you must add one Matrix item for each
plate to the Report/Export Content. See Designing multi-plate
reports
9.
Save the protocol. And, you're ready to run it in an experiment: File> New
Experiment. 0.
216 | Chapter 11: Multi-Plate Protocols
Running a Multi-Plate Assay Experiment
If you've already created a multi-plate single-assay protocol, here are a few tips for
running it in an experiment.



Read each plate individually, as you would in any other experiment:
highlight the plate in the menu tree and click Read
Inter-plates is a special view provided only for this type of protocol.
Since data reductions are performed across the plates, the inter-plate view
combines the statistics from all the plates into one table and shows any curves
plotted from all the data points.
Designing the Reports and Export parameters for these kinds of assays
requires extra attention: when adding Matrix items to the output content you
must designate which plate it represents. Gen5 opens the Edit dialog to
facilitate the process:
1.
Add a Matrix item in the Available Data Views to add it to the Content box.
2.
Now, double-click the matrix in the Content box to open its Edit dialog.
Change the Plate number in the Selection tab to identify the Plate.
Multi-Plate Assay Protocols | 217
3.
Repeat Steps 1 and 2 until there is one Matrix item in the Content for each
plate.0.
You can fine tune the protocol while running it in an experiment, but if you like the
changes, be sure to select File>Save Protocol As to save the changes to the original
protocol for future use in another experiment.
218 | Chapter 11: Multi-Plate Protocols
Processing a Batch of Samples
Gen5™ offers several ways to process a large batch of samples. The method you
choose depends on the requirements of your protocol.
The procedure described here use's Gen5's Multi-Plate Assay feature to define a
protocol to process a batch of samples with one method. Gen5™ lets you assign up to
10 plates to an experiment. Plates can have the same or different layouts, but all other
Protocol elements are the same.
Note: This is one of several options for achieving the same goal. You
may want to try other methods to determine which approach best
meets your needs. Check out Gen5’s Help to learn more.
How to:
1.
2.
3.
4.
5.
6.
7.
Begin by creating a new protocol: File>New Protocol
In the menu tree, open the Protocol Options and highlight Protocol Type
Select the button next to Multi-Plate Assay Protocol. Enter the number of
plates required in the field, maximum 10. In this example, each plate has a
different layout to distribute standards to some plates, and to continue sample
numbering across several plates.
Define the Plate Layout for each plate. (See Plate Layout for Multi-Plate
Protocols on page 210.)
Define the Procedures for reading the plates.
Define the Data Reduction steps.
Define the Report requirements.0.
When these steps have been completed the protocol is ready to run in an Experiment.
Chapter 12
Preparing Plates
This chapter describes Gen5’s tools for defining the Plate Layout,
including assigning concentration values to samples, standards, and
controls, and how to customize their Well IDs. It also covers
assigning Sample IDs or names to associate test samples with
specific test subjects.
Defining the Plate Layout .......................................................... 221
Assign Standards, Controls, and Blanks ...................................... 223
Customize Well IDs .................................................................. 223
Assign Concentrations/Dilutions ................................................. 226
Custome Plate Layout............................................................... 229
Plate Information ..................................................................... 230
Runtime Prompts ..................................................................... 231
Assign Sample IDs ................................................................... 231
220 | Chapter 12: Preparing Plates
Overview
Gen5™ needs to know the layout of samples, standards, controls, and blank wells on
the actual microplate(s) of your experiment to perform data reduction, curve analysis,
and other calculations. It is not necessary to define a plate layout to simply read the
plate and report the measurements. But to take advantage of Gen5's full array of data
reduction features, define the plate layout, including any concentrations or dilutions of
samples, controls or standards, before defining the data reduction calculations.
Plate Type for a protocol or experiment is defined in the Procedure.
Plate Type is selected from the Plate Types Database (covered in a
System Management chapter)
Gen5 supports 6-, 12-, 24-, 48-, 72-, 96-, 384- and 1536-well microplates. However, your
reader may not support all of these configurations. Select the Plate Type when defining
the Procedure and then open the Plate Layout to see how Gen5 formats the plate map:
all columns are numbered and all rows are designated with a letter(s). Well A1 is
always in the top left corner of the grid, for example:
 96-well plates are mapped as 8 rows A-H and 12 columns 1-12
 1536-well plates are mapped as 32 rows A-Z, AA, AB, AC, AD, AE, AF and 1-48
columns
Adding a new plate to an Experiment
Click the
button to add another plate to an experiment. The plate takes on the
currently-defined plate attributes. Right-click on the plate and select Custom
Layout to create a unique plate map.
Defining the Plate Layout | 221
Defining the Plate Layout
Protocol> Plate Layout
It's easy to define the plate layout with Gen5's tools for identifying samples, standards,
controls and blanks. Follow these steps:
1.
In the Well Settings box in the top-left corner, select the Type of specimen
2.
Customize the ID or Well Identifiers, if necessary:
3.
Define the Concentration or Dilution, if applicable:
4.
Assign the well IDs to their corresponding locations in the plate grid by
clicking in the wells in the matrix. 0.

When you select a corresponding starting # the ID changes
accordingly for assignment to the plate.
 Use the Auto Select and Replicates options to speed up your work: set the
options and click and drag to fill multiple wells at once. Click a column or
row header to fill it.
The type of plate, e.g., 96-well, is defined in the Procedure and
displayed in a representative matrix or grid format in the Layout and
Transformation screens
 Helpful Hints:
 Set up your preferred default Well IDs in the Default Protocol. For example,
you can define PC (for Positive Control) instead of CTRL1 for Assay Controls.
Well IDs defined in the Default Protocol are available when defining the Plate
Layout for all newly-created protocols/experiments
 Use the Undo button at the bottom of the screen to undo the last action. Up to
10 previous actions can be undone
 To clear the grid and start over, right click and select Empty Layout, or to
clear selected cells, set the Type of Well Settings to Empty and select the cells
you want to clear.
 You can Print the plate layout. 384-well plates print out in two sections,
columns 1-12 and 13-24. 1536-well plates print in eight sections to fit all 48
columns and rows from A to AF.
 To copy the contents of the grid to Windows' virtual clipboard to paste into a
text/external file, right click and select Copy Layout. Open the receiving file,
e.g. Word® or Excel® and right click and select Paste. Generally, plates larger
than 96-wells do not fit completely in a standard-sized Word or text file, a
spreadsheet is required.
222 | Chapter 12: Preparing Plates
 For Samples - unknown test specimen - Gen5 lets you assign and track data
points in addition to the Sample ID. You can create "Additional Identification
Fields."
 To copy the contents of the grid to Windows' virtual clipboard to paste into a
text/external file, right-click and select Copy Layout. Open the receiving file,
e.g. Word® or Excel® and right-click to select Paste. Generally, plates larger than
96-wells do not fit completely in a standard-sized Word or text file, a
spreadsheet is required.
 Each instance of a Sample and Sample Control Well ID, and each Assay Control
group can have a unique concentration/dilution value. Gen5 assigns a dilution
index to the Well ID to keep track each instance.
 Use the Dilutions Only/Concentrations Only button to apply only dilution
or concentration values (that you have previously defined) to selected wells
without altering the well's identifier. See Assign Concentrations or Dilutions to
Samples, Standards, Controls on page 226.
 Use the shortcut for filling the entire plate with the selected Well Settings: click
in the top-left (unlabeled) corner of the matrix, i.e. between A and 1.
 When assigning concentrations/dilutions, well selection must be compatible
with the Replicate, Auto Select, and Filling option settings
 You can resize the plate view in the standard Windows® way: click and drag
the outer borders of the view, or click the maximize button in the top-right
corner. You can resize the rows and columns: hover your mouse over a grid
line between two numbered columns or alpha-labeled rows until the cursor
changes to a separator, then, click and drag.
Assigning Well IDs | 223
Assigning Well IDs
Protocol> Plate Layout
Gen5™ recognizes the significance of commonly-used elements in an experiment:
 Standards or calibrators for generating a standard/calibrator curve
 Blanks for blank wells subtraction
 Controls for multiple purposes: Assay Control generally used as controls, cutoffs, or for validating the assay, and Sample Control generally used in
association with a specific sample, e.g., spiked or known-concentration
samples.
 Samples represent the test specimen or unknowns to be processed.
When defining the Plate Layout, you can customize the Well ID and on-screen
appearance, and you can assign concentration or dilution values to Standards, Controls
and Samples.
Use the drop-down lists and 3-dot buttons in the upper-left corner of the Plate Layout
dialog to select, customize and assign standards, controls and blanks to the plate. For
details see:
 Customize Well IDs (below)
 Customize Sample IDs or assign them additional ID fields on page 224
 Assign Concentrations or Dilutions to Samples, Standards, Controls on page
226
Customize Well IDs
To save the customized IDs for use in all newly-created protocols/experiments,
perform these steps in the Default Protocol at System> Preferences> Default
Protocol
1. Type
Use the drop-down list to select the Type of specimen,
(except for the Empty option, which is used to clear a previously assigned well).
224 | Chapter 12: Preparing Plates
2. ID
Gen5 displays the default label or name for the selected Type. Click
(3-dot button)
to customize the name and color code. Click in the fields to replace the text and select
the color.
Depending on the Type, one of three dialogs opens, here are two examples:
 ID for Standards, Assay Controls and Blanks can be up to 10 characters, the ID
Prefix for Samples and Sample Controls can be up to 6 letters, numbers and
underscores, without any blank spaces. It cannot end in a number, nor be
identical to a formula operand, e.g., X, MIN, MAX, and so on, and cannot be
identical to a well coordinate, e.g., A1, H12. Click in the field, and enter text to
edit it. The ID can be used in data reduction formulas.
 Name can be up to 20 alphanumeric characters and can be used in reports
 The selected Color or Color Sequence will be applied to the matrix view of the
plate. Click in the field to activate the drop-down list of color choices
Customizing Sample Wells
With Sample selected, click the 3-dot button next to the ID field to access these
controls.
Sample wells are the unknown samples to be processed. To save customized IDs for
use in all newly-created protocols/experiments, perform these steps in the Default
Protocol at System> Preferences> Default Protocol
About Sample Identification Fields
Identification Fields provide a way to assign and track additional data points related to
an unknown sample. For example, in a clinical trial you may have a patient number,
Assigning Well IDs | 225
age, gender, and other information to be analyzed for trends. This data must be kept
with the measurement results. There are numerous scenarios for assigning additional
data to a sample. Use an Identification Field to create a category or class for this data.
Then, collect the data in the experiment.
In the Gen5 Experiment, data, like Name, Age, etc., can be assigned to each sample on
the plate. When you create Identification Fields in this dialog, they become data fields
in the Plate's Sample ID table. You can also display the data in custom data views for
online viewing and reports.
Gen5's system-generated views: the Layout matrix, Statistics and Well IDs tables
automatically include all Identification Fields marked as "Show." This facilitates the
Matrix data-entry option.
How to customize Sample wells:
1.
2.
3.
4.
In the Plate Layout, set Well Type to Sample, click the 3-dot button next to
the ID field.
On the Display tab, click in the field to overwrite the default Samples ID
prefix: SPL.
The ID can contain letters, numbers, and underscores, up to 6 characters. IDs
cannot end in a number and cannot contain spaces. IDs cannot conflict with
well coordinates, A1, H12, etc.
Click in a Color Sequence field to enable the drop-down options, click on the
desired color to select it. The first color selected is applied to SPL1, the second
color is applied to SPL2, and so on. Gen5 reapplies the colors, starting with the
first one, when the entire list has been used.
Click the Identification Fields tab to create or modify these data categories.
226 | Chapter 12: Preparing Plates
5.
6.
For each "Add. Field#" or additional identification field, enter a Title or name
for this data category.
Mark the field to Show in Gen5's system-generated data views. This enables
the Matrix data-entry option referenced below.
To populate the Identification Fields
The Title of the Identification Field becomes a category for data input. For every
Sample assigned in the Plate Layout, you can collect the data for each category when
you run an experiment. There are two ways to input the data:
 Fill in the Samples ID Table on page 236
 Edit the Matrix to Input Data on page 237
 Use the Batch IDs creator to "Apply to Fields," see page 239
Assign Concentrations or Dilutions to Standards, Samples, Controls
In the Plate Layout screen, under Well Settings, the label changes to either Conc. or
Dil. (for Concentration or Dilution) depending on the Type selected and your input.
This is a must-do
for plotting a
Standard Curve:
assign the
expected
concentrations of
the Standards
First, define the concentrations or dilutions, then, assign them to the plate.
Define the Concentrations or Dilutions
After selecting the Type and the ID, click the 3-dot button next to Concentrations
or Dilutions. When Standards are the selected Type, the cells in this table are labeled
accordingly, e.g. STD1 (or STDB1 when multiple standard curves are created [see the
Data Reduction Options chapter]). Gen5 applies an indexing notation for all other
Types of Well ID, e.g. CTL1:1
1.
In ascending or descending order, enter the values in the consecutivelynumbered fields. For a shortcut, select one of the two Auto entry tools:
 Increment when the dilutions are based on a fixed number to increment
your starting entry by. For example, starting at 10, increment by 10 to define
concentrations as 20, 30, 40.
 Factor when the dilutions are based on a fixed number to multiply your
starting entry by. For example, starting at 1, factor by 10 to define them as
10, 100, 1000 and so on.
Assigning Well IDs | 227
 In the first field, enter the starting number
2.
3.
4.
 Click in (or use the down arrow key to move to) each successive field to
apply the incremented or factored value
When the well type is other than Standards, select Concentrations or Dilutions
with the buttons underneath Conc./Dil. Type.
If applicable, enter an abbreviation for the measurement Units.
Assign the location of concentrations or dilutions to the plate, in the same
manner as assigning Samples. Set the Well Settings and click the well to assign
that ID and Conc/Dil value to. Or, use the Replicates and Auto Select options
and select a row, column, or click and drag over the area of the plate to assign
the IDs.0.
228 | Chapter 12: Preparing Plates
 Helpful Information:
 Important: You can assign unique concentration/dilution values to individual
Sample, Sample Control Well IDs, and Assay Control groups. For example,
SPL1 can be defined as dilutions of 5, 15, and 45, while, SPL2 is defined as
dilutions of 10, 25, and 50. Change the ID and click the 3-dot button for
Conc/Dil to define a unique concentration/dilution-values table for each
individual ID. The values table is not saved for that Well ID until they have
been assigned to the plate
 You can define multiple standard curves: described in the Data Reduction
Options chapter
 In the Plate Layout dialog, you can use the Dilutions Only/Concentrations
Only button to apply only dilution or concentration values to selected wells
without altering the well's identifier
 When assigning concentrations/dilutions, the well selection must be
compatible with the Replicate, Auto Select, and Filling option settings
 Set up your preferred default IDs and define regularly used
concentration/dilution values for Samples, Standards and/or Controls in the
Default Protocol
Custom Plate Layout | 229
Custom Plate Layout
Gen5 let's you create individual custom layouts for experiments with multiple plates »
not to be confused with Multi-Plate Protocols. Exercise judgement when using this
option, keep in mind any Data Reduction formulas that reference Well IDs. You cannot
set up Data Reduction steps that reference the custom layout only.
How to create a custom layout:
1.
After adding plates, select the
3.
Double click the plate's Custom Layout icon to open the Plate Layout screen,
for that plate only!0.
2.
in the menu tree, and right click
Select Custom Plate Layout from the pop-up menu.
A new Custom Layout icon is added to the menu tree for that plate.
 Helpful Info:

In the menu tree, Gen5 highlights plates with an asterisk to
indicate the plate varies from the protocol in some way
 Keep in mind the differences between the Protocol's plate layout in Data
Reduction steps, Data Views and Report Builder. For seamless integration of a
custom layout, make sure any Well IDs referenced by a Data Reduction step are
included in the custom plate
230 | Chapter 12: Preparing Plates
Plate Information
Plate> Information
About the Plate Information
Every plate added to an experiment comes with an Information component. The
Information is collected when the plate is read. Runtime Prompts (described on the
next page), set up for the Protocol, define the information requested when the plate is
read.
Reviewing the Plate Information
Double click the Information element under the Plate in the menu tree to review or
modify the information collected when the plate was read.
Printing the Plate Information
You can include the Plate Information in a report or export file using Field Groups
Runtime Prompts | 231
Runtime Prompts
Protocol> Runtime Prompts
Use these controls to set up the Runtime Prompts presented to users when they Read
a plate in an Experiment based on this Protocol. The Prompts you define become the
labels for input fields in the "Plate Reading" screen Gen5 presents when a plate is read.
The Plate Reading data is retained in the experiment as Plate Information.
The Runtime Prompts become input fields in the Plate Reading dialog. Example:
When the Prompt Name is "Name" for prompt 1, users are prompted to enter their
name when they read a plate.
 Clear the default text from any unused prompts for the best appearance at run
time.
How to:
Find descriptions of these prompt attributes:
 Prompt Name on page 232
 Prompt Type on page 232
 Data Reduction Variable Names on page 233
 Remember Recent Values on page 233
 Skip runtime prompts on page 234
232 | Chapter 12: Preparing Plates
Reviewing the Plate Information
You can review (and modify) the Information entered when the
plate was read in the Information component of the Plate in the menu tree
Printing the Plate Information
You can include the Information in a report or export file using Field Groups
Bar-Code Scanning the Plate ID: If you have a compatible bar-code scanner, you
can use it to input the plate's barcode and any other prompts. Replace the keyboard
with the scanner and use it to capture the information just before reading the plate.
Creating a Runtime Prompt:
Prompt Name
When defining Runtime Prompts the Prompt Name becomes the data-input field name
in the Plate Reading dialog. Up to 6 prompts can be defined. Prompt Names must be
unique or empty, independent of case. LOT and Lot are not acceptable variations, for
example.
Field names are limited to 32 characters. Their corresponding data-entry fields support
up to 255 characters.
When a prompt is defined as "required" its Prompt Name is marked with an asterisk in
the Plate Reading dialog.
Delete unused "Prompt #'s" for the best appearance in the Plate Reading dialog.
The fields will appear blank instead of displaying the prompt number.
Prompt Type
When defining Runtime Prompts use the drop-down list to select the Prompt Type:
 Optional: gives the user an opportunity to enter data, but the field can be
skipped. When all prompts are optional, the Plate Reading dialog can be
turned off, blocked from appearing before a plate read.
 Required: requires the user to enter data in the field before reading the
plate. Required "Prompt Names" are marked with an asterisk in the Plate
Reading dialog. Required fields disable the ability to "Skip the Plate
Reading dialog."
Runtime Prompts | 233
 Data Reduction Variable: requires the user to enter a numeric value for use
in data reduction formulas. The entered value replaces the Variable Name,
which is used as a placeholder when writing the formulas. Numeric values
can be decimal or scientific notation in accord with the computer's Regional
Settings. Data Reduction Variables, also called "runtime variables" can be
used in these data reduction steps:
 Transformation
 Curve Interpolation
 Cutoff
 Validation
 Well Analysis Formula
Data Reduction Variable Names
When defining Runtime Prompts for Data Reduction Variable Prompt Types, the
Variable Name is used when writing formulas. The Variable Name is a placeholder for
the numeric value Gen5 users are prompted to enter before reading the plate.
Although, the value can be modified in the Plate Information dialog at a later time.
At the Plate Reading dialog, Gen5 verifies the user has entered a valid numeric value
for the variable. They can be integers, decimals or scientific notation in accord with the
computer's "Regional Settings."
Gen5 gives you a headstart when defining a variable name. It repeats the Prompt
Name text preceded by an exclamation point (!), because this is the required syntax.
Syntax for Variable Name:
 Must start with "!"
 Other characters must be alphanumeric (a-z; A-Z; 0-9); they are character
case dependent
 Up to 32 characters can be used
 Must be unique (to the protocol)
Data Reduction Variable prompts are "required" entry fields.
Remember Recent Values
When defining Runtime Prompts this option lets you give users a shortcut for data
entry. It remembers the last 5 values entered for the prompt and provides them in a
drop-down list for easy selection. Gen5 retains the values with the Protocol, so the list
is available in any experiment based on that protocol.
Recent Values are managed with the Database Maintenance tools.
234 | Chapter 12: Preparing Plates
Skip Runtime Prompts
You can speed up plate reading by skipping the "Plate Reading" dialog when:
 it is not necessary to collect miscellaneous data about each plate
 none of the Prompts are "Required" entry fields
 none of the Prompts are Data Reduction Variables
Open the Runtime Prompts screen, empty the table is necessary and select
Skip Plate Reading dialog during plate read
Assigning Sample IDs | 235
Assigning Sample IDs
Plate> Sample IDs
Gen5 provides tools for pairing labeled patient/test samples with their reading and
data reduction results. This feature reflects the customization and definition of
unknown "Sample" wells in the Plate Layout, e.g. SPL1. For each Sample well assigned
in the Plate Layout you can attach an ID or Name, and when you have defined
"Additional Fields" you can input related data for each Sample well.
The Samples IDs (Names) and other Identification Fields are unique to each test plate.
They provide the ability to explicitly relate a test sample to a test subject. Learn more
about the Identification Fields that are created in the Plate Layout.
You must be in an Experiment, not a Protocol, to assign Sample IDs.
And, the Plate Layout must be defined before Sample IDs can be
defined and applied to the plate.
You can:
 Import Sample IDs from a Text File (page 242)
 Manually Enter Sample IDs (page 235)
 Batch Sample IDs (page 239)
 Create a replicate of a previously defined plate (page 242)
 Use a BarCode Scanner to enter Sample IDs (page 237)
 Export Sample IDs to a text file (page 243)
 Print the Sample IDs after entering them, in list or matrix format. Matrix
depicts the plate layout. To include them in a report or export file, add the Well
IDs table to the Report Content or Export Content in the respective Report or
File Export Builder, or using the Power Export toolbar.
 Clear/Remove Sample IDs from a plate after they've been assigned: Select
Plate>Sample IDs and click Clear All
 Delete a column of data: highlight column in the Samples ID table and press
Delete
Manually Enter Sample IDs
Gen5 provides three ways to manually enter Sample IDs and data for "Additional
Identification Fields:
 Fill in the Sample IDs table (described below), or
 Edit the Plate View Matrix (described on page 237), or
 Barcode Scan Sample IDs to enter data (described on page 237)
236 | Chapter 12: Preparing Plates
 Helpful Hints:
 Use the Batch Sample IDs feature for more advanced sample naming described
next
 When Sample well identifiers are not consecutively numbered in the Plate
Layout, Gen5 does not skip them in the Sample IDs table, but indicates their
absence by graying out and putting an asterisk at their label. When automated
methods are used to ID samples, Gen5 skips the missing SPL identifiers.
Fill in the Sample IDs Table
This data-entry method is an alternative to editing the Matrix.
1.
2.

Locate Sample IDs under the Plate in the menu tree
and double-click to open it.
Gen5™ lists the consecutively numbered Sample well identifiers (SPL) from
the Plate Layout. Enter their corresponding IDs or names or other data:0.
Select Auto Numbering to automatically increment a
numeric suffix or a standalone number. For example, enter ABC10 in the
first cell of the table and using your down-arrow key or a mouse click,
select the next downward cell to assign the next samples ABC11, ABC12,
and so on.
 Use the buttons to print the Sample IDs in a List or Matrix format
 Select the contents of a cell and use Ctrl+C to Copy and Ctrl+V to Paste
 Use the Clear All button to empty the table: contents of all columns and
rows will be deleted. Click Cancel to recover data.
To delete rows, columns or blocks of contiguous cells, select them and click
Delete. To select a row or column click on its header. Click and drag over a
block of contiguous cells to select them.
 Copy Sample IDs from Another Plate: Instead of manually entering or
importing IDs, when you have multiple plates in an experiment, use the
spin buttons or enter the number of the plate you want to copy IDs from
and click Copy.
Assigning Sample IDs | 237
Edit the Matrix to Input Sample Data
Gen5 lets you enter Sample Identification Fields data in the Matrix:
Prerequisite:
There are two ways to display the Sample Identification Fields in a Matrix view so they
can be input/edited:
 they must be defined to Show in the Identification Fields dialog, this makes
them automatically appear in the Layout view
 or, they have been included in a custom Data View
How to:
1.
2.
3.
4.
5.
With the experiment open and the desired plate selected in a multi-plate
experiment, open the Plate View.
Select the Matrix tab and from the Data drop-down list select Layout or a
custom data view that contains Name or Additional Identification fields.
Click the Edit button.
Click in a well to reveal placeholders for the fields (if data has not yet been
entered). Replace the placeholders or previously entered data with your
desired input. Multiple wells can be changed in a session.
To apply the changes, click the OK (green check mark) button.
Click the cancel button to ignore your entries, and restore the original
values.0.
Use the right-click options to copy and print the matrix.
This data-entry method is an alternative to filling in the table.
Barcode Scanning Samples IDs
Prerequisite
You must have a wedge-type bar-code scanner that replaces or mimics keyboard input.
Follow the manufacturer's instructions for installing and setting up the scanner for
carriage return line feed.
Added Bonus: If you do have a compatible bar-code scanner you can
also use it to input a Plate ID and other Plate Information collected
by Gen5 when the plate is read.
238 | Chapter 12: Preparing Plates
How to
1.
2.
3.
Open the experiment and locate Sample IDs under the
Plate in the menu tree, and double click to open it.
Gen5™ lists the consecutively numbered Sample well identifiers (SPL) from the
Plate Layout. Use your mouse to select the starting point, e.g. SPL1, and make
sure Auto Numbering is de-selected, i.e. unchecked.
Operate the scanner according to the manufacturer's instructions to enter the
corresponding IDs or names.0.
Assigning Sample IDs | 239
Assign Sample IDs for Multiple Plates (Batch)
Plate> Batch Sample IDs
Use the Batch Sample IDs screen to assign sample IDs or names to multiple plates
simultaneously. Samples IDs or names are specific to each test plate, and are intended
to relate a test sample processed by Gen5 to a test subject. The batch process offers
more advanced auto-numbering methods than the single-plate Sample IDs tool.
The Plate Layout must be defined before Sample IDs can be applied to
the plates.
Auto Number
Select Auto Number to manually create a naming/numbering convention for samples
for one or more plates:
240 | Chapter 12: Preparing Plates
When you have created additional Sample ID Fields
during the Plate Layout, you can use this Batch ID feature to populate these fields. Use
the Apply to Field drop-down list to select the ID field you want to auto-number.
1.
2.
3.
4.
5.
In the Base Name text field, enter text that Gen5 will append with a numeric
suffix, if desired. Leave the field blank to consecutively number samples
without additional text.
Enter the Initial Suffix — the number to apply to the first sample (of the first
plate)
Set the Increment for sample IDs. Gen5 will leave the defined number of
numbers unassigned between each sample. For example:
If desired, set the Minimum Suffix Width to enforce a uniform appearance to
the numbering convention
Optionally, set the Start next plate at the next multiple of number. Gen5 will
increase the next plate's Initial Suffix by the defined "next multiple," as long as
that number has not already been used in a plate.
For example: For a 96-well plate, if samples are numbered consecutively with
an increment of 1, and the next multiple is 100, the second plate's samples will
be numbered 101, 102, 103, ..., and the third plate's samples will be numbered
201, 202, 203, and so on.
For a 384-well plate, in the same scenario, the next plate's samples will be
numbered 401, 402, and the third plate must begin with 801,
More on Next Multiples: Applying the Next Multiple prefix is determined by
the number of samples on the plate and the Increment factor. When sample
numbering for the plate exceeds 100, and the "next multiple" is set to 100, Gen5
applies the next unused multiple to start numbering the next plate. Thus, for
384-well plates the default next multiple is 1000, which produces the best
results for large numbers of samples.
Watch the effect of your choices in the Example space of the screen.
6.
In the Plates section, define which plates to apply the naming convention to:0.
 All currently defined plates. This feature will not automatically apply the
naming convention to plates added to the experiment after it has been
executed. You must execute the feature again when more plates are added
to the experiment.
Assigning Sample IDs | 241
 Selection is filled by Gen5 when you select plates in the menu tree before
initiating this feature: hold the Ctrl key while clicking multiple plates, they
will be highlighted. Then, select Plate>Batch Sample IDs to see this option
selected.
 Range to define a contiguous selection of plates
All plates selected for sample naming will be affected, even if Sample
IDs have already been defined for them, i.e. the batch process will
overwrite existing IDs.
Use Same IDs for each plate
This option assigns the same Sample IDs or names to all selected plates:
1.
2.
Click the Edit Sample IDs button and enter IDs
Define the plates to apply sample IDs to in the Plates section (see step 6 above
for details).0.
Import From File
Gen5 lets you import a text file of Sample IDs. The file can contain the IDs or names of
samples, each one separated by a hard return, and any "Additional" sample
identification fields you've defined. When the additional ID fields are included in the
text file they must be separated from the Name or Sample ID by the symbol defined in
the Read From File Settings.
The text file format requires data for each sample to be in a separate row: Name; ID
field; ID field, when the "read from file" separator is a semi-colon (;), for example. Use a
hard return or "carriage return" to separate each sample's data..
Enter the full path and filename or click the 3-dot button to
locate the text file containing the Sample IDs for this plate and click Open.
1.
File Name
2.
Define the plates to apply sample IDs to in the Plates section (see step 5 above
for details).0.
Beginning with the first text item, Gen5 fills the Samples ID table of the first plate with
the corresponding number of IDs. Additional plates are subsequently processed. Extra
text is ignored, and insufficient text to fill all the sample cells results in blank name
spaces.
Clear Sample IDs from Multiple Plates
You can use the Batch Sample IDs feature to clear or erase the sample names applied to
multiple plates:
1.
2.
In a multiple-plate experiment, highlight the plates in the menu tree (hold the
Ctrl key while selecting the plates with Sample IDs you want to remove)
Select Plate> Batch Sample IDs, under Sample Names, select Use Same
IDs for each plate
242 | Chapter 12: Preparing Plates
3.
4.
Click the Edit Sample IDs button, Gen5 opens the Samples dialog.
Click Clear All and click OK. Gen5 returns to the Batch Samples ID screen.
5. Click OK. Click Yes at the warning message that all IDs will be cleared.0.
erase sample names clear sample IDs for multiple plates
Create a replicate of a previously defined plate
Gen5 automatically creates a replicate of a plate, when you add a plate to the
experiment. The currently-defined Plate Layout is applied to the new plate. Gen5 also
provides tools for copying Sample IDs from another plate.
Choose your preference:
 Adding (a replicate) plate to an Experiment (see below)
 Copy Sample IDs from one plate to another on page
Perform both steps to create an identical copy of the plate!
Import Sample IDs from a Text File
Gen5 lets you import a text file of Sample IDs and "Additional" sample identification
fields.
These instructions are for a single plate, for more than one plate see:
Batch IDs
The file can contain the IDs or names of samples, each one separated by a hard return,
and any "Additional" sample identification fields you've defined. When the additional
ID fields are included in the text file they must be separated from the Name/Sample
ID by the symbol defined in the Read From File Settings.
1.
2.
3.
Locate Sample IDs under the Plate in the menu tree and
double click to open it.
Click Import. Gen5 opens the standard Windows® open file screen.
Locate the text file containing the Sample IDs or names for this plate and click
Open.0.
Gen5 assigns the first text item to the first sample well, and fills the Samples ID table
with the exact number of IDs. Extra text (i.e. for undefined SPL wells) creates
additional cells in the table to hold the extra data. Similarly, when the samples were
not consecutively numbered in the Plate Layout, Gen5 does not skip them in the
Assigning Sample IDs | 243
Sample IDs table, it assigns them an ID. Both extra text and "missing" samples are
indicated in the table as grayed out fields.
Gen5 offers to delete the extra or "invalid" data/IDs when you modify
or review the Samples ID table. Answer No to the question: Do you
want to keep this data? to delete it.
Import File Format
The import file format requires data for each sample to be on a separate line: Name; ID
field; ID field, when the "read from file" separator is a semi-colon (;), for example. Use a
hard return or "carriage return" to separate each sample's data. Leave the row/line
blank to skip the sample identifier.
When the "Read from File Setting" is a Tab and one additional ID field is defined the
text file for the first 5 samples should look like this, without the title row:
Well Identifier
Sample ID
Additional ID
SPL1
S4532
F
SPL2
S8765
F
SPL3
S2310
M
SPL4
G5876
M
SPL5
T4326
F
The title row is only shown for illustration purposes. It should be omitted from the
import file.
Export Sample IDs
Gen5 lets you export a text file of Sample IDs. The file will contain only the IDs or
names of samples, each one separated by a hard return.
1.
2.
3.
Locate Sample IDs under the Plate in the menu tree and
double click to open it.
Click Export. Gen5 opens the standard Windows® save file screen.
Locate the directory where you want to save the text file containing the Sample
IDs for this plate and click Save.0.
244 | Chapter 12: Preparing Plates
Chapter 13
Data Reduction Options
Gen5’s robust and flexible Data Reduction options are described in
this chapter.
Setting up Data Reduction ........................................................ 246
How to use a Runtime Variable in a Formula................................ 248
Define Transformations............................................................. 249
Plotting a Curve ....................................................................... 261
Multiple Curves ................................................................... 282
Kinetic Analysis ....................................................................... 288
Well Analysis ...................................................................... 290
Define Cutofs .......................................................................... 296
Validation Criteria .................................................................... 301
246 | Chapter 13: Data Reduction Options
Setting up Data Reduction
Protocol> Data Reduction
There are several options available for interpreting the results of your experiment.
Gen5™ automatically creates the most commonly applied data reduction steps (based
on previously defined Protocol parameters). You can design your own or modify the
calculations.
Top 6 Things to Know about Data Reduction
1.
2.
Reductions are StepWise™, they can be built one upon another, based on their
sequence in the Data Reduction dialog: a data set created in a previous step can
be used in a later transformation, curve, cutoff, validation or well analysis, if
applicable.
Gen5 creates four types of data reduction steps automatically:
 When blanks (BLK) are assigned to the plate, Gen5 automatically creates a
Blank Subtraction data set. Gen5 subtracts the mean of the blanks from all
other wells on the plate.
 A Well Analysis step is created when a multi-read index Read step is
defined: Kinetic, Spectrum, Area or Linear Scan. If applicable, blanksubtraction results are used to perform the well analysis.
 A Pathlength-Corrected data set is created when this option is selected in
an Absorbance read step.
3.
4.
5.
 The Fluorescence Polarization (FP) transformation is performed
automatically when this reading mode is selected in the Read step. If
applicable, blank-subtraction results are used to perform the FP reduction.
In kinetic experiments, well analysis is based on the FP transformation
results.
Important! Once the Data Reduction dialog is opened and saved, (i.e. OK is
selected to close it) Gen5-created reductions are no longer added, deleted, or
changed. Keep this in mind when modifying a protocol or experiment.
Plate-specific Data Reduction Variables can be collected from users when they
read the plate so Gen5 can use them in data reduction calculations. First, you
define the variable in the Runtime Prompts, then, write a formula using the
variable name as a placeholder. At runtime, when the measurements and
variables are obtained, Gen5 performs the calculation using the input value.
Raw data sets used in Data Reduction steps are named according to Gen5's
Data Set Naming Convention, which is based on the number of Read steps
defined in the Procedure. When the number of read steps is changed, any
previously defined Data Reduction steps are voided, because the data set name
is also changed. When you add or remove a Read step, you must update the
effected Data Reduction steps.
Setting up Data Reduction | 247
6.
In the Data Reduction dialog, you can:0.
 Drag and drop Data Reduction steps to change their sequence order,
 Select a step and right-click to delete it,
 Double click an event to open it for modification or deeper review (or rightclick and select Edit).
Data Reduction Options

Transformation

Curve Analysis

Well Analysis

Cutoffs

Validation

Fluorescence Polarization

Gen5 shows an invalid data reduction step by blocking out its icon.
Changing the Procedure, e.g. reading parameters or sequence of
events, renaming a Read step or data set, or other changes can
invalidate a data reduction step. Generally, it is easiest to delete the
invalid step and recreate it, selecting valid options.
248 | Chapter 13: Data Reduction Options
How to use a Runtime Variable in a Formula
You can acquire a plate- or assay-specific variable for use in data reduction formulas
using the Runtime Prompts. When the plate is read, users will be prompted to enter
a value that will be used in the calculations.
Follow these steps to write a formula using a Data Reduction Variable:
1.
Create the Data Reduction Variable in the Runtime Prompts:
1.
Select Protocol>Runtime Prompts
3.
Set the Prompt Type to Data Reduction Variable
2.
2.
3.
4.
4.
Enter a Prompt Name for the variable: this is the name of the field users
will see in the Plate Reading dialog when they read a plate
Assign it a Variable Name0
Write the formula: create the applicable Data Reduction Step and include the
Variable Name in the formula
Save the protocol and create a new experiment based on it.
Read the plate. Enter the value for this runtime variable in the Plate
Reading screen that opens just before the plate is read. Gen5 will calculate the
formula using the entered value.0.
In Calibrator-Plate Protocols, Data Reduction Variables created for
and populated by the calibrator plate(s) can be used in data reduction
steps defined for the Other Plates. The converse is not true: variables
created for the Other Plates cannot be applied to a calibrator plate.
Any variable defined for a calibrator plate can be used to create
formulas applied to the Other Plates. Variable names must be unique
in a protocol, they cannot be reused from plate to plate.
In Multi-Plate Assay Protocols, Gen5 only recognizes the
variable(s) collected for the first plate (Plate 1). Users will be
prompted to enter the data reduction variable(s) for every plate, but
only the data entered for Plate 1 will be used in the calculation(s).
Define Transformations | 249
Define Transformations
Protocol> Data Reductions> Transformations
About Transformations
In Gen5™, the Transformation dialog is the workspace to define plate- and welllevel calculations. If you are familiar with spreadsheets, like Excel, you can write
formulas in a similar way.
You can perform calculations using:
 any previously-defined raw data, e.g. measurements obtained from the
reader
 already-transformed data sets,
 concentrations determined from standard curves,
 well-analysis results
 up to 4 valid data sets
Gen5's StepWise Data Reduction lets you perform a Transformation on the results of
any previous data reduction step.
The sequence of data reduction steps determines the availability of the data sets:
previous steps provide input for subsequent steps. So you can build a series of
calculations, defining new calculations to be performed on the results of a previous
one.
Well IDs, like blanks (BLK) and standards (STD), etc., must be defined in the plate
layout before they can be used in a formula. The matrix in the Transformation dialog
reflects the current Plate Layout
????? — This symbol in Transformation results indicates a value could
not be determined, or an out-of-range or biased value was used in the
calculation. Check the Protocol Options>Calculation Options
settings.
250 | Chapter 13: Data Reduction Options
Basic Steps
In the top left corner of the Transformation dialog:
1.
Select Data In
3.
Enter the formula in the Plate Formula field to apply it to the whole plate (all
wells) or
de-select Use single formula for all wells and define the Current Formula
field for individually selected wells: click in the matrix cell to apply the formula
to that well of the plate0.
2.
Enter a name for the resulting data set in New Data Set Name
Note: When formulas are applied to individual wells you can right
click and Copy the formula, then Paste it into the Current Formula
field to see it, reuse it, or modify it. You can also resize the columns to
view formulas.
For more details about setting up data transformations:
 Selecting Multiple Data Sets on page 251
 Formula Syntax and Examples on page 252
 Apply calculation to entire plate on page 256
 Apply calculation to individual wells on page 256
Don't forget to update your Report to include your transformations.
Define Transformations | 251
Multiple Data Sets
In the Transformation dialog, click the Select multiple data sets… button:
Use these controls to select the data sets for the Transformation. Click the radio button
to enable selection of a data set, and use the drop-down lists to select the content of the
data set.
 Plate: When multiple plates have been defined for a protocol, you can create a
data set using other than the default value of Current Plate
 Data In: The drop-down list offers any raw data, or results of previouslydefined calculations or curves
 Read(s): Kinetic and scanning raw data offers All or the results of a specific
reading or sampling number to define the data set. Selection is limited in two
ways:
 If you want to use a combination of All and individual reads, set DS1 to
All, and the subsequent data sets to the individual reads, otherwise,
individual read points can be selected for all four data sets
 When more than one kinetic or other multiple-index data set is available
you can only select All for more than one data set when their read counts
(indexes) exactly match. Otherwise, individual readings from different data
sets can be selected.
When selecting multiple data sets with read indexes, the first data set selected: DS1,
determines the read index count of the resulting data out: New Data Set produced by the
transformation.
252 | Chapter 13: Data Reduction Options
Transformation Formula Syntax and Examples
Here are the Symbols and Functions that can be used in Transformations, in formulas
applied to the whole plate or individual wells.
Symbol
Description
x or X
Represents the current well
value
Well Coordinates
Represent the value of a
particular well
A2 or H12
Multiple Data Sets
(DS#)
When referencing multiple
data sets use the DS#. To
identify a specific well within a
data set, use a period to
separate the data set and the
well coordinate
DS1.H6 = well H6 of
data set 1
DS1.X or DS1 = current
well of DS1
<well>.<plate>
When referencing a well
coordinate in a multi-plate
experiment, identify the specific
well and plate using a period
B3.3 = well B3 on Plate
3
DS1.H6.2 = well H6 of
data set 1 on Plate 2
Well Identifiers
The value of a specific well. The
ID assigned to a specific well,
including a Conc/Dil index
value, if applicable:
<ID><index>:<Conc/Dil
Index> The last number is the
Conc/Dil index, not the
concentration/dilution value.
SPL3
<wellID>:<conc
index>
Use : as a separator to identify
individual well IDs of a specific
concentration/dilution level.
CTL2:3 = the average
value for all CTL2 at the
third concentration or
dilution level
Data reduction
variable
Represents a value collected
with the Runtime Prompts
!KitFactor
Function Operators
Add +, subtract -, divide /,
multiply *, combine ( )
CTL3+H5, STD3-25,
DS1/DS2, SPL_ALL*2,
(STD1/STD6)*100
<data set>.<well>
wellID_ALL
The well index can be replaced
by _ALL for Samples and
Sample Controls, which returns
the mean of all indexes of the
well type. Does not apply to
STD, BLK or Assay Controls
Example
SPL_ALL
SPLC_ALL:3 = the mean
of SPLC at the 3rd conc
value
STD3.3 = STD3 on Plate
3
Define Transformations | 253
Figures/Scientific
notation
Any numeral, including those
expressed with scientific
notation
2.45E-08
Function
Description
Example
Mean(<ID>)
Represents the mean of the
specified well identifier or
variables; the mean of any set of
variables can be expressed
Mean(SPL1;SPL2;SPL3)
Note: Gen5 automatically
uses the mean of all likenamed wells on the plate
SD(<ID>)
Represents the standard
deviation of the specified well ID
or variables
SD(SPL10)
CV(<ID>)
CV(x;y;z;...)
Represents the coefficient of
variation for the specified well ID
or variables, expressed as a
percent
CV(CTL2)
DIL(<ID>) or
Dil(X); CONC(X)
or Conc(<ID>)
Returns the defined dilution or
concentration of the specified well
ID or current well
Dil(CTL3)
Round(x;y)
Rounds x to the y number of
significant digits. x can be any
valid symbol or expression.
Round(X;2)
(X represents the value of
the current well)
Truncate(x;y)
Truncates x to the y number of
significant digits. x can be any
valid symbol or expression.
Truncate(CTL3;3)
Log(x)
Represents the Log10 function
Log(SPL_ALL)
POW(x;y)
Represents the value of x raised
to the power of y
POW(STD1;2)
POW(10;x)
Calculates the Anti-Log of the
current well
POW(10;x)
SQRT(x)
Represents the square root of x
SQRT(A1*B1)
MIN(x;y;z;...)
Returns the minimum of the
defined variables.
Min(CV(SPL1);CV(SPL2))
MAX(x;y;z;...)
Returns the maximum of the
defined variables.
MAX(A1;B1;C1)
Mean(x;y;z;...)
SD(x;y;z;...)
SD(23;75;45)
CV(1;2;3)
CONC(STD2)
Conc(X)
254 | Chapter 13: Data Reduction Options
Functions allow a
combination of
expressions
(x;y) Any expression that represents a single value, including
well identifiers, locations, numerals, a function that results in a
single value, can be included in the formula, if it's a valid
expression. Functions described with the ellipsis (x;y;z;...) allow
up to 10 expressions.
Well IDs are case sensitive, i.e. they must be entered exactly as they
are defined in the plate layout. Other symbols and the functions are
case insensitive.
Formula Examples
Formula
Description
X+(A5+A6)/2
The result of this formula is the sum of the current well
value and the mean of the A5 and A6 wells.
DS1/DS2
This is the ratio calculation of data set 1 and data set 2.
Log(X/PC)
The result of this formula will log the ratio of the current
well over the mean of PC (user-defined identifier).
MAX(A1;A2;A3)MIN(B1;B2;B3)
This formula calculates the difference between the
maximum value of A1, A2, A3 and minimum value of B1,
B2, B3.
CTRL1-3*SD(CTRL1)
The result of this formula is the mean of the wells
containing the identifier CTRL1 minus three Standard
Deviations of these wells. It is the equivalent of
MEAN(CTRL1)-3*SD(CTRL1)
X*Dil(X)
The result of this formula is the current well value times
its dilution factor
((SPL4-BLK)/(SPLC4BLK))*100
This formula can be used for toxicology assays, in this
example to calculate the toxicity percentage of SPL4.
More on Min/Max
The MIN/MAX calculations are limited to 10 arguments, but by combining them you
can apply up to 100 arguments:
 1 level: MIN(A1;B2;C3;D4;E5;F6;H7;A8;B9;C10) works for 2 to 10 arguments
 2 levels:
MIN(MIN(A1;B2;C3;D4;E5;F6;H7;A8;B9;C10);MIN(F1;G2;H3;A4;B5;C6;D7;E
8;F9;H10);...) works for up to 100 arguments if you use 10 MIN statements
inside a higher level one.
Define Transformations | 255
Note: you cannot use Min/Max for one Well identifier, like Min(STD1)
or Max(NC). You must use the well locations to determine the min and
max of a well ID's replicates.
For example: If you use "MIN(NC;POS)", this translates as
"MIN(MEAN(NC);MEAN(POS))" and does not return the value that
corresponds to the minimum value of all wells where you either put NC
or POS. It returns either MEAN(NC) or MEAN(POS), whichever is lower.
Round or Truncate to control results
While Gen5 provides a way to control the number of significant digits or decimal
places to display in reports and on-screen, when performing data reduction operations,
Gen5 uses all the digits (up to 15) regardless of the numeric format applied for display.
Use the Round(x;y) and Truncate(x;y) functions to control the number of digits used in
and/or generated by a calculation.
Adding and Selecting Data Sets
Protocol> Data Reduction> Transformation
Gen5™ provides enormous flexibility in designing data reductions by letting you build
up a series of data sets. The variables or data sets for your calculations can be raw data
or the results of a previously-defined Data Reduction step.
When one or no data sets selected
Multiple data sets already selected
The Transformation dialog changes when multiple Data In data sets have been
selected, as demonstrated above. Initially, the dialog offers the Select multiple data
sets button. Use the drop-down list to select one data set. Click the button to select
multiple data sets.
When multiple data sets have been selected, the selected data sets (DS1, DS2, up to 4)
are displayed with a three-dot button.
256 | Chapter 13: Data Reduction Options
Both buttons lead to the Multiple Data Sets dialog, where you can select from raw
data or results data from previously defined transformations, well analysis formulas
and curves.
Apply calculation to entire plate
Select Protocol> Data Reduction> Transformation and retain the default settings
to apply a formula to all the wells of the plate:
In the Formula section of the Transformation dialog, affirm with a check mark "Use
single formula for all wells."
In the Plate Formula field, enter the calculation formula to apply to all wells.
Apply calculation to individual wells
Select Protocol> Data Reduction> Transformation and de-select "Use single
formula for all wells." This changes the input-field label from Plate Formula to
Current Formula.
1.
First, de-select Use single formula for all wells by clicking the checkbox to
remove the check mark.
The formula field label changes to Current Formula and additional auto-entry
options are enabled:
 Current Formula, selected by default, refers to the formula entered in the
field
 Difference Between Columns
2.
 Difference Between Rows
In the Current Formula field, enter a formula to apply and then select (click
in) one or more wells to apply that formula to them.0.
 Helpful Hints:
 Right click a well or field for tools: Copy, Paste, Cut, Undo
 Use the Undo button (which retains 10 past actions) to reverse an action
 Resize the window and/or the grid's columns to see the formula written to a
well; (the formula is truncated when it is too long to display):
 Hover the mouse between two columns to engage
and drag to the desired column width
(the resize tool), click
 Resize the window using standard Windows® tools: click and drag the twoheaded arrow icon at the window's corners or edges
Define Transformations | 257
 Reference specific wells in a formula: often, after creating a data set based on
individual-well formulas, it is necessary to reference the specific well or wells
in a subsequent transformation using that data set.
Correcting a formula
Use the right-click pop-up menu if you need to make small corrections to a previouslyapplied formula:
1.
Right click as you're highlighting or selecting the well to be fixed
3.
Paste the formula in the Current Formula field, with a right click or Ctrl+V
2.
4.
5.
From the pop-up menu select Copy
Make the needed changes to the formula
Apply the revised formula to the desired cell with a regular left click.0.
Individual-Well Formula Example 1
Here's an example of the need to reference a specific well in a transformation formula.
An assay kit requires subtracting the average of the "non-specific binding" wells (NSB)
from the "maximum binding" wells (MB) to determine the corrected maximum
binding, which is used in a subsequent transformation.
The wells to be referenced are assigned to the first column of the plate layout:
1
A
B
C
D
E
F
G
H
BLK
BLK
NSB
NSB
MB
MB
MB
SPL1
Transformation 1: MB - NSB = DS1 (data set 1). This formula can be applied to the whole
plate, even though only the specifically referenced wells will be affected by it. Viewing the
output data set shows the results, the corrected maximum binding, are assigned only to
the applicable wells: C1, D1, E1, F1, G1.
Transformation 2: X-NSB/DS1.C1*100 can be applied to the whole plate or individually to
the sample wells. Notice the reference to well C1 of the data set (DS1), this could have been
any of the relevant wells, i.e. referencing F1 would also work.
258 | Chapter 13: Data Reduction Options
How to perform Dual-Wavelength Subtraction
A common way to improve the accuracy of your results is to read the plate at two
wavelengths and perform a dual-wavelength subtraction data reduction. Here are
step-by-step instructions for endpoint and kinetic (multi-index) reads:
Endpoint Analysis
First define the Read step with two wavelengths:
1.
Select Protocol>Procedure and add steps as needed, e.g. Set Temperature
3.
Define the Plate Layout of samples, blanks, standards, etc.
2.
4.
5.
6.
7.
8.
9.
Click Read and select 2 wavelengths
Select Protocol>Data Reduction and click Transformation
Gen5 opens the Multiple Data Set dialog
Select the button for DS2
Use the drop-down list to select Data In for DS1 and DS2, the first read
measurement for DS1 and the second read data set for DS2. Click OK when
you're done.
In the Transformation dialog, enter a name for the New Data Set Name in
the text field, e.g. Delta OD
Define the dual wavelength subtraction formula in the Plate Formula text
field, e.g. DS1-DS20.
Now you can use the results of this calculation, Delta OD, in subsequent data
reduction steps, if desired.
Kinetic Analysis
First define the Read step with a kinetic loop and two wavelengths:
Define Transformations | 259
1.
2.
3.
4.
5.
6.
7.
Select Protocol>Procedure and add a Kinetic loop and other steps as
needed, e.g. Set Temperature
Click Read and select 2 wavelengths
Define the Plate Layout of samples, blanks, standards, etc.
Select Protocol>Data Reduction. Gen5 opens the StepWise™ Data
Reductions dialog
Highlight the first Well Analysis step and click Transformation.
StepWise Data Reductions let us use the results from all previous calculations
in subsequent steps. By making the dual-wavelength subtraction the first step
we can use the results in all other steps. (Later, we can modify the Gen5generated Well Analysis steps to use the dual-wavelength results.)
Gen5 opens the Multiple Data Set dialog
Select the button for DS2
8.
Use the drop-down list to select Data In for DS1 and DS2, the first read
measurement for DS1 and the second read data set for DS2.
9.
Set the Read(s) for both DS1 and DS2 to All. Click OK when you're
done.
10. In the Transformation dialog, enter a name for the New Data Set Name in
the text field, e.g. Delta OD
11. Define the dual wavelength subtraction formula in the Plate Formula text
field, e.g. DS1-DS20.
Now you can use the results of this calculation, Delta OD, in the Well Analysis data
reduction steps, if desired. In the StepWise Data Reductions dialog, to modify the
Gen5 generated steps, double click a step to open it in edit mode, and change the
Data In to Delta OD. Or, create a new well analysis step.
Subtracting Blank Wells
When there is one or more Blank defined in the Plate Layout, Gen5™ automatically
creates a Transformation or "blanked" data set.
Gen5 uses the "blank" (blank-subtracted) data sets in any subsequent
system-generated data reduction steps, like Pathlength Correction and
Well Analysis calculations in kinetic experiments.
For single- and multi-wavelength reads:
For each raw data set, Gen5:
1.
2.
Calculates the mean of the raw measurement values in wells identified as blank
Subtracts the mean from the raw measurement value in each well on the plate
to generate a "Blank" data set containing each well’s measurement result after
blank well subtraction
260 | Chapter 13: Data Reduction Options
3.
Displays the Blank well Mean in the Statistics data view.0.
For Specific Read Types:
Within any protocol, if one or more wells are defined as ‘Blank’ in the Plate Layout,
Gen5 automatically generates Blank-Wells Subtraction data sets for each wavelength:
 Endpoint read: For each wavelength defined in the protocol, the average of the
blank well(s) is subtracted from every well on the plate
 Kinetic analysis: For each wavelength defined in the protocol, within each
kinetic read, the average of the blank wells is subtracted from every well on the
plate
 Spectrum scan: A blank average is calculated for each wavelength in the
spectrum reading range. The blank average for each wavelength is then
subtracted from the absorbance read at the corresponding wavelength in each
well
 Linear and Area scan: For each wavelength defined in the protocol, within each
read index, the average of the blank wells is subtracted from every well on the
plate
Plotting a Curve | 261
Plotting a Curve
Data Reduction> Curve Analysis
Select Curve Analysis in the Data Reduction dialog to create a standard or titer curve
for your experiment. Other than kinetic curves, there are two scenarios for using a
curve to determine the concentration of samples:
Gen5™ provides two general ways to use its curve plotting feature:
 Standards, Controls, and/or Samples, for which concentrations or dilutions
have been defined, are read on one or more microplates, along with the
test/unknown samples.
 A Multi-Plate Calibration Protocol defines one plate as the calibrator
(containing the Standards or Controls), and plots a curve against the calibrator
plate to determine the concentration of test/unknown samples on one or more
other plates. Refer to the Multi-Plate Protocols chapter for details.
Gen5 lets you generate multiple standard curves (up to 6) from one plate
Prerequisites for generating a Curve:
1.
2.
3.
Define Standards (STDn), Controls (Assay or Sample), and/or Sample
Dilutions (SPL) in the Plate Layout with corresponding concentrations or
dilutions (Learn about Multiple Standards on page 282)
Define the minimum number of standards/dilutions for the desired Curve Fit
(Minimum STDs on page 269)
Create at least one read step in the Procedure. 0.
To View a Curve:
After you've defined the Curve Analysis, and acquired the data, e.g. read the plate,
open the Plate View, and select the Graph tab.
 Curve Fitting Results: The default table displays the parameters used to
plot the curve including the Curve Formula, its elements and the R2
coefficient (for all curve fits except point-to-point).
 Curve Fitting Details: Select the Details table to view best-fit results for
each parameter, including standard error (SE) and 95% confidence
intervals.
 Curve Interpolations: When one has been defined for the curve, Gen5
builds a table listing the interpolation formula and the X and Y values for
that point on the curve.
262 | Chapter 13: Data Reduction Options
To Output a Curve:
Gen5 provides several ways to print a curve:

Click Quick Export to instantly send the current curve to Excel
 Add it to the Content in Report Builder
 Right-click to copy or save it as an image for use in a word-processor
application
 Export it to Excel® using Power Export
How to Create a Standard Curve
Gen5 lets you create one or more standard or calibration curves for determining the
concentration of samples:
1.
Select File> New Protocol
3.
Select Plate Layout:
2.
4.
Select Procedure and define the Read step (and any other required steps)
 Define the concentrations of the Standards (see below)
 Assign the location of the standards, samples, and controls and blanks (if
any) on the plate
Select Data Reduction> Curve Analysis
 Gen5 may have generated a "corrected" data set: if you assigned blanks to
the plate or selected Pathlength Correction in the Read step, you'll want to
select these data sets for Data In for the Y-Axis Data when plotting the
curve
 For Kinetic reads, Gen5 creates a Well Analysis step. The default kinetic
well analysis is “Mean V,” which can be easily changed to any of the wells
analysis options. The output of the well analysis step is typically used as the
Data In for the Y-Axis in quantitative assays.
5.
6.
7.
On the Data In tab, use the drop-down to select the Y-Axis Data
On the Curve Fit tab, choose a curve fit method
Other options and requirements when defining multiple curves:
 Curve Name: replace the default "Curve" with a more meaningful or unique
name
 On the Data Out tab, replace the default "Conc" for the Data Set Name with
a more meaningful or unique name
8.
 On the Data Out tab, define interpolations to plot on the curve
Define the reporting or export requirements and Save the protocol. Now,
you're ready to run an experiment: File> New Experiment to read the plate
and generate the curve.0.
Plotting a Curve | 263
Define Standards
In the Plate Layout dialog:
1.
2.
3.
Set the Type to Standard
Gen5 sets the ID to STD:
 You can change the abbreviation using the 3-dot button
 Use the drop-down list to define multiple standards.
Click the 3-dot button at the Conc. field to enter the expected concentrations for
the Standards:
 In ascending or descending order, enter the values in the consecutivelynumbered fields: STD1, STD2... For a shortcut, select one of the two Auto
entry tools
Be sure to assign the Minimum Number of Standards: see page 269
4.
Assign the location of the Standards on the plate, in the same manner as
assigning unknown Samples.0.
264 | Chapter 13: Data Reduction Options
Curve Fit
Data Reduction> Curve Analysis> Curve Fit tab
Curve Name: assign each curve a unique alpha-numeric name that does not include
spaces or symbols used as mathematical operators (+, *, -, /). Characters must be
alphabetic, numeric, or the underscore.
Select the Curve Fit Method that will best model the data for your experiment. The
parameters selected for Curve Fit can be modified at any time without invalidating the
data. You may want to experiment with the options to assess the best method for your
experiment.
If the options on the Curve Fit tab are disabled (grayed out), Data In
is set to "Use Curve from Calibrator Plate," which is only applicable to
Calibration Plate Protocols.
Gen5 offers several curve fit methods and lots of flexibility in defining or influencing
the best-fit calculation. All the options are intended to fit data to a model that defines Y
as a function of X, i.e. X values must be known. Gen5's StepWise™ Data Reduction
feature lets you transform the data prior to fitting the curve, if necessary. And, you can
apply constraints to the parameters or weighting to the sum-of-squares after viewing
the curve, as well as before it is plotted.
Linear Regression
Linear Regression is a simple, best-fit, straight line. See page 265.
Polynomial Regression is an extension of the Linear Regression equation. See page 268
Curve Fit | 265
Non-Linear Regression
4 Parameter is characterized by a symmetrical sigmoidal plot that eventually becomes
asymptotic to the upper and lower standard values. See page 266.
5 Parameter is similar to 4P but it is better able to model data that is asymmetrical at
the upper and lower asymptotes. See page 267.
Logit-Log is a restricted form of 4P that has been offered in BioTek readers' onboard
data reduction (PDR) software and KCjunior™. See page 268.
Other
Point-to-Point follows each standard point with no averaging of the values to smooth
the curve. Minimally two standards are required.
Spline with Smoothing is a curve defined piecewise by polynomials, joining a set of
data points by a series of straight lines, which is then smoothed by the Smoothing
Factor.
The curve will appear smoother as the Smoothing Factor is increased. The zero factor
will force the curve fit through all data points.
This curve is most useful when you have a very large data set. Minimally 4 standards
are required to plot a Spline curve.
Linear Regression
Linear regression: y = ax + b (or Y = intercept + slope x X).
y represents unknown response
x represents theoretical concentration (in this context should we be using the word
expected?)
a represents the slope of the linear regression
b represents the intercept to the y axis
 The linear regression fit uses the least squares technique. The better the quality of
the fit the more the absolute value of R tends to 1. This type of curve fitting
technique can be used when you think the data will fall in a predictable linear
pattern. It may be necessary to transform the x and/or y components using
Logarithmic axes.
 You can enable or disable Use average of replicates in the curve calculation. By
default, the mean of replicates is used. This is recommended when the replicates
are not independent. Contrarily, when the source of experimental errors is the
same for all replicates, you should consider plotting each point separately.
 You can apply Parameter Constraints, but generally, linear regression determines
the best-fit curve without constraints.
266 | Chapter 13: Data Reduction Options
Nonlinear Regressions are Iterative
Nonlinear regression is performed in a series of steps, each adjusting the parameters to
improve the goodness-of-fit.
Here are the steps that every nonlinear regression program follows:
1.
Start with an initial estimated value for each variable in the equation.
3.
Adjust the variables to make the curve come closer to the data points. There are
several algorithms for adjusting the variables. Gen5 uses the Newton-Rapshon
method.
2.
Generate the curve defined by the initial values. Calculate the sum-of-squares
(the sum of the squares of the vertical distances of the points from the curve).
4.
Adjust the variables again so that the curve comes even closer to the points.
6.
Report the best-fit results. The precise values you obtain will depend in part on
the initial values chosen in step 1 and the stopping criteria of step 5. This means
that repeat analyses of the same data will not always give exactly the same
results.
5.
Keep adjusting the variables until the adjustments make virtually no difference
in the sum-of-squares.
4 Parameter Curve
The four parameters are left asymptote, right asymptote, slope, and the value at the
inflection point. Gen5 performs an iterative series of calculations (using the NewtonRaphson algorithm) to determine the best curve fit - the least squares method to
minimize the residual error. The iterations stop when no further improvement to ERR
is detected. You can refine the calculation using Parameter Constraints and/or
Weighting.
4 Parameter logistic fit:
a = (theoretical) response at concentration = 0
b = measure of slope of curve at its inflection point
c = value of x at inflection point
d = (theoretical) response at infinite concentration
x = concentration
y = response (OD)
The minimum number of standards is 4.
IC50/EC50: typically, the c parameter is equal to the IC50 or EC50 value
Curve Fit | 267
It is recommended that:
 at least one standard is not far from each asymptote
 at least 2 standards fall within the linear area of the curve, one either side of the
inflection point
You can plot the IC50/EC50 value on the 4P curve by updating Gen5's Curve
Analysis step before reporting the results.
5 Parameter Curve
As you would expect, the five parameter curve is nearly identical to the 4 Parameter
except for an additional parameter e (which is equal to 1 in a 4P curve and makes the
curve symmetrical). With e, the 5P curve fit is better able to model asymmetric
experiment results. You can refine the calculation using Parameter Constraints and/or
Weighting. Gen5 ends the iterative calculations when no further improvement to ERR
is detected.
This five-parameter logistic is also called the Richards equation.
a = minimal curve asymptote; (theoretical) response at concentration = 0
b = measure of slope of curve at its inflection point
c = value of x at inflection point
d = maximal curve asymptote; (theoretical) response at infinite concentration
e = quantifies the asymmetry
x = concentration
y = response (OD)
The minimum number of standards is 5.
It is recommended that:
 at least one standard is not far from each asymptote
 at least 3 standards fall within the linear area of the curve, one at the inflection
point and one on either side of it.
You can calculate and plot the IC50/EC50 value on the 5P curve by manually
performing the calculation and then updating Gen5's Curve Analysis step before
reporting the results.
268 | Chapter 13: Data Reduction Options
Polynomial Regression Curve Fit
The calculation of the Polynomial fit parameters is based on a least squares method
that results in a series of equations. Then, a Gaussian Elimination algorithm is applied
to the augmented matrix of the series to calculate the parameters.
n represents the Degree of the polynomial regression.
 The Degree must be less than or equal to the number of standards minus 1. If
this condition is not met, Gen5 automatically reduces the degree of the
polynomial to the number of defined standards having different X values
minus one.
 The unknown concentrations are calculated by using an approximate
calculation method, linear interpolation between 1000 points evenly spaced on
the X axis.
 When a Y Axis Intercept value is defined it determines the coefficient a of the
polynomial equation:
y = g*x6 + f*x5 + e*x4 + d*x3 + c*x2 + b*x + a
This is equivalent to defining an advanced parameter constraint with a fixed.
Logit-Log Curve
Gen5's Logit-Log curve is identical to the 4 Parameter Curve except it is does not
perform an iterative series of calculations to minimize residual error. Instead, the
asymptotes of the curve (parameters a and d) are determined from experimental data
(y values). And, the inner portion of the curve (b and c) is solved using a logit-log
linear regression. This prohibits the application of Parameter Constraints and
Weighting.
Gen5's logit-log algorithm is derived from BioTek readers' onboard
data reduction (PDR) software and KCjunior™.
Curve Fit | 269
Curve Fit: Minimum Number of Standards
Here are the minimum number of standards that must be defined for each Curve Fit
Method:
Curve Fit Method
Minimum STDs
Linear Regression
2
4-Parameter
4
5-Parameter
5
Logit-Log
4
Point-to-Point
2
Spline with Smoothing 4
Polynomial Regression Degree +1
Degree: 2
3
Degree: 3
4
Degree: 4
5
Degree: 5
6
Degree: 6
7
More Curve Fit Controls:
Axis Transformation:
In the bottom left corner of the Curve Fit tab, you can alter the default Transformation
for the X and Y axes used to calculate the curve.
 None - the default value, retains the Formula displayed at the bottom of the
dialog to calculate the curve (no transformation is applied to the selected data,
X or Y.)
 Log (logarithmic) - alters the formula used to calculate the curve by applying
log10 (10x) to the selected data, X or Y. Any change is reflected in the Formula
displayed at the bottom of the screen. Log transformations fail when the data
includes a negative or null value. And, they are not applicable to the Nonlinear
Regression curves.
Y Axis Data:
Use average of replicates
This check box offers a Yes or No option to calculate and apply the average of
replicates when plotting the curve or to calculate each data point individually. The
270 | Chapter 13: Data Reduction Options
default setting is yes, to average the replicates, but some types of assays consider
results to be more accurate when each sample is plotted separately. This option is
disabled for Point-to-Point and Spline curves.
Weighting: Use the drop-down list to apply a weighting factor to the curve fit
formula. (See below for more info.)
Extrapolation Factor: The extrapolation factor range must be between 1 and 3.
(See below for more info.)
Parameter Constraints:
 None (Estimate All)
 Y Axis Intercept is limited to Linear and Polynomial Regression fit methods.
This option forces the curve to intercept the Y axis at the value you input. See
page Error! Bookmark not defined..
 Advanced
page 272.
: Click the 3-dot button to define constraints for the curve. See
Weighting in a Curve Fit
Gen5 offers three options for weighting the curve fit to normalize or minimize-theeffect of an uneven distribution of data points from the curve. Select the most
appropriate option for your experimental data:
1/Y - Poisson Weighting
This weighting option is available to refine data that follows a Poisson distribution.
Where the standard deviation among the replicates is almost equal to the square root
of their mean.
1/Y2 - Relative Weighting
When you expect (or discover) the average distance of the points from the curve to
increase as Y increases, you can use this weighting option to minimize the sum-of-thesquare of the relative distances. Relative weighting can ensure that all points have an
equal influence on goodness-of-fit.
1/Std Dev Y2 - Reciprocal-Variance Weighting
Curve Fit | 271
When you have a large range of data values, variable error in the data or a relatively
large error in the data you have good reason to consider applying a weight to each
data point. This method of "weighting by observed variability" assumes that the mean
of replicates with a large standard deviation (std dev) is less accurate than the mean of
replicates with a small std dev. This is not always true.
This method is only reliable when you have a large number of replicates.
The setting: Protocol> Protocol Options> Calculation Options>
Standard Deviation Weighting N-1 or N is used to determine SD
prior to its use in this weighting scheme.
At times Gen5 may not be able to calculate one or more weights.
Calculation Warning messages will alert you to the situation and
describe the remedy Gen5 implemented, e.g. the highest valid weight
was used
Extrapolation Factor in Curve Fitting
For all curves except Spline and Point-to-Point, you must define an Extrapolation
Factor in the Curve Fit tab or use the default setting: 1.1. The Extrapolation Factor must
be between 1-3.
Using a factor of 1 eliminates the extrapolation, using the upper and lower Standards
as the limits for concentration/dilution interpretation. An Extrapolation Factor >1 lets
you extend the upper and lower limits of the calculation.
 Example: Assuming a linear X axis, we wish to extend the upper and lower
limit by 20%. The lower limit denoted by the first standard is 50 units. The
upper limit denoted by the last standard is 150 units. The dynamic range
therefore is 150-50 = 100 units. Imposing the 20% extension means that the new
range will be: 100 x 1.2 = 120 units. This represents an increase in the dynamic
range of 10 units at the lower limit and 10 units at the upper limit. Therefore
the new lower limit will be 50-10 = 40 units. The new upper limit will be 150 +
10 = 160 units.
Important: Exercise caution when using extrapolation (Factor >1), as
the implied assumption is that the relationship of the x and y variables
is valid outside the range defined by the standards. This type of
extrapolation should only be applied when prior knowledge of the
relationship is known. Typically this feature is used in assays where
linear relationships are known. Inappropriate use of the
Extrapolation Factor may invalidate results generated from
data falling into the extrapolation zone.
272 | Chapter 13: Data Reduction Options
FYI: Gen5 calculates the values that fall into the new limits. Those
that fall outside these limits will be assigned > than or < than,
respectively. Negative concentrations shall not be reported for any (y)
value through extrapolation. If a value intersects the curve below 0 on
the x-axis, Gen5 shall report a concentration of <0 for the well.
Advanced Parameter Constraints
Gen5 lets you apply one of two types of constraint on your curve parameters to
produce a more informative curve. (Detailed information about parameters is provided
below.)
Select a constraint for a parameter:
1.
Click in the Mode field of a parameter to enable a drop-down list to select:
 Start from: is offered for the nonlinear regressions that use an iterative
calculation process to determine the best fit. For 4P and 5P curve fits you
can tell Gen5 to start the iteration process with a given value.
 Fixed: lets you assign a fixed parameter value for Gen5 to use in the
calculation. When you fix certain parameter values Gen5 will use them to
determine the best-fit values for the other parameters.

2.
 Estimate: does not apply a constraint. It lets the curve fit determine the
parameter value.
Enter a Start From or Fixed value in the Value field when applicable. 0.
Helpful Information
 Constraints can be useful when you have not collected sufficient data to map
all the parameters in your model and you know or expect a parameter to equal
a certain value.
 4P and 5P regressions require that B, C, and E parameters are positive (nonnegative) integers. Gen5 prevents input of a negative or null value for these
parameters with an error message.
 For Linear and Polynomial Regressions, fixing the B or A parameters
(respectively) to 0 is similar to setting the Y Axis Intercept to 0
 Constraints can be added or modified at any time, before or after the data has
been collected. When the regression calculation using initial, non-constrained
values generates a curve that is far from the data, you may be able to generate a
better fit using a Start From or Fixed constraint.
Curve Fit | 273
About Curve Parameters and Values
Depending on the curve fit method, Gen5 calculates and reports the values for these
parameters. They can also be used in a Validation formula to test the results of your
experiment.
Fitting Parameters
The coefficients used in the equation to calculate the curve are the fitting parameters,
potentially: A, B, C, D, E, F, G. These values can be constrained or determined by the
curve fit. Gen5 reports SE and 95% CI for each parameter, except when Parameter
Constraints have given them fixed values.
For example, A, B, C, D are the 4 parameters in the 4P curve formula:
Goodness of Fit
R2 - Coefficient of Determination
The value R2 quantifies goodness of fit. The coefficient of determination of the
regression ranges from 0.0 -1.0. It is computed by comparing the sum-of-the-squares
distances from the best-fit curve and from a model defined by the null hypothesis, e.g.
horizontal line through the origin.
 When R2 = 0.0 the curve does not come close to the data. Knowing X does
not help you predict Y.
 When R2 = 1.0 all points lie exactly on the curve with no scatter. If you know
X you can calculate Y exactly.
274 | Chapter 13: Data Reduction Options
R2 is one criterion for determining if your curve fit is reasonable. Review the other
Curve Data, like confidence intervals, to confirm the value of a high R2.
Standard Error (SE)
Gen5 constructs a "Hessian Matrix", evaluates the WSS and DoF to calculate the
asymptotic Standard Error of Estimate of each parameter. A low Standard Error
indicates one or more of these conditions:
 the curve fit models the data well
 lots of data points
 less scattered data
 narrow confidence intervals
SE is not reported for fixed parameters.
95% Confidence Interval: Min and Max
Review the 95% CI range for each parameter to evaluate the curve's goodness-of-fit. A
narrow range assures you of a true best fit, but a wide range signals a weakness in the
experiment or in the model selected to fit the data.
If you plotted the minimum and maximum CI values that Gen5 reports for each
parameter it would produce a confidence band on equal sides of the curve. This
standard statistics calculation tells you, with 95% certainty, the best-fit curve falls
within the confidence band.
See Calculating the Confidence Interval using t-distribution on page 276.
SE and 95% CI are not reported for fixed parameters.
General Metrics
R - Correlation Coefficient
Gen5 calculates R by taking the square root of the coefficient of determination: R2.
The correlation coefficient ranges from -1 to 1. A value of 1 shows that a linear
equation describes the relationship perfectly and positively, with all data points lying
on the same line and with Y increasing with X. A score of -1 shows that all data points
lie on a single line but that Y increases as X decreases. A value of 0 shows that a linear
model is inappropriate – that there is no linear relationship between the variables.
Err - Error
ERR, also known as the "root mean squared error" (RMSE), is the difference between
the actual measurements and the values predicted by the model. It can be used to
determine whether the model fits the data or not.
Curve Fit | 275
SS — Sum of Squares
The sum of the squares of the vertical distances of the points from the curve. It is useful
when comparing curve fits. The less scattered the data the smaller the SS and Std Err.
When weighting is applied to minimize the relative distance squared, the WSS is used
to assess goodness-of-fit.
Covariance Metrics
Degrees of freedom (DF)
DF = p - n
where p is the number of data points
and n is the number of parameters
t-Distribution (T)
t-distribution is a statistic whose values are given by:
t = [ x - ì> ] / [ s / sqrt( n ) ]
where x is the sample mean, ì is the population mean, s is the standard deviation
of the sample, n is the sample size, and t is the t score.
See Calculating the Confidence Interval using t-distribution on page 276.
Weighted Sum of Squares (WSS)
When you apply a weighting factor to the curve, Gen5 calculates the weighted sum
of squares (WSS), then uses it to determine the SE for a parameter ak:
where wi is the weight of (xi,yi)
and p is the number of data points
and n is the number of parameters
Interpolations
Gen5 reports the user-defined interpolations Y Formula and the values it produces
for X and Y.
276 | Chapter 13: Data Reduction Options
Calculating the 95% Confidence Interval using t-Distribution
The 95% Confidence interval for a parameter ak is calculated with the following
formula:
Where t0.025,df is the 97.5th percentile of the Student t distribution, given in the following
Upper Tail Probability table:
Degrees of
Freedom
Pr(T > t)
Degrees of
Freedom
Pr(T > t)
1
12.706
31
2.040
3
3.182
33
2.035
2
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
4.303
2.776
2.571
2.447
2.365
2.306
2.262
2.228
2.201
2.179
2.160
2.145
2.131
2.120
2.110
2.101
2.093
2.086
2.080
2.074
2.069
2.064
2.060
32
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50 to 59
60 to 69
70 to 79
80 to 89
90 to 99
100 to 119
2.037
2.032
2.030
2.028
2.026
2.024
2.023
2.021
2.020
2.018
2.017
2.015
2.014
2.013
2.012
2.011
2.010
2.009
2.000
1.994
1.990
1.987
1.984
Curve Fit | 277
Degrees of
Freedom
Pr(T > t)
Degrees of
Freedom
Pr(T > t)
26
2.056
120 to 139
1.980
28
2.048
180 to 199
1.973
27
29
30
2.052
2.045
2.042
140 to 179
200 to 499
500 to 999
1000 and greater
1.977
1.972
1.965
1.962
Data In for Curve Analysis
Data Reduction> Curve Analysis> Data In tab
Generate Curve from Current Plate
A prerequisite for this option is defining in the Plate Layout:
 Standards, Controls, or Dilution Samples
and
 Concentrations or Dilutions for the standards, controls or samples
278 | Chapter 13: Data Reduction Options
In each of the three fields, use the drop-down options to select the parameters for the
curve:
 Well ID is the Standards, Controls or Dilution Samples to plot on the X axis
 for SPL (samples) and SPLC (sample controls), select All or one ID (see page
283)
 X Data is the source for the values to plot on the X-axis, by default it is set to
use the map of the selected Well IDs <Plate Layout>
 Y Data is the source for the values to plot on the Y-axis
Use Curve from Calibrator Plate
This option only applies to Other Plates in a Calibrator Plate Protocol described in the
Multi-Plate Protocol chapter
Data Out for Curve Analysis
Data Reduction> Curve Analysis> Data Out tab
The data sets created here will be available for viewing, reporting, and exporting. You
may also be able to use them to perform additional data reductions.
Options Grayed Out?
Data Out options are only available when the curve is plotted for standards,
controls or samples with Concentration values (not Dilution values).
Curve Fit | 279
For Calibrator-Plate Protocols Only
Y-Data: Select the data set to use for plotting the curve, based on the standard
curve from the Calibrator Plate.
Concentrations
Gen5™ lets you define multiple curves for an experiment or protocol, the only
requirement is defining a unique name for each one in the Data Set Name and
Curve Name fields.
Calculate Concentration x Dilution
If sample dilutions have been defined for this protocol in the Plate Layout, you can
use this feature to perform the common Titer Curve requirement of calculating the
actual concentration of diluted samples. You must define a unique name, Data Set
Name, for each data output generated based on a different curve.
Interpolations
In the Interpolations table, you can enter up to 20 Y-Axis values or formulas to
view and report the results. Well IDs (that have been previously) defined in the
Plate Layout can be used. Review the Formula Syntax for Interpolations. Gen5
plots the interpolations in the generated curve if possible, Example.
Interpolation Formula Syntax
Symbol/Function Definition
Example
-
Subtraction or negation
BLK-0.010
*
Multiplication
STD1*0.10
/
()
Numeric value
Well coordinates
Well ID
Well_All
Division
Represents inclusion
Represents y value
The location of a specific well
The value of a specific well. The
ID assigned to a specific well,
including a Conc/Dil index value,
if applicable:
<ID><index>:<Conc/Dil
Index> The last number is the
Conc/Dil index, not the
concentration/dilution value. The
well index can be replaced by
_ALL for samples and sample
controls, which returns the mean
of all indexes of the well type.
CTL1/CTL2
(CTL1/CTL2)*100
0.500, 54000
A1/B1
STD3
CTL1:2
SPL_ALL
SPLC_ALL:3
280 | Chapter 13: Data Reduction Options
MEAN(<ID>)
Mean(x;y;z;...)
SD(<ID>)
SD(x;y;z;...)
CV(<ID>)
CV(x;y;z;...)
Round(x;y)
Truncate(x;y)
Dil(<ID>) or
Conc(<ID>)
LOG(x)
POW(x;y)
SQRT(x)
MIN(x;y;z;…)
MAX(x;y;z;…)
Data reduction
variable
Functions allow a
combination of
expressions
The mean of the specified well
identifier, well coordinates or
variables
MEAN(POS1)
MEAN(A1;A2)
The coefficient of variation of the
specified well identifier or
variables
CV(STD1)
CV(A1;SPL3;50)
Truncates x to the y number of
significant digits
Truncate(STD2;5)
Represents the LOG10 function
LOG(SPL10)
The square root of <x>
SQRT(A1*B1)
The maximum of the defined
variables
MAX(A1;B1;C1)
The standard deviation of the
specified well identifier or
variables
SD(BLK)
SD(22;33;44)
Rounds x to the y number of
significant digits
Round(SPL3;4)
Returns the defined dilution or
concentration of the specified
well ID
DIL(SPL1)
Conc(CTL2)
The value of x raised to the
power of y
POW(STD1;3)
The minimum of the defined
variables
Represents a value collected with
the Runtime Prompts
MIN(CV(CTL1);CV(CTL2))
!Lot#
(x;y) Any expression that represents a single value,
including well identifiers, locations, numerals, a function
that results in a single value, can be included in the
formula, if it's a valid expression. Functions described with
the ellipsis (x;y;z;...) allow up to 10 expressions.
Curve Fit | 281
Interpolation Example
Interpolate the IC50 or EC50
When using the 4 Parameter or 5 Parameter curve fit methods, you can show the IC50 or
EC50 value in the curve results using Gen5's Interpolate function.
1.
2.
First, define the Gen5 protocol and run the experiment as you normally would
to capture the measurement results.
After Gen5 has calculated the best fit curve, locate and make note of the Curve
Parameters:
 4P: C
3.
 5P: A and D. Then, calculate the IC50/EC50 value using this formula: ((AD)/2)+D
Return to and edit the Data Reduction>Curve Analysis step: select the Data
Out tab and enter the value determined in the previous step in the
Interpolations table under Formula.
In the Plate View select the Graphs tab to see the interpolated IC50 or EC50 value. You
will also see the value plotted when you include the curve in a report or PowerExport.
282 | Chapter 13: Data Reduction Options
Multiple Curves
Gen5's Multiple Curves Options
Gen5 offers several methods for generating multiple curves in an experiment. Follow
the link for the method that best fits your needs:
 Generating Multiple Standard Curves: you have two or more standards and
want to plot a standard curve for each
 Generating Curves based on Sample Dilutions: you have samples with
multiple dilutions and want to plot curves based on the expected dilution
values
 Plotting Sample Dilutions on a Standard Curve: you have unknown samples
of various dilutions and want to determine their concentration from a standard
curve
 Kinetic curve for each well: you are conducting a kinetic or time-course
analysis and want to plot kinetic curves to determine Max V, Integral, etc.
Generating Multiple Standard Curves
Gen5 lets you create up to six standard curves in an experiment. The standards can
have the same or different concentration values.
How to:
Generating multiple standard curves requires applying multiple standards to the plate:
1.
Create a new Protocol and define its Procedure in the usual way. When
defining the Plate Layout, assign the first set Standards to the plate as usual
You can change the default IDs for
the Standards, learn how in the
Preparing Plates chapter
2.
3.
Use the ID Prefix drop-down list to select the next standard, e.g. STDB, to
assign to the plate
Optionally, click the 3-dot button for Conc. to define different concentration
values for the next standard. Overwrite the first set of concentration values,
Multiple Curves | 283
4.
5.
6.
with those for the current standard. Skip this step to use the same
concentrations
Assign the location of the additional standards on the plate
Assign the location of the test samples and any controls to the plate
Go to Data Reduction> Curve Analysis to set up the curves. Create a Curve
Analysis step, in the usual way, for each set of standards defined (one curve for
each standard group).0.
To View Multiple Standard Curves:
As with a single standard curve, after you've acquired the data, e.g. read the
plate, open the Plate workspace, and select the Graph tab. Use the drop-down list
in the Curve field to select the curve to view.
Curve Fitting Results: In addition to displaying the curve, Gen5 displays, in a
table beneath the curve, the data points used to calculate all the standard curves.
Combine the Curves in One View: Gen5 lets you create a new curve to overlay
multiple curves in one graph.
To Report Multiple Curves:
Gen5 lets you report/print the curves separately or combined:
 Create a New Graph to overlay curves and add the new curve to the
Content in Report Builder/Power Export Builder or add each curve
independently to report them separately
 For any curve, display it in the Graph tab of the Plate workspace and RightClick to copy or save it as an image for use in a word-processor application
 Export it to Excel®
Samples and Sample Controls Curves
Data Reduction> Curve Analysis> Data In
Gen5 will plot a curve for each sample ID or sample control ID, using the expected
dilutions/concentrations for the X-Axis and the user-selected measurement values for
the Y-Axis. Titer assays, for example, use this feature to plot a titer curve.
Well ID
After setting the Well ID to SPL or SPLC (assuming the default IDs were retained), tell
Gen5 to generate one curve for All (each of) the IDs for which a concentration or
dilution has been defined, or for only one particular ID:
284 | Chapter 13: Data Reduction Options
 Keep the check mark for All IDs to generate one curve for each ID
 Or, de-select All and enter the number of the Sample ID or Sample Control
ID group for which you want only one curve plotted.
Viewing
Just like standard curves, after you've read the plate, open the Plate View and select the
Graph tab. Use the Curve drop-down list to select the curve to display. Gen5 appends
the Well ID (e.g. SPL1) group name to the curve name: Curve_SPL1 for example, to
name the curves.
Reporting
You can report/print the curves just like standard curves, repeating the procedure for
each curve generated, as needed.
If the Samples or Sample Controls used to plot the curves are
assigned Concentrations, rather than Dilutions, you can elect to
Calculate Concentrations and Concentrations x Dilutions. When
the Well ID to plot the curves is set to All IDs, the results will only be
calculated for the samples used in generating each single curve. For
example, concentrations for SPL1 will be calculated using the SPL1
curve, concentrations for SPL2 will be calculated using the SPL2 curve,
and so on.
How to generate Sample-Dilution Curves
When you have multiple dilutions of your samples, Gen5 makes it easy to plot a curve
for each sample based on the known dilution values. The critical factor is assigning the
dilution values to the Samples in the Plate Layout. Gen5 recognizes sample dilutions
as valid X-axis values.
How to:
1.
Select File>New Protocol
3.
Select Protocol>Plate Layout:
2.
Select Protocol>Procedure and define the Read step (and any other required
steps)
 Define the Sample Dilutions
 Assign the location of the sample dilutions, and blanks (if any) on the plate
Multiple Curves | 285
For example:
This example shows three samples with the same dilution values. Gen5 will create
three curves, one for each sample. Gen5 assigns a dilution index to keep track of the
multiple instances of a sample, e.g. SMP2:3 is the third dilution index of Sample 2.
4.
5.
Select Protocol>Data Reduction
 When Blanks (BLK) are assigned in the Plate Layout, Gen5 automatically
creates the Blank-Subtraction transformation
 Depending on your assay requirements you may need to define another
transformation or data reduction to normalize the data used in the curves,
as in this Toxicity/Cytotoxicity assay
Click Curve Analysis0.
 On the Data In tab, set the Well ID to SPL (or the customized Well ID) for
sample dilutions
 Select the Curve Fit tab to select the best curve fit method
286 | Chapter 13: Data Reduction Options
Viewing and Reporting Sample Dilution Curves
You can overlay multiple sample dilution curves in one graph for viewing and
reporting. After defining the Procedure, Plate Layout, and Data Reduction steps,
Create a New Graph in Data Views. The data views become Available Data Views in:
 Report Builder to generate a print out
 Power Export Builder for transfer to Excel®

To view the new curve online, select the Graph tab and use the Curve:
drop-down list to select it
Multiple Curves | 287
Plotting Sample Dilutions on a Standard Curve
When you have unknown samples and want to determine their concentration, it may
be most efficient to test them in various dilutions/concentrations against a standard. In
Gen5, you can take advantage of multiple features to accomplish this task.
How to:
1.
Select File>New Protocol
3.
Select Protocol>Plate Layout:
2.
Select Protocol>Procedure and define the Read step (and any other required
steps)
 Define the Sample Dilutions
 Define the Standards and their expected concentrations
4.
5.
6.
7.
 Assign the location of the sample dilutions, standards and blanks (if any) on
the plate
Select Data Reduction> Curve Analysis to create the standard curve
 Gen5 may have generated a "corrected" data set: if you assigned blanks to
the plate or selected Pathlength Correction in the Read step, you'll want to
select these data sets for Data In for the Y-Axis Data when plotting the
curve
On the Data In tab, set the Well ID to STD and use the drop-down to select
the Y-Axis Data
On the Curve Fit tab, choose a curve fit method
On the Data Out tab, define Interpolations to plot select Sample dilutions on
the curve. For example, in the Interpolations Formula table enter SPL1:1,
SPL1:5, SPL2:1, etc. to easily identify them in the graph0.
Viewing results: Select the Graphs tab, after reading the plate, to view the curve.
Use the drop-down for the Results field (at the top, right corner) to select the
Interpolations table to enhance the view
288 | Chapter 13: Data Reduction Options
Troubleshooting Curve Fits
Gen5 gives you a lot of flexibility in curve fitting, some of them can be used to improve
a curve fit:
 Collect more data: the most certain way to improve a curve fit is to collect
more data: widen the range of X values, for example.
 Simplify the model: Linear regression and 4P fits are easier to calculate and
have fewer unknowns than a 5P fit, your data may better fit a simpler
model. (You can also use constraints to simplify the model, i.e. reduce the
number of unknowns.)
 Apply constraints when the curve is far from the data: by constraining the
initial values (Start From) or assigning a Fixed value you may be able to
generate a better fit.
 Constraints can also be useful when you have not collected sufficient data
to map all the parameters in your model and you know or expect a
parameter to equal a certain value.
Gen5 lets you modify the settings used to plot the curve, as suggested above, so
you can experiment with the different options. Alternatively, you can create multiple
curves using the same data but with variant settings (add more Curve Analysis steps
to the Data Reduction), so it is easier to compare the various results. Then, you can
overlay the curves in one view, if that is helpful: see Create a New Graph.
Kinetic Analysis Options | 289
Kinetic Analysis Options
Learn more about the Well Zoom in the Kinetic Analysis chapter.
Gen5 offers a full complement of options for analyzing your Kinetic Reading raw data
results.
Data Reduction Options
In the Data Reduction> Well Analysis dialog, you can set up multiple steps, taking
advantage of some or all the available options:
 Mean V
 Max V (Gen5 creates this Data Reduction step automatically. It also
calculates the Y Intercept, R & R2, time at Max V, and Lag time)
 Mean Min/Max OD/RFU/RLU
 Onset OD/RFU/RLU
 Onset OD%/RFU%/RLU%
 Integral
Combine Data Sets
Gen5 lets you combine the measurements collected from multiple kinetic readings
performed in one experiment. When multiple kinetic loops are defined in the
Procedure, Gen5 offers the Append to previous Kinetic data option in the second and
subsequent kinetic read steps.
The read steps in the kinetic loops must be identical, and Gen5 enforces this rule when
the Append option is selected. In a Synchronized Mode block, this feature is
mandatory and Gen5 automatically applies it to the second and higher kinetic read
steps.
Append to previous Kinetic data results in one data set containing all the
measurement values acquired from the reader during the all the kinetic loops. Do not
use this option if you want separate data sets for data reduction purposes.
Dispensing Reagent in a Kinetic Analysis
Gen5 lets you include dispensing in a kinetic analysis: learn about Dispensing Reagent
in a Kinetic Analysis Protocol in Gen5’s Help.
290 | Chapter 13: Data Reduction Options
Perform Well Analysis
Data Reduction > Well Analysis
About Gen5's Well Analysis
 Well Analysis is available as a Data Reduction option when a Kinetic analysis
has been set up in the Procedure
 Well Analysis is also available when Spectrum, Area Scan, or Linear Scan is
defined as the Read Type
 Well Analysis produces a special data view that lets you zero-in on each
individual well to see the measurement values and analysis results: Well Zoom
 Well Analysis also produces a special table of results for viewing, reporting and
exporting the calculation results of each well
 In the StepWise Data Reduction dialog, you can create multiple Well Analysis
events to obtain multiple types of results. Assign a unique Label/name to each
well analysis step.
How to:
1.
2.
3.
Label - Identifies the results for data views, report building, etc. Enter a unique
name/ID to be used in the resulting data set name. Data Set Name Rules. You
must enter a unique Label when a data set is used in more than one Data
Reduction step.
Data In - Click the down arrow to select a data set, e.g. raw data or results of
previously-defined Transformation (based on All Reads)
Calculation Type - Use the buttons to select the type of computation to
conduct. Each option displays the results it will produce in the Generated Data
box on the right side of the screen (see below)0.
 Calculation Options correspond to the Calculation Type selected. Click the
Calculation Options button to alter the default settings for the selected
Calculation Type.
 Formula Syntax for Well Analysis: describes the symbols and functions
supported to perform a calculation using the individual read points of each
well (on page 292).
Kinetic Analysis Options | 291
Kinetic and Scanning Data Reduction Outputs Listing
Set up the Well Analysis option that generates the desired data output
Read Type
Kinetic
Calculation Type
Mean V
Max V
Mean Min/Max OD
Mean, Std, CV
Onset OD
Integral
Spectrum
Min / Max OD
New Data Sets
Mean V
R (correlation coefficient)
R2 (coefficient of
determination)
Y Intercept
Max V
R (correlation coefficient)
R2 (coefficient of
determination)
t[1] at Max V
Lagtime
Max V Calc - t min
Max V Calc - t max
Y Intercept
Mean Min OD[2]
t at Mean Min OD
Mean Max OD
t at Mean Max OD
Mean OD
Std Dev OD
CV OD
Onset Time
Onset OD
Basis Time
Basis OD
Integral
Mean Min OD
W[3] at Mean Min OD
Mean Max OD
W at Mean Max OD
292 | Chapter 13: Data Reduction Options
Read Type
Linear Scan
Calculation Type
Mean, Std, CV
Mean Min/Max
Area Scan
Integral
Mean, Std, CV
New Data Sets
Mean OD
Std Dev OD
CV OD
Mean Min OD
Read Pos[4] at Mean Min OD
Mean Max OD
Read Pos at Mean Max OD
Integral
Mean OD
Std Dev OD
CV OD
OD assumes absorbance reads. Substitute RFU or RLU/sec as appropriate.
[3] W = Wavelength
[4] Pos = Horizontal Reading Position
Formula Syntax for Well Analysis
The Well Analysis Formula lets you perform calculations using the individual read
points or indexes in "multi-index" readings: kinetic and spectral scan. Formulas can be
written similar to Transformations, using the symbols and functions listed below. Also
see some Examples on page 295.
Symbols and functions are not case sensitive.
Kinetic Analysis Options | 293
Symbol/Function Description
Example
R#
Read point or index of a
kinetic read
W#
Read point or index of spectral W2
read
Function
Operators
Numeric value
Add +, subtract -, divide /,
multiply *, combine ( )
Any numeral, including those
expressed with scientific
notation
Mean(R#/W#;...) The mean of a set of read
Mean(x;y;z;...)
points or variables
R1
R2+R4, R6-R10,
W3/W8, R1*R15,
(R4/R1)*100
2.45E-08
Mean(R2;R4;R8)
Mean(1;2;3)
SD(R#/W#;...)
The standard deviation of
specified read points or a set
of numerals
SD(R12;R22)
SD(23;75;45)
CV(R#/W#;...)
CV(x;y;z;...)
The coefficient of variation of
specified read points or any
set of numerals, expressed as
a percent
CV(W5;W6;W7)
CV(1;2;3)
Round(x;y)
Rounds x to the y number of
significant digits.
Round(W2;5)
SD(x;y;z;...)
Truncate(x;y)
Log(x)
Truncates x to the y number of Truncate(R3;3)
significant digits.
Represents the Log10 function Log(R3)
Represents the value of x
raised to the power of y
POW(W10;2)
POW(10;x)
Calculates the Anti-Log of the
current well
POW(10;R4)
SQRT(x)
Represents the square root of
x
SQRT(R1*R5)
MIN(x;y;z;...)
Returns the minimum of the
defined variables.
Min(R5;R6;R7;R8)
MAX(x;y;z;...)
Returns the maximum of the
defined variables
MAX(W1;W2;W3)
POW(x;y)
294 | Chapter 13: Data Reduction Options
Symbol/Function Description
Functions allow a
combination of
expressions
Example
(x;y) Any expression that represents a single value,
including well identifiers, locations, numerals, a function
that results in a single value, can be included in the
formula, if it's a valid expression. Functions described
with the ellipsis (x;y;z;...) allow up to 10 expressions.
Using individual Kinetic read points in a Formula
In addition to Gen5's Transformation option, you can perform calculations using the
individual reading points of a well in a Kinetic or Spectral analysis with the Well
Analysis Formula function. The formula will generate a single value for each well.
Gen5 names the resulting data set "Formula Result [nm]", where nm is the wavelength
or filter set defined in the read step. When a Label is defined it precedes the naming
convention: "Label: Formula Result [nm]"
After setting up the Kinetic loop or spectrum read step in the Procedure:
1.
2.
3.
Select Data Reduction>Well Analysis
Select the multi-index data set to use for Data In
Select the Formula button and write the calculation in the text field0.
Kinetic Analysis Options | 295
Examples:
1. For an ORAC Antioxidant Test:
0.5+(R2/R1)+(R3/R1)+(R4/R1)+(R5/R1)....+(Rn/R1)
Where R1 is the reading at initiation of the reaction and Rn is the last measurement. A
step-by-step description for using this formula in an experiment is described in the
Kinetic Fluorescence Assay Example in the Assay Examples chapter.
2. To determine the mean of certain read points: (r1xr2xr3xr4)/4
Viewing/Reporting Results
Gen5 automatically generates a Matrix view and two tables when a Well Analysis
Formula is created. In Data Views, and the Report Builder and export options, you'll
find:
 Matrix: Formula Result [nm]
 Statistics: Formula Result [nm]
 Well Analysis Results: Formula Result [nm]
Well Zoom during a Kinetic Read
Learn more about the Well Zoom in the Kinetic Analysis chapter.
1.
2.
Select the Curves data set from the Data drop-down list before Reading the
plate.
Zoom into a specific well: click on the desired well to display the Well Zoom
screen. It will display the results as they're measured.0.
Tip: If necessary, drag the progress dialog out of the way for an unobstructed view:
click and drag the title bar of the dialog to move it out of the way.
Caution: In some cases, displaying the Curves data set during a Kinetic read can
consume excessive resources resulting in computer-performance degradation. Learn
more in the Troubleshooting chapter. You can follow the steps above to monitor the
progress of one well, then, leaving the Well Zoom open, change the Matrix Data to a
numeric view
296 | Chapter 13: Data Reduction Options
Define Cutoffs
Protocol> Data Reduction> Cutoffs
About Cutoffs
Gen5™ lets you define cutoffs as fixed or variable margins against which results are
compared. Gen5 creates a Symbols data set based on your definition of cutoffs that
shows how each well fits into the defined categories. Gen5 also adds another tab to the
Plate View to show the Cutoff Values, the results of cutoff formulas. Up to 40 formulas
(of increasing value) can be defined for each data set and multiple Cutoff steps, one
Cutoff step per data set, can be defined in the StepWise Data Reduction.
In the Cutoffs dialog, notice that the number of Symbols fields exceeds the number of
cutoff formula fields by one. During data reduction, if the value of a well is less than
the first cutoff, the first symbol is applied to it. If the value of a well is greater than or
equal to the first cutoff but less than the second cutoff, the second symbol is assigned
to the well, and so on.
Out-of-Range Symbols are applied to concentration values (calculated from a
standard curve) when the concentrations are outside the extrapolation range of the
curve: below the minimum or above the maximum. You can change the OUT+ and
OUT- labels applied to these values by clicking in the text fields and replacing the
content.
Data In data sets presented for selection are determined by the current protocol
excluding multi-index data sets. Cutoffs cannot be determined in multiple-read
measurements like kinetic analysis and scanning results. For these types of analysis a
transformed or processed data set must be used.
????? — This symbol in Cutoff results, i.e. the Symbols data set, indicates an out-ofrange or biased value was used in the calculation. Check the Protocol
Options>Calculation Options settings.
See an example and explanation of cutoffs on page 298
How to set up cutoffs:
1.
Begin by selecting the Data In data set on which to apply the cutoffs.
Hint: The Data In drop-down list offers the data sets resulting from all
previously defined reads (raw data) and calculations, except for multi-index
readings, e.g. kinetic. Cutoffs cannot be evaluated against multiple-index reads.
2.
Define the cutoffs, beginning with the lowest value, by entering a formula or
data point in the Cutoff Formula 1 field. In the Symbols fields that straddle the
cutoff formula field, in the top field, enter a symbol (or call) to apply to wells
with values less than the formula. In the next Symbol field, enter the symbol to
Define Cutoffs | 297
apply to values greater than or equal to the Formula. (See the Formula Syntax
table on page 298.)
Important: Cutoffs must be defined in increasing order, from the
lowest value to the highest. Gen5 will issue a Calculation Warning and
will be unable to assign Symbols to wells if the reading results do not
affirm the increasing values of the cutoff formula
3.
4.
Customize the appearance of the symbols, change the font and color, by
clicking the 3–dot button next to the Symbol field.
Continue defining cutoffs and symbols in the same manner, always defining a
higher value cutoff formula.0.
How to view the cutoffs:
1.
2.
3.
After reading the plate (or otherwise acquiring data), open the Plate View and
select the Matrix tab
At the Data field, use the drop-down list to select the Symbols data set
Select the Cutoff Values tab to view the values (formula results) upon which
the Symbols data set was based0.
 Important Information:
 When cutoffs, or calls, are defined, Gen5 adds a tab to the Plate View to
display the values or results of the cutoff formulas

Up to 40 cutoff formulas can be defined for one data set. Use the scroll controls at
the top of the dialog to display additional cutoff formula and symbol fields.
 Multiple Cutoffs can be defined (in the Data Reduction dialog) for a protocol: one set of
cutoffs per data set, i.e. you can only reference a data set one time for cutoffs
 Gen5's rounding function in Data Views may cause unexpected results in the
Cutoffs' reporting. Gen5 does not round the values before applying the cutoff
formula, so it's possible to see conflicting outputs. More:
298 | Chapter 13: Data Reduction Options
Cutoffs Example
For this example, we customized the Assay Control well type in Plate Layout to put
Positive (PC) and Negative (NC) controls on the plate. Then, setting up the cutoffs as
shown in this image, Gen5 will apply NEG to any well with a value less than the NC.
It will apply the EQV symbol to any wells that are greater than or equal to the NC but
less than the PC. It will assign POS to any wells equal to or greater than the PC. Any
wells with values considered out-of-range will be assigned OUT- if the concentration is
below the minimum, and OUT+ if the concentration is higher than the maximum.
To view the cutoffs, after reading the plate, in the Plate workspace, select Symbols
from the Data field drop-down list.
Formula Syntax for Cutoffs
Symbol/Function Description
+-*/
()
Numeric value
Example
Mathematical operators
CTL1+0.100
Represents inclusion
(CTL1/CTL2)*100
Any numeral, including those
0.500, 54000, 1e10
expressed with scientific notation
Define Cutoffs | 299
Symbol/Function Description
Well ID
Well coordinates
wellID_ALL
MEAN(<ID>)
Mean(x;y;z;...)
SD(<ID>)
SD(x;y;z;...)
CV(<ID>)
CV(x;y;z;...)
DIL(<ID>);
Conc(<ID>)
Round(x;y)
Truncate(x;y)
LOG(x)
POW(x;y)
SQRT(x)
MIN(x;y;z;…)
MAX(x;y;z;…)
Data reduction
variable
The value of a specific well. The
ID assigned to a specific well,
including a Conc/Dil index value,
if applicable:
<ID><index>:<Conc/Dil
Index> The last number is the
Conc/Dil index, not the
concentration/dilution value.
The well index can be replaced
by _ALL for Samples and
Sample Controls, which returns
the mean of all indexes of the
well type. Does not apply to
STD, BLK or Assay Controls.
Example
A1
STD3
CTL1:2
SPL_ALL
SPLC_ALL:3
The mean of the specified well
identifier or variables
MEAN(SPL1)
Mean(A1;22;SPL2)
The coefficient of variation of the
specified well identifier or
variables, expressed as percent
CV(STD1)
CV(SPL10;33;B2)
The standard deviation of the
specified well identifier or
variables
Returns the defined dilution or
concentration of the specified
well ID
SD(BLK)
SD(4;H12;CTL2)
Dil(CTL3)
CONC(STD2)
Rounds x to the y number of
significant digits. x can be any
valid symbol or expression.
(Learn more below)
Round(SPL1;4)
Represents the LOG10 function
LOG(SPL10)
Truncates x to the y number of
significant digits. x can be any
valid symbol or expression
Truncate(CTL3;3)
The value of x raised to the
power of y
Pow(STD1;3)
The square root of x
SQRT(A1*B1)
The maximum of the defined
values
MAX(A1;B1;C1)
The minimum of the defined
values
Min(CV(CTL1);
CV(CTL2); 45)
Represents a value collected with
!KitFactor
the Runtime Prompts
300 | Chapter 13: Data Reduction Options
Symbol/Function Description
Example
Functions allow a (x;y) Any expression that represents a single value, including
combination of
well identifiers, locations, numerals, a function that results in a
expressions
single value, can be included in the formula, if it's a valid
expression. Functions described with the ellipsis (x;y;z;...)
allow up to 10 expressions.
Rounding Issue with Cutoffs
It's possible to see apparent discrepancies in the cutoff results:
For Example: a value of .9998 will be rounded to 1 when the numeric format for the
view is set to 3 Decimal places (the default setting). In the Matrix view you'll see 1
for the well, but if Cutoffs are set to identify values less than 1, it will be reported
as <1 in the Symbols view/report.
Two ways to avoid this inconsistency:
 Create a Transformation that rounds the data set, and apply the cutoffs to
the new data set. Transformation formula: Round(X;3) for example. The
resulting reports and views of the data set and cutoffs will be consistent.
 Revise the numeric Format, i.e., the number of decimal places or significant
digits, of the Data View to more precisely view and report the values. Find
instructions at Numeric Format. In the above example, increasing the
number of decimal places to 4 would eliminate the inconsistency. This
option may or may not be appropriate for your results.
Validation | 301
Validation
Data Reduction> Validation
Many assay kits define conditions which must be met to validate the results of an
experiment. The Validation dialog lets you set up these conditions to compare to
selected results (data sets). The Validation Formulas can be fixed thresholds or
algebraic formulas.
Top 5 Things to Know about Validation Criteria:
1.
2.
3.
4.
5.
Multiple Validation steps can be defined in the StepWise Data Reduction, but
only one set of criteria for each data set is permitted
Up to 50 conditions or formulas can be defined in a Validation step
When data points that cause a Validation failure are masked or changed, the
Validation can change from fail to pass
Validation results can be included in reports and/or export content
Most often, validation formulas combine well IDs with a less than, greater than,
or equal sign, e.g. STD1>=1.5:0.
<
less than
>
greater than
<=
>=
less than or equal to
greater than or equal to
Setting up Validation Criteria
1.
Select Data Reduction>Validation
3.
In the Formula fields, enter conditions (up to 20) that must be met for the
experiment's results to be considered valid.
2.
4.
Use the drop-down list to select a Data In data set against which the criteria
are evaluated
Optionally, in the text fields on the right-side of the screen, e.g. Valid Text, click
inside the field and overwrite the default text to change it for the results output
and reports.0.
302 | Chapter 13: Data Reduction Options
Formula Syntax for Validation
In conjunction with a conditional operator: <, <=, =, >, >=, you can use the following
elements to define a formula as a validation or quality control condition:
Symbol/Function
Description
Example
+
Addition
CTL1+0.100<3.5
-
Subtraction or negation
BLK-0.010
/
*
Division
()
Multiplication
CTL1/CTL2
Represents inclusion
(CTL1/CTL2)*100
Numeric value
Well ID
Well coordinates
wellID_ALL
WellID#
WellID:#
WellID#:#
wellID:conc index
Any numeral, including
those expressed with
scientific notation
The value of a specific
well. The ID and index
assigned to a specific well.
The well index can be
replaced by _ALL for
samples and sample
controls, which returns the
mean of all indexes of the
well type.
To evaluate all of the
specified wells individually,
returns the mean value of
each separate well index.
The Conc/Dil index can
also be represented with
#.
SPL#:# performs the
evaluation on each dilution
of each sample group.
Use : as a separator to
identify individual well IDs
of a specific concentration
or dilution, if applicable:
<ID><index>:<Conc/Dil
Index> The last number is
the Conc/Dil index, not the
concentration or dilution
value.
STD1*0.10
0.500, 54000, 2.45E-08
A1
STD3
SPL_ALL
SPLC_ALL:3
STD# performs the
evaluation on each STD
group, e.g. STD, STDB,
STDC, etc.
SPLC2:# performs the
evaluation on each SPLC2
dilution
STD:# performs the
evaluation on each
concentration of the STD
group, e.g. STD1, STD2
CTL2:3 the average value for
all CTL2 at the third
concentration value
Validation | 303
Symbol/Function
Description
Example
The difference between the two "all" identifiers extends to their results output: using
_ALL produces a one line result for all wells: valid or invalid (if one well is invalid, the
report is invalid); the # produces individual invalid results: if one or more wells are
invalid, each well result is reported; if all wells are valid a one line report is given.
_All does not apply to STD, BLK or Assay Controls
SD(<ID>)
SD(x;y;z...)
CV(<ID>)
CV(x;y;z...)
ROUND(x;y)
Truncate(x;y)
Conc(<ID>)
DIL(<ID>)
SQRT(x)
LOG(x)
POW(x;y)
MIN(x;y;z;...)
MAX(x;y;z;…)
Curve(<x>;<y>)
The standard deviation of the
specified well identifier or
expression
SD(BLK)
SD(A1;STD3;45)
Rounds x to the y number of
significant digits
Round(SPL1;4)
Returns the defined
concentration of the specified
well ID
CONC(CTL4)
The square root of x
SQRT(A1*B1)
The value of x raised to the
power of y
POW(STD1;3)
The coefficient of variation of
the specified well identifier or
expression
CV(STD1)
CV(SPL12;33;B2)
Truncates x to the y number
of significant digits
TRUNCATE(STD1;5)
Returns the defined dilution
of the specified well ID
Dil(SPL3)
Represents the LOG10
function
LOG(SPL10)
The minimum of the defined
variables
MIN(CV(CTL1);CV(CTL2))
The maximum of the defined
variables
MAX(A1;B1;C1)
Returns the value of the
selected curve result
Curve(CurveA;R2)>8.8
Curve(<x>;<y>;<z>) Returns the value of the curve Curve(CurveB;C;SE)<=1
result for the selected
parameter. See explanation
below.
Data reduction
variable
Represents a value collected
with the Runtime Prompts
!KitFactor
304 | Chapter 13: Data Reduction Options
Symbol/Function
Functions allow a
combination of
expressions
Description
Example
(x;y) Any expression that represents a single value,
including well identifiers, locations, numerals, a function that
results in a single value, can be included in the formula, if
it's a valid expression. Functions described with the ellipsis
(x;y;z;...) allow up to 10 expressions.
Defining curve results and parameters
When you have generated a standard curve, Gen5 lets you define validation criteria using
the Parameters and Values calculated by the curve as the variables in the validation
formula. For example, you can define a validation condition specifying the value of R2:
0 < Curve(CurveC;R2) < 1.0
Two types of curve formula are possible:
 Curve(Curve_name;y) to express a whole curve variable, such as R2, DF, or SS
 Curve(Curve_name;y;z) to identify a parameter and parameter-specific
variable, like SE or 95% CI
Note: you can select any data set in the experiment for this curve
formula application; but, keep in mind Gen5's limitation of one
Validation step per data set.
Find more details in Gen5’s Help. Look for Validation: Curve Formula
Validation Examples
1.
From an assay kit: "The absorbance of the Negative Control (NC) must be less
than 70% of the cutoff (CO) value. The mean absorbance of the cutoff should be
greater than 1. The ratio Positive Control (PC)/CO should be greater than or
equal to 1.3."
2.
Another assay kit says: "Individual negative control (NC) absorbance values
must be less than or equal to 0.150 and greater than or equal to -0.005.
Individual positive control (PC) absorbance values must be greater than or
Validation | 305
equal to 0.600. Individual positive control values must be within the range of
0.5 to 1.5 times the mean of the positive control."
3.
In a kinetic analysis, during the first of several readings, the mean value of
STD1 must fall between 0.200 and 0.300 OD. The mean value of STD2 must fall
between 0.900 and 1.300 OD.
And, the Mean OD of every sample replicate group must be greater than 0.
Viewing the Validation Results
Gen5 applies a status to each formula defined in the Validation step:
 Valid if the condition was met
 Not Valid if the condition was not met (i.e. failed).
 Unable to Evaluate, if:
306 | Chapter 13: Data Reduction Options
 The selected data set was not available,
 A well ID in the formula was not found in the Plate Layout,
 A value could not be determined for a cited Well ID (e.g., all wells with that
ID are masked, or over-ranged).
You can change the status labels, replacing them with terms that have
more meaning for your organization.
Gen5 issues a Calculation Warning when out-of-range or biased values
are used in a validation formula, see Calculation Options
 Gen5 adds a tab to the Plate View to display Validation results
 Failed validations or when Gen5 was "Unable to Evaluate" a criteria are
reported immediately after a plate is read in the Calculation Warning popup. You can reopen the message anytime by selecting Calculation Log
under the respective Plate in the menu tree. If the condition is Verified,
Gen5 does not present a message.
Reporting Validation Results

Add the Validation table to Report Content in the Report Builder.
Similarly, you can export the results.
Fluorescence Polarization | 307
Fluorescence Polarization
Data Reduction> Polarization
About Fluorescence Polarization Data Reduction
Gen5 automatically performs data reduction when Fluorescence Polarization (FP) is
the selected read type. You can retain, modify, or delete the auto-generated data
reduction step.
When Blanks are assigned to the Plate Layout, Gen5 performs a blank-subtraction
before calculating polarization. When FP is performed in a kinetic loop, Gen5 uses the
polarization results to automatically perform a Max V Well Analysis determination.
Blank subtraction is performed before the Well Analysis, if applicable.
Polarization and Anisotropy
The basic polarization formulas use:
 Parallel Intensity (raw or blanked data from parallel measurement
 Perpendicular Intensity (raw/ blanked data from perpendicular
measurement x G Factor
 G Factor: a coefficient used to calculate the polarization value. It corrects for
the optical variations between the parallel and perpendicular emission
paths unique to each reader. Gen5's default value is 0.87.
Gen5 automatically performs the Polarization calculation option. You can modify the
automatically-generated FP data reduction step to change the output to Anisotropy, or
to select both options.
The raw and transformed data sets created by FP are available for selection/use in all
other applicable data reduction options, e.g. Transformations, Curve Analysis.
308 | Chapter 13: Data Reduction Options
FP Formulas
 Parallel Intensityraw data from parallel measurement
 Perpendicular Intensityraw data from perpendicular measurement X G
Factor
 G Factor: coefficient used to correct for the optical variations between the
parallel and perpendicular emission paths. Gen5's default value is 0.87
 spl = test sample; blk = blank
The G Factor is used in the FP calculation to normalize the polarization value obtained
on fluorescein to 20 mP (known reference value of unbound fluorescein). Gen5 ships
with a "G Factor Determining Protocol" that you can run to determine your reader's
specific G Factor for fluoroscein.
Chapter 14
Viewing Results
Learn Gen5’s naming conventions and the meaning of symbols and
notations in this chapter. Instructions and suggestions for
customizing online views and report outputs are provided also.
Plate View ............................................................................... 313
Data Views.............................................................................. 315
Gen5’s Tables.......................................................................... 320
Data Set Naming Conventions ................................................... 316
Symbols and Notations ............................................................. 317
Modify/Customize Views/Data ................................................... 323
Change the Time Format........................................................... 326
310 | Chapter 14: Viewing Results
Viewing Results
You can instantly view the results of an experiment in Gen5's main workspace using
the Plate View:
 After reading the plate (or otherwise acquiring data), in the Plate View use the
drop-down list for Data to display the raw data and any data reduction results

Click the Quick Export button to instantly open the current view in Excel®.
Learn more about Gen5's Export Options

Click the 3-dot button next to a data set to customize the view's appearance.
This feature is also available in the Data Views dialog.
 ** Asterisks are used to signal a change: in Gen5's title bar an asterisk indicates
the current file has been changed but not-yet saved. When a data set is enclosed
by asterisks it has been become invalid. Generally this is because a Read step or
Data Reduction step has been altered. Edit custom-made data views to select
valid data sets

384- and 1536-well plates require resizing to effectively see the data. Gen5
adds a button to the Plate View to zoom in on the top-left quadrant of the plate
and zoom out to view the entire plate. After zooming in, use the scroll bars to
bring the other quadrants into focus. Find more on resizing the views below.
 Multi-index readings offer another viewing option. Kinetic and scanning reads
generate views based on the number of read intervals, wavelengths, or
positions defined. Use the spin buttons or enter the desired read index and
click Show to display it. Gen5 displays the time, wavelength, or position of the
selected read number.
Viewing Results | 311

Kinetic and Scanning protocols can generate Well Analysis data sets
labeled Curves, in the Matrix tab, open the Curves data set and click on a well
for a Well Zoom. (Note: 384- and 1536-well plates show a magnifying glass in
the well instead of a curve.)
Starting at the Curves data set, you can display multiple well zooms
simultaneously by holding down the Ctrl key while selecting (up to 8) wells
 You can also select Create new Matrix to define a new view
 Select the Statistics tab to view a table of data reduction results
 Select the Graphs tab (when available) to view any Curves, except kinetic
analysis curves, which Gen5 calls Well Analysis and is described above
 Select the Cutoffs tab (when available) to view the values or results of the
cutoff formulas
 Select the Validation tab (when available) to view the values and results of the
validation formulas
 Important Notes:
 Gen5 may not display some data points by default; to see them you must
create your own Data Views. If you expected to see certain results that are
not currently displayed, try creating your own views.
 All data views are also available for Reporting and/or Exporting
 Modify a data view to change the way results are reported, including the
number of decimal places and significant digits (page 323)
 Gen5 always uses your computer's Regional Settings to display and input
data
 Learn the meaning of the Symbols and Notations displayed on page 317.
Opening the Plate View/Workspace
In an Experiment, if it is not already open in the main view of Gen5™:
 from the menu tree: Double-click the desired
 Or, select Plate> View
item
312 | Chapter 14: Viewing Results
Resizing the Plate View
Use the standard Windows® Maximize and Minimize buttons to resize the Plate View
For more precise control, hover your mouse at the corner of the window, and with
the two-headed arrow click and drag it to the desired size
You can also resize the columns and rows: hover your mouse on a border and
drag the two-arrowed pointer to the desired column/row size
Changing the window, column & row size typically enables the
standard Windows® scroll bars, which you'll need to use to see all of
the wells
Viewing Results | 313
Resize columns
Hover your cursor over the division between columns until the cursor turns into a
two-arrow I-beam. Then click and drag the column to the desired size. Just like Excel®
and other programs! In some Gen5 views this option works for rows, as well.
Plate View (Workspace)
Plate> View
Use the Plate View or Plate Workspace to instantly view the results of an experiment
and, if needed, to mask or alter the results.
About the Plate View
Gen5 always provides the Matrix and Statistics tabs, and when applicable, adds a
Graphs, Cutoff Values and Validation tab
What you can do:

After reading the plate (or otherwise acquiring data), in the Plate View use
the drop-down list for Data to select the data set (raw data or data reduction
results) to display

Click the 3-dot button next to a data set to customize the view's appearance.
This feature is also available in the Data Views dialog.

Click the Quick Export button to instantly open the current view in Excel®.
Learn more about Gen5's Export Options, including the right-click options:
Copy to Clipboard and Save As
314 | Chapter 14: Viewing Results

In the Matrix and Curve tabs, use the Edit and Mask buttons to change or
mask selected data

In the upper-right corner, below the minimize, maximize, and close
buttons, click the duplicate view button to open another instance of the Plate
View. Use this feature to view the raw data results of a reading in one window
and simultaneously display a curve plotted from the results in another
window, for example

Use the read index spin buttons to consecutively advance the
view of a Kinetic or Spectrum read, or enter a read/wavelength index in the
field and click the Show button
How to set the default view
To determine the first data set or data view to open for each tab of the Plate View:
1.
2.
3.
Select Data Views from the menu tree
For each category, Matrix, Table, Graph, ..., highlight the data set you want to
be shown first, i.e. during and immediately after reading the plate, when its
corresponding tab is selected in the Plate View
Click Set as default0.
The Set as default button only appears when an eligible data set is highlighted. The
button appears grayed-out when the current default is selected, and it disappears
when a non-eligible data set or another item in the Data Views is selected.
Data Views | 315
Data Views
Protocol> Data Views
Gen5™ offers this menu-tree control box for selecting and modifying the way data is
presented on-screen and in reports and export files. The selections and modifications
made for on-screen viewing (Data Views) become the settings for the Report Builder,
Power Export Builder, and File Export Builder.
Create your own Data Views for the most precise control of content and
appearance.
Gen5 lists all the data sets available for viewing under a display category:
 Matrix = a grid that represents the microplate
 Table = a columnar presentation of the data
 Graph = a standard curve or well zoom generated from a Curve or Well
Analysis
 Field Groups = user-selected or defined data points to include in reports
Protocol Summary is another category offered for reports and
exports only. You'll find it in the Report Builder, File Export Builder,
and Power Export Builder.
The function buttons: New, Edit, and Hide/Show are enabled or disabled in sync
with your selections in the menu tree.
 Highlight an item in the tree and click Edit to modify its appearance.
Depending on the type of item, you can change its:
 Numeric Format and Font, e.g. number of decimal places,
 Range of data/wells to include in views and reports,
 Sort order, layout and other characteristics.
 Highlight a display category to enable the New button. Modifying the systemprovided views is limited, but you can create your own views to display
exactly the data elements of interest, in the most pleasing format.
The Set as default button only appears when an eligible data set is
highlighted. The button appears grayed-out when the current default is selected, and it
disappears when a non-eligible data set or another item in the Data Views is selected.
Use the button to determine the first data set to open in the Matrix tab of the Plate
View. Gen5 displays the first raw data set (measurements obtained from the reader),
unless another data set has been set as the default.
316 | Chapter 14: Viewing Results
Data Set Naming Convention
Gen5™ names the data sets it creates this way:
Name
Meaning
Example
wavelength
Absorbance wavelength
450
wavelength[#]
When 2 or more identical read
steps are defined in the same
Procedure, the wavelengths are
numbered
450[2]
ex/bw & em/bw
Fluorescence filter sets:
excitation/bandwidth and
emission/bandwidth or excitation
and emission wavelengths for
mono reads
360/40, 580/40
em/bw
Luminescence emission
wavelength/bandwidth
460/40
Lum
Luminescence using Hole/empty
position in the filter wheel
Read 3:Lum
Spectrum
Absorbance Spectrum scan
Read 1:Spectrum
ex, em
EX Spectrum
EM Spectrum
Curves [nm]
Curves
[ex/bw,em/bw]
Fluorescence Monochromatorbased spectrum scans
Kinetic curves are automatically
generated during kinetic analysis;
they lead to Well Zooms
485,528
Read 1: EX Spectrum
Read 2: EM Spectrum
Curves [490]
Curves [360/40, 460/40]
Curves [EM Spectrum]
[Spectrum]
Spectrum scans also plot curves
for each well: OD*/wavelength;
they lead to Well Zooms
Read #:nm
When more than one read step is
defined, the Read number names
the data set
Read 2:410
Blank nm
Blank well subtraction data set
(created automatically by Gen5)
Blank Read 2:360/40
Corrected [nm]
Pathlength corrected data set
(Absorbance read option)
Corrected [405]
Polarization
Data transformed per
fluorescence polarization formula
Polarization
*OD also represents
RFU/RLU
Symbols and Special Notations | 317
Parallel Intensity
Raw/ blanked data from parallel
measurement
Parallel Intensity
Perpendicular
Intensity
Raw/ blanked data from
perpendicular measurement x G
Factor
Perpendicular Intensity
ex/bw,em/bw
[Parallel] or
[Perpendicular]
Raw data from parallel or
perpendicular measurement
485/20, 590/35 [Parallel]
Anisotropy
Data transformed per anisotropy
formula
Anisotropy
485/20, 590/35
[Perpendicular]
Data Reduction steps produce data sets named with the type of calculation and the
raw data set name. For example, Well Analysis steps could generate: Mean V [340/40,
520/40] and Onset [Blank Read 2:490]
When a Step Label is entered for the Read or Data Reduction Step, the label is
included in the name of the data set. For example: a Step Label in an Absorbance read
step of Test1 would result in a raw data set of "Test1:450" and an automaticallygenerated blank-subtraction data set would be "Blank Test1:450".
Symbols and Special Notations
Depending on the current view, report, or exported text you may see any of the
various symbols and notations that Gen5 applies to call your attention to special
conditions:
Symbol
Description
>(highest conc.)
<(lowest conc.)
After fitting a standard curve and calculating the concentrations,
Gen5 denotes wells falling outside the abscissa range with >(upper
limit concentration) or <(lower limit concentration); <0.00 is
displayed rather than negative concentrations, unless it's called in
an interpolation
?????
????? appears in a well in certain Matrix and Statistics views when
data for that well has not been obtained; cannot be calculated; is
based on out-of-range values; or has been failed by the reader
####
#### appears in a well when the size of the grid is not large
enough to show the value in the well. Resize the view to see the
contents. Or, change the Font used to display the value, choosing a
different "clipping" method
[ ]
In Well Zoom views when the original read range is reduced, Gen5
318 | Chapter 14: Viewing Results
plots the revised Calculation Zone with brackets: [ ]
*1234*
Gen5 displays Masked values in data views and reports between
asterisks
!1234!
When Gen5 uses an out-of-range value in statistics calculations, it is
considered a biased result and will be reported between exclamation
points
*
Asterisks are displayed next to plate icons and in the title bar of an
experiment when a change is made or an action is taken but the file
has not yet been saved
**dataset**
Asterisks identify invalid data sets. This is generally caused by
changing the source Read step or Data Reduction step after the
data set was initially created
#N/A
Indicates an invalid data reduction item
INJECT
Synchronized Mode Procedures with multiple, appended kinetic
loops and one or more dispense steps, use this symbol to identify
when dispensing occurred
OVRFLW
Measurements are not being collected, most likely due to
inappropriate read parameters for the test specimen (overflow)
MISSED
The reader did not capture a value for every Xenon flash
measurement taken for this well. The reader missed a measurement
and cannot report a reliable value.
Note: Biased values may appear in a Statistics table when
Calculation Options are set to include out-of-range values. If, for
example, the concentration for one of three standard replicates is
reported as >40, the Standard Deviation and CV% values are
considered suspect. Gen5 surrounds the values with exclamation
points to indicate that it is the user’s responsibility to determine
whether or not the results are valid.
Well Analysis Results Table
When a Well Analysis Data Reduction step is defined, Gen5 shows the calculation
results in a table beneath the curve. The "Curves" or "Scan" data set that leads to a well
zoom, must be the subject of a Well Analysis step; raw data well zoom views do not
include a Well Analysis Results table.
Calculation Zone
The range of reads considered for analysis is determined by the Calculation Zone
setting of the Well Analysis. When the original range is reduced, Gen5 plots the
revised Calculation Zone with brackets: [ ]
Data Points Reference | 319
Viewing Appended Kinetic Results
When one or more kinetic reads are appended, Gen5 combines them into one data set.
When a Dispense step occurs between the kinetic loops, Gen5 represents the event as a
blue diamond on the X-Axis timeline.
FLx800 with Injectors may show the "Dispensing" event occurring
in the same interval as a Read. This is a limitation of the reader's
basecode or on-board software.
Data Points Reference
When customizing or creating a new view in Gen5, the following data points may be
available depending on the Procedure (reading parameters) and Data Reduction steps:
Data
Description
Well ID,
Plate Layout well assignments
Conc/Dil, Conc/Dil type
Concentration or dilution values and setting
in Plate Layout
Unit
User-defined in Plate Layout
Name
Sample IDs
Bitmap [nnn]
Kinetic/Spectrum Curves or Area/Linear
Scan image
Formula [nnn]
Transformation formula
Label: nnn [nnn]
User-defined labels for read and data
reduction steps
320 | Chapter 14: Viewing Results
Gen5's Tables
About Gen5's Tables
Based on the type of plate reading and the data reduction steps defined, Gen5
automatically creates tables to display, report, and export the data. You can make
slight modifications to the system-generated tables, like changing the font and numeric
format of an item. And, you can create your own -custom-made- tables.
You can view the tables in the Plate View:
 Statistics tables can be viewed using the Statistics tab,
 Curve Fitting results are shown below the curve in the Graphs tab,
 Well Data and Well Results tables can be viewed in the Well Zoom.
Some tables, like Validation results, can only be printed (or Print Previewed) and
exported.
Curve Results Table
Gen5's Tables | 321
Potential Tables
Depending on the protocol, specifically the type of read and data reduction steps,
and the level of Gen5 software, the following tables may be available for viewing,
reporting and exporting data.
 Statistics — show the results of a data reduction step. The system-generated
tables display the Well (well coordinate), Well ID, and
Concentration/Dilution assigned in the Plate Layout; the Sample IDs or Name
assigned to the Well ID; the Count or number of replicates; and the Mean,
Standard Deviation and Coefficient of Variation percentage (%), if available.
 Curve Results — Gen5 generates three tables to show the curve fitting
Parameters and Values of a curve. The "Curve Fitting Results" table includes
the curve name, formula, parameters, and R2. The "Curve Interpolations" table
shows the interpolation data. And, the "Curve Fitting Details" table lists the
parameters and their calculated value, standard error and 95% confidence
interval. You can display these tables underneath a curve in the Graphs tab of
the Plate workspace when viewing them online. You should review the details
to assess the goodness-of-fit of your curve. Depending on the Curve Fit
Method, numerous other parameters and values can be displayed/reported in
a custom-made table.
 Well Data — show the well-specific details for multiple-reading Read Steps
like kinetic analysis, spectrum, and linear scans. Well Data 2D is the Area Scan
rendition. They are used in Well Zooms to toggle the display between View
Data and View Chart. When adding this kind of table to a report or export file,
it is necessary to select the specific wells, by their well coordinate, e.g. A1, that
you want reported.
 Well Analysis Results — show the generated data of a Well Analysis Data
Reduction step. They are viewed in a related Well Zoom, beneath the curve.
Note: The "Curves" or "Scan" data set that leads to a well zoom, must be the
subject of a Well Analysis step; raw data well zoom views do not include a Well
Analysis Results table. When adding this kind of table to a report or export file,
it is necessary to select the specific wells, by their well coordinate, e.g. B2, that
you want reported.
 Cutoff Results — show the cutoff formula as defined and the value of the
formula. While the results of the cutoff criteria can be viewed online, using the
Symbols data set, the Cutoff Results table can only be reported and exported.
You can use the Print Preview feature to view this report component online.
 Validation Results — show the validation Formula as defined and the Value
result of the formula. The Validation Results table can only be reported and
exported. You can use the Print Preview feature to view this report component
online.
 Audit Trail — shows the entries, i.e. change history, logged in the Audit Trail.
Depending on your level of Gen5, one or more types of audit trails are
maintained and can be reported: Data, Protocol, and Calculation Warning. This
322 | Chapter 14: Viewing Results
table is only used for reporting and exporting, as Gen5 offers the Audit Trail
viewer in the menu tree for online viewing. The audit trails tables list date,
user, event and user's comment logged at the time of the event.
 Signatures — shows the date, time, reason and signatory of each signing event.
Also included is a "Document modified" record whenever the protocol or
experiment is changed after a signing event. Refer to the audit trail to
determine how the file was changed.
 Procedure Summary — lists the steps, in sequence, defined in the StepWise
Procedure for reports and export files
When building reports, using the Report Builder, group together related items, like
the Curve and its Curve Results table, and a Well Zoom and its Well Data, for the best
results.
Print Preview to see Tables
This is a sample report of the Cutoffs, Validation, and Audit Trail tables, using Print
Preview.
Modify/Customize Views/Data | 323
Modify/Customize Views/Data
Numeric Format for Results
Gen5 provides controls for changing the numeric format for results. You can choose
between Scientific notation, Decimal and Best Fit formats. Then you can define the
number of significant digits or decimal places to display/report. Scientific notation is
also known as Standard index notation.
How to change the numeric format:
The numeric format is set individually for each applicable data set.
After defining the protocol, open Data Views (select Protocol>Data Views):
1.
Highlight the data set you want to format in the tree and click Edit
3.
In the Format column, click inside the applicable table cell (row) to enable a 3dot button that leads to the Numeric Format control for that data point
2.
4.
Select the Data tab
Click the 3-dot button and use the controls to define the format. Select a
Format and define the level of Precision. The Samples section of the control
shows the affect of your selections on sample data.0.
Data views/data sets can also be Edited in the Plate View and after
they have been added to report and export content. Click the 3-dot
button next to the Data field of the Plate View. Double click an item
added to the Report/Export Content in the respective builder.
Gen5's Numeric Formats explained:
Gen5 provides these display options for numeric results in reports and on-screen.
"Display options" being the operative description. When performing data reduction
operations, Gen5 uses all the digits (up to 15) regardless of the numeric format applied
for display. Use the Round(x;y) and Truncate(x;y) functions to control the number of
digits used in/generated by a calculation.
Format options:
Decimal
Standard, unmodified numeral
Scientific
Notation
A way to write very small or large numbers. Numbers
are separated into two parts, a real number with an
absolute value between 1 and 10 and an order of
magnitude value written as a power of 10. The '10' is
omitted and replaced by the letter E or e, which is
short for exponent.
Best Fit
Gen5 determines, based on the size of the display
area, the format, Decimal or Scientific
324 | Chapter 14: Viewing Results
After selecting the format, define the level of precision for the display of numeric
results. Select and set the number of Decimal places or Significant digits:
Example
Decimal places = 3
Significant digits = 3
0.000123456
0.000
0.000123
12.34567
12.345
12.4
123456
123456.000
123456
Modify Data Files
After data has been retrieved from the reader (or entered manually, or imported from a
file), Gen5™ permits authorized users to edit or mask measurement values. Gen5
automatically logs an event in the experiment’s Data Audit Trail any time data is changed
or masked.
Important! Changing or masking wells may significantly alter or even
invalidate results.
 Only raw measurement values can be changed. Data sets generated from
Data Reduction calculations cannot be changed, only masked.
 When a well is masked, Gen5 excludes its value from further calculations.
 In most views and reports, masked values appear sandwiched between
asterisks, e.g. *6879* and edited values are shown in parenthesis, e.g. (6879)
Change a Measurement Value
After data has been retrieved from the reader, Gen5™ permits authorized users to edit
or mask measurement values. Gen5 automatically logs an event to the file’s Data Audit
Trail any time values are changed.
1.
2.
3.
With the experiment open, and the desired plate selected in a multi-plate
experiment, open the Plate workspace
In the Plate workspace, select the Matrix view and from the Data drop-down
list, select the desired data set (it must contain raw measurement values); or in
Well Zoom view, click the View Data button
Click the Edit button
The System Administrator can protect the use of this function. If the
button is grayed out, you may not be authorized to use it.
4.
Click on and change the value of one well at time in the grid. Multiple wells
can be changed in a session.
Modify/Customize Views/Data | 325
5.
To apply the changes, click the OK (green check mark) button. Gen5 will
recalculate results.
Click the cancel button to ignore your entries, and restore the original
values.0.
Mask (Exclude) a Data Point
Most data views let you mask or ignore one or more data points:
1.
2.
3.
With the experiment open, and the desired plate selected, open the Plate
workspace
In the Plate workspace, select the desired view, Matrix or Graph. Depending on
the view, click the Data or Curve drop-down list to select a data set. Or go to
the Well Zoom view, where you can either View Data or View Chart
In the Matrix/View Data view, click the Mask button. (This is not
necessary in Curve/Chart view.)
The System Administrator can restrict the use of the Mask function. If
the options are grayed out, you may not be authorized to use it.
4.
Click a well in the matrix or a point in a curve to mask it. (Click again to
unmask.) Multiple data points can be masked in a session.
5.
To apply the changes, click the Apply (green check mark) button to
recalculate results.
Click the Cancel button to ignore your entries, and restore the original
values.0.
In curve views, right click or click & drag for more masking options: you can mask and
unmask multiple points simultaneously

Mask and Edit functions are done in a "session." If you change
the view, e.g. change the Read Index in a kinetic analysis, or close the
plate view, experiment, or Gen5, without first applying the changes,
Gen5 prompts you to Apply or Cancel the modifications you've made,
before it can close the session.
326 | Chapter 14: Viewing Results
Change the Time Format
For viewing and reporting Kinetic or Well analysis results, you can change the time
format using Gen5's Edit tool for data views.
In the Report and Export Builders:
(Not shown: In Data Views, highlight the item and click Edit.)
On the Data tab, in the Format column for the data point,
After defining a Procedure and Data Reduction steps based on a time format:
1.
2.
Open the Data View, Report Builder, or Export file builder, and locate the
Matrix, Table or Curve that contains the data you want to modify and click
Edit or double-click to open the item. (In Report & Export Builders, first
Add the view to the selected Content box.)
In the Edit dialog:
 for a Matrix or Table select the Data tab and locate the time format you
want to change in the Format column, then, click inside the cell to enable a
3-dot button
 for a Curve select the X-Axis tab, locate the Format field under Labels
3.
4.
Click the 3-dot button in the Format column/field to open the Time Span
Format selector.
Fill the checkboxes to select the desired time-format options. 0.
Modify/Customize Views/Data | 327
Modify protocol parameters in an experiment:
After a plate is read, the Procedure cannot be changed. Other changes to the
experiment are permitted:
1.
With the experiment open, select an option from the Protocol menu tree, other
than Procedure. Double-click the element you want to modify, such as Plate
Layout, Data Reduction, Report, and so on.
Warning: Making changes to the Protocol elements may have an
unintended effect that ripples through your protocol. For example,
deleting or altering a Data Reduction step whose results are used in a
subsequent step, could invalidate the subsequent step.
2.
Within the appropriate protocol dialog, make the desired change and click OK
to recalculate results.0.
The System Administrator can protect some or all protocol parameters
from being modified. If you are trying without success to modify these
parameters, you may not be authorized to do so.
Gen5 Secure automatically updates the Audit Trail to reflect any changes made.
328 | Chapter 14: Viewing Results
Modify the Matrix View
You can change the number of decimal places or significant digits expressed and customize
the font used, among other options.
There are two ways to access this feature:

Select Protocol> Data Views, highlight
the desired data set under Matrix in the
menu tree and click Edit

In the Matrix tab of the Plate View,
select the Data to modify and click the
3-dot button
Report and Export Builders offer the same options. Generally, it is more efficient to
modify the matrix using these approaches, so you see the changes both on-screen and
in the Report and Export outputs.
Edit
Except for custom-made matrix views (Create New Matrix), modification options are
limited to Format, Font, and Selection
Format
Click inside a cell in the Format column
to enable a 3-dot button, and click on
the 3-dot button to open the Numeric
Format dialog.
You can select the desired Format
using the drop-down list and set the
number of Significant digits or
Decimal places
Use the Samples window to judge the
effect of your selections on the
appearance of the data
Modify/Customize Views/Data | 329
Font
Title
To change the font used to display and report values: click inside a cell in the Font
column to enable a 3-dot button that leads to the Font dialog. Use this standard
Windows® Font option to make selections.
Customize the Title of the data set by clicking in the field and typing over the Auto or
default text. The title appears as a Tool Tip when the mouse is hovered on a data point
in the Matrix view.
Selection
Modifying a matrix via Data Views and the Report/Export Builders offers the
Selections tab. It is most useful in multiple-read experiments, e.g. kinetic, that produce
multiple results sets. Use the Selections tab to define a range of results sets to include
in reports and export files.
330 | Chapter 14: Viewing Results
Modify a Graph
Gen5™ provides tools to change the appearance of a graph. You can display or hide the
legend and change the title, labels, font, and colors.
There are two ways to access this feature:


Select Protocol> Data Views, highlight
the desired curve (under Graph in the
menu tree) and click Edit
In the Graphs tab of the Plate view,
select the curve to modify and click the
3-dot button
The Report Builder offers the same options. Generally, it is more efficient to modify
the graph using these approaches, so you see the changes both on-screen and in print.
Layout
Select the Layout tab to:
 Define a Title for the curve; position the title on the page/screen; and select the
font
 Display or hide the Legend; and select the font for the legend
X Axis/Y Axis
On the X Axis and Y Axis tabs, you can:
 Define a Title or label for the axis; select the font; Show (or hide) Gridlines for
the axis;
 Change the Scale of the display using Linear (1, 2, 3) or Log (10, 20, 30)
numbers; Auto applies the method selected when the curve was created in the
Curve Analysis step of Data Reduction
 Change the numeric Format and Font of the Labels, i.e. the numbers/data
displayed on each axis. Try out the various options to determine which
combination works best for your reporting and viewing requirements.
Click the 3-dot button for Format to change the scientific notation, decimal
places or significant digits displayed in the view/report/export
Plots/Curves
Select the Plots tab to further modify the appearance of the graph. You customize the
appearance of the error bars and fitting line, for example. (The Curves tab is displayed
for user-created curves, select a curve and click Edit after to enable these functions):
Modify/Customize Views/Data | 331

Click in a cell in the table to enable a 3-dot button that leads to formatting
options for the selected item (line, marker, text, or pattern):
 Automatic is the default setting. It is most useful in Well Zooms, when
more than one well is selected for simultaneous viewing. Gen5 displays a
different color scheme for each well selected.
 Select Hide (or None) to remove the item from the view.
 Select Custom to modify it. Use the drop-down options to apply different
colors, symbols, styles and/or line weight.
Select the Plot tab to turn-off the Text that may be obscuring the details in a
Well Zoom curve: select the table cell containing the offending text, click the
activated 3-dot button. At the Text tab, select Hide
332 | Chapter 14: Viewing Results
Chapter 15
Reporting Results
This chapter describes Gen5’s Report Builder for generating printready data output for your experiments. Instructions for creating
Field Groups to report inherent data points, how to change the
Font, and other useful tips are provided.
Building Reports ...................................................................... 334
How to create and customize a report ........................................ 336
Customizing Reports ................................................................ 338
Reporting Well Analysis Results ................................................. 340
Change the Font ...................................................................... 344
Edit Report Items..................................................................... 344
Fields and Field Groups............................................................. 346
Create a Header and Footer ...................................................... 349
334 | Chapter 15: Reporting Results
Building Reports
Protocol> Report Builder
About the Report Builder
Gen5™ provides this tool to define exactly:
 what to include in the report
 how to format an item in the report
 where to place the item in the report.
Define the Data Views and Default Protocol to speed up this step! Create Headers
and Footers and add the Protocol Summary report sections in the Default Protocol so
they appear in all newly-created protocols.
Report elements should be defined for each Protocol:
1.
2.
In the menu tree, under Protocol, select Report Builder
Highlight Available Data Views and Add them to the Report Content box
 You can also Drag and Drop items into the Report Content box
 Drag and drop to change the sequence order of items in the Report Content
box
 Edit an item in the Report Content box with a double click or use the rightclick menu
 Highlight an item in the Report Content box and click Remove to de-select
it (or use the Delete key)
 To clear the slate and start over, click Remove All to de-select all items.
 In multiple-read (multi-index read) protocols, like kinetic analysis, it is
necessary to select a range of reads or a range of wells to include in an
export item. Certain data elements, like Well Data, Well Results, and Well
Zoom, require manual selection of the specific wells to include. Except for
area scan results, you can select multiple wells for simultaneous reporting
in the resulting table or graph. For details see Reporting Well Analysis
Results on page 340.
Gen5 opens report items in Edit mode when a selection is required. For example,
when you select a Matrix item to report a multi-index/kinetic read, you must select a
Range of read numbers. One matrix or grid will be reported for each read number.
Building Reports | 335
3.
4.
5.
Highlight an item in the Report Content box and click Page Break to add a
page break to the report. Gen5 inserts it just above the highlighted item. You
can drag and drop the Page Break to move its sequence order. (This step often
works best after you've read the plate and can use Print Preview to assess the
layout of the report.)
Set up Headers and Footers, if desired. (page 349)
When the report is defined, in an experiment, click the Print button to
generate the report.0.
** Items marked with asterisks indicate 1 of 3 conditions:
1. You must select specific data points from a very large (multi-read)
data set or
2. The experiment did not generate the expected results, an error
occurred or
3. The Procedure and/or Data Reduction steps that generated the item
have been changed making it invalid **
Click Print Preview to assess the report layout!
Using the Default Protocol
Using the controls in the Default Protocol, you can input text and select protocol and
experiment data to be included in all your reports. Your selections can be modified,
removed, or replaced in individual protocols without affecting other experiments.
System> Preferences> Default Protocol > Report Builder
Content options in the Default Protocol may be limited by the lack of a
defined Procedure.
Important: Default Protocol Settings are applied "going forward,"
they do not affect existing protocols. They are applied only to newlycreated protocols.
336 | Chapter 15: Reporting Results
How to create and customize a report
These step-by-step instructions are intended to introduce you to Gen5's tools and
method for outputting results. While this example uses the Report Builder, the options
and process is the same when building export files.
Important first step
You must define the Procedure (read parameters) and the Plate Layout before you can
define Data Reduction steps. Likewise, you must define these and other elements of
the Protocol (to generate the content of reports and export files) before you can create
and customize the report.
After you've defined the Procedure, Plate Layout, Data Reduction, and Runtime
Prompts, you're ready to build the report.
Create a Field Group to report details
Field Groups can be used to report all of the details affecting your experiment:
1.
Open Data Views from the menu tree
2.
Highlight the Field Group label at the bottom of the tree and click New
4.
Click in the first cell of the table to enable a 3-dot button, and click the 3-dot
button. The Fields dialog opens.
3.
5.
6.
7.
8.
9.
Enter a Name for the field group at the top of the Edit dialog. For this exercise,
we'll name it Read Step.
Use the drop-down list to set the Category to Procedure for this exercise.
At Field: use the drop-down list to select a data point. Select Measurement 1 for
this exercise.
At Label: click in the text field, and overwrite the default label with a more
fitting label for this data point. For this exercise, we'll call it Wavelength 1
because we have multiple wavelengths.
Click OK to close the Field dialog.
Repeat steps 4-8 for the other cells in the table, adding Rows and Columns as
needed. Explore the fields offered in the other Categories, like Plate
Information, to find all the details you want to include. When you've added all
the desired fields, click OK to save and close the Field Group.
10. At Data Views, click Close.0.
How to create and customize a report | 337
Here’s an example of the Field Group:
Build the Report
1.
2.
3.
4.
Open the Report Builder from the menu tree
Locate the Field Group category at the bottom of the tree and highlight the
just-made field group (Read Step for this exercise). User-defined field groups
appear in bold text. Click Add to include it in the Report Content.
Scroll up the tree of Available Data Views, selecting and adding the desired
items to the Report Content. The order of the items listed in Report Content is
their order in the printed report. Drag and drop items to change their position.
After adding an item to the Report Content, double-click it to open it in Edit
mode. Now you can customize the output. For example, on the Data tab, in the
Format column, click in the cell to enable a 3-dot button that lets you change
the number of decimal places or time format; on Selection or Well tabs define
the range of data to report. Editing Curves lets you define the X- and Y-Axis
titles. You can even combine multiple curves in one graph, if applicable.
In Edit mode, change the Name at the top of the screen to customize the section
heading in the report
5.
Click OK to save your work and close the Report Builder.
6.
If you're performing these steps in an experiment, click Print Preview to
assess the report layout. If you're performing these steps in a protocol, save the
protocol and create a new experiment based on it. Then use Print Preview to
judge the output. Return to Report Builder to make any changes to the selected
content.0.
338 | Chapter 15: Reporting Results
Customizing Reports
Gen5™ offers extraordinary flexibility in customizing reports and export files. Almost
everything you can view in Gen5 can also be reported. And, once you learn a few basic
steps, you'll be able to define exactly what to include and exclude from reports and onscreen views.
Basic Rules:
 Data elements that are created or modified in Data Views become available
for selection when defining the Report and Export parameters. This
includes hiding a data set, which removes it from selection. Setting up the
views in the Default Protocol (if possible) makes them available in all
newly-created protocols.
 Create your own Data View for the most precise control over content and
appearance. You can create a matrix, table or graph that displays and
reports the information you've selected. You can include multiple data sets
in one view, for example. And, exclude default data points that do not
apply to your experiment.
 Include the Protocol Summary options: Procedure and Data Reduction
Summary to report protocol elements used to obtain the measurements
being reported. They are a good candidate for the Default Protocol.
 Create Field Groups to include miscellaneous information and data
points in your reports/export files. Gen5 captures numerous details like
temperature and shake duration, Plate ID and other run-time entries, and
print date and page count. Virtually all of the details affecting your
experiment can be reported.
 In multiple-read protocols, like kinetic analysis, it is necessary to select a
range of reads, or a range of wells to include in a report item. Certain data
elements, like Well Data, Well Analysis Results, and Well Zoom, require
manual selection of the specific wells to include in the report. You can
select multiple wells for simultaneous reporting in a table or graph.
 Select the Font option when editing content to define the "clipping"
method to apply to data points that are too long to fit completely in a report
column. Several choices are available to hide, truncate, or display as much
as possible of an extra-long data point.
 Select the Format option when editing content to define the number of
decimal places or significant digits to report or to change the time format of
a report item.
 Attributes applied to data elements in Data Views and the Report and
Export Builders take effect going forward. They do not replace, update, or
overwrite an item that has been previously assigned to a Report/Export.
You must refresh the selected contents after making any changes to a data
Customizing Reports | 339
element. And, any previously-saved Experiment will not reflect the content
or formatting changes.
 When you Edit data elements in the Report Builder, your changes only
apply to the Report. They will not be reflected in the Data Views or Export
options. And, unless you use the File>Save Protocol As option, your
changes will not be applied to any future experiments based on this
protocol.
 384- and 1536-well plate matrixes are reported in segments that best fit the
data to the page. Generally, the first 12 columns are reported in one matrix,
the next 12 columns in another and so on, unless the page orientation is
changed to landscape or the font size is reduced. Unless otherwise directed,
Gen5 reports the entire matrix on as many pages as needed to display all
the data.
Best Practices:
 Create your own Data Views for the most freedom-of-choice in reporting
and online viewing.
 Print Preview your reports to make sure you're happy with the layout
before printing them.
 Curve Results tables work best just below or above the curve they describe.
Drag and drop the Curve or the Curve Results in the Report Content to
arrange them this way.
 Limit the number of wells in a Well Zoom graph to 8 for best results.
 Changing the page orientation from "portrait" to "landscape" may be the
best use of the space and improve the appearance and readability of the
report, especially when reporting 384-well and larger plates.
To change the page orientation:
1.
2.
Select File>Print Setup...
Select the desired Orientation 0.
You must be have the experiment file open to change the Print Setup
340 | Chapter 15: Reporting Results
Reporting Well Analysis Results
Protocol> Report/Export Builder> for the selected Content
By its nature, the individual well results of Well Analysis make reporting them a bit
tricky. Well Analysis results, like Well Zoom graphs and Well Data tables, require an
extra step when defining reports and exports. See Report Examples on page 342.
In the Report Builder and for applicable export routines, in the Export Builders, when
you select any of the following:
 Well Data table
 Well Data 2D table (for area scans)
 Well Analysis Results table
 Well Zoom graphs
 Area Scan Zoom graphs
Be sure to open (Edit) the item to select one or more wells as the content to
report/export.
In the Report or Export Builder:
1.
Add a well analysis item from Available Views to Report/Export Content
3.
Select the Wells tab or the Curves tab (depending on the type of report item)
2.
4.
5.
If the item doesn't open in Edit mode, double click it
Select one well at a time to report on: enter a well location in the Well field;
Gen5 displays the Well ID and concentration or dilution assigned to the
location, or
Select multiple, adjacent wells using a hyphen to define the range, A1-H12,
for example, would include all wells in a 96-well plate
Important: Some report items require limiting the number of wells that can be
successfully included in an instance of it. You may need to add multiple
instances of the item to report all the desired wells. Use Print Preview to
determine how many wells can fit on the page.
Click Add to move the well into the Selected box. Except for Area Scan results,
you can select multiple wells for each report item. (See Tip for Area Scan
below.)
Reporting Well Analysis Results | 341
Tables and Curves respond differently to this treatment. Curves: Well
Zoom graphs, overlay the results for each well in one curve. (Limit the
number of wells to 8 for the best results.) Well Data tables present
the data for each well in a column or row, adding another column/row
to the table for each well. To best fit the data in a report it is often
necessary to add multiple instances of an item. And, for each
instance select the maximum number of individual data points that fit
cleanly. Likewise, to report well zoom graphs individually, rather than
overlaying them, you must add multiple instances of the Well Zoom
graph. Use Print Preview (after the plate is read) to determine the
best fit for your data. It's a "trial and error" process, selecting and
revising the Report Content, and assessing the layout with Print
Preview, until the report is satisfactory.
Exporting the data does not require the same level of precision when
selecting content. Gen5's File Export Builder delimits data points
without restriction (and does not support curves) and Power Export
exploits Excel's spreadsheet capabilities to handle limitless data
transfer.
6.
(Optional when available) Highlight a well in the Selected box and click the
Edit button to modify its formatting.0.
You can remove multiple wells from the Selected box
simultaneously: hold the Ctrl key while selecting non-contiguous wells or hold
the Shift key while selecting adjacent wells, then click Remove
Tip for Area Scans
You must add multiple instances of the Area Scan Well Zoom and Well Data 2D table
to the Content to report /export multiple area scan wells. For best results, identify the
selected well in the Name field when adding each well, one well at a time, to the report
content. The Name becomes a sub-heading in the report output, so you can easily
distinguish between reported wells, e.g. Scan: B3.
342 | Chapter 15: Reporting Results
Report Examples
Here are some sample report outputs of well analysis results:
Using Gen5's Report Builder to output well analysis results involves some trial and
error to determine the maximum number of wells that can fit neatly on the page. Here
are some examples of the offerings:
Well Zoom Graph
Limit the number of wells to 8 when reporting a well zoom graph for the best results
Well Data Table
Well data tables report each well in a column. The number of wells that can be successfully
included depends on the number of digits in the results and the paper orientation (portrait or
landscape).
Reporting Well Analysis Results | 343
Well Analysis Results Table
Well Analysis results tables are generally easy to include, i.e. all wells can be safely selected,
because each well is reported in a row.
344 | Chapter 15: Reporting Results
Edit Report Items
Protocol> Report Builder
In the Report Builder, double click an item in the Report Content window to edit its format,
font and other attributes specific to the selected item. The editing options available are
context sensitive, depending on the attributes of the selected item: matrix, table, or graph.
Change the Font
Clicking the 3-dot button in the Font column of a Data View or Report Builder Edit
screen leads to a standard Windows® Font selector (watch the Report Builder Tutorial for a
demonstration):
 In Data Views, highlight the item and click Edit
 In Report Builder, add the item to the Report Content, then double click to
open it in Edit mode
Selecting the Font, Style, Size, and Effects is the same as any Windows program. The
fonts available for selection are set by your PC's operating system.
Select method for displaying extra-long text items:
In the lower-right corner of the Font screen, use the drop-down lists:
 Clipping to select the way to format data points that have too many characters
to fit completely in a report or table column and in the cells of a Matrix:
 None fits as much text as possible, using the selected Alignment method
Edit Report Items | 345
 text... fits as much text as possible and truncates it using the ellipsis
 ### replaces all the content with the pound sign or hash mark
 c:\...\file.ext only applies to path and filename content, it fits as much text
as possible beginning with the filename and extension and progressively
truncates the directory's path
 Alignment to define the text alignment: left, center, right
Font settings are not retained by the File Export Builder because
they are not supported in the resulting text file
346 | Chapter 15: Reporting Results
Fields and Field Groups
For reporting and exporting data, Gen5™ automatically provides data fields and field
groups based on inherent information. You can create your own field groups, as well.
 Learn About Field Groups (below)
 Create New Field Groups on page 347
 Assign Fields to Reports on page 350
About Fields and Field Groups
For reporting and exporting purposes, Gen5™ provides data fields based on inherent
information. You can create your own Text field, as well, to add custom information to
a report header or to create a report title, for example.
The responses to Runtime Prompts, the steps in the Procedure, and the Reading Date
and Time (logged by Gen5 your computer's calendar and clock) are examples of the
numerous data points Gen5 turns into Fields that can be added to a Field Group for
reporting or inserted in a report header or footer. One field group is installed with
Gen5: an empty Field Group is available in the Data Views, and the report and export
builders. You can modify this Field Group and/or create your own in Data Views.
Basic Rules
 Field Groups are a collection and arrangement of fields
 Creating and modifying Field Groups is done in Data Views; however, field
groups can be modified for individual instances after they are included in
Report or Export content
 Field Groups can be included in Reports and Export files and Fields can be
added to report Headers and Footers in the Report Builder
 Once Field Groups are added to reports and export content their properties are
fixed. Changes made to field groups only take effect going forward, i.e. when
you edit a field group in Data Views, the changes are NOT applied to those
field groups that are already included in Report and Export Content. You must
Remove the original and Add the updated field group in the Report Builder,
Power Export Builder and File Export Builder to capture the changes.
 Field Categories include Text for user-created information/text and Blank for
use when editing a field group, header or footer to remove a field.
 A Field Categories reference table is provided on page 348
how to clear remove a field from a field group
Fields and Field Groups | 347
Creating and Modifying Field Groups
To create a new field group:
1.
2.
3.
Open Data Views (Protocol>Data Views)
Highlight the Field Group label at the bottom of the tree and click New
Enter a Name for the field group in the Edit dialog. Follow the instructions
below to define the content of the group.0.
To modify a field group:
1.
2.
Open Data Views
Highlight the Field Group you want to modify and click Edit. Follow the
instructions below to define the content of the group.0.
You can also Edit a field group in the Report Builder, but your
changes will only apply to the Report for the current experiment. They
will not be reflected in the Data Views, will not be available for Export,
and will not be applied to any future experiments based on this
protocol. Keep this in mind when you're formatting a field group — in
most cases it is more efficient to work in Data Views than in Report
Builder.
To define the content of a field group:
1.
2.
3.
Use the Add Row or Add Column buttons as needed to set up the desired
number of rows and columns.
Click in a cell in the table to enable a 3-dot button that leads to the Fields dialog
to select and format the content of the field. Click the 3-dot button, and select
the Category and Field you want to add to the group.
You can insert, delete, and merge rows, and insert and delete columns using a
right-click: select the row or column by clicking its number, then right-click for
a menu.0.
Another shortcut: you can drag and drop rows and columns to change
their position. Click in the column/row you want to move until the pointer
changes to drag and drop mode, drag it into place, watching for the red
location indicator, and release to drop it into the desired position.
348 | Chapter 15: Reporting Results
Field Categories Reference
Category
Field
Hint
Text
User-defined Text
Use this option to define your own
report titles
Experiment
Information
Experiment File Name
.xpt file must be saved to have a file
and path name
-Plates per Assay is only applicable to
multi-plate protocols.
Experiment Path Name
Plates per Assay
Procedure
Read step and related
data, examples:
Plate Type
Reading Zone
Kinetic Interval
Measurement #
Sensitivity
These fields are created by the steps
you define in the StepWise Procedure.
If there is more than one Read step
the fields will be numbered
accordingly, i.e. every read-related
field will be numbered to correspond
with its read step. When multiple
Kinetic loops are defined, they are
similarly numbered.
Plate size reports the number of
columns x rows
Temperature
Step 1 Description
Protocol Options
Protocol Type
Std Dev Weighting
Plate Information
Experiment-specific
details, examples:
Reports user inputs at read time
Reading Date and
Time
Plate ID
Runtime Prompts
Barcode
Reader Serial Number
Reader Basecode
Plate Comment
Printing Options
Print Date/Time
Page Number
Especially useful for Headers or
Footers
Fields and Field Groups | 349
System
Information
User Name
User Group
Software version
Blank
Empty
User information is only useful for
Gen5 Secure users
Software version reports Gen5's
version number
Use to delete a previously-added field
Creating a Header and Footer
You can set up a default header and footer that will be applied to all reports, and/or
you can create a header and footer for each protocol individually. (Modify the
header/footer for individual experiments to override the Default Protocol settings.)
 To assign headers and footers to the Default Protocol (for all newly-created
protocols/experiments), select System> Preferences> Default Protocol
Setup
 To create headers and footers in a Protocol/Experiment (only for the
current protocol/experiment): in the menu tree, select Protocol> Report
Builder
To create a header or footer:
1.
In the Report Builder, select the appropriate tab: Header or Footer
3.
Click in a cell in the table to enable a 3-dot button that leads to the Fields
dialog to select and format the content of the field
2.
4.
5.
Use the Add Row or Add Column buttons as needed to set up the desired
layout
You can insert, delete, and merge rows, and insert and delete columns using a
right-click: select the row or column by clicking its number, then right click for
a menu
As needed, select the option to "use custom header/footer on first page" to add
another tab to this dialog. If unselected, all pages of the report will have the
same header and footer. 0.
Another shortcut: you can drag and drop rows and columns to change their
position. Click in the number of the column/row you want to move until the
pointer changes to drag and drop mode, drag it to the new place, watching for
the red location indicator, and release to drop it into the desired position. Note:
when a row has been merged, columns cannot be moved.
350 | Chapter 15: Reporting Results
Assigning Fields to Reports
Fields can be used in two ways:
 Used in a header or footer when defining reports, see Creating Headers and
Footers (described above)
 Used to define a Field Group to include in a report or export file
In Report or Export Builder:
1.
2.
3.
4.
5.
6.
In any of the Header or Footer tabs or after adding a Field Group to the
Report or Export Content and opening it to Edit, click in a cell in the table to
enable a 3-dot button, and click it.
In the Category field, use the drop-down list to select either Text or a category.
In the Field field, use the drop-down list to select a field, unless you selected
Text.
In the Label field, enter the text you want included in the report. You can
customize the label by typing over the default text or remove the label by
deleting the text.
Use the 3-dot buttons at the Font and Format fields (if applicable) to modify the
default settings. You can replace the default content for the field Value the
same way:
 Use the Font dialog to define the Alignment of the content in the field: left,
center, right. And, if there's a chance the text will overrun the length of the
field, choose a Clipping format to replace the missing text. Your choices are
not displayed in the header or footer table, use Print Preview to assess the
effects.
Click OK to save and apply your choices.0.
Chapter 16
Exporting Results
Learn about Gen5’s numerous data-exporting options in this
chapter. You must have Microsoft Excel 2000 or higher installed
on your computer to run the Quick Export and Power Export
features. If you do not have Excel your options are limited to the
File Export or Right-Click options.
Exporting Results ..................................................................... 352
Quick Export ........................................................................... 354
Right-Click Options................................................................... 356
Export to File........................................................................... 358
Power Export........................................................................... 362
352 | Chapter 16: Exporting Results
Exporting Results
Gen5 provides these exporting tools:

Quick Export: to instantly export the current view to a Microsoft® Excel
worksheet
 Power Export: to export selected data to Microsoft Excel
 File Export: to export selected data, excluding curves, to a text file (for use in
another software application)
 Right-Click Menu Options - Copy to Clipboard and Save As: to copy or save
the current selection for use in another software application
Prerequisites
For the Quick Export and Power Export features, you must have Microsoft Excel
2000 or higher installed on your PC. Use the File Export or Right-Click options if
you do not have Excel.
About the Export Tools:
 The Power Export and File Export methods require selecting the content you
want included in the output file before executing the export for a designated
plate
 You can save your export selections with the Protocol, to reuse them every time
you run an experiment based on that protocol
 Exporting data is like generating a report, it is done individually for each
plate*. While you can select the export content in a protocol, you must run (or
execute) the export in an Experiment (after selecting a plate or multiple plates)
 In an experiment, to run the export, you can select a plate in the menu tree and
right click for a menu that offers the Power Export and File Export options
[* except in multi-plate assays: refer to the Multi-Plate Protocol chapter]
To preview the export-file output on-screen before generating an export file, use the
Report Builder and Print Preview: add the same elements to a report as you do to
the export, then click Print Preview to view the results online.
Exporting Results | 353
Export Multiple Plates to One File
When you run multiple plates in an experiment you can export all the data to one text
file:
1.
2.
In the menu tree, select/highlight multiple plates (by holding down the Ctrl
key)
Right-click and select File Export0.
Make sure the File Export Settings are defined to automatically
append the data
354 | Chapter 16: Exporting Results
Quick Export
Click the Quick Export button to instantly create a copy of the current screen in
Excel®.
Where it works:
Wherever you see the Quick Export button, you can export the view. And almost
every Data View has a Quick Export button. For example, the Matrix, Statistics, Cutoff
and Validation tabs offer it and the Graph tab has two, one for the curve and another
for the Curve Results Table.
If you don't have MS Excel:
Use one of these options to select content and export it for use in another software
application:
 File Export Builder: to export selected data to a text file (see page 356)
 Right-Click Menu Options - Copy to Clipboard and Save As: to copy or save
the current selection for use in another software application (see page 356)
Quick Export Settings
Protocol> Protocol Options> Export Options> Quick Export Settings
System> Preferences> Default Protocol> Protocol Options> Export Options>
Quick Export Settings
You can define default settings for Quick Export, which can be overridden in
individual protocols. Use the controls in the Default Protocol to base all new Protocols
on them. Override the default settings in individual protocols using the Protocol
Options.
Important: Default Protocol settings are applied "going forward,"
they do not override existing protocol settings. They effect only newly
created protocols.
Export Row and Column Headers
Select this option to include the Matrix and Statistic table row and column headers with the
data exported to Excel™
Text Options
 Formatted Text: exports text as defined in Gen5, retaining the selected font and
any customizations
 Text Only: exports text as characters only, without an associated font or any
customization performed in Gen5
Quick Export | 355
Excel Target
Select a method for positioning the exported content in Excel:
 New Workbook and Target Cell: opens a new workbook and aligns the
content starting at the target cell
 New Worksheet and Target Cell: creates a new worksheet (within a workbook)
and aligns the content starting at the target cell
 Current Worksheet: adds content to the current worksheet
Gen5 will launch Excel with a new worksheet if necessary. When multiple Excel
sessions are open, Gen5 will prompt you to select a worksheet before
performing the Quick Export.
 Target Cell: aligns content beginning at the target cell, fill the Target Cell
field when you select this option
 Current Selection: places content beginning at the currently selected cell
 Append to Bottom: places content beginning at the next available row
Ask me when I export: This option lets you determine the Excel Target every time
you use Quick Export. Gen5 will prompt you for a placement option prior to executing
the Quick Export.
356 | Chapter 16: Exporting Results
Right-Click Menu Options
In addition to the Quick Export option available in most views, Gen5 offers three other
features for "exporting" the current view for use in other software applications.
Simply right-click to select the entire current view for a quick output. Or, to limit
the output: click and drag to select contiguous cells or hold down the Ctrl key and click
to select noncontiguous cells, then right-click for an option.
Copy to Clipboard
1.
Right-click in almost any view and select the Copy to Clipboard feature
3.
Paste the selected content. Try:
2.
Open another software application, e.g. Microsoft® Word, WordPad, Paint,
Outlook and similar products offered by other manufacturers, where you want
to use the Gen5 content

Ctrl-V
 Right-click and select Paste
 From the menu, select Edit> Paste 
Quick Print
After selecting specific content or a current view, right-click and select the QuickPrint
feature.
It is similar to printing from the Report Builder, you can select a local printer. The
current view or selected content is printed in formatted text with row and column
headers.
Save As
In any graph, i.e. Curve or Well Zoom, you can:
1.
Right-click and select the Save As feature
Right-Click Menu Options | 357
2.
Gen5 opens the standard Save As dialog so you can browse to any
file/directory available to your computer to choose the Save In location
3.
Use the drop-down list to select the Save as type: 0.
 Portable Network Graphic (.png)
 24-bit Bitmap (.bmp)
 CompuServe Graphics Interchange Format (.gif)
 JPEG Format (.jpg)
 Windows Enhanced Meta File (.emf)
358 | Chapter 16: Exporting Results
Export to File (File Export Builder)
This option creates a text (.txt) file of the selected content for use in another software
appliation.
Protocol> File Export Builder
Using the File Export Builder
Select the Content to Export
Highlight items in the Available Data Views and Add them to the Export Content
box:
 You can Drag and Drop items into the Export Content box
 Drag and drop to change the sequence order of export items in the output
file
 Change the format and data sets associated with an item in the Export
Content box: Highlight an item and double click, or right click and select
Edit
 Highlight an item and click Remove, to remove it from selection
 In multiple-read (multi-index read) protocols, like kinetic analysis, it is
necessary to select a range of reads or a range of wells to include in an
export item. Certain data elements, like Well Data, Well Results, and Well
Zoom, require manual selection of the specific wells to include. Except for
area scan results, you can select multiple wells for simultaneous reporting
in the resulting table or graph. For details see Reporting Well Analysis
Results in the (previous) Reporting Results chapter
Gen5 opens report items in Edit mode when a selection is required. For example,
when you select a Matrix item to report a multi-index/kinetic read, you must select a
Range of read numbers. One matrix or grid will be reported for each read number.
Limitation: "Curves" and "Scan" data sets, created from kinetic
analysis and area scans, cannot be exported with this feature. If you
have Excel®, use the Quick or Power Export options.
Export Multiple Plates to One File
When you run multiple plates in an experiment you can export all the data to one text
file. After defining the export content, (and making sure the File Export Settings do not
prevent it):
1.
In the menu tree, select/highlight multiple plates (by holding down the Ctrl
key)
Export to File (File Export Builder) | 359
2.
Right-click and select File Export0.
You can also use the File Export Settings to do this automatically:
 make sure the plates do not result in unique filenames,
 set the "prompt before saving" option to Never and Append
** Items marked with asterisks indicate 1 of 3 conditions:
1. You must select specific data points from a very large (multi-read)
data set or
2. The experiment did not generate the expected results, an error
occurred or
3. The Procedure and/or Data Reduction steps that generated the item
have been changed making it invalid **
Using the Default Protocol
You can define default settings for File Export, which can be overridden in individual
protocols:
 Use the controls in the Default Protocol to base all new Protocols on them.
 Override and refine the default settings in individual protocols using the File
Export Builder
Content options in the Default Protocol may be limited by the lack of a
defined Procedure.
Important: Default Protocol Settings are applied "going forward,"
they do not affect existing protocols. They are applied only to newlycreated protocols.
File Export Settings
Protocol> Protocol Options> Export Options> File Export Settings
System>Preferences>Default Protocol>Protocol Options>Export Options>
File Export Settings
You can define default settings for File Export, which can be overridden in individual
protocols:
 Use the controls in the Default Protocol to base all new Protocols on them
 Override the default settings in individual protocols
File Naming Convention
Set up a naming convention to apply to the export file:
 File Name: use the text field to build a naming convention. You can put any
combination of text and Gen5-provided data points in the field to become the
name applied to consecutively-saved files:
360 | Chapter 16: Exporting Results

Click the options arrow at the end of the field to select from the Gen5provided data points.
 Add or replace default text with your own text
 Notice the underscores Gen5 places between data points, they can be
retained or removed according to your preferences. Generally, it is good
practice to use filenames without spaces.
 Example: Gen5 displays an example of the file name you create
The filename must comply with Microsoft® filename conventions, e.g. it
must not contain so-called offending characters: \ / : # ? " < > |
Separator
Export files contain "delimited" data, i.e. data separated by a user-defined symbol
or character. Select or enter the desired Separator using the buttons for Tab, semicolon, comma or Other. If Other, enter the symbol or character in the text field.
File Location
Specify the location for Saved files:
 Last folder used: puts the Excel file in the folder last used by Gen5's File Export
engine
 Folder: select an existing folder or define a name to apply to a newly-created
folder


Use the 3-dot button to browse to the desired location for file storage
Use the options arrow to name a newly-created folder using the Gen5provided data points.
 You can add text for naming a newly-created folder, if desired
 Example: Gen5 displays an example of the folder name you create
When Exporting, prompt before saving file:
 Always prompt users by opening the Save As screen whenever they export
a plate file, allowing users to alter the file name and location on-the-fly
 Only if the file already exists: open the Save As screen for saving export
files only if Gen5 generates a filename that already exists
 Never, if it the file already exists: never open the Save As screen
 Append: add this plate's data to the bottom of the existing file
 Overwrite: replace the existing data with this plate's data
Include:
Use the checkboxes to include any of the items offered:
Export to File (File Export Builder) | 361
 Headings: includes the Name of selected data elements as a section heading
in the export file (just like the section headings in a Gen5 report)
 Matrix ...: includes the well location column and row labels, e.g. A-H and 112
 Statistics ...: includes column headers of the tables, e.g. Well ID, Name,
Well, Conc/Dil.
362 | Chapter 16: Exporting Results
Power Export
Prerequisite
You must have Microsoft® Excel 2000 or higher installed on your PC to use Power
Export.
Power Export Explained
Gen5 joins forces with Microsoft Excel to give you high-powered results reporting.
Gen5 compiles all the data and customizations made in an experiment and exports it to
Excel, along with a Gen5 toolbar.
In Excel, you design the report using the Gen5 toolbar to select the desired experiment
content. Then you can use Excel's native tools to perform complex calculations and
customize the report's appearance.
Using Power Export is a two step process: first, ideally when setting up a protocol, you
select the content for export. Second, after running an experiment, you execute the
Power Export for each plate.
Whenever you select a Power Export option, Gen5 launches Excel. Initially, to select
the content of the export, which inserts placeholders in the worksheet for the data to be
generated in the experiment. Later, when you execute Power Export in the experiment,
the selected data fills the placeholders.
With Power Export you can:
 Take full advantage of Excel’s document customization features to generate
publication-quality reports
 Include pictures, drawings, and company logos in reports
 Create custom formulas in Excel to perform additional calculations on the
Gen5 experiment data
 Take advantage of Excel’s charting capabilities to create bar graphs, pie
charts, etc.
Before defining the Power Export, customize the Data View elements in Gen5 that
you'll include in the Excel report. While, you can make changes to Gen5's data
elements when using Power Export in Excel, it is faster and easier to make the bulk of
your choices first in Gen5.
Watch the Tutorial for a demonstration on how to use Power Export
Power Export | 363
About the Power Export Toolbar
Gen5's Power Export Builder launches Excel® with a custom toolbar:
The selection buttons of the toolbar mirror the categories in Data Views (except
Protocol Summary, which is only offered in the reporting tools). Use the buttons to
select the content you want included in the Power Export. When you make a selection,
Gen5 puts a "Results Object" or placeholder for the information in the Excel worksheet.
The placeholder is filled in with results data (after the plate is read) during Power
Export execution.
In Office 2007 the Power Export Toolbar is placed in the Add-Ins
tab/ribbon, which is added to the default ribbons when Excel is
launched by the Power Export Builder.
 Protocol Summary = two pre-defined listings of the Procedure and Data
Reduction steps defined in the protocol
 Matrix = a grid that represents the microplate
 Table = a columnar presentation of the data
 Graph = a standard curve or well zoom generated from a Curve or Well
Analysis
 Field Groups = user-selected or defined data points useful for reports
Power Export Execution
When you execute the Power Export in an experiment (i.e. highlight a plate in the
menu tree, right click and select Power Export) , Gen5 launches Excel with the data
from the experiment filling in the placeholders selected with the Builder. You can run
Excel as you normally do. he connection between Gen5 and Excel is severed. To
modify a report element use the Power Export Builder.
BioTek recommends customizing the Data View elements in Gen5 before
selecting them for the Excel report. You can make changes to Gen5's data elements
using the Power Export toolbar in Excel, but it is faster and easier to make the bulk
of your choices in Gen5 first.
364 | Chapter 16: Exporting Results
How to use Power Export
1.
When setting up the protocol, after customizing the Data Views, select Power
Export Builder from the Protocol menu tree. This launches Excel with Gen5's
Power Export Toolbar.
In Office 2007 the Power Export Toolbar is placed in the Add-Ins
tab/ribbon, which is added to the default ribbons when Excel is
launched by the Power Export Builder.
2.
3.
4.
In Excel, use the Power Export toolbar to select the content you want to import
from each plate (described below).
Define the Power Export Settings (page 365).
When you run an experiment based on the protocol, highlight a plate in the
menu tree, right click and select Power Export.0.
Whenever you select Power Export, Gen5 launches Excel. Initially, to select the export
content, inserting placeholders for the data in the Excel worksheet. When you run
Power Export in the experiment, the selected data fills the placeholders. Then, you can
use Excel's native toolset to prepare the report for publication.
To modify a report element you must use Power Export Builder.
Do NOT "protect" the worksheet in Excel when building the report with Power
Export Builder; that is do not engage Excel's Tools>Protection settings.
Using the Power Export Toolbar in Excel
Gen5's Power Export Builder launches Excel® with a custom toolbar for selecting
content for the export.
How to select content:
1.
2.
3.
Select the starting cell in the Excel worksheet where you want the Gen5 content
to begin.
Click the down arrow of a selection button: Protocol Summary, Field group,
Matrix, Table, or Graph on the Power Export toolbar and select an item. Gen5
presents a Selection/Data/Format dialog specific to the selected item.
Make selections and/or modifications to the data format, as required for the
item. Just like Customizing Gen5 Data Views and Reports. You can limit the
Range of data points or change the Format/Font, as needed.
Power Export | 365
Certain data elements, like Well Data, Well Results, and Well Zoom,
require manual selection of the specific wells to include in the
export. Except for Area Scans, you can select multiple wells for
simultaneous reporting in the resulting table or graph.
4.
Repeat steps 1-3 to select all the specific data items you want included in the
Power Export, filling the worksheet with the required placeholders.
5.
Click
to return to the Gen5 workspace. 0.
Now you're ready to execute Power Export in an experiment: highlight a plate
in the menu tree, right click and select Power Export.
How to modify selected content:
When you select content for the Power Export, Gen5 puts a button above each data
view in the Excel spreadsheet, right next to the starting cell for the content.
Click the button to modify the selected content, i.e. open it in Edit mode
Running Power Export
Highlight the plate in the menu tree> right click> Power Export
 After you've selected the content to export using the Power Export Builder
 And read the plates in an experiment
Highlight the plate in the menu tree and click the Power Export button on the
toolbar or right click and select Power Export. Gen5 launches Excel® with the selected
content. You can then use Excel as normal.
Power Export Settings
Protocol> Protocol Options> Export Options> Power Export Settings
System>Preferences>Default Protocol>Protocol Options>Export Options>
Power Export Settings
366 | Chapter 16: Exporting Results
You can define default settings for Power Export, which can be overridden in
individual protocols. Use the controls in the Default Protocol to base all new Protocols
on them. Override the default setting in individual protocols using the Protocol
Options.
Select method:
Save after Export: select this option to enable Gen5's file naming and saving routine,
then define your preferences below. They will be executed when the Excel file is saved.
When this option is not selected, Power Export performs as expected but does not save
or name the resulting file.
Close after Export: select this option to run Power Export in the background. This
feature creates, saves, and closes the Excel file using the defined settings after
obtaining the content selected with the Power Export Builder. If you do not select this
option, Gen5 will keep Excel open until you close it.
File Naming Convention
Set up a naming convention to apply to the Excel files created with Power Export:
 File Name: use the text field to build a naming convention. You can put any
combination of text and Gen5-provided data points in the field to become the
name applied to consecutively-saved Excel files:

Click the options arrow at the end of the field to select from the Gen5provided data points
 Add or replace default text with your own text
 Notice the underscores Gen5 places between data points, they can be
retained or removed according to your preferences. Generally, it is good
practice to use filenames without spaces.
 Example: Gen5 displays an example of the file name you create
The filename must comply with Microsoft® filename conventions, e.g. it
must not contain so-called offending characters: \ / : # ? " < > |
File Location
Specify the location for Saved files:
 Last folder used: puts the Excel file in the folder last used by the Power Export
engine
 Folder: select an existing folder or define a name to apply to a newly-created
folder


Use the 3-dot button to browse to the desired location for file storage
Use the options arrow to name a newly-created folder using the Gen5provided data points
Power Export | 367
 You can add text for naming a newly-created folder, if desired
 Example: Gen5 displays an example of the path and folder name based on
your input
When Exporting,
Prompt the user to confirm the path and filename by showing Excel's Save dialog:
 Always: whenever the save occurs
 Only if the file already exists: when the same name is applied to an
existing file
 Never (overwrite the file if it already exists): do not show the Save dialog,
replace the existing file with the current one when a file with the same
name exists
Export Row and Column Headers
Select this option to include the Matrix and Statistic table row and column headers
with the data exported to Excel™
Text Options
 Formatted Text: exports text as defined in Gen5, retaining the selected font and
any customizations
 Text Only: exports text as characters only, without an associated font or any
customization performed in Gen5
Important: Default Protocol settings are applied "going forward,"
they do not override existing protocol settings. They effect only newly
created protocols.
368 | Chapter 16: Exporting Results
Chapter 17
Managing Files
This chapter offers instructions and suggestions for managing your
Gen5 experiment and protocol files, with a focus on Gen5’s
database. Methods for recovering from Database Errors are
provided.
Managing Files......................................................................... 370
File Storage............................................................................. 371
Database Management ............................................................. 372
Database Errors....................................................................... 379
370 | Chapter 17: Managing Files
Managing Files
Gen5 offers two methods for storing its protocol (.prt) and experiment (.xpt) files. You can
use a secure database called SharedDB (and its companion LocalDB) provided by Gen5 or
you can use the Windows® File System. Both options let you set up Gen5 files to be shared
by multiple users. Conversely, you can prohibit file sharing by only installing Gen5 locally,
on an individual's PC.
The SharedDB ships with Gen5, and for all software levels, it contains security information
and the Plate Types Database. Except for Gen5 Secure, the File Storage option must be
changed to use the database for storing .prt and .xpt files.
Gen5 Secure is intended to be used with the SharedDB, it is a major component of making
it "secure." In Gen5 Secure the SharedDB contains user accounts and a System audit trail,
in addition to the security information and the Plate Type database, and it is set up by
default to store .xpt and .prt files and their associated audit trails.
How to manage files
Gen5 provides Database Management tools when its Shared database (SharedDB) is used
for file storage. The SharedDB can be moved to a shared, network directory, where all
required users can access it. When the Windows file system is used for file storage, you
manage files using Windows Explorer. In addition to storing the files online, files can be
stored on CD or diskette.
File Storage | 371
File Storage
System> Preferences> File Storage Mode
Use this control to select a method for storing protocol and experiment files.
Attention Gen5 Secure users: To ensure 21 CFR Part 11 compliance
retain the setting to use the Gen5 Database
About File Storage
Gen5 provides two methods for storing protocol and experiment files. You can use the
secure, shared-access database provided with Gen5, which is required for compliance
with the FDA's 21 CFR Part 11 regulation on electronic records submission.
Alternatively, you can use the file system provided with the Windows® operating
system on a local computer or network (LAN). If your organization is unconcerned
with FDA regulations, the choice is a matter of preference. However, one advantage to
using the Gen5 Database is its ability to recover from a system crash. New and
modified files are saved as Temporary Files in the database and can be used to recover
information that wasn't saved before a system failure.
Clarity™ Luminometer protocol files, with a .bpf extension, cannot be
stored in Gen5’s shared database. They are typically stored in the
C:\Program Files\BioTek\Clarity\protocols folder.
How to
Select an option for storing Experiment and Protocol files:
 Gen5 Database: all actions related to managing and maintaining files, like
File>Open, File>Save, Browse..., and so on, will occur in Gen5's SharedDB.
 Windows File System: Gen5 will not control the management of files. Actions
related to managing and manipulating files will be determined by the
Windows operating system, e.g. you can use Windows® Explorer. Generally
during file management activities like File>Open, Windows begins at the last
directory and folder used.
AutoSave Feature: Gen5 offers this feature to give you additional
control over the storage of saved files.
372 | Chapter 17: Managing Files
Database Management
Organize Your Database Files
During regular installation, Gen5 Secure installs and enables the
shared database to store experiment and protocol files. All other
levels of Gen5 must elect to use the database at System>
Preferences> File Storage
All of your file management requirements can be fulfilled using Gen5's secure
databases. You'll be most satisfied with the final structure if you spend some time
planning it up-front. In a multiple-user environment, you can set up Gen5's database
on a shared-network drive (LAN) so multiple users can access the same protocol and
experiment files, including the Default Protocol.
Multiple Databases: You can create multiple copies of the clean, installed SharedDB,
renaming them with meaningful titles for use by various projects or teams or
researchers. Within each database you can set up a consistent file structure, e.g. specific
folders for specific types of Protocols and Experiments, or a different folder for each
user. The possibilities are endless.
Backups: Performing backups on a regular schedule is highly recommended to
preserve your data. And, Gen5 provides a tool to schedule backups to occur
periodically. See below.
 File Management Recommendations
 Put a copy of the SharedDB on a shared-network drive where all your Gen5
users can access it. Be sure to set each user's Database Configuration to point to
the correct location.
 Before moving the SharedDB to a network location, make a copy of it to use as
a template for future use:
1.
In the default SharedDB folder, highlight the original, right-click and select Copy
3.
Highlight the copy, right-click and select Rename
2.
4.
De-select the original (click elsewhere in the dialog), right-click and select Paste
Give the copy a unique name, like SharedDB_original.mdb0.
 Consider setting up shared databases for different projects or teams within
your organization. You can follow the steps defined above to create multiple
databases in the same folder (or directory), or you can move the unique
databases to a different network location/folder. Use Database Configuration
to point user's Gen5 sessions to the correct database.
Database Management | 373
 Regularly archive and backup the database to preserve your records. There are
numerous ways to do this, so BioTek recommends following your
organization's existing policy for securing data. For example, if you put the
shared database on the network and your network is backed up every night,
this may be sufficient. You can use Gen5's Optimize and Backup Settings to
facilitate your data-protection policy.
 Consider using Gen5's automatic Save feature to create a new, date-stamped
folder for storing experiment records. This is an especially good practice for
large labs with multiple users who run hundreds of plates per day. Gen5 will
keep all that data organized by date. Define this kind of file management
setting in the Default Protocol so it will apply to all newly-created protocols
(System>Preferences>Default Protocol>Protocol Options>Save).
 Gen5 handles multiple, simultaneous users performing database management
tasks by giving precedence to the user with the greater administrative rights.
About Gen5 Databases
All levels of Gen5 install two databases during regular installation: SharedDB and
LocalDB. Only Gen5 Secure is initially set up to use the Gen5 Database for experiment
and protocol file storage. All other levels of Gen5 must elect to use the database to
store experiment and protocol files at System> Preferences> File Storage
 SharedDB can be set up on a network for sharing information amongst
multiple users. It contains all protocol and experiment data files and their
associated audit trails, the plate types, and reader-diagnostic history data. In
Gen5 Secure, SharedDB also contains security settings, user accounts, and a
system audit trail for shared events. This database can be moved, renamed, and
copied. So, if desired, you can create a unique database for individual projects,
teams, or other classification.
 LocalDB contains the local setup information, including the Reader
Configuration. For Gen5 Secure, this database also contains an audit trail for
local events. LocalDB is stored on the computer’s hard drive, and it cannot be
moved or renamed.
 Default database location: During normal installation, Gen5 installs its
databases:
 Windows XP and 2000 systems: C:\Documents and Settings\All
Users\Application Data\BioTek Instruments\Gen5 (software
edition)\(version #)\SharedDB or LocalDB
 Windows Vista: Windows XP and 2000 operating systems: C:\Program
Data\BioTek \Gen5 (software edition)\(version #)\SharedDB or LocalDB
You may need to change your operating system settings to view the
Application Data folder. In Windows® Explorer, select Tools>Folder
Options>View and make sure it is set to "Show hidden files and
folders."
374 | Chapter 17: Managing Files
 Max Size: the maximum size of the database files is 2 gigabytes (Gb). At
startup, Gen5 checks the remaining size of the database. Warning messages are
displayed when the database size exceeds 1536Mb. Use Gen5's maintenance
and backup features to archive your database records.
 Gen5 has built-in error recovery modes, when your connection to the database
is lost for any reason, Gen5 saves any unsaved files as Temporary Files. After a
system failure, the next time you open an affected protocol or experiment file,
Gen5 offers to replace the unsaved files with the Temporary Files. Say Yes to
recover any changes made to the files before the system failure, say No to open
the files as they were last saved, before the unsaved changes were made.
Newly-created files are saved as Temporary Files, also. Following a system
failure, you can rename these temporary files with the proper filename
extension (.xpt or .prt) using Gen5's Maintain Files controls.
 File locking: When a file is opened in Gen5 it is “locked” to protect it from
being modified (saved or renamed) by a different user. When a second user
attempts to open the file, they will receive a message stating: “File <filename>
is already in use. Do you want to open it in read-only mode?”
 Gen5 offers automatic backup: you can define settings for regularly and
automatically backing up and optimizing databases with Gen5's AutoOptimize feature.
Database Configuration
System> Database Configuration
Prerequisite
Some features of this dialog require System Administrator privileges. Contact your
System Administrator if you are unable to perform actions as expected.
When Gen5 is installed, there are two primary databases, a shared and a local
database. They are named SharedDB.mdb and LocalDB.mdb respectively. The
LocalDB cannot be moved or renamed. The SharedDB can be moved and renamed. All
operations affecting them take place using their respective tabs, except the upgrade
utility.
Troubleshooting
When launched, Gen5 attempts to connect to the Gen5 databases. Review this
information if errors occur: Database Errors (page 379)
Gen5 presents the Reset Connection button only when it detects an
error that can be repaired by its functionality. Click it, several times if needed, until it is
grayed-out. Review the Database Errors information if the button doesn't fix the error.
Database Management | 375
Source
Gen5 displays the current location of the database.
 LocalDB: You cannot move or rename the LocalDB database, thus the 3-dot
button is disabled. If necessary to see the full pathname of its location, you can
click inside the text field and scroll to the right.
 SharedDB: Click the 3-dot button to view the current location of the database.
You can move, rename or copy the SharedDB database. Learn how in the
Getting Started Guide shipped with the product CD.
Test
Use the Test button to check the connection to the Gen5 database.
 Potential error messages are referenced in the Troubleshooting section above.
Stats
Use the Stats button to assess the number of files and amount of
space used in the Gen5 database.
 Generally, the most important information is Size: reported as used/available.
If the used value is nearing the available value, it's time to move some files. Use
the DB maintenance tools to archive files not currently being used.
 Occasionally using the Optimize option (described below) helps keep the DB in
good shape.
Optimize
Click the Optimize button to engage Gen5's corruption-repair and sizecompacting functions. Learn more in Gen5’s Help.
Periodically Optimize and Backup: to direct Gen5 to automatically backup and
optimize the database on a regular basis. Select the option and define its settings. Use
the 3-dot button to modify the settings. (See page 377)
Upgrade
There are two uses for the Database Upgrade Utility:
 install an updated version of the software
 install a higher level of software, e.g. upgrade Gen5 to Gen5 Secure
376 | Chapter 17: Managing Files
Maintaining Files
System> Maintain Files
Use this dialog as you would Windows® Explorer to manage your Protocol (.prt) and
Experiment (.xpt) files. Gen5 Secure tracks activities, like creating, moving, and
deleting files, in its System Audit Trail.
Important: the DB (database) this dialog opens is
controlled by Database Configuration. It is the SharedDB defined as Source.
Tools:

Toggle the view between Details and Icons of the files and folders. In
Details view, click on a column header to set the sort order. For example, click
Type to organize the files by file type, or click Modified (once or twice) to sort
them in the desired ascending or descending date order.

Create a new folder to save certain files separately

Refresh or update the view to show files or folders added by another user

Move up one folder/directory level with this button

Right-click menu: highlight one or more items (folders or
files) and right click for a pop-up menu. Notice the Hidden option: system
administrators can hide/reveal selected files to prevent other system users
from accessing them. Warning for Windows XP users...
 Ctrl+C to copy, Ctrl+V to paste, and the Delete key are also supported

Highlight a file or folder and Delete it with this button. You must delete
sub-folders (i.e. folders within a folder) before you can delete their parent or
higher-level folder

Column Headers can be used to sort the files:
click on a header to sort the files in ascending/descending order by that
category. For example, click Modified to sort the files by "last modified" date.
Click the same column header to reverse the order.
Database Management | 377
Tasks:
Find step-by-step instructions for performing these tasks in Gen5’s Help:
 Organize your files
 Copy to CD, diskette or other portable media
 Export a file
 Import a file
 Reduce the database size
Optimize and Backup Database
System> Database Configuration
Optimize Now
Click the Optimize button to run Gen5's database compacting and
backup program.
Before "optimizing" the database, close all protocol or experiment files.
When to do it:
 After restoring database connections following an error
 After exporting and deleting records to reduce the database size (Maintaining
Files)
 After system audit trail events are exported or deleted
Gen5 creates a backup copy of the database (in its present location
unless a different storage location was selected in the Optimize
Periodically settings) before beginning optimization. It is named:
<original filename>_yymmdd_hhmmss.mdb (year, month, day_hour,
minute, second). .mdb is the filename extension. Backup files can be
used to repair Gen5 when the current database file is corrupt, for
example.
378 | Chapter 17: Managing Files
Periodic Optimization
Use this option to schedule Gen5 to conduct
Optimization on a regular basis. BioTek suggests once per week.
Use these controls to define the rules for regular, automatic database optimization.
Important: Only use this automatic method for backing up files when
you're saving them to a network or external drive. Do not use it to
save a backup to the same (local) hard drive used to store the original
database. Manually backup your database if you are limited to one
hard drive/PC, unconnected to a network.
How it works:
Whenever Gen5 is launched it checks the contents of the backup location to determine
if optimization is due. When it is, Gen5:
1.
2.
3.
4.
Renames and moves a copy of the current database to the Backup location. The
naming convention is:
Auto_Backup_<original filename>_yymmdd_hhmmss.mdb.
Executes the repair and compact operations on the current database
As needed, it deletes the oldest archived (or previously backed-up) database
file to correspond to the current settings
Gen5 displays a status gauge on screen to tell users the operation is underway
0.
How to define the settings:
1.
Set the number of days to run the optimization in the Optimize every _ days
field
2.
Backup: you can retain Gen5's default location for storing a backup copy of
the database, or click the 3-dot button and select an alternative location.
3.
Define the number of previously backed-up or archived database files to keep
in the backup location in the Keep _ last archived databases field0.
Database Errors | 379
Database Errors
Certain conditions can cause database-related errors:
 The database file is not available. Potential causes: the shared database is on a
network and the cable is unplugged, or the file is locked by another user
 The database file is corrupt. Potential cause: an incomplete write operation
occurred because Gen5 was closed unexpectedly due to a power outage or
hardware problem
 Verification of the database capacity failed. Potential cause: the maximum
size of the database (2 gigabytes) has been exceeded
 File importation failure. Potential causes: the filename extension is wrong, a
protocol file was misnamed with an .xpt filename extension instead of .prt
Fixing the errors
1.
First, make sure non-Gen5-system issues are resolved, for example:
 network cables are plugged in and the network is up and running;
 another Gen5 user is not currently performing database maintenance
routines;
2.
 the Database Configuration for both the SharedDB and LocalDB databases
point to the expected locations;
Then, follow these instructions for fixing the errors:
 Fixing a Database Connection Error (page 379)
 Fixing a Corrupted File Error (page 380)
 Fixing a Database Capacity Error (page 381)
3.
 Fixing a File Importation Error (page 381)
If the above solutions do not work, try Restoring an archived database (page
382). 0.
Fixing a Database Connection Error
Connection to SharedDB failed.
This type of error is most commonly caused by a network timeout or
disconnection, or corruption to the SharedDB file residing on a network.
To fix:
1.
Make sure you are properly connected to your network, if applicable, i.e.
cables/wires installed and the network server is live.
380 | Chapter 17: Managing Files
2.
Click Reset Connection at the Database Configuration screen.
Gen5 immediately opens the Database Configuration screen after displaying
the error message. Otherwise, select System> Database Configuration
Important: Click the Reset button several times, if needed, until it is
grayed out.
Quit: If Gen5 cannot restore the network connection, usually because
of external factors, e.g. the network is down, when you click Quit at a
secondary error message, Gen5 will save any currently opened and
modified files to the Windows Temp directory. When the database is
restored you can import the files from the Temp folder to the
database.
3.
When the database connection has been repaired, click Optimize.
If Reset button fails:
If your network is performing as expected, and you've checked the cabling from your
PC to the network, and the Reset button fails to re-establish a connection with the
shared database:
1.
Reboot your PC
2.
Restore a previous version of the database or contact your System
Administrator to inspect and repair your system connection.
If the same message is displayed:
Fixing a Corrupted File Error
Database file is corrupt
There are two potential ways to fix a corruption error:
 Reboot your PC to try to clear the error by restarting the system.
 Install an archived version of the LocalDB.mdb: use Windows® Explorer to
locate and restore a backup of the database.
Windows® Explorer provides an option to hide certain folders from
view, if you cannot find the Application Data folder (C:\Documents
and Settings\All Users\Application Data) it is probably hidden. In
Explorer, select Tools>Folder Options>View and enable Show hidden
files and folders
If these options fail to repair Gen5's behavior, contact BioTek TAC.
Database Errors | 381
Fixing a Database Capacity Error
When the cumulative size of the files in your database nears or exceeds its capacity (2
gigabytes) Gen5 displays an error message or warning. You must reduce the size of the
database. There are numerous ways to accomplish this, the least invasive method, to
remove files, is described here.
Prerequisite
This function is only available to the System Administrator. You must login,
System>Administrator Login, as the Administrator to access these controls.
Optimize the database before proceeding to see if Gen5 can compact
the database sufficiently to comply with its size limits. Select
System>Database Configuration>Optimize. When the process is
finished click the Stats... button to check the current size.
To reduce the size of your database:
1.
Select System> Maintain Files
3.
Right click and select Export to Disk from the pop-up menu
2.
4.
5.
6.
Highlight multiple database records: hold down the Ctrl key while selecting
records
Select a folder (using the standard Windows dialog) where you want to save or
archive the Gen5 records
Back in the Maintain Files dialog, highlight the same records, and click the
Delete button (or right click and select Delete)
Finally, Optimize the database to ensure it's running in top form.
Fixing a File Importation Error
File importation failure
The requested file may be a Protocol file
The requested file may be an Experiment file
Gen5 tests the file's format when you perform certain operations like importing a file
and File>Open. One of these error messages may be displayed when an
incompatibility is found.
Change the filename extension to fix these errors
1.
Locate the offending file: depending on the current File Storage mode:
 using the Gen5 Database, select System> Maintain Files
 using the Windows File System, use Windows® Explorer
382 | Chapter 17: Managing Files
2.
3.
Highlight the file, right click and select Rename:
 change the filename extension for a misnamed Protocol file from .xpt to .prt
 change the filename extension for a misnamed Experiment file from .prt to
.xpt
Retry the desired action, e.g. open the file, import the file
Restore an archived database
When Gen5's error recovery processes cannot resolve database errors, a final-resort
solution is to replace the current database file with an archived or backup copy of it.
Ideally, you or your System Administrator has regularly (or at least recently) backed up or
archived the database. Gen5's Optimize tools can perform backups regularly, for instance.
Check the Auto-Optimize Settings, if they were defined, to determine the location of
the last-saved backup file.
How to
1.
2.
3.
4.
5.
6.
Using Windows® Explorer, locate the last-saved archived or backed-up
database file.
Copy and Paste it to the desired location. Rename the database file, too. (All of
these commands are available from the right-click menu.)
In Gen5, select System> Database Configuration
Select the SharedDB tab
Next to the Source field, click the 3-dot button and browse to the location
selected in Step 2.
Click OK. 0.
Chapter 18
Security
Primarily for Gen5 Secure users, this chapter describes Gen5’s tools
for managing security issues, including audit trails, electronic
signatures and user accounts.
Changing your password........................................................... 385
Login/Password Controls ........................................................... 386
FDA’s 21 CFR Part 11 ............................................................... 388
Signing Protocols ..................................................................... 389
Audit Trail ............................................................................... 391
User Accounts ......................................................................... 398
384 | Chapter 18: Security
Security
To meet the FDA's electronic records requirements, Gen5 Secure offers several
tools to enable a secure software environment. In addition to the content provided
here, you can find detailed information about these features in the Gen5 Help:
 Audit Trail on page 391
 Electronic Signatures on page 389
 System Administrator's "To Do List" on page 8
 Manage User Accounts:
 Setting Up New Users on page 398
 Changing a User's Passwords on page 385
 Changing a User's Privileges on page 401
 About 21 CFR Part 11 on page 388
Changing Your Password | 385
Changing Your Password
For Gen5™ Secure Only
System> Security> Users
Users other than the System Administrator are limited to changing their own login
password.
How to change your password:
1.
Select System> Security> Users
3.
Enter your current password in the Current Password field
2.
4.
5.
Identify and open your user account: highlight and click Edit (or double click)
Enter your new password in both the New and Confirm password fields
Click OK.0.
The password will take effect the next time you log into Gen5.
Contact your System Administrator if you've forgotten your password.
He/she can change your password without knowing the current one.
386 | Chapter 18: Security
Login/Password Controls
For Gen5™ Secure Only
System> Security> Login
Prerequisite
Only the System Administrator can access these controls. You must login:
System>Login/Logout, as the Administrator to change the settings.
Important: The default settings shipped with Gen5 Secure, and
shown in the screenshot below, comply with the FDA's 21 CFR Part 11
requirements (page 388) on controls for identification passwords.
Login
 Lock user account after: Specify the number of successive failed login
attempts a user may make before being locked out of Gen5. This feature does
not apply to System Administrator accounts and only a System Administrator
can reinstate a locked out account. Valid entry range: 2-10. When this feature is
unchecked, users login attempts are unlimited. Compliance with 21 CFR Part
11 requires setting a limit for failed login attempts.
 Lock session after: Specify the number of minutes that a Gen5 session can be
idle before it is locked and requires successful user login to reactivate. A
Login/Password Controls | 387
session is considered idle when there is no keyboard or mouse activity and
Gen5 is not controlling a reader activity. Valid entry range: 1-1440 minutes.
Compliance with 21 CFR Part 11 requires setting an idle-time limit.
 Force user to type ID: apply this control if your security rules require users
to enter their ID at login and to apply their Signature. When this feature is
unchecked, the last user's ID is displayed in the login and signature screens and
users can select an ID from a drop-down list of users. This is not a requirement
for compliance with 21 CFR Part 11.
Password
 Minimum password length: Specify the minimum number of alphanumeric
characters required for a valid password. Valid entry range: 2-10 characters.
 Password expiration: Specify the number of days a password can be used
before users are required to change it. When users let their password expire
without changing it, their accounts are locked out and only a System
Administrator can reinstate a locked out account. Valid entry range: 1-10000
days. If this feature is unchecked passwords do not expire. Compliance with 21
CFR Part 11 requires an expiration period.
Lock out: when a user's password has expired, the system
administrator has two choices:
= manually remove the Locked out flag: this resets the password
expiration period allowing the user to login using his/her current
password.
= enter a new password for the user (which unlocks the account) and
tell the user to login with the password you have assigned him/her.
Advise the user to change the password after logging in.
 Advise user: If password expiration is set, specify the number of days before
their password expires to alert users to change their password. Valid entry
range: 1-30 days, but cannot exceed the number of days to Password
Expiration.
 Password reuse: Specify the number of passwords Gen5 will remember for
each user's account to prevent a recently used password from being reused.
Valid entry range: 2-20.
388 | Chapter 18: Security
FDA's 21 CFR Part 11
This is a description of the FDA's electronic-records submission requirements
and how they are satisfied by Gen5™ Secure.
A significant component of this secure software environment is the ability to create
individual user accounts to ensure that only authorized users can gain access to the system
and to any restricted functions. A site-designated System Administrator creates and
maintains the user accounts.
Gen5 Secure complies with FDA's Electronic Signatures rule, 21 CFR Part 11:
 System Administrator — The System Administrator creates and maintains user
accounts and user groups to specify which Gen5 functions shall be protected
from use by limited-access users, e.g. masking data. The System Administrator
sets special password and login characteristics including minimum password
length, password aging, and idle session time-out. The System Administrator is
also responsible for managing the database of Gen5 files and audit trails.
 Support for Multiple Users — Each user is identified by a unique combination
of User ID and encrypted password. Users must log in to Gen5 Secure with
these identifiers to gain access.
 Time-stamped Audit Trails — Activities such as user login/logout, protocol
and experiment creation and modification, and plate reading are permanently
logged in a secure database.
 Embedded Signatures — Authorized users can electronically sign protocol and
experiment files. Electronic signatures are permanent and remain a part of the
overall data record for the life of that file.
 Secure Record Storage — Gen5 proprietary files (.prt and .xpt) are stored in a
secure shared-access database. Activities performed on files within this
database (such as rename, move, copy, overwrite, and delete) are performed
within the Gen5 environment, and every change is tracked in an audit trail. In
addition, the System Administrator can configure the system so that these
activities may only be performed by Power Users or high-level users.
 Protected Functions — The System Administrator can protect a variety of
functions from use by limited-access users, e.g. Standard Users. These functions
include the deletion, renaming, modification, and overwriting of various record
types.
Signing Protocols | 389
Signing Protocols
For Gen5™ Secure Only
System> Security> Signature Reasons
Gen5 Secure provides users the ability to sign (i.e. sign off on) a protocol or
experiment file. Your System Administrator can define the Signature Reasons to give
meaning to each signature recorded. Gen5 ships with three reasons: Authorship,
Review, and Approval. These terms can be kept, modified, or added to.
When users create, review, or perform any other activity on a Protocol or Experiment
for which a signature or sign-off is required, they use the Sign option, select a Reason,
and enter their password to confirm the action.
Representatives can sign off on files for another user. Gen5 provides an option for two
users to digitally sign records as representatives of a third user.
What do you want to do:
 Create/Modify Signature Reasons (below)
 Sign a Protocol or Experiment (page 390)
 Include Signatures in the Experiment Report:
To include Signatures in a report or export file:
1
2
Open the preferred reporting tool: Report Builder, File Export
Builder or Power Export Builder
In the Available Data Views or Excel report objects, find Table, and
add Signatures to the report content.
Gen5 reports the Signatory, Reason, and Date
Signature Reasons
For Gen5™ Secure Only
System> Security> Signature Reasons
Prerequisite:
This function is only available to the System Administrator. You must login:
System>Login/Logout as the Administrator to access this control
390 | Chapter 18: Security
How to create/modify Signature Reasons:
Simply, click in the text fields of the Signature Reasons table to add new or replace
existing reasons for signing protocols and experiments.
Sign
Protocol> Sign
Plate> Sign
To sign off on a Protocol, select Sign from the Protocol menu or click the Sign button
 To sign off on an Experiment, highlight a plate in the menu tree, select Sign
from the Plate menu (or right click and select Sign, or click the Sign button)
Sign Off on a file:
1.
Use the appropriate option (described above) to open the signature screen
2.
Reason: Use the drop-down list to select the reason for signing the file.
Your System Administrator creates and maintains the Reasons selection list .
3.
4.
5.
User: Gen5 sets this to match the user who is currently logged in. Use the
drop-down list to change it, if necessary.
Password: Enter your password.
Click
0.
If the file hasn't already been saved, Gen5 opens the Save dialog.
Sign as a Representative:
Two users are required to sign as a Representative of another user. Follow steps 1 and
2 above, then:
1.
2.
3.
Select the checkbox for Representative of and use the drop-down list to
identify the user being represented.
Gen5 adds 2 tabs to the dialog, one for each representative.
Each representative must select their user ID and enter their password.
Click
0.
If the file hasn't already been saved, Gen5 opens the Save dialog.
Audit Trail | 391
Audit Trail
About Audit Trails
Depending on the level of Gen5 you're running, one or more Audit Trails keep track of
certain activities and build a "change history" log of events. The protocol and data
audit trails cannot be edited or deleted. They are part of the permanent record of the
protocol or experiment file.
When the Audit Trail Notification feature is deployed in Gen5 Secure, users are
prompted to enter comments into the record each time a logging event takes place. You
can view and report the audit trail and calculation warning logs, as needed.
Audit Trail Types:
 Data Audit Trail — All levels of Gen5 — logs values-masking and -editing
events, plate addition and deletions, and other related events. Data audit trails
occur at the Experiment level to log the experiment-related events, like which
protocol it was based on, and at the Plate level for plate-related events, like the
read's status/progress
 Protocol Audit Trail — Gen5 Secure Only — logs all events related to the
creation and modification of protocol files, like changes to plate layout and data
reduction steps
 System Audit Trail — Gen5 Secure Only — logs system-level events, like user
login/logout and reader-setting modifications, maintenance and updates to
database folders and files, and so on. System events can be archived and
deleted from the database.
All the audit trails include an Event description, a time and date stamp, Gen5
Secure logs the ID of the user logged in at the time of the event, and any userentered comments
Audit Trail Notification Options
For Gen5™ Secure Only
System> Security> Audit Trail
Prerequisite
Only the System Administrator can access these controls. You must login:
System>Login/Logout, as the Administrator to change the settings.
About Audit Trail Notification
These controls turn on or off notification to users when an audit-trail-logging event
occurs. When Notification occurs, users are provided an opportunity to add a
Comment to the record. If the system-generated text does not provide as much detail
392 | Chapter 18: Security
about the event as you'd like, you can use the Comments feature to encourage users to
enter more useful information. For example, when the plate layout of a protocol is
changed, Gen5 simply logs the event as "Plate Layout changed", while the user can add
details to the record like, "Added blanks: H11, H12."
Notification and comment control for each type of audit trail can be selected
individually using the checkboxes and drop-down lists.
How to
1.
Turn on Notification: for each type of audit trail using the checkbox to turn
on or off (remove the checkmark) notification of an event. Notification
identifies the event with a brief description and provides a text area for users'
Comments
2.
Prompt user for a comment: if Notification for an audit trail is turned on,
select a comment-required setting:0.
 Accept an empty comment: user is not required to enter text in the
Comment area
 Invite user to type a comment: if user does not enter a comment during
notification of an event, the Message inviting the user to enter a comment:
defined in the text box below, will be presented to them. You can replace
the default text with your own wording
 Comment required: if user does not enter a comment during notification of
an event, the Message requiring the user to enter a comment: defined in
the second text box below, will be presented to them. You can replace the
default text with your own wording. Users will not be permitted to
quit/exit the audit trail notification without entering some text in the
Comment area
Exporting Audit Trail Events
For Gen5™ Secure Only
System> Audit Trail> Export button
Use this feature to export System Audit Trail events for archiving and to generate a
report of the events. Exported records can be deleted from the system during the
export process to maintain the size of the database, and to remove unnecessary
records.
Important: Gen5 does not retain control over the exported text files.
It is your organization's responsibility to ensue the security of the
exported audit trail records.
Audit Trail | 393
To export audit trail events:
1.
Select System> Audit Trail
3.
Click Export
2.
4.
5.
6.
7.
Click the Shared or Local tab to select the source database of the records you
want to export
Enter a date range of the events you want included in the export file
Check or ignore the Delete events after exportation option
Set the Save in field to the location you want to send the text file to. Use the
standard Windows® browse tools to select the location
Click Save to export the events0.
After export, compact the database:
If the Delete events after exportation option was used, the System Administrator
should:
1.
Make sure there are no users are currently logged into to the shared database
3.
In the Shared or Local database, as appropriate, click Optimize0.
2.
Select System> Database Configuration
After exporting the file, you can open it with Notepad® or a word processor, to
review or print it.
394 | Chapter 18: Security
Data Audit Trail
Each plate and each experiment has a Data Audit Trail, a change history or log of
automatically-recorded events. An event is an action like:
 Plate read started
 Plate successfully read
 Plate read failed with message "Reader error: 0IE0"
 Modify Value - Well A2 - 390 - Old: 2.180 - New: 2.080
When values are masked or edited, Gen5 logs the event as Mask or
Modify Value <Well>-<Data set name><read index for
kinetic/scan><position for scan>; old and new values are provided
when the value is changed.
What events are logged:
The level of software determines the types of events logged by the data audit trail:
 Gen5: All Gen5 levels log data changing/masking and plate addition and
deletion events, and plate-read status and warnings
 Gen5 Secure also logs digital signature events
 All audit trails contain a description of the Event, a time and date stamp. Gen5
Secure also contains the ID of the user logged in at the time and any userentered comments (if Audit Trail Notification is turned on)
Viewing Audit Trails:
Reporting/Printing Audit Trails:
In the menu tree, each Plate
has a Data Audit Trail, and
so does the Experiment
You can also open them from
a menu:
Plate>Audit Trail
File>Audit Trail (for the
Experiment)
You can include the Data Audit Trail in reports and export files, and copy and paste
items to an external file:
Audit Trail | 395
 In the Report Builder and Export Builder, look for Audit Trail under Table in
the Available Data Views tree, to add an item to the Report or Export Content
 Copy and Paste: In the audit trail screen, highlight event details and use Ctrl+C
to copy. Open Notepad or a word processor, and paste it with Ctrl+V
Security:
Data audit trails cannot be edited or deleted. They remain a permanent part of the
Experiment file for the life of that file.
Protocol Audit Trail
For Gen5™ Secure Only
Each protocol has an audit trail that automatically logs all events related to its creation
and modification. For example:
 Copy of protocol X (the full path and filename)
 Plate Layout modified
 Data Reduction modified
What events are logged:
 Procedure
 Data Reduction steps
 Plate Layout
 Report and Export definitions
 Miscellaneous protocol options
 A description of the Event, a time and date stamp, the ID of the user logged
in at the time (if applicable) and any user-entered comments (if Audit Trail
Notification is turned on)
Viewing the Audit Trail:
 In the menu tree, expand the Protocol branch to locate its Audit Trail
 In a multi-plate calibrator or single-assay protocol, the Protocol Audit Trail
is split into a main log and separate Method Audit Trails for each
Calibration Plate and Other Plates.
Reporting/Printing the Audit Trail:
 In the Report Builder and Export Builder, look for Audit Trail under Table
in the Available Data Views tree, to add an item to the Report or Export
Content
396 | Chapter 18: Security
 In the audit trail screen, highlight event details and use Ctrl+C to copy.
Open Notepad® or a word processor, and paste it with Ctrl+V
Security:
Protocol audit trails cannot be edited or deleted. They remain a permanent part of the
Protocol and/or Experiment file for the life of that file.
System Audit Trail
For Gen5™ Secure Only
System> Audit Trail
System-level events, like user login/logout and reader-setting modifications, are
automatically recorded in the System Audit Trail. For example:
 Logout (computer and user ID)
 File "database + filename" created
 File "database + filename" pasted from clipboard
What events are logged:
 User login and logout
 System security updates (user accounts, login and password parameters,
protected functions, audit trail notifications, and file location and format)
 Plate Type Database modifications
 System Test and Test Plate runs, and adding and modifying Test Plates
 Reader settings changes (reader type, probe selection, communication
parameters, and filters/wavelengths)
 System setup changes (protocol defaults, format settings, start-up options,
and database settings)
 User-customizable application settings (such as toolbar and position/size of
main window)
 A description of the Event, a time and date stamp, the ID of the user logged
in at the time and any user-entered comments (if Audit Trail Notification is
turned on)
Viewing the System Audit Trail:
Select System>Audit Trail to open the viewer.
Audit Trail | 397
Reporting the System Audit Trail:
You must export Audit Trail Events to print them from a text or word processing file.
Exporting Audit Trail Events:
Gen5 provides a quick and easy method for exporting the System Audit Trail. Use this
feature to establish a regular schedule for "archiving" past events and to generate a
report of the events, if needed. The export action itself is logged in the audit trail.
Exported records can be optionally deleted from the system.
Important: Gen5 does not retain control over the exported text files.
It is your organization's responsibility to ensure the security of the
exported audit trail records.
398 | Chapter 18: Security
User Accounts
About User Accounts
For Gen5™ Secure Only
System> Security> Users
Prerequisite
This function is only available to the System Administrator. You must login: System>
Login/Logout as the Administrator to access all the controls. Non-administrators are
limited to changing their own password and selecting a Startup Action and Protocol
Folder.
How to Create, Modify or Delete User Accounts
Only an Administrator can add, modify, or delete users. Except for the Administrator,
any user account can be changed or deleted:
Click New to set up a new user


(Double-click or) Highlight a user and click Edit to modify its
name, password, or Group assignment
 Highlight a user and click Delete to remove the user account
Setting User's Permissions
Gen5 Secure: System> Security> Users> Edit
All other Gen5 levels: System> User Setup
Prerequisite
This function is only available to the System Administrator. You must login, System>
Administrator Login, as the Administrator to access these controls
Depending on the level of software, User's are given permission to perform tasks based
on their Group assignment in Gen5 Secure or the User Permissions given to all users
in all other levels of Gen5.
Gen5 Secure
User Permissions are defined by the User Group. When you select or change a user's
Group assignment you're simultaneously assigning their permissions:
1.
Select Security> Users
3.
Use the drop-down list to change the Group assignment0.
2.
Highlight the user and click Edit (or double click the user record)
User Accounts | 399
 See Modifying User Permissions (on page 401) to change the
permissions assigned to a group
Gen5, Gen5 ELISA, Gen5 Reader Control
For all levels of Gen5, except for Gen5 Secure, there are only two types of users: System
Administrator and User (non-administrator). The System Administrator can set or
change the User Permissions for non-administrators. Gen5 provides all user rights and
privileges to administrators.
To change User Permissions:
1.
Login as the System Administrator
3.
Add or remove a tick mark for each permission to give or deny access to it to
all non-administrator users0.
2.
Select Security> User Permissions
About User Groups
For Gen5™ Secure Only
Gen5 Secure uses Groups to manage the rights or permissions granted to users. When
creating (or maintaining) a group, you define the level of access and the controls
available to certain types of users, and then assign actual users to the groups. Gen5
ships with three groups: Administrator, Power User, and Standard User.
The System Administrator and Power User groups are given access rights to all
functions. The Administrator's rights cannot be changed, and include additional rights
to manage user accounts that are not extended to Power Users. When Gen5 Secure is
installed, the Standard User is limited to the following permissions. The System
Administrator can change these controls as needed:
 Quick Read/Use Default Protocol
 Add a New Plate
 Create/Edit Sample IDs
 Edit Plate Information
 Edit Report Builder
 Create folder in database
How to create new and modify existing groups:
Only a System Administrator can add, modify, or delete groups. Except for the
Administrator group, any group can be changed or deleted, and any group can be
renamed.
400 | Chapter 18: Security
Click New to set up a new group


Highlight a group and click Edit to modify its name and
permissions

Highlight a group and click Delete to remove it as an option. First
you must reassign any users to another group. You cannot delete a group with
users assigned to it.
Creating/Maintaining User Accounts
For Gen5™ Secure Only
System> Security> Users
Prerequisite
Most options for user accounts are only available to the System Administrator. Nonadministrators are limited to changing their own password and selecting a Startup
Action and Protocol Folder.
User ID
Enter a unique ID using 1 to 16 alphanumeric characters. The user will enter or select
this ID when logging into Gen5 and when signing files.
Full Name
Enter the user’s name. This name will be associated with events logged by this user’s
actions and with the digital signature applied by this user.
Group
Choose a Group membership to assign access rights and permissions to the user. Users
receive the rights assigned to the Group.
Status
The checkbox shows whether or not the user’s account is currently locked. The System
Administrator can lock or unlock the account. When a user’s account is locked, the
user cannot log into Gen5 and cannot sign files. A user’s account may become locked
due to one of three events:
 Intentional lock by the Administrator through this dialog
 Automatic lock if the user exceeded the number of successive failed login
attempts
 Automatic lock if the user’s password expired
See important information about expired passwords on page 387.
User Accounts | 401
Startup Action
Use the drop-down to select the preferred method for starting Gen5:
 Startup Window is the default setting, it offers several options including
creating a new item or opening a recently used item
 Create new experiment opens Gen5 with the Protocol selection dialog
open, as if the user had selected File>New Experiment
 Start at main menu opens Gen5 showing the File, System and Help menus
only. Since neither a protocol or experiment is open, the workspace is blank.
Protocol and Experiment Folders
Browse to or enter the full path and directory to define the folder in which the current
user will typically store protocol and experiment files. If a folder is not specified, Gen5
will default to the most recently-accessed folder.
Password
Assign a password for the user to enter the first time he/she logs in to Gen5. Instruct
users to change their password after the first login using the Password you've
assigned. Users can only change their own password. System Administrators can
change any user's password.
Modifying User Permissions in Gen5 Secure
For Gen5™ Secure Only
System> Security> Groups> Edit
User's are given permission to perform tasks based on their Group assignment in Gen5
Secure.
Prerequisite
This function is only available to the System Administrator. You must login,
System>Login/Logout, as the Administrator to access these controls
How to Change User Permissions:
1.
2.
Select System> Security> Groups, highlight the group and click
Edit to change the permissions or access rights of group members. Or click
New to create a new user group.
Add or remove a check mark for each function to grant access or deny it.0.
402 | Chapter 18: Security
Denying user permissions usually results in making the applicable dialog Read
Only.
Permissions
Protocol/Experiment Controls
This table describes the capability each Permission gives users. The Audit Trail icon
shows when Gen5 Secure logs the activity in the Protocol or Data Audit Trails. Links
are provided to learn more about the function.
Function
Create a new Protocol: Access to menu options File>New Protocol,
File>Save As, and Startup Page options to create a new protocol file
Open a Protocol: Access to File>Open, Recent Files List and Startup Page
options to open an existing protocol
Perform a Quick Read/Use default protocol: Access to creating an
experiment from the default protocol
Add a New Plate: Access to menu options and toolbar buttons for Adding
one or multiple plates to an experiment
Delete a plate: Access to Plate menu option to Delete, i.e. remove the plate
information and all data associated with the plate (if any) from an experiment
Create/Edit Sample IDs: Access to Plate menu and menu tree options to
enter or modify Sample IDs for each plate or in a Batch for multiple plates
Edit Plate Information: Access to Plate menu and menu tree options to
modify the Plate Information. Note: Information is intended to be captured at
run-time, for each plate in an experiment
Mask/Unmask values: Access to Mask button in data views to select
individual wells and mark them to be ignored in data reduction and curve
plotting
Edit values: Access to Change button in data views to select individual wells
and change/enter alternative data for use in curve plotting and data reduction
Re-read plate: Access to Read button after plate has been read to overwrite
the current measurement results with newly acquired measurements
Simulate Read: Access to Simulate option of the Plate Read dialog to let
Gen5 simulate a reading instead of actually reading the plate. (Useful for
Gen5 training/tutorials.)
Read from File (import): Access to Read From File option of the Plate Read
dialog to acquire/import reading data from a text file
Audit
Trail
User Accounts | 403
Enter Manually (raw data): Access to Enter Manually option of the Plate
Read dialog to manually enter (type in) reading data instead of actually
reading a plate
Edit Protocol: This switch gives or denies access to the next nine related
functions. You can override it by individually selecting the permissions and
assigning access
Edit Procedure: Access to the Procedure dialog to alter the reading
requirements and related events, like Delay, Shake. Gen5 always prohibits
users from changing an experiment's Procedure after the first plate is read
Edit Plate Layout: Access to the Plate Layout dialog to change the plate
layout, Well IDs, Concentrations/Dilutions
Edit Data Reduction: Access to the Data Reduction dialog to change data
reduction steps, add new steps or alter existing ones
Edit Report Builder: Access to the Report Builder to create or modify the
report definitions
Edit Runtime Prompts: Access to create or modify the "prompts"
(information requests) presented to users at read time. Users' responses
become Plate Information
Edit Data Views: Access to alter the format/font of data views items; create
custom data views
Edit File Export Builder: Access to select and modify the content for export
to a text file; define the filename and format settings for export files
Edit Power Export Builder: Access to select and modify the content for
export to Excel®
Edit Protocol Options: Access to define miscellaneous, protocol-related
parameters
System Controls
This table describes the capability each Permission gives users. The Audit Trail icon
shows when Gen5 Secure logs the activity in the System Audit Trail
Function
Manage and Maintain Systems: This switch gives or denies access to the
next five items. You can override it by individually assigning access to the
permissions
Edit Default Protocol: Access to define or modify the Default Protocol
Settings
Edit file storage mode: Access to menu option System>Preferences>File
Storage to alter the option: database or Windows® file system
Audit
Trail
404 | Chapter 18: Security
Edit Read from File options: Access to menu option
System>Preferences>Read from File Settings to alter the designation of the
text delimiter for importing data via text files
Manage and maintain Database: Access to change the location of the local
and shared databases, and their backups. Run maintenance tasks and tests,
and repair errors. Only when File Storage "uses the SharedDB"
Delete System Audit Trail Events after export: Access to delete records
after exporting them to a text file. All users can export records, only users
with this permission are able to delete them
Manage and Maintain Devices: This switch gives or denies access to the
next four related permissions. You can override it by individually assigning
access to them
Edit Reader Settings: Access to Reader Configuration to set up and alter
the settings. Denying access restricts the user's ability to change a reader's
filter/wavelength settings in Gen5
Edit Plate Types: Access to create, modify or delete records in the Plate
Type Database
Define Universal Plates: Access to Diagnostics options to set up and modify
the Universal Test Plate records used to conduct testing
Delete Diagnostic Test History: Ability to delete test records. All users can
view the test history, only users with this permission can delete the records
Manage and Maintain File Storage: This switch gives or denies access to
the next seven related permissions. You can override it by individually
assigning access to them. They are only applicable when File Storage "uses
the SharedDB"
Create folder in Database: Ability to create a new folder while maintaining
database files and when saving protocol and experiment files. Users denied
this function are limited to saving files in existing database folders
Delete/Overwrite folder in Database: Ability to delete or overwrite (Save
As) folders and files from/in the database
Export file from Database: When maintaining database files, ability to use
the right-click menu to Export to Disk
Rename folder/file in Database: Ability to rename database files and
folders in the database
Move folder/file in Database: Ability to relocate folders and files within the
database
Import file to Database: Ability to import, paste from clipboard, or drag
and drop files from another location
Chapter 19
Reader Control
This chapter supplements the Getting Started Guide instructions for
attaching a reader to Gen5 with more in-depth information about
how to control, configure and test your reader.
Reader Configuration................................................................ 408
Controlling the Clarity............................................................... 409
About Com Ports...................................................................... 410
Reader Settings ....................................................................... 413
Absorbance Wavelengths...................................................... 415
Fluorsecence/Luminescence Filters ........................................ 416
Dispenser Settings .............................................................. 418
Reader Control Panel ................................................................ 417
Preheating.......................................................................... 417
Testing the Reader................................................................... 422
406 | Chapter 19: Reader Control
When you have Two Readers
Gen5 lets you set up and control two readers simultaneously. Here's how Gen5
determines which reader to deploy when you have two readers attached to your PC.
Note: Fluorescence and Luminescence protocols are not instantly
interchangeable between Synergy 2/4 and other BioTek readers. (The
Synergy 2 and Synergy 4 have newer basecode.) When you try to read
a plate using a protocol defined on a different reader, Gen5 will alert
you of the need to edit the Read step. To use a protocol created with a
different reader, open all the Read steps while communicating with the
current reader. This action will update the protocol to match the
current reader's capabilities.
Compatibility
Gen5 tests the readers for compatibility with the Procedure when you:
 Edit/Open an Existing Procedure
1.
 Read a plate
All available, i.e. not busy, readers are tested for compatibility. A reader
performing a read is considered busy.
Compatibility is determined by these criteria:
 If the protocol was created for the Clarity, then the reader must be a Clarity.
If the protocol was not created for the Clarity, then the reader cannot be a
Clarity
 If it is not a Clarity protocol, Gen5 tests the reader's capability to perform
the required detection method:
 Absorbance: minimum and maximum wavelengths supported
 Fluorescence
 Luminescence
 Spectrum Scans
 Linear Scans
 Area Scans
 Gen5 tests the reader's capability to perform:
 Incubation: minimum and maximum temperature supported
 Shake
 Dispense: number of dispensers available
 Gen5 tests the reader's capability to perform:
 Well Mode: maximum number of reads, shakes, and dispenses
 Synchronized Plate Mode: maximum number of synchronized plate reads,
shakes, and dispenses
When you have Two Readers | 407
2.
3.
4.
 Pathlength Correction
If exactly one reader meets the criteria, it is automatically selected to edit the
Procedure or read the plate
If more than one reader meets the criteria, Gen5 determines if one of them was
last used to edit the Procedure or read the plate. If so, then it is selected. If not,
the user is prompted to select which reader to use.
Gen5 checks the Protocol for a reader type and serial number to determine
which reader was last used. If it does not find an exact match, but only one of
the readers is the same type, that reader is selected.
If none of the readers matches the criteria:0.
 Gen5 will display an error message and offer to Continue or Cancel. Users
who select Continue can modify the Procedure to make it compatible with
their reader
408 | Chapter 19: Reader Control
Reader Configuration
System> Reader Configuration
Use these controls to tell Gen5 about the attached reader(s) and to retrieve software
version information for tech support or other purposes. The status of an instrument is
displayed as Ready or Busy: Ready to perform a read or Busy doing so.
Special note for Clarity users: Configuration parameters and port
settings can only be defined through the Clarity PC software. See
Setting up the Clarity Luminometer in the Getting Started Guide
Add a Reader
Click the Add button to connect up to two readers to the system. You'll select the
Reader Type and the Communication Port its plugged into on your PC (see page 410),
and if necessary, define Setup properties.
and
lead to Reader Settings on page 413
Modify a Reader
Highlight a reader and click Modify (or double click a reader) to change the reader's
Com Port or Setup properties
Delete a Reader
Highlight a reader and click Delete to eliminate it from potential use by Gen5.
ActiveX Version
Click the Active X button to retrieve the latest software version number:
You may need to provide this information when seeking assistance from BioTek's TAC
(Technical Assistance Center)
Controlling the Clarity | 409
Controlling the Clarity
System> Reader Control> Clarity
Microplate Holder Control
The Clarity’s microplate holder can be opened and closed only through software
control. Under Move Plate:
 Click Out to extend/open the microplate holder
 Click In to retract the microplate holder into the reading and heating
chamber
Important: Do not forcibly push in or pull out the microplate holder!
If for any reason you cannot control the holder using the software, use
the Allan key supplied with the instrument to extend or retract the
holder. Refer to the Clarity™ Operator’s Manual for more information.
Prime
The reagent lines and injectors should be primed with the dispensing fluid before
running the protocol. Click Priming to open the Priming Parameters dialog.
Refer to the Clarity Operator’s Manual for complete priming
instructions.
To prime the injectors:
1.
Fill the reagent bottle(s) with the fluid to be dispensed.
3.
Click on the injector’s check box. The drop-down list box Direction, Volume
[µl] and Strokes are enabled.
2.
4.
5.
Select System>Reader Control>Clarity and click Priming for the Priming
Parameters dialog. All installed injectors are displayed. Injectors marked by an
asterisk (*) have yet to be initialized. Initialization takes place automatically
when the injector is used.
Set the Direction To Mpl. Specify the Volume [µl] and the number of Strokes or
cycles. The total liquid volume is displayed as the Total Volume.
Click Prime to prime the injector(s). 0.
Heating
The Clarity’s optional incubator is controlled via software. Click the Incubation...
button to access the Sample Incubation dialog.
Refer to the Clarity Operator’s Manual for complete heating
instructions.
410 | Chapter 19: Reader Control
About Com Ports
Com Ports are communication ports that allow your computer (PC) to connect to and
control other devices. BioTek ships the required serial and/or USB cables with the
reader. You must tell Gen5 which com port is used to connect to a reader. (More on
page 413)
Serial cable (see samples on page 411)
Generally, Windows®-compatible PCs have two serial com ports, which it assigns as
Com1 and Com2. If you're uncertain which com port the serial cable is plugged into,
try Com1 and Test Communication. If you receive an error, try Com2.
Advanced users can attach additional com ports to a PC, and can use Window's
Control Panel to identify or modify the com port number.
USB cable (see samples on page 412)
For compatible instruments, BioTek ships USB-Driver software along with the USB
cable. Follow the instructions provided for USB installation, e.g. installing the USB
Driver software, and review the ComPort Guide to learn how to identify or modify the
com port number.
Troubleshooting
Review the information provided in the Troubleshooting chapter for resolving
communication errors.
Controlling the Clarity | 411
Serial Communication Cables and Ports 9-pin and 25-pint
412 | Chapter 19: Reader Control
USB Communication Cables and Ports
Reader Settings | 413
Reader Settings
System> Reader Configuration> Add/View
 Prerequisite: You must be authorized to make changes to the
Reader Configuration. If the options are grayed out, contact your
System Administrator for access rights.
Special note for Clarity users: Configuration parameters and port
settings can only be defined through the Clarity PC software.
Use these controls to tell Gen5 the type of reader, communications port and baud rate
to use:
1.
2.
3.
Click the down arrow to select the Reader Type
Enter number of the Com Port in the text field
BioTek recommends retaining the default Baud Rate or transmission speed. If
you have a compelling reason you can select another rate from the list
Baud rate settings can cause "serial read" errors: when the baud
rate is set to a non-default setting for Synergy and PowerWaveXS
readers, Gen5 will be unable to communicate with them if they are
turned off and then turned on again while Gen5 is running.
4.
Generally, the Setup option is not needed. Gen5 communicates with the reader
to obtain the probe sizes and configuration of the filter/wavelengths tables. 0.
Reader Types
Gen5 only needs to know the basic model of reader, then Gen5 can communicate with
the reader to learn its specific capabilities, e.g. Incubation, Dispensing. BioTek
recommends installing the latest version of basecode for your reader, which is
generally free-of-charge and easy to obtain and install. Contact BioTek.
Com Port
Enter the serial communications port number. When using a USB connection to the
PC, the Windows® operating system sets up a "virtual" Com Port. Follow the
instructions below:
All BioTek Readers except the Clarity
1.
2.
Plug in the USB cable
For first time set up, Windows recognizes New Hardware, and prompts you to
install the required driver. Follow the installation directions provided with the
driver. When the wizard is finished installing the driver, a new "COM port"
will be available.
414 | Chapter 19: Reader Control
3.
4.
Go to Control Panel>Administrative Tools>Computer Management>Device
Manager>Ports(COM & LPT) to see the new virtual Com port assigned to the
USB.
Enter this port for the reader. 0.
Clarity Luminometers
1.
2.
3.
Connect the Clarity to the PC with the USB cable.
Launch the Clarity software, and go to Options>Com Port Settings. Select
USB.
Once you get this set up initially, you won't have to do it again unless you
switch to a serial port connection.
Close the Clarity software and launch Gen5. 0.
Gen5 will automatically use whatever connection was specified in the Clarity
software. All connection information is controlled by the Clarity software only.
Baud Rate
Make sure the Baud Rate matches the reader's settings. Consult your reader's
operator's manual for the correct rate. Readers without keypads, Synergy and
PowerWaveXS, will issue a "serial read" error when it is powered down and then up
again while Gen5 is running if the baud rate is set to other than the default setting.
Test Communication
Use this button when adding or modifying a reader to test the Com Port setting. Gen5
attempts to communicate with the reader and reports its results in an on-screen
message.
Setup
Generally, the Setup option is not needed. Gen5 communicates with the reader to
obtain the information it contains. Occasionally, you may want to view or modify:
 Absorbance Wavelengths (next page)
 Fluorescence/Luminescence Filters (on page 416)
Reader Settings | 415
Absorbance Wavelengths
System> Reader Configuration> Add/Modify button> Setup button
Use the Absorbance Wavelength tab to ensure that Gen5’s wavelengths table is aligned
with the reader’s internal table. Depending on the reader, you can specify up to six
wavelengths to be made available as default selections in the Read Step dialog
(Protocol>Procedure>Read).
 Get Wavelengths: retrieve wavelength values from the instrument
 Send Wavelengths: download and calibrate wavelength values. Enter the
desired values in the Wavelength fields and then click Send Wavelengths.
The values will be downloaded to the instrument, overwriting its existing
wavelength table.
Note: To exchange wavelength information between Gen5 and the
reader, the two must be communicating, i.e. the reader must be
turned on and correctly configured in Gen5.
Reader-Specific Information
Reader Series
Wavelength
range
Wavelength selection
ELx-Series
340-900
Filters: Update the reader
when changing filters
µQuant and PowerWave
series
200-999
Monochromator: selectable
by 1nm increments
Synergy HT and
Synergy 2/4
200-999
Monochromator: selectable
by 1nm increments
depends on specific
model
depends on specific
model
Note: You must conform to the specific BioTek reader procedures
when altering the reader's configuration. For filter-based readers, it is
your responsibility to ensure that the filters are positioned correctly
and recorded here accurately.
ELx-Series Filter-Based Readers
BioTek updates the on-board software with the current configuration of filters before
shipping the reader to you. Unless you change the filters without updating the onboard software, Gen5 will capture the filter-wheel configuration when it initiates
communication with the reader.
If you do change the filter-wheel configuration, you can use Gen5 to update the reader:
1.
Precisely record the wavelength and position of the filters before reinstalling
the filter wheel
416 | Chapter 19: Reader Control
2.
3.
4.
5.
In Gen5, select System>Reader Configuration and click the View/Modify
button
Click the Setup button, and select the Absorbance tab
Fill in the Wavelength table to match the filter-wheel configuration
Click Send Wavelengths. 0.
Fluorescence/Luminescence Filters
System> Reader Configuration> View/Modify button> Setup button
Normally, these controls are only needed when you are changing a filter wheel
The Filter Wheel Library can also update the reader's
Fluorescence/Luminescence Filters table. See the Filters and Mirrors
section beginning on page 173.
To change the current settings and download them to the instrument:
1.
2.
Select the filter Type using the drop-down list for each Filter position in the
Excitation and Emission filter wheels.
When applicable for the filter Type, enter Wavelength and Bandwidth values
in the fields.
The Wavelength value and its accompanying Bandwidth, in
nanometers, are etched into the filters. For example, the
Wavelength/Bandwidth combination of 485/20 will transmit light from
475 to 495 nm (10 nm on either side of the center). See the reader's
operator’s manual for details.
3.
When all values have been entered, click Send Values. The values will be
downloaded to the instrument, overwriting its existing wavelength table. 0.
To retrieve filter wheel settings from the instrument:
 Click Get Values. This reports the values in the reader's on-board memory.
Since the reader does not have the ability to mechanically determine the filter
configuration, these values may NOT truly represent the current filter wheels.
Find additional information about changing Filter Wheels and recommended
configurations in the Filters and Mirrors section beginning on page 173.
Reader Control Panel | 417
Reader Control Panel
System> Reader Control
or, click on the reader button in Gen5's toolbar to open the control panel.
If supported by the current reader, you can use this feature to view information about the
attached reader, control the reader door or plate carrier, and control incubation.
The reader must be connected, turned on, and properly communicating with Gen5™ for
the controls to be enabled. This means the reader must be "ready" not busy reading a plate
or running a system test, for example.
 Information
 Door/Carrier
 Pre-Heating (below)
 Dispenser (page 418)
 Tungsten Lamp (page 422)
Detailed information about the Filter Wheel and Mirror tabs is provided
earlier in this guide.
Pre-Heating Parameters
System> Reader Control> Pre-Heating
In the control panel for readers with incubation capability:
 The Set Temperature Procedure defined for the Protocol offers the ability to
activate Pre-Heating. This screen reflects the parameters defined in the protocol
 To use the reader as incubator in between experiments: enter the temperature
in the Requested field and then check On to begin pre-heating. Most BioTek
readers allow a temperature range of 20-50°C.
 The temperature will rise or fall to the Requested temperature, as appropriate.
Off disables the incubation unit; the temperature will return to ambient.
 The Actual field reports the current temperature (Celsius) of the incubation
unit.
 The Total Time field reports the total time elapsed since the On box was
checked. Associated with the Total Time field, you can use the Beep after
checkbox to direct Gen5™ to "beep" continuously after the specified
duration. The clock starts when the incubation unit is turned On.
 The Time Since Reached field reports the total time elapsed since the
incubation temperature reached the Requested temperature. Associated
418 | Chapter 19: Reader Control
with the Time Since Reached field, use the Beep after checkbox and field to
tell Gen5 to "beep" continuously after a specified duration. The clock starts
when the incubation temperature reaches the Requested temperature.
 Temperature Reached is displayed when the incubation temperature reaches
the Requested temperature.
Note: As the temperature of the incubation unit approaches the
Requested temperature, it may take a few minutes to settle within an
acceptable tolerance (+/- 0.5° C). During this settling period, the
Temperature Reached indication may appear for a few seconds,
disappear, then reappear moments later. The Time Since Reached field
will automatically reset to 00:00:00 each time the indication appears.
If the Beep after checkbox associated with Time since reached field is
enabled and set to, for example, 10 minutes, Gen5 will "beep" 10
minutes after the incubation temperature has consistently settled
within +/- 0.5° C of the Requested temperature.
Dispenser Settings
System> Reader Configuration> Add/Modify button> Setup button
Read Only: for everyone except BioTek qualified technicians, these
controls provide information, they do not let you alter it.
Use the Reader Control Panel to position the dispensers for performing
maintenance.
Calibration Volumes
Gen5 shows the minor differences between the expected (Target) dispensing volumes
and the actual (Measured) volumes, as determined at the BioTek factory.
 Click Get Values. Actual measured values will be uploaded from the reader's
current internal tables.
Injector Position
Gen5 shows the current position of the injector, if applicable to the reader.
 Next to Top Probe
 Above Bottom Probe
Also see: Special filter position requirements for the Synergy HTTR w/Injectors on
page Error! Bookmark not defined..
Reader Control Panel | 419
Dispenser Control and Maintenance
System> Reader Control> Dispenser
In the control panel for readers with dispensing or injection capability:
Dispenser: up to two dispensers may be attached to the reader, use the drop-down
list to select the one you want to control or review information about.
Dispenser Information
The fields on the left side of the screen display the current state of the selected dispenser:
 Connected: the reader detects a live connection (Yes) via serial cables with
the dispenser module. "No" indicates a faulty connection. Check the
cabling.
 Initialized: Prior to performing a dispense step the dispenser module must
be initialized. Click the Initialize button if this status reports "No."
 Primed: Prior to performing a dispense step the dispenser must be primed.
Place the priming plate on the carrier and click the Prime button if this
status reports "No."
 Injector position: Gen5 reports the position of the injector in relation to the
reader's probe
Dispenser Routines
Ensure normal and correct communication between the
dispenser module and reader
Prime the tubing with fluid
420 | Chapter 19: Reader Control
Remove and recover fluid from the tubing
Move the dispenser's syringe pump into maintenance
position for installation or replacement
When defining a Dispense Step in the Procedure you can also define
Tip Priming
Priming the Dispenser
This routine is only applicable for Readers with Injectors. Refer to your reader's
Operator's Manual for specific and more detailed maintenance guidelines.
Priming the tubing with reagent (dispensing fluid) is an important first step when
running an experiment. Likewise, flushing the tubing of reagent after each use is an
important maintenance step. The priming routine is used for both steps.
When dispensing volumes less than or equal to 20 µl/well, we
recommend specifying a tip prime volume that is equal to the dispense
volume. For dispense volumes greater than 20 µl/well, we recommend
a tip prime volume of 20 µl.
To prime the dispenser:
1.
2.
3.
4.
5.
6.
7.
8.
Fill the supply bottle(s) with the dispensing fluid when running an experiment
or with deionized or distilled water when performing maintenance. Insert the
supply (inlet) tubes into the bottles.
Place the priming plate on the carrier.
Select System> Reader Control> Dispenser
Set Dispenser to 1
Set the Volume to at least:
 1000 µl for pre-experiment priming
 5000 µl for maintenance
Set the dispense Rate (BioTek recommends 275 for priming)
Click Prime to start the process.
When the process is complete, carefully remove the priming plate from the
carrier and empty it.
Repeat the process for Dispenser 2, if applicable.0.
Maintaining the Tubing: Leave DI water in the system overnight or until the
instrument will be used again. Purge the fluid from the system and then prime with
the dispense reagent before running an assay.
Reader Control Panel | 421
Purging the Dispenser
This routine is only applicable for Readers with Injectors. Refer to your reader's
Operator's Manual for specific and more detailed maintenance guidelines.
Purging the dispenser is an important part of the recommended daily maintenance
routine. Gen5's purging capability can also be used to recover and preserve expensive
reagents.
To purge the dispenser of fluid:
1.
Remove the inlet tubes from the supply bottles.
3.
Select the Dispenser number: 1 or 2
2.
4.
5.
6.
Select System> Reader Control> Dispenser
Set the Volume (2000µl guarantees all fluid in the system's tubing is removed).
Click Purge to start the process.
When the purge is complete, repeat the process for the other Dispenser, if
applicable. 0.
After purging the system, you may wish to run a quick DispenseOnly experiment to visually verify the dispense accuracy.
Dispenser Prime/Purge Rate
The allowable volume ranges for each dispense rate are:
Rate (ul/sec) Volume Range (ul)
225
5-5000
250
15-5000
275
25-5000
300
30-5000
BioTek recommends using the default rate of 275 for priming.
422 | Chapter 19: Reader Control
Tungsten Lamp Control
System> Reader Control > Tungsten Lamp
Use this control to turn off the Tungsten Lamp when it is not needed. Follow the menu
path shown above to access the controls. Note: when the tungsten lamp is not required
in a Procedure, Gen5 turns off the lamp.
Conversely, you can use the Turn Lamp On button. The lamp takes approximately
180 seconds to warm up before measurements can be taken. When the lamp is not
warmed up before a reading is requested Gen5 displays a message that counts down
this warm up period before prompting you to put the plate on the carrier.
Testing the Reader | 423
Testing the Reader
Gen5™ provides the following options for testing the reader:
 Run a System Test
 If you've purchased BioTek's Gen5 Reader Diagnostics Utility:

Run the Absorbance Test Plate
Reader System Test
System> Diagnostics> Run System Test
The System Test for the Clarity™ Microplate Luminometer must be
performed using the Clarity PC software. Refer to the Clarity
Operator’s Manual for instructions.
Run the Test
Most BioTek readers perform a self test every time they're turned on, but when you
want to view and/or print the results of a system (aka optics) test:
1.
Select System> Diagnostics>Run System Test
3.
When the test is completed: 0.
2.
When there is more than one reader attached to the PC, select the desired
reader and click OK
1.
2.
3.
Test History
Fill in the text fields, User, Company, Comments, to be included in
the report of the test results. Then, click OK.
Print the report to retain a hard copy for your records
Save As to convert the results to a text file. This is especially useful
when troubleshooting a reader. You can email the text file to BioTek
TAC. 0
Gen5 keeps the results of System Tests when they are performed using the menu
controls. To review or print them, select System> Diagnostics> History...
424 | Chapter 19: Reader Control
System Test Results
System> Diagnostics> History
Immediately after running a system test on the reader, Gen5 displays the results, and
then stores them in History (in the shared database).
Print
Click Print to generate a paper version of the results.
Save As
Click Save As to convert the results to a text file. This is especially useful when
troubleshooting a reader. You can email the text file to BioTek TAC.
 Gen5 opens the standard Windows® file save dialog, and sets the file type to .txt
Text files are the default format for Notepad® and is recognized by most word
processing programs.
 Optionally, click in the File Name field to modify the default name:
SystemTest. Add the date, instrument name, or other information to ensure the
file has a distinguishable name.
 Use the drop-down list and other tools to navigate to the Save In location
Reader Test History
System> Diagnostics> History
Gen5™ keeps this database of test results from System (formerly-called Optics) Tests and
Diagnostic Tests, if applicable. It is stored in Gen5's shared database.
 Double-click the desired test to open it on screen and to print it or save it as a
text file
Use the options in the Test History dialog to:

Click the Refresh button to capture any tests that were conducted since
the dialog has been opened

Use the drop-down lists in the Selection area to filter the list of tests shown
by reader (Device) and user (Operator), if applicable
 Column Headers can be used to sort the tests: click on a header to sort the files
in ascending/descending order by that category. For example, click Status to
sort the files by Pass/Fail. Click the same column header to reverse the order
 Highlight a test and click:
 View: to open it for viewing, printing, saving as a text file
 Delete: to delete it, erase it from the database.
Chapter 20
System Management
This chapter supplements the Getting Started Guide shipped with
the Gen5 product CD, which you should consult first for installation
and intial set up instructions.
System Requirements .............................................................. 426
Gen5’s System Administrator .................................................... 427
Changing your password (Gen5 Secure) ..................................... 428
Changing your Startup Preferences ............................................ 429
Customizing the Toolbar ........................................................... 430
Plate Type Database................................................................. 431
426 | System Management
System Requirements
Before installing Gen5™ make sure your hardware meets the minimum requirements.
Computer Requirements
For Gen5 to run successfully, the computer must meet the following requirements:
 Windows XP or Windows 2000 (Professional Editions)
 Pentium III-Class PC (or compatible) processor (500 MHz or higher)
 512 MB RAM or higher
 2 GB Hard Drive space or higher
 Designed for XGA Resolution at 1024 x 768 or higher
 CD-ROM Readable Drive
 Keyboard & Mouse
 Microsoft Internet Explorer v 5.0 or higher (for online Help)
 Serial or USB port for BioTek instrument
Reader Requirements
Verify that the Base Code and Assay Code built into your BioTek reader is compatible
with Gen5. BioTek has validated the following list of base codes. Any instrument with
the base codes listed below or higher is compatible with Gen5.
If your instrument has a base code with a version lower than these
please contact TAC to download and install updated software
Instrument
Base Code
Powerwave
1.21.1
PowerwaveXS
1.06
Synergy 4
Synergy 2
1.03
1.03
Synergy HT
2.24
FLx800
1.15
ELx800
3.07
ELx808
3.15
µQuant
2.02
Gen5's System Administrator | 427
Gen5's System Administrator
For all levels of Gen5 except Gen5 Secure
It is necessary to login as the System Administrator to change User Permissions and
Database Configuration, and to access any features which are denied as Users
Permissions
How to change the System Administrator's password:
This function is only available to the System Administrator. You
must login, System> Administrator LogIn, as the Administrator to
access these controls
1.
Select System> User Setup, and select the Administrator tab
3.
Enter the new password in both the New and Confirm password fields
2.
4.
Enter the current password in the Current Password field. Gen5 ships with the
password set to "admin."
Click OK. 0.
How to maintain Users Permissions:
Except in Gen5 Secure, access to Gen5's functions, like reading a plate, modifying a
protocol, and masking values, is defined equally for all users except the System
Administrator, who has all "permissions."
428 | System Management
Changing Your Password
For Gen5™ Secure Only
System> Security> Users
Users other than the System Administrator are limited to changing their own login
password.
How to change your password:
1.
Select System> Security> Users
3.
Enter your current password in the Current Password field
2.
4.
5.
Identify and open your user account: highlight and click Edit (or double click)
Enter your new password in both the New and Confirm password fields
Click OK. 0.
The password will take effect the next time you log into Gen5.
Contact your System Administrator if you've forgotten your password.
He/she can change your password without knowing the current one.
Changing Your Startup Preferences | 429
Changing Your Startup Preferences
For all levels of Gen5 except Gen5 Secure
System> User Setup
How to change your startup preferences:
1.
2.
Select System> User Setup
Use the drop-down to select the preferred method for Startup Action:
 Display Welcome dialog is the default setting, it opens Gen5 with a screen
that offers several common tasks including creating a new item or opening
a recently used item
 Create new experiment opens Gen5 with the Protocol selection dialog
open, as if the user had selected File>New Experiment
 Start at system menu opens Gen5 showing the File, System and Help
menus only. Since neither a protocol nor experiment is open, the workspace
is blank.
3.
4.
Use the 3-dot button to change your Protocol and Experiment Folders:
browse to the full path and directory to define the folder where you will
typically store protocol and experiment files. Gen5 will point to these folders
when you save and open a protocol or experiment.
Click OK. 0.
The changes will take effect the next time you log into Gen5.
Contact your System Administrator if you need assistance.
430 | System Management
Customize the Toolbar
Double click the toolbar, anywhere without a button, to open the Customize Toolbar
tool or select System> Preferences> Customize Toolbar
 Gen5 has two toolbars, Protocol and Experiment. Set the current state to
correspond to the toolbar you want to customize: select either File>New
Protocol or File>New Experiment, accordingly
 You can remove unused buttons. Add favorite buttons. Insert separators
between buttons to make them easier to distinguish.
 The Customize Toolbar dialog opens with the Current Toolbar Buttons
displayed in the box on the right and any unused buttons and the separator in
the box on the left. The Separator is always available and there is no limitation
on its use.
To remove buttons from the toolbar:
1.
2.
Highlight the button you want to remove from the toolbar in the Current
toolbar buttons box on the right
Click Remove
The button is moved into the Available toolbar buttons box and removed from
the toolbar when you click Close. 0.
To add buttons to the toolbar:
1.
2.
3.
Highlight the button you want to add to the toolbar in the Available toolbar
buttons box on the left
In the Current toolbar buttons box, highlight the button or Separator before
which you want to place the button
Click Add
The button is moved into the Current toolbar buttons box and added to the
toolbar when you click Close.0.
Use the Reset button to restore the toolbar to its default configuration.
To rearrange the buttons on the toolbar, first remove them and then add them in
the desired location
The toolbar configuration corresponds to the user logged into
Windows® at the time it is customized.
Plate Types Database | 431
Plate Types Database
System> Plate Types
About the Plate Types Database
All of the default and custom plate types currently stored in the database are
listed. When a reading is initiated, Gen5 sends the appropriate plate-type details
to the reader. The reader uses this information to precisely position the plate
when taking measurements. Most readers support only the Default Plate Types:
click the button to view this list. Consult your reader’s operator’s manual for a list
of supported plate sizes.
Gen5™ comes with details for more than forty industry-standard microplates. If
your reader supports custom plates, you can add your own microplates by
selecting Add, or Import them from a previous version of Gen5 or KC4.
Plate Types Database Tools:

Click the Default Plate Types button to view the list and
dimension details of the plate types supported by all BioTek readers
 Double click a plate type in the Default or Custom lists to review its
dimensions, such as width, length, height, and the number of rows and
columns. Or highlight the plate and click View
Important: Only BioTek's Synergy and PowerWaveXS readers support
Custom Plate Types.
 Add: to add a new plate type to the database. Take and record careful
measurements of its size before creating the new record.
 View/Modify: to change or update the details of a plate.
Warning! Modifying the dimensions of the installed plate types is not
recommended; consider adding a new plate type instead. Please
contact BioTek with any questions regarding the current dimensions.
 Export and Import: to transfer custom plate types from KC4 or to and from
another Gen5 system. Learn more... Since the Plate Type Database is stored in
Gen5's SharedDB:
 you do not need to use the Export-Import tools to archive or backup the
database
 when the SharedDB resides on a network, all users connected to the
SharedDB reference the same Plate Types Database, so you do not need to
transfer custom plate types between system users
 Click Delete to remove a selected plate type from the database.
432 | System Management
Plate Type Measurements
When creating or updating plate dimensions, taking precise measurements is essential.
Use calipers with precision to 0.01 millimeters (mm) to gather the following
measurements. A standard ruler is not precise enough. Note: when entering values based
in 10 micron increments, values always end in 0 (zero).
Important! Dimension values are used by the software to calculate
reading positions. Any inaccuracies in these dimensions could
significantly affect your results.
Dimensions
 Number of Columns is the number of vertical columns of wells when viewing
the plate in its normal orientation. There are 12 in a 96-well plate.
 Number of Rows is the number of horizontal rows of wells when viewing the
plate in its normal orientation. There are 8 in a 96-well plate.
 Length is the longest dimension of the plasticware (the x axis).
 Width is the shorter dimension of the plasticware (the y axis).
Plate Types Database | 433
 Height is the distance from the bottom mounting surface of the plate to the top
face of the plate.
 Well Diameter is the diameter of any well.
 Top Left X is the distance from the left side of the plate to the center of well A1.
 Top Left Y is the distance from the top of the plate to the center of well A1.
 Bottom Right X is the distance from the left side of the plate to the center of the
last well on the plate. In a 96-well plate, this is H12.
 Bottom Right Y is the distance from the top of the plate to the center of the last
well on the plate. In a 96-well plate, this is H12.
Import and Export Plate Types
System> Plate Types
Gen5 provides the Export and Import feature to transfer custom plate types from KC4
or to and from another Gen5 system. It may be necessary, for example, to import a
custom plate type associated with a Gen5 protocol you've received from BioTek or
another Gen5 system user.
The Import routine examines the plates in the import file and compares them to the
current plate type files. New plate types are added to the database. Existing plate types
with new dimensions will replace the existing dimensions after user confirmation.
Existing plates with identical dimensions are ignored. Gen5 Secure logs the event in
the System Audit Trail.
How to Import Plate Types
When you have one or more custom plate types exported from KC4 or Gen5 (and
therefore in the proper file format):
1.
2.
Click Import. Gen5 opens the standard Windows® browse dialog.
Locate the plate type file and click Open.
Gen5, by default, looks for files with the .ptf extension, but, it will accept a file
with any extension, as long as the data is correctly formatted. Change the Files
of type: using the drop-down list to see all file types. 0.
How to Export Plate Types
When you want to export one or more custom plate types:
1.
2.
3.
Highlight the files in the Custom Plate Types box. Hold the Ctrl key to select
multiple files.
Click Export. Gen5 opens the standard Windows® Save As dialog.
Browse to the storage location for the files, enter a File name and click Save.
Gen5, by default, assigns the .ptf extension to the file, but you can change it, if
desired, by typing a different filename extension. 0.
434 | System Management
Chapter 21
Troubleshooting
This chapter is intended to help you resolve or recover from error
messages or other system trouble. The Fluorescence and
Luminescence chapter also contains troubleshooting suggestions
particular to those detection methods.
Communication Errors .............................................................. 437
Error Messages ........................................................................ 438
Calculation Warnings ................................................................ 439
Restoring Optimal Performance.................................................. 442
System Administrator's Password............................................... 442
436 | Troubleshooting
Troubleshooting
Here are some guidelines for error recovery, find additional information in Gen5’s Help:
 First Response: Run a System Test on the reader to restore the reader's initial
settings and computer communication capability. Note: to stop the alarm on
readers without keypads (e.g. Synergy) press the plate-carrier button
 Reboot your Computer and Reader: When you can't run a system test, e.g.
Gen5 is not responding, or when running a system test doesn't resolve the
issue, turn off your computer and reader, check all the cabling, i.e. make sure
your serial or USB cable is in good condition and is properly connected to the
PC and reader, and then, power on your computer and reader. This should
refresh the devices and reset communication parameters
 Communication Errors: PC to Reader on page 437
 Database Error Recovery in the Managing Files chapter
 Calculation (Data Reduction) Warnings on page 439
 Reader Error: #### on page 438
 Handling Other types of Error Messages refer to Gen5’s Help
 Unknown System Admin's Password on page 442
 Computer Performance Slowdown on page 442
 Troubleshooting Fluorescence/Luminescence Measurements in a previous
chapter on page 169
 Excel® errors refer to Gen5’s Help
Visit BioTek's website for useful suggestions on getting the most from your reader:
http://www.biotek.com/products/technotes.php.
 Other Known Issues
Gen5 installs a Read Me file in the root directory, the default path is
C:\Program Files\BioTek\Gen5 (software level)\ReadMe.txt. It lists known
issues you may have encountered. Locate and review the file and contact
BioTek TAC for additional information or support.
 Synergy 2/4 to non-Synergy 2/4 readers (and vice versa)
Protocols created with a Synergy 2 or Synergy 4 reader are not instantly
compatible with other readers, and vice versa. You must re-validate the
Procedure with the current reader: open the Procedure and click Validate.
Generally, this corrects the error. If not, open each step in the Procedure and
review it for compatibility with the current reader.
Communication Errors: Reader to Computer | 437
Communication Errors: Reader to Computer
Important Information:
 To prevent damage to the reader, always turn OFF the reader or the computer
before removing or inserting a communications (serial or USB) cable
 Gen5™ and the reader-communication parameters will supersede the
Windows® settings. Windows communication port configuration settings
should not need adjustment to enable proper communications
When the computer (PC) won't communicate with the reader:
1.
2.
3.
4.
5.
6.
7.
Confirm that the reader passes its system self test. Most readers perform a self
test when turned on. Refer to the reader's user guide for more details. The
reader will not communicate if it fails an internal system test. If the reader fails,
refer to the user's guide to resolve the failure.
Make sure the serial or USB cable is in perfect condition and properly
attached to the port defined in the Reader Configuration dialog (e.g. COM 1).
Correct and reboot both PC and Reader. Test communication.
Confirm the Baud rate (or transmission speed) defined in Gen5's Reader
Configuration matches the reader's settings. Consult your reader's user guide
for the correct rate. Correct Gen5's Reader Settings to match the reader and
reboot both PC and Reader. Test communication.
Disable the Calculation Option: Perform data reduction after each read to
give Gen5 sufficient time between obtaining measurements to perform
calculations
Confirm that the serial cable was obtained from BioTek. Serial cables are not
universal. Consult the reader’s user guide for proper cable configuration or
contact BioTek customer service to purchase a factory tested cable. After
installing a known, good cable, reboot both PC and Reader. Test
communication.
Confirm with your computer supplier or a local PC technician that the serial
port has been enabled. For example, the IBM Thinkpad® was originally
shipped with the serial port disabled. Correct and reboot both PC and Reader.
For advanced PC users, the serial port of the reader and PC can be
independently tested using an independent serial-communication software
package such as Windows Terminal™, Hyper Terminal™, or ProCom™.
BioTek does not support or sell these programs. 0.
 Select flow control for “XON/XOFF” and send an ASCII asterisk symbol (*)
to the reader. The reader should initiate a self test and return the results to
the PC. If the reader fails to communicate, test the reader on an alternative
PC to confirm which device is at fault. Please contact BioTek if the reader is
diagnosed to be faulty.
438 | Troubleshooting
Error Messages
Here are some guidelines to help you quickly resolve an error:
1.
Make note or take a "print screen" of the error message
3.
Call BioTek's Technical Assistance Center (TAC) if you are unable to resolve
the issue yourself. 0.
2.
Locate and follow the specific instructions/suggestions for the error provided
in the reader's operator's manual
Potential Error Messages and their Resolutions
 Reader Error ###: refer to the reader's Operator's Manual to identify the
specific error. You may be able to resolve it yourself.
 File Not Found: there are several potential causes for this error. In a shared
database environment, another user may have the file open. Check with your
colleagues to eliminate this as the cause. When using the Windows® File
System for file storage, use Windows Explorer to verify the location of the file.
 Bandpasses overlap: the selected Excitation and Emission filters are too close.
Change one of the selected filters. Learn more in the Fluorescence and
Luminescence chapter.
 Baud rate settings can cause "serial read" errors: when the baud rate is set to a
non-default setting for Synergy and PowerWaveXS readers, Gen5 may be
unable to communicate with them if they are turned off and then turned on
again while Gen5 is running. Gen5 may reset the baud rate to the default
setting in this scenario. Run a System Test to return readers to their initialized
state
Calculation Warnings | 439
Calculation Warnings
When Data Reduction steps generate an error or cannot be calculated, Gen5 displays
and logs a Calculation Warning. Here are some guidelines for pinpointing and
correcting the source of the error.
Curve Fit
 Not enough data points to fit
If the plate was read successfully, i.e. all the data points obtained, make sure
you have defined the minimum number of X-Axis points, e.g standards, for the
selected curve fit. See Curve Fit: Minimum Number of Standards in the Data
Reduction chapter.
 Too many data points
The Spline curve fit is the only option with a limit on the number of X-axis
points. Either change the curve fit method or reduce the number of standards,
dilution samples, or calibrators, i.e. the number of X-data points.
 The selected curve fit method does not accept data points with identical X
values
The Spline and 4-P curve fits cannot be plotted when X-axis values are
identical. Either:
 select a different curve fit
 change the Data In selected for the X-axis
 if the selected X-axis data is based on a Transformation, rewrite the formula
to suppress duplicate values in the results
 The degree of the polynomial regression fit has been reduced
If desired, you can either:
 Reduce the Degree
 Add more X-axis points, e.g. standards
 Math overflow error
Check the Extrapolation setting
440 | Troubleshooting
or Interpolation formulas (on the Data Out tab) to make sure they are not
raising values to too high a value.
 Curve fit generic error
Is the curve fit 4-P?
Formula: Y = (A-D)/(1+(X/C)ˆB) + D
If so, this error may be indicating that the calculated B parameter <=0
 Curves do not support multi-indexed data sets
It is possible the Procedure was changed from an endpoint read to a kinetic
analysis (or other multi-index option) without revising the curve generator.
Review the Data Reduction steps and make the necessary adjustments, e.g.
Well Analysis may be a better fit.
 The 4-parameter fit is not convergent. It is probably not the best fit
Gen5 performs multiple approximations to plot a 4-P curve. It is expected that
the err (error) will decrease with each approximation, indicating a better fit is
being determined during each iteration. Gen5 displays this message when the
err does not decrease.
Select another curve fit method.
 Error during calculation. Data to fit not compatible with axis type
Review the Data Reduction> Curve Analysis definition, is the Axis Data set
to Log? and some of the Data In values are <0?
If yes, change these settings to eliminate the error.
Validation
 At least one validation condition failed
This message alerts you to the results of a Data Reduction>Validation
formula. A criterion of your experiment may not have been satisfied. Review
the results.
Cutoff
 Cutoffs do not support multi-indexed data sets
It is possible the Procedure was changed from an endpoint read to a kinetic
analysis (or other multi-index option) without revising a Data Reduction>
Cutoff step.
Review the Data Reduction steps and make the necessary adjustments, e.g. it
may be possible to use a Validation formula in place of Cutoff results.
Calculation Warnings | 441
 Cutoffs are not in increasing order. Symbols can not be determined
Review the Data Reduction> Cutoff formulas. They must be input in
ascending order, from the lowest (obtained or calculated) value to the highest.
 Some cutoffs could not be calculated. Symbols cannot be determined
Review the Data Reduction> Cutoff formulas. Try rewriting them, making
sure to reference valid Well IDs, non-masked data values and logical formulae.
Well Analysis
 Well Analysis requires multi-indexed data set
It is possible the Procedure was changed from a kinetic analysis (or other multiindex option) to an endpoint read without revising the Well Analysis step.
Review the Data Reduction steps and make the necessary adjustments or
update the Procedure to define kinetic or scanning analysis to generate a multiindex data set.
442 | Troubleshooting
Restoring Optimal Performance
Numerous factors can affect your computer's performance. If you notice a slowdown
in Gen5's performance, follow these suggestions:
 Close all other applications, including Internet browsers, when running
Gen5
 Do not display Gen5's "Curves" data in the Plate View while performing a
kinetic analysis. Wait until the read step is finished before viewing the
"Curves" data set. Displaying the Curves data set during a Kinetic read can
consume excessive resources resulting in performance degradation. You can
drill down to a Well Zoom to monitor the progress of one well, then,
leaving the Well Zoom open, change the Matrix Data to a numeric view
 Disable the Calculation Option "Perform data reduction after each read"
to give Gen5 sufficient time between obtaining measurements to perform
calculations
 Disable the auto-Save options for interim reads: Save Options can be set to
free up resources.
System Administrator's Password
Contact BioTek Customer Care if you've lost or forgotten the System Administrator's
password: BioTek Customer Care
The System Administrator's password does not expire, but if a change in personnel, or
some other cause has resulted in your team not knowing the password, you can
contact BioTek for a new one.
Gen5 ships with the System Administrator's password set to "admin."
Index
Symbols
!exclamation points!....................................317
* Asterisks explained ..........................102, 310
.glb...................................................................39
.pla...................................................................39
.prt ...............................................39, 45, 47, 376
.xpt...............................................39, 45, 47, 376
?????...............................................................317
[brackets] ................................................39, 317
ß-Galactosidase............................................112
A
A260/A280...................................................112
About
Audit Trails ................................................391
AutoSensitivity ..........................................159
Data Reductions .................................116, 246
Fields and Field Groups .............................346
Fluorescence Analysis ...............................150
Gen5's Tables.............................................320
Luminescence Analysis .............................153
Multi-Plate Protocols .................................207
Plate Workspace.........................................313
the Menu Tree..............................................38
Access rights ................................................401
Acquiring data.............................110, 116, 246
Add
Buttons to the toolbar.................................430
New Plate Type..........................................432
New User .............................................15, 400
Text to a report...........................................346
Adding fields to a report............................349
Administrator, Power User .................18, 399
Aligning text in views and reports ...........344
Append to kinetic file .................................189
Apply calculation
entire plate..................................................256
individual wells.......................................... 256
Applying calculation to raw data............. 256
Area Scan ..................................... 127, 191, 200
Assay Control.............................................. 223
Assay Description....................................... 346
Assign Calibrators ...................................... 223
Assign Concentrations ............................... 226
Assign Sample Names
Multiple Plates........................................... 239
Assign Standards ........................................ 223
Audit Trail Notification ............................. 391
Audit Trails
About ......................................................... 391
Exporting ................................................... 392
User Comments ......................................... 391
Audit Trails.................................. 394, 395, 396
Automatic Sensitivity Adjustment
Fluorescence/Luminescence .............. 159, 169
Automatic Sensitivity Adjustment........... 156
Automatically-generated data reduction 246
B
Backup files.................................. 374, 379, 380
Bandwidth Verification.............................. 169
Bandwidth Verification Failed.................. 169
Basics .............................................................. 28
BioTek’s Technical Assistance Center........ 41
Bitmaps......................................................... 319
Blank Read1 ................................................. 316
Blanks
In plate layout ............................................ 223
Subtracting blank plates............................... 58
Subtracting blank wells ..................... 246, 259
Blanks ..................................................... 58, 223
Block light between reads.......................... 129
Build
Export File ................................................. 358
Report ........................................................ 334
Buttons
444 | Index
explained......................................................36
rearrange toolbar ........................................430
C
Calculation Options
Linear Scan ................................................202
Calculation Zone
Defining in Well Analysis .........................196
Symbols .....................................................317
Calculation Zone .........................................191
Calculations
formula syntax ...........................................252
Calibration Curve................................101, 262
Calibrator Plates ..................206, 208, 212, 214
Calibrator/Standards Plate Protocol112, 212
Cell growth studies.....................................189
CFR Part 11 ....................................................44
Change the Format of data values
In a curve....................................................330
In a report...................................................344
Change the Time Format............................326
Changing
Filter Cartridges/Wheels ............................173
Filter Wheel ...............................................416
Font ............................................................117
On-screen appearance ........................117, 315
the Procedure/Protocol...............................114
User's Permissions .....................................398
Well IDs .....................................................223
Your Password...................................385, 428
Your Startup preferences ...........................429
Check wells periodically ............................144
Clarity
Controlling .................................................409
Setup ............................................................23
Clipping text ................................................344
Close light between reads ..................129, 416
Comments
Audit Trail..................................................391
Communication errors ...............................437
Concentrations
Assigning ...................................................226
Determine by Curve Fit .............101, 262, 278
Concentrations/Dilutions..........................278
Connecting a Reader.....................................21
Continuous Shake .......................................139
Controlling the reader ................................123
Controls
Assign ........................................................223
Customize IDs ........................................... 223
Quality or Validation ................................. 301
Reader Control Panel................................. 417
Controls........................................................ 223
Copying
Copy and Paste images .............................. 356
Copyright information................................ vii
Corrected...................................................... 316
Corrected data sets ..................................... 259
Creating
Header and Footer for Reports .................. 349
New Experiment ........................................ 109
New Protocol ............................................. 112
Standard Curve .................................. 101, 262
Current Password............................... 385, 428
Curve
4 Parameter ................................................ 266
Change the appearance .............................. 330
Generate multiple standard curves............. 282
Minimum number of standards.................. 269
Polynomial................................................. 268
Remove/hide text....................................... 330
Standard............................................. 101, 262
Titer ........................................................... 283
Using curve from another plate ................. 214
Curve ............................................................ 320
Curve Analysis
Data In ....................................................... 277
Curve Analysis.................................... 116, 246
Curve Fit Method........................................ 269
Custom Plate Layout.................................. 229
Custom Plate Type ..................................... 431
Customize Well IDs.................................... 223
Customizing
Data Views ................................................ 117
Reports....................................................... 338
Toolbar....................................................... 430
Well IDs..................................................... 223
Well Zoom View ....................................... 194
Cutoffs
About ......................................................... 297
Formula Syntax.......................................... 298
Cutoffs Example.......................................... 298
D
Data
Change or mask raw data........................... 324
Mask/unmask values.................................. 324
Data Audit Trail .......................................... 394
E | 445
Data Files
File Storage ................................4, 12, 47, 371
Maintaining Files ...............................370, 376
Organizing your Files ..........................10, 372
Data In for Curve Analysis ........................277
Data points
not showing................................................344
Data Reductions
How to set up .....................................116, 246
Top 5 things to know .................................246
Validation/Quality Control ........................301
Data Reductions ..................................116, 246
Data Set Naming Convention....................316
Data Views
Customizing ...............................................117
Modifying ..................................................330
Data Views ...................................102, 310, 315
Database Configuration .............................374
Database Management
Database Utilities .......................373, 376, 379
Error recovery ............................................379
Maintaining files ........................................376
Optimize performance ...............................377
Plate Types Database .................................431
Reduce the size ..........................................381
Setting up ...................................................374
Test connection ..........................................374
Decimal places
in Data Reduction ......................................255
Setting number of...............315, 323, 328, 330
Default data reduction ...............................246
Default Protocol...................................120, 223
Default Report .....................................338, 349
Define method to display data when it's too
long............................................................344
Defining
Concentrations/Dilutions ...........................226
Filter cartridges ..........................................175
Procedures..........................................113, 122
Reporting requirements..............................334
Timelines .............................................69, 186
User's Permissions .....................................398
Delay .....................................................143, 146
Delay before integration (Time-Resolved
Fluorescence) ...........................................156
Delay Before Sampling...............................156
Delay Between Samples .............................156
Delete
Files............................................................376
Plates from an Experiment................. 109, 114
Delta OD ...................................................... 258
Design
Export ........................................................ 352
Protocol...................................................... 112
Difference Between Columns.................... 256
Difference Between Rows.......................... 256
Digital signature ......................................... 390
Dilution Factor ............................................ 252
Dilutions............................................... 226, 278
Dispense reagent
Dispense Rate ............................................ 141
in a Kinetic Analysis.............................. 94, 97
in an Endpoint Analysis............................... 95
Dispenser control
Priming ...................................................... 420
Purging....................................................... 421
Dispenser control........................................ 419
Display measurements....................... 102, 310
DNA Purity.................................................. 169
Dual Wavelength
Data Reduction .................................. 116, 246
How to perform dual-wavelength subtraction,
Endpoint................................................. 258
Duration
Kinetic time course.................................... 186
Long/discontinuous kinetic........................ 189
Pre-Heating................................................ 417
Shake Step ................................................. 139
E
Edit Report Items ........................................ 344
Editing
Procedure................................................... 114
Report elements ......................................... 338
Electronic Signature............................ 389, 390
Email............................................................. 356
Email Support................................................ 41
Endotoxin Analysis ...................................... 89
Endpoint Absorbance
Protein Quantification.................................. 66
Error bars ..................................................... 330
Error Messages
Communication Errors .............................. 437
Database Errors.......................................... 379
Error Messages............................................ 438
Essential Concepts ........................................ 44
Excel®
446 | Index
Shortcuts not working ................................436
Excel® ...................................................105, 363
Experiment
multiple plates............................................208
printing results ...........................................104
setting up....................................................109
Experiment vs Protocol ................................45
Export Builder
Using..........................................................358
Export Builder .....................................117, 359
Export Content ............................................358
Export File Settings .....................................359
Export Multiple Plates................................353
Exporting
Results........................................................352
Sample IDs.................................................243
System Audit Trail.....................................396
F
Fast Kinetics ...................................................97
FDA Electronic Records Compliance .44, 388
FDA requirements
Signature ................................................389
Fields and Field Groups .....................347, 350
File locations ..................................................47
File Management...................10, 370, 372, 376
File Storage...........................4, 12, 47, 370, 371
File types ........................................................47
Filter Cartridges
Changing a filter cartridge .........................173
Filter Cartridges ..................................173, 416
Filters ....................................................175, 415
Fluorescence Analysis ................................150
Fluorescence Experiment
Filter Set Options .......................................156
Monochromator-based ...............................133
Processing Modes Comparison..................166
Read Step ...................................................129
Time Resolved ...........................................154
Fluorescence/Luminescence
Automatic Sensitivity Adjustment .............159
Background too high..................................169
Measurement Options ................................156
Readings too low........................................169
Troubleshooting measurements .................169
Fluorescence/Luminescence .....................159
FLx800.....................................................21, 419
Font
Change ....................................................... 344
Changing.................................................... 117
Font ....................................................... 117, 344
Force the curve through the origin........... 268
Formula
Data point .................................................. 319
Easily Make Corrections............................ 256
Formula ........................................................ 256
Formula Syntax
Cutoffs ....................................................... 298
Transformations......................................... 252
Validation/QC criteria ............................... 302
G
Gen5 Secure ................................................. 398
Gen5™ Secure Only ............................. 18, 399
Getting Technical Assistance ...................... 41
Getting to Know Gen5 ........................... 28, 44
Glow Luminescence ................................... 112
Graph
Change the appearance .............................. 194
Modify ....................................................... 330
Graph.................................................... 117, 194
Groups
change........................................................ 398
Groups............................................ 18, 398, 399
H
hash mark..................................................... 344
Header/footer ............................................. 349
Help>About Gen5™..................................... 41
Hide the Legend.......................................... 330
How to
Set up Kinetic/Time course analysis........ 69
Set up kinetic analysis ............................. 69
Create a standard curve.......................... 101
View results ........................................... 102
Print results ............................................ 104
Set up Data Reduction ........................... 116
Resume a Stop/Resume step.................. 146
Set up Kinetic/Time course analysis...... 186
Set up kinetic analysis ........................... 186
Use the minimum kinetic interval.......... 188
Determine kinetic rate............................ 196
Set up Data Reduction ........................... 246
Perform dual-wavelength subtraction.... 258
Create a standard curve.......................... 262
View results ........................................... 310
Mask or change data points/values ........ 324
I | 447
Create and customize reports .................336
Change your password...........................385
Change your password...........................428
I
Icons
explained......................................................36
Import Sample IDs......................................242
Importing data.............................................110
Improve the transfection............................169
Incubation ....................................................417
Individual Well Auto Scaling......................39
Industry-standard microplates .................431
Initial Setup Tasks...........................................8
Initialize the dispenser ...............................419
INJECT..........................................................317
Injection assays..............................................97
Injectors ..........................................................94
Install Gen5 Secure..........................................8
Instrument Not Achieving Desired
Fluorescence Detection Limit ................169
Instrument Over-ranging...........................169
Interpolations
Curve Analysis...........................................278
Example .....................................................281
Formula syntax...........................................279
Introduction ...................................................28
K
KC4..................................................................39
Kinetic
Fast Kinetics for Absorbance.......................97
Long Interval, Discontinuous.....................189
Monitoring in real time ..............................295
Kinetic...................................................191, 295
Kinetic Absorbance Assays........................112
Kinetic Analysis.....................................69, 186
Kinetic Data Reduction Options listing ..196,
291
Kinetic Fluorescence .............................69, 186
Kinetic Multi-Detection Protocols
Restrictions ................................................183
Kinetic Multi-Detection Protocols ............184
Kinetic reads
How to create a protocol ......................69, 186
Setting the minimum time interval.............188
Kinetics Time format ..................................326
Known-concentration samples..................223
L
Lag time........................................................ 196
Lamp
tungsten...................................................... 422
Lanthanide ions........................................... 154
LD50........................................................ 86, 112
Learn About
Buttons......................................................... 28
FDA Electronic records submission .......... 388
Gen5 Databases ......................................... 373
Plate Workspace ........................................ 313
Legend
show/hide in graphs ................................... 330
Light shutter ................................................ 129
Linear Scan................................................... 127
LocalDB ........................................................ 370
Login
changing another user's password........ 15, 400
changing your password .................... 385, 428
controls/parameters.............................. 17, 386
Long-period kinetic analysis..................... 189
Low UV Applications................................. 112
Lowry Protein Assay............................ 66, 112
Lum............................................................... 316
Lum/E............................................................ 39
Luminescence
About Luminescence ................................. 153
Read Step................................................... 135
Troubleshooting......................................... 169
M
Maintain Files .............................................. 401
Manually entering data.............................. 110
Matrix
Modify ....................................................... 330
Matrix ................................................... 102, 310
Max V ........................................................... 196
Mean Maximum OD................................... 196
Mean Minimum OD ................................... 196
Mean V ......................................................... 196
Measurement Mode.................................... 162
Measurement Options........................ 150, 156
Menu Tree...................................................... 38
Microplate
Layout samples .................................. 115, 221
Plate Types ................................................ 431
Quick Read ................................................ 100
Read........................................................... 110
448 | Index
Read a blank plate........................................58
Microsoft Word .............................39, 352, 356
Microsoft® Excel 2000 ..........................39, 352
Minimum kinetic interval ..........................188
Minimum Number of Standards ..............269
Minimum Requirements ............................426
Mirrors
Dichroic .....................................................177
Mirror Holder Library................................180
Setting up a mirror .....................................178
Mixing...........................................................123
Modify
Fields and Field Groups .............................347
Graph .................................................194, 330
Matrix View...............................................328
Reports .......................................................338
Monitor Wells ..............................................144
Monochromator-based reads
About Fluorescence Monochromator.........151
Monochromator-based reads ....................133
Multi-detection kinetic ...............................183
Multi-Detection Protocols
Examples....................................................184
Multi-Detection Protocols ..........................182
Multi-index reads................................102, 310
Multi-Mode Reading
See
Multi-Detection......................................182
Multi-Plate Protocols
Plate Layout for..........................................210
Running a...................................................209
Using calibrator/standard curve .........212, 214
Multi-Plate Protocols ..........................207, 208
Multiple curves in one view ..............191, 330
Multiple plates.............................................229
Multiple reads..............................................123
Multiple standard curves...................226, 282
N
Naming
Data points .................................................319
Data Sets ....................................................316
New User Accounts ..............................15, 400
Numeric Format
Scientific, Decimal, Best Fit ......323, 328, 330
O
Onset OD......................................................144
Optics Position .................................... 150, 169
Optics Test ........................................... 108, 423
Optimize the database................................ 377
OUT+/OUT-................................................ 297
Outlook......................................................... 356
Out-of-range values.................................... 317
Overflow (OVRFLW) ................................. 317
Overlay multiple curves in one view....... 191
P
Page Break
add to report............................................... 334
Password
expired ......................................................... 18
Password, Changing your ................. 385, 428
Pathlength Correction ................................ 246
Perform
Calculation................................................. 256
Kinetic analysis.................................... 69, 186
Multiple detection methods ......... 69, 182, 186
Quick Read ................................................ 100
Performance degradation .......................... 436
Periodically check wells............................. 144
Permissions.................................... 18, 399, 401
Plate In/Out ................................................ 146
Plate Information ........................................ 230
Plate Layout................................. 223, 226, 229
Plate Reading....................................... 100, 110
Plate Types................................................... 431
Plate types currently stored....................... 431
Plate Types Database.......................... 431, 432
Plate Workspace
Resizing ............................................. 312, 313
Plate Workspace.......................................... 313
Plate#
About the workspace ................................. 313
Information ................................................ 230
Viewing results .................................. 102, 310
Plate>Audit Trail ........................................ 394
Plots
Curves........................................................ 330
Select ......................................................... 330
Plots .............................................................. 330
PMT Sensitivity........................................... 159
Polynomial Regression............................... 269
Polynomial Regression Curve Fit............. 268
Positive Control........................................... 223
Pound sign ................................................... 344
Q | 449
Power Export
Run.............................................................365
Power Export ...............................................365
Power Export Designer ..............................363
Power Export toolbar..................................363
Power User.............................................18, 399
Preferences
Startup..........................................15, 400, 429
Pre-Heating ..................................................417
Pre-Read Blank Plate ..............................39, 58
Pre-read for specific value .........................144
Print Preview ...............................................334
Printing
Defining the Report....................................334
Headers and Footers...................................349
Quick Print .................................................104
Reader test results ......................................424
Results........................................................118
Printing.................................................104, 334
Privileges
User Permissions........................................401
Procedure
Delay..........................................................143
Discontinuous Kinetic................................189
How to change ...........................................114
Monitor wells .............................................144
Read Step ...................................................200
Validating...................................................125
Procedure .....................................113, 122, 123
Procedure Summary ...................................320
Procedure, set up.........................113, 122, 123
Protein Quantification
Endpoint Absorbance...................................66
Protein Quantification ..................................66
Protein Quantitation ...................................112
Protocol
Applying Signature ....................................389
Default Setup .............................................120
Protocol Folder...............................................5
Protocol.........................................................389
Protocol Type
Default Protocol .........................................119
Multi-Plate .................................................206
Protocol vs Experiment ................................45
Protocol's Procedure ...........................113, 122
Q
Quality Controls..........................................301
Question marks ........................................... 317
Quick Read .................................................. 100
R
R and R Squared ......................................... 320
Read Step
About the Procedures................................. 123
Fluorescence .............................................. 129
Luminescence ............................................ 135
Spectrum Analysis..................................... 136
Read Step ..................................... 100, 135, 136
Read Type .................................... 127, 150, 153
Reader
Connecting................................................... 21
Reader............................................................. 21
Reader Control .............................. 44, 123, 417
Reader System Test............................. 108, 423
Reader Test History.................................... 424
Reading Parameters.................................... 123
Reading Procedure
Defining..................................... 100, 113, 122
Read-only permission ................................ 401
Reagent dispensing................................. 94, 95
Reduce database size.................................. 381
Reduce photo bleaching............................. 129
Reduction Requirements ................... 116, 246
Remove buttons .......................................... 430
Repair/compact the database ........... 377, 381
Report Builder ............. 117, 334, 338, 344, 349
Report Content.................................... 334, 344
Reporting
method to display data when it's too long.. 344
Reporting Engine ........................................ 334
Reports
Adding fields to ......................................... 350
Customizing....................................... 117, 338
Defining..................................................... 334
Headers and Footers .................................. 349
Include Sensitivity value............................ 161
Meaning of symbols, asterisks................... 317
Rules and Best Practice ............................. 117
Well Analysis Results................................ 340
Reports ......................................................... 334
Requirements for plotting a curve.... 101, 262
Reset Connection button............................ 374
Resize columns and rows .......................... 313
Resize the windows.................................... 312
Resolutions .................................................. 438
450 | Index
Restrictions and liabilities........................... vii
Results
Meaning of symbols, asterisks ...................317
Viewing......................................102, 117, 310
Results...........................................316, 317, 320
Results Object ..............................................363
Resume button.....................................110, 146
Rights and privileges..................................401
RNA Quantitation.......................................112
Running
Multi-Plate Experiment..............................209
Run-Time Prompts
Creating......................................................231
In experiments............................................230
Include in reports .......................................346
S
Sample Control Wells
Spiked or Known-concentration ................226
Sample Control Wells.........115, 221, 223, 283
Sample Dilutions.........................115, 221, 283
Sample IDs
Batch creation ............................................239
Erase/Clear IDs ..........................................239
Export.........................................................243
Import.........................................................242
Sample IDs ...................................235, 242, 243
Sample naming............................................235
Sample Protocols...............................28, 58, 66
Samples.........................................................223
Save
Curves/Graphs as pictures..........................356
Experiment...................................................45
Protocol......................................109, 112, 125
Save .................................................................48
Scales for Kinetic Reads................................39
Scan Options ........................127, 191, 200, 203
Scanning Data Reduction Options listing291
Scientific notation and significant digits
in Data Reduction ......................................255
Scientific notation and significant digits.323,
330
Security
Audit Trails ................................................391
Digital Signatures.......................................389
File Storage ......................................4, 12, 371
User Accounts......................................15, 398
Selecting Data Sets ......................................255
Sensitivity
Determine optimal setting.......................... 159
Lower/Raise............................................... 169
Report the Sensitivity setting..................... 161
Sensitivity............................................. 156, 169
Serial read errors......................................... 438
Set Temperature Procedure............... 145, 417
Setting
Start-up Preferences................................... 429
User's Permissions ..................................... 398
Shake the plate ............................................ 139
Shared Database.................................... 10, 372
SharedDB ............................................. 370, 374
Show
Plate Layout............................................... 313
Reading results .................................. 102, 310
Sign a protocol or experiment................... 390
Sign off.......................................................... 389
Signature Reasons....................................... 389
Signatures .................................................... 389
Significant digits ......................................... 323
Slow response time from Gen5 ................. 437
Software performance degradation ......... 437
Spectrum ...................................................... 316
Spectrum Analysis
Read Step................................................... 136
Viewing ..................................................... 191
Spectrum Analysis...................................... 203
Spiked samples.............................................. 89
Stand-Alone Multi-Detection Protocol .... 182
Standard Curve ... 101, 212, 214, 223, 262, 313
Standard User........................................ 18, 399
Standards
Assigning........................................... 223, 263
Minimum Number ..................................... 269
Startup Preference ...................................... 429
Statistics
Inter-Plates................................................. 209
Statistics................................................ 102, 310
StepWise™................................................... 123
Stop/Resume............................... 110, 143, 146
Subtracting a blank plate read .................... 58
Symbols and special notations.................. 317
Synergy 2...................................................... 131
Synergy 4...................................................... 133
Synergy HTTR............................... 21, 182, 183
Synergy HTTR w/Injectors ......... 94, 416, 419
Syntax
T | 451
in formulas
Cutoffs....................................................298
Interpolations .........................................279
Transformations .....................................252
Validation/Quality Control ....................302
System Administrator
Changing password......................................14
To Do List ......................................................8
System Audit Trail
Exporting ...................................................396
Viewing......................................................396
System Test ..........................................108, 423
System> Security.........................................384
System-generated data reduction .............246
T
Table..............................................................320
TAC .................................................................41
Technical Assistance.............................41, 438
Temperature
Incubation during an experiment ...............145
Pre-heading the Reader ..............................417
Temporary Files...........................................373
Text
not fully displayed......................................344
Time
hours, seconds format ................................326
Time to Peak ................................................196
Time-Resolved Fluorescence .....................154
Titer Assay ...................................................112
Titer Curve ...................................................283
Toolbar
Buttons and Icons Guide..............................36
Customize ..................................................430
Top Probe Vertical Offset...........................169
Trademarks ................................................... vii
Transformation............................................256
Transformation formula syntax ................252
Troubleshooting
Communication Errors...............................437
Fluorescence/Luminescence Measurements
...............................................................169
Restore optimal performance.....................442
Troubleshooting ..........................................436
Truncated text..............................................344
Tungsten lamp control ...............................422
Turn on/off incubator ................................145
Turn on/off lamp........................................422
Tutorials ......................................................... 28
U
Upgrade utility............................................ 374
Use first filter set sensitivity.............. 156, 159
User Groups
Defining/Modifying................................... 401
User Groups................................... 18, 398, 399
Users ..................................... 5, 15, 18, 398, 399
User's Permissions
Changing your password ................... 385, 428
Setting................................................ 398, 401
User's Account..................................... 15, 400
User's Permissions ...................................... 401
V
Validate
Procedures ................................................. 125
Set up quality controls for experiment....... 301
Validation Criteria ...................................... 301
Validation Examples .................................. 304
Viewing
Audit Trails................................ 394, 395, 396
AutoSensitivity .......................................... 161
Excel® ....................................................... 358
Results ............................................... 102, 310
System Audit Trail..................................... 396
Well Analysis ............................................ 191
Viewing Data
Customizing views ............................ 117, 194
Defining Data Views ................................. 315
Masking data point .................................... 325
Modify views..................................... 328, 330
Well Zoom................................................. 191
Viewing Data............... 117, 191, 194, 320, 330
Viewing Preferences............................. 24, 328
Viewing Results
Method to display data too long to fit........ 344
Viewing Results ............................ 24, 102, 310
W
Well Analysis Data Reduction . 191, 196, 246,
290
Well Analysis Results Table ...... 191, 320, 340
Well IDs................................................ 223, 252
Well Settings................................................ 226
Well Zoom
Modify view ...................................... 194, 330
452 | Index
Monitor experiment ...................................295
Report multiple wells simultaneously........340
View multiple wells simultaneously..........191
Well Zoom View
Customizing ...............................................194
Well Zoom View .........................................194
Wells to Monitor..........................................144
Windows Explorer ........................................47
WordPad ......................................................356
Workspace
Introduction ................................................. 28
Plate View.................................................. 313
Wrong pH .................................................... 169
X
X Axis/Y Axis ............................................. 330
Y
Y Axis Intercept........................................... 268
Was this manual useful for you? yes no
Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Download PDF

advertisement