яюю я R otor - G ene A ssay M anager M anual

October 2012
Rotor-Gene AssayManager
Core Application User Manual
Sample & Assay Technologies
Trademarks: QIAGEN®, QIAlink™, QIAsymphony®, QuantiTect®, Rotor-Disc®, Rotor-Gene®, Rotor-Gene
AssayManager™ (QIAGEN Group); Microsoft®, Windows® (Microsoft Corporation); Intel® (Intel Corporation); SYBR® (Life
Technologies Corporation).
10/2012 © 2012 QIAGEN, all rights reserved.
Registered names, trademarks, etc. used in this document, even when not specifically marked as such, are not to be
considered unprotected by law.
Rotor-Gene AssayManager User Manual
3
Contents
1
Core Application User Manual - October 2012
1-2
1.1
................................................................................................................................... 1-3
Safety Information
1.2
................................................................................................................................... 1-10
Introduction
Provided User ..........................................................................................................................................................
Manuals
1-10
About this User
..........................................................................................................................................................
Manual
1-11
General Inform..........................................................................................................................................................
ation
1-11
Getting Help .......................................................................................................................................................... 1-12
1.2.1
1.2.2
1.2.3
1.2.4
1.3
...................................................................................................................................
1-14
General
Description of Rotor-Gene AssayManager
1.4
1-17
Getting...................................................................................................................................
Started
1.4.1
1.4.2
1.4.3
1.4.4
1.4.5
1.5
1.5.1
1.5.2
1.5.3
1.5.4
1.5.5
1.5.6
Installing Rotor-Gene
..........................................................................................................................................................
AssayManager
1-17
Requirements......................................................................................................................................................... 1-18
......................................................................................................................................................... 1-19
Internationalization
Installing Core..........................................................................................................................................................
Application and Plug-ins
1-19
.........................................................................................................................................................
1-19
Installing the Core
Application
.........................................................................................................................................................
1-30
Installing Plug-ins
Uninstalling the..........................................................................................................................................................
Rotor-Gene AssayManager
1-35
First Login
.......................................................................................................................................................... 1-36
First Configuration
.......................................................................................................................................................... 1-37
...................................................................................................................................
1-37
Basic Concepts
and General Software Usage
Concepts
.......................................................................................................................................................... 1-37
......................................................................................................................................................... 1-37
Modes
......................................................................................................................................................... 1-39
User Management
......................................................................................................................................................... 1-44
Session Management
.........................................................................................................................................................
1-46
Rotor-Gene AssayManager
and other QIAGEN Products
.........................................................................................................................................................
1-48
Experiment vs. Assay
General Softw are
..........................................................................................................................................................
Usage
1-49
Use of Color ......................................................................................................................................................... 1-50
.........................................................................................................................................................
1-52
Displaying Errors
and Warnings
.........................................................................................................................................................
1-54
Entering Data
.........................................................................................................................................................
1-56
Working w ith Tables
.........................................................................................................................................................
1-59
Working w ith Graphs
Rotor-Gene AssayManager
..........................................................................................................................................................
Workspace
1-65
General Elem ents
.......................................................................................................................................................... 1-67
......................................................................................................................................................... 1-67
Menu
Main Toolbar ......................................................................................................................................................... 1-69
......................................................................................................................................................... 1-70
Messages Area
Button Bar ......................................................................................................................................................... 1-71
Status Bar ......................................................................................................................................................... 1-72
Environm ents .......................................................................................................................................................... 1-73
......................................................................................................................................................... 1-74
Setup Environment
.........................................................................................................................................................
1-109
Cycler Environment
.........................................................................................................................................................
1-121
Approval Environment
.........................................................................................................................................................
1-143
Archive Environment
.........................................................................................................................................................
1-146
Service Environment
.........................................................................................................................................................
1-152
Configuration Environment
General Work..........................................................................................................................................................
Flow
1-196
Rotor-Gene AssayManager User Manual
4
1.5.7
1.6
Rotor-Gene AssayManager User Manual
Plug-in Concept
.......................................................................................................................................................... 1-199
1-199
Using ...................................................................................................................................
Rotor-Gene AssayManager
1.6.1
Standard Tasks
.......................................................................................................................................................... 1-200
.........................................................................................................................................................
1-201
Logging In and
Logging Out
1-206
Locking and .........................................................................................................................................................
Unlocking
1-210
Setting up a .........................................................................................................................................................
Run
......................................................................................................................................................... 1-228
Starting a Run
1-231
Finishing and.........................................................................................................................................................
Releasing a Run
1-236
Approving a.........................................................................................................................................................
Run
1-240
Working w ith.........................................................................................................................................................
Reports
1-243
Working w ith.........................................................................................................................................................
Audit Trails
1.6.2
Adm inistrative
..........................................................................................................................................................
Tasks
1-245
.........................................................................................................................................................
1-245
Managing Assay
Profiles
.........................................................................................................................................................
1-251
Managing Report
Profiles
......................................................................................................................................................... 1-259
Managing Cyclers
......................................................................................................................................................... 1-265
Managing Users
......................................................................................................................................................... 1-274
Managing Archives
1-276
Customizing .........................................................................................................................................................
Settings
1.7
................................................................................................................................... 1-276
Maintenance
1.8
................................................................................................................................... 1-278
Troubleshooting
System Setup.......................................................................................................................................................... 1-280
Operation
.......................................................................................................................................................... 1-281
Error Messages
..........................................................................................................................................................
and Error Codes
1-283
1.8.1
1.8.2
1.8.3
1.9
................................................................................................................................... 1-298
Abbreviations
1.10
................................................................................................................................... 1-299
Glossary
1.11
................................................................................................................................... 1-318
Appendices
1.11.1
1.11.2
1.11.3
File Endings .......................................................................................................................................................... 1-318
Liability Clause
.......................................................................................................................................................... 1-318
License Term..........................................................................................................................................................
s
1-319
.........................................................................................................................................................
1-322
Microsoft Softw
are License Terms
.........................................................................................................................................................
1-324
Microsoft .NET Framew ork 4
.........................................................................................................................................................
1-324
Microsoft Reportview er 2010
Rotor-Gene AssayManager User Manual
1. Core Application User Manual - October 2012
1-2
1
Core Application User Manual - October 2012
Core Application User Manual - October 2012
QIAGEN Rotor-Gene AssayManager™ Online Help
Recommended readings
For all users
Introduction
Basic concepts
Using Rotor-Gene AssayManager
Troubleshooting
Abbreviations
Glossary
Appendices
For operators
For administrators
For approvers
Operators set up and start a run. Administrators are responsible for Approvers assess the results of a
the initial installation. They
run and make decisions on the
manage all assets (e.g., cyclers,
validity of an experiment.
assay profiles, users) necessary for
working with Rotor-Gene
AssayManager.
Setting up a run
Starting a run
Finishing/releasing a run
Getting started
Managing assay profiles
Managing report profiles
Managing users
Managing cyclers
Approving a run
Working with reports
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1.1
1-3
Safety Information
The user-friendly Rotor-Gene AssayManager™ has been specifically developed for
use with up to 4 different Rotor-Gene® Q instruments. Before using Rotor-Gene
AssayManager, it is essential that you read this user manual carefully and pay
particular attention to the safety information. The instructions and safety information
in the user manual must be followed to ensure safe operation of the cycler and to
maintain the instrument in a safe condition.
The Rotor-Gene AssayManager user manual does not provide detailed information
about the Rotor-Gene Q instrument hardware and maintenance. The Rotor-Gene
AssayManager manual only describes the functionality of the Rotor-Gene
AssayManager software in combination with Rotor-Gene Q instruments.
Note: The terms "Rotor-Gene Q" and "Rotor-Gene Q instrument", used in this manual,
apply to all Rotor-Gene Q and Rotor-Gene Q MDx instruments (not available in all
countries) unless otherwise specified.
Safety information for the Rotor-Gene Q cycler
The following types of safety information appear throughout the Rotor-Gene Q cycler
manual.
WARNING
The term WARNING is used to inform you about situations that
could result in personal injury to you or other persons.
Details about these circumstances are given in a box like this
one.
CAUTION
The term CAUTION is used to inform you about situations that
could result in damage to the instrument or other equipment.
Details about these circumstances are given in a box like this
one.
The advice given in the Rotor-Gene Q cycler manual is intended to supplement, not
supersede, the normal safety requirements prevailing in the user’s country.
Proper use
WARNING/
CAUTION
Risk of personal injury and material damage [W1]
Improper use of the Rotor-Gene Q may cause personal injuries or
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damage to the instrument.
The Rotor-Gene Q must only be operated by qualified personnel
who have been appropriately trained.
Servicing of the Rotor-Gene Q must only be performed by
QIAGEN Field Service Specialists.
QIAGEN charges for repairs that are required due to incorrect maintenance.
WARNING/
CAUTION
Risk of personal injury and material damage [W2]
Rotor-Gene Q is a heavy instrument. To avoid personal injury or
damage to the instrument, take care when lifting.
WARNING/
CAUTION
Risk of personal injury and material damage [W3]
Do not attempt to move the Rotor-Gene Q during operation.
CAUTION
Damage to the instrument [C1]
Avoid spilling water or chemicals onto the Rotor-Gene Q.
Damage caused by water or chemical spillage will void your
warranty.
Note
In case of emergency, switch off the Rotor-Gene Q at the power switch at the back of
the instrument and unplug the power cord from the power outlet.
WARNING/
CAUTION
Risk of personal injury and material damage [W4]
Do not try to open the lid during an experiment or while the
Rotor-Gene Q is spinning. Otherwise, if you overcome the lid lock
and reach inside, you risk contact with parts that are hot,
electrically live, or moving at high speed, and you may injure
yourself and damage the instrument.
WARNING/
CAUTION
Risk of personal injury and material damage [W5]
If you need to stop an experiment quickly, turn off the power to
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1-5
the instrument, then open the lid. Let the chamber cool before
reaching inside. Otherwise you risk injury by touching parts that
are hot.
WARNING/
CAUTION
Risk of personal injury and material damage [W6]
If the equipment is used in a manner not specified by the
manufacturer, the protection provided by the equipment may be
impaired.
WARNING/
CAUTION
Risk of personal injury and material damage [W7]
Loose paper underneath the Rotor-Gene Q interferes with
instrument cooling. It is recommended that the area beneath the
instrument is kept free of clutter.
CAUTION
Damage to the instrument [C2]
Always use a locking ring on the rotor. This stops caps from
coming off tubes during an experiment. If caps come off during
an experiment, they may damage the chamber.
If you touch the Rotor-Gene Q during an experiment, while you are charged with static
electricity, in severe cases the Rotor-Gene Q may reset. However, the software will
restart the Rotor-Gene Q and continue the experiment.
Electrical safety
Disconnect the line power cord from the power outlet before servicing.
WARNING
Electrical hazard [W8]
Any interruption of the protective conductor (earth/ground lead)
inside or outside the instrument or disconnection of the protective
conductor terminal is likely to make the instrument dangerous.
Intentional interruption is prohibited.
Lethal voltages inside the instrument
When the instrument is connected to line power, terminals may be
live, and opening covers or removing parts is likely to expose live
parts.
To ensure satisfactory and safe operation of the Rotor-Gene Q, follow the advice
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below:
The line power cord must be connected to a line power outlet that has a protective
conductor (earth/ground).
Do not adjust or replace internal parts of the instrument.
Do not operate the instrument with any covers or parts removed.
If liquid has spilled inside the instrument, switch off the instrument, disconnect it from
the power outlet, and contact QIAGEN Technical Services.
If the instrument becomes electrically unsafe, prevent other personnel from operating
it, and contact QIAGEN Technical Services; the instrument may be electrically unsafe
when:
It or the line power cord appears to be damaged.
It has been stored under unfavorable conditions for a prolonged period.
It has been subjected to severe transport stresses.
WARNING
Electrical hazard [W9]
The instrument has an electrical compliance label which
indicates the voltage and frequency of the power supply as well
as fuse ratings. The equipment should only be operated under
these conditions.
Environment
Operating conditions
WARNING
Explosive atmosphere [W10]
The Rotor-Gene Q is not designed for use in an explosive
atmosphere.
WARNING
Risk of explosion [W11]
The Rotor-Gene Q is intended for use with reagents and
substances supplied with QIAGEN® kits. Use of other reagents
and substances may lead to fire or explosion.
CAUTION
Damage to the instrument [C3]
Direct sunlight may bleach parts of the instrument and cause
damage to plastic parts.
The Rotor-Gene Q must be located out of direct sunlight.
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Biological safety
Specimens and reagents containing materials from biological sources should be
treated as potentially infectious. Use safe laboratory procedures as outlined in
publications such as Biosafety in Microbiological and Biomedical Laboratories, HHS
http://www.cdc.gov/biosafety.
Samples
Samples may contain infectious agents. You should be aware of the health hazard
presented by such agents and should use, store, and dispose of such samples
according to the required safety regulations.
WARNING
*
OSHA
†
ACGIH
‡
COSHH
Samples containing infectious agents [W12]
Some samples used with this instrument may contain infectious
agents. Handle such samples with the greatest of care and in
accordance with the required safety regulations.
Always wear safety glasses, 2 pairs of gloves, and a lab coat.
The responsible body (e.g., laboratory manager) must take the
necessary precautions to ensure that the surrounding workplace is
safe, and that the instrument operators are suitably trained and
not exposed to hazardous levels of infectious agents as defined in
the applicable Safety Data Sheets (SDSs) or OSHA,* ACGIH,† or
COSHH‡ documents.
Venting for fumes and disposal of wastes must be in accordance
with all national, state, and local health and safety regulations
and laws.
Occupational Safety and Health Administration (United States of
America).
American Conference of Government Industrial Hygienists (United
States of America).
Control of Substances Hazardous to Health (United Kingdom).
Chemicals
WARNING
Hazardous chemicals [W13]
Some chemicals used with this instrument may be hazardous or
may become hazardous after completion of the protocol run.
Always wear safety glasses, gloves, and a lab coat.
The responsible body (e.g., laboratory manager) must take the
necessary precautions to ensure that the surrounding workplace is
safe and that the instrument operators are not exposed to
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hazardous levels of toxic substances (chemical or biological) as
defined in the applicable Safety Data Sheets (SDSs) or OSHA,*
ACGIH,† or COSHH‡ documents.
Venting for fumes and disposal of wastes must be in accordance
with all national, state, and local health and safety regulations
and laws.
*
OSHA
†
ACGIH
‡
COSHH
WARNING
Occupational Safety and Health Administration (United States of
America).
American Conference of Government Industrial Hygienists (United
States of America).
Control of Substances Hazardous to Health (United Kingdom).
Risk of fire [W14]
When cleaning the Rotor-Gene Q with alcohol-based disinfectant,
leave the Rotor-Gene Q door open to allow flammable vapors to
disperse.
Only clean the Rotor-Gene Q when worktable components have
cooled down.
Toxic fumes
If working with volatile solvents or toxic substances, you must provide an efficient
laboratory ventilation system to remove vapors that may be produced.
Waste disposal
Used consumables and plasticware may contain hazardous chemicals or infectious
agents. Such wastes must be collected and disposed of properly according to local
safety regulations.
Mechanical hazards
The lid of the Rotor-Gene Q must remain closed during operation of the instrument.
WARNING
Moving parts [W15]
To avoid contact with moving parts during operation of the RotorGene Q, the instrument must be operated with the lid closed.
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WARNING/
CAUTION
Risk of personal injury and material damage [W16]
Open and close the lid of the Rotor-Gene Q carefully to avoid
trapping fingers or clothing.
CAUTION
Damage to the instrument [C4]
Make sure that the rotor and locking ring are installed correctly.
If the rotor or locking ring show signs of mechanical damage or
corrosion, do not use the Rotor-Gene Q; contact QIAGEN
Technical Services.
CAUTION
Damage to the instrument [C5]
The Rotor-Gene Q must not be used if the lid is broken or if the lid
lock is damaged.
Make sure that the rotor and locking ring are installed correctly.
Only use rotors, locking rings, and consumables designed for use
with the Rotor-Gene Q. Damage caused by use of other
consumables will void your warranty.
CAUTION
Damage to the instrument [C6]
When Rotor-Gene Q is started immediately after delivery in cold
climates, mechanical parts can block.
Allow the instrument to acclimatize to room temperature for at
least one hour before turning the instrument on.
WARNING
Moving parts [W17]
In case of breakdown caused by power failure, remove the power
cord and wait 10 minutes before attempting to manually open
the lid.
WARNING
Risk of overheating [W18]
To ensure proper ventilation, maintain a minimum clearance of
10 cm at the sides and rear of the Rotor-Gene Q.
Slits and openings that ensure the ventilation of the Rotor-Gene Q
must not be covered.
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Heat hazard
1.2
WARNING
Hot surface [W19]
The Rotor-Gene Q chamber can reach temperatures above 120°
C (248°F). Avoid touching it when it is hot.
WARNING
Hot surface [W20]
When a run is paused, the Rotor-Gene Q will not be cooled
completely to room temperature. Exercise caution before
handling the rotor or any tubes in the instrument.
Introduction
Thank you for choosing Rotor-Gene AssayManager. We are confident it will become
an integral part of your laboratory.
Rotor-Gene AssayManager is a software for routine testing in combination with RotorGene Q instruments. Rotor-Gene AssayManager is able to read in sample
information, set up experiments, control up to 4 different Rotor-Gene Q cyclers,
acquire data from these instruments, automatically analyze results, and create
reports.
Rotor-Gene AssayManager consists of different components working together. The
core application is complemented by different plug-ins that contain assay type
specific analysis and visualization of the results. The core application is mandatory for
working with Rotor-Gene AssayManager. Optionally additional plug-ins can be
installed. At least one plug-in must be installed. Not all plug-ins are available in all
countries. Refer to the www.qiagen.com/Products/Rotor-GeneAssayManager.aspx to
discover our continuously expanding range of plug-ins.
1.2.1
Provided User Manuals
The core application and every available plug-in have their own user manual with
specific information about the functionality of the different Rotor-Gene AssayManager
components. Rotor-Gene AssayManager provides a context sensitive help that can be
started by simply pressing the "F1" key.
When installing additional plug-ins, the corresponding user manuals are
automatically added to the existing help system. Alternatively the different user
manuals can be accessed, read, and printed as *.pdf files.
Rotor-Gene AssayManager
core application user
Provides a description of the software
Describes functions that are the same for the core
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manual
1-11
application and all different plug-ins
Provides information about troubleshooting
Rotor-Gene AssayManager Provide details on
plug-in user manuals
How to use the assay type specific plug-ins
Their functionalities.
1.2.2
About this User Manual
This user manual provides information about Rotor-Gene AssayManager Core
Application in the following sections:
1.
2.
3.
4.
5.
6.
7.
8.
9.
The
Introduction
Intended use of Rotor-Gene AssayManager
Getting started including installing Rotor-Gene AssayManager
Basic concept and general software usage
Using Rotor-Gene AssayManager
Maintenance
Troubleshooting
Abbreviations
Glossary
appendices contain the following:
File endings
Liability clause
License terms
Note
The screenshots show examples of how to use the Rotor-Gene AssayManager
software. Some of the names used in this manual are only examples and may look
different in the lab of the end user. This particularly applies to the use of cycler
names.
In this manual, the cycler names "Cycler 1", "Cycler 2", "Cycler 3", and "Cycler 4" are
used. Further information about how to configure cycles can be found under
Managing cyclers and Cycler management.
1.2.3
General Information
Policy Statement
It is the policy of QIAGEN to improve products as new techniques and components
become available. QIAGEN reserves the right to change specifications at any time.
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Core Application User Manual - October 2012
In an effort to produce useful and appropriate documentation, we appreciate your
comments on this user manual. Please contact QIAGEN Technical Services.
Version Management
This document is the Rotor-Gene AssayManger Core Application User Manual,
version 1.0, which provides information about Rotor-Gene AssayManger Core
Application version 1.0.0.
1.2.4
Getting Help
Rotor-Gene AssayManager comes with a detailed help system. The help is provided
as *.pdf file and as *.chm file (compiled help file). The following image shows the help
page corresponding to the login screen as an example:
Rotor-Gene AssayManager has a context-sensitive help system. After pressing the "F1"
key in dialogs, a context-sensitive help page is shown.
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1-13
Using Rotor-Gene AssayManager Help
The help file contains two functional areas:
Tool bar
Tabs
The tool bar contains the following buttons:
Name
Icon
Description
"Hide" or
"Show"
Hides the left-hand side navigation tab. To display
the navigation tab again, click "Show". This button
appears instead of "Hide".
"Back"
Returns to the previous screen.
"Forward"
Returns to the screen displayed before using the
"Back" button.
"Print"
The user has the choice:
1) Print the selected topic
2) Print the selected heading and all subtopics
Select one option and confirm with "OK" or select
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"Cancel" to go back.
"Options"
Opens the options menu with the following entries:
The navigation tab contains the following tabs:
1.3
Name
Description
"Contents"
In the "Contents" tab the help content can be browsed by topics.
"Search"
Specific help topics can be found by entering search terms.
"Favorites"
Shortcuts to individual help topics can be added and managed
General Description of Rotor-Gene AssayManager
Product Configuration
Rotor-Gene AssayManager is a software for routine testing in combination with the
Rotor-Gene Q real-time PCR instruments.
The software consists of a core application and modular plug-ins and assay profiles.
The specific combination of core application, plug-in and assay profile determines a
specific routine testing application. Rotor-Gene AssayManager allows control and
operation of the Rotor-Gene Q instrument and contains algorithms for analysis of
data generated with the Rotor-Gene Q. Rotor-Gene AssayManager supports the user
in importing sample specific information and in performing all aspects of the
experiment result analysis procedure. The result analysis is started and processed fully
automatically after finishing an experiment, and appropriate result reports can be
generated.
Rotor-Gene AssayManager does not replace the standard Rotor-Gene Q software with
its full breadth of functionalities. Rather it allows running and analyzing PCR tests in a
highly controlled environment making use of assay profiles dedicated to specific PCR
assays, as well as automated result reporting, thus giving maximum process safety
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1-15
and reliability.
Product Functions
Rotor-Gene AssayManager includes these 3 main functionalities:
1) Cycler control: Rotor-Gene AssayManager controls the Rotor-Gene Q cycler, i.e.,
the software will provide all functions to set up, start, and run real-time PCR
experiments on up to 4 Rotor-Gene Q cyclers in parallel. Rotor-Gene AssayManager
can also be used for experiment result approval and reporting only. In this case the
software can be installed on a computer not necessarily connected to a Rotor-Gene Q
cycler.
2) Data analysis: Rotor-Gene AssayManager analyzes the real-time PCR raw data
according to well defined assay specific rules and generates result reports comprising
information on the validity or invalidity of the assay and individual samples.
3) Data management: Rotor-Gene AssayManager imports sample-specific
information from QIAsymphony® or via a LIMS. Data from the PCR experiment are
then used for analysis. After analysis the system is able to export data.
Modes of Operation
For cycler control and data analysis, Rotor-Gene AssayManager offers 2 modes of
operation to the user, the Closed Mode and the User Defined Test Mode.
Closed Mode
User Defined Test Mode
(UDT Mode)
The Closed Mode is used for assays that
have been created and validated by
QIAGEN. These assays can only be
modified by QIAGEN.
The User Defined Test Mode is used
for assays that have been created and
validated by a user of the Rotor-Gene
Assay Manager with the user role
“UDT Mode Assay Developer".
In Closed Mode, assays are run and
analyzed without the permission to modify
the corresponding assay profiles.
In User Defined Test Mode, assays are
run and analyzed without the
permission to modify the
corresponding assay profiles.
The analysis in Closed Mode includes core The analysis in UDT mode includes
analysis, assay and sample analysis, and, only the core analysis and the assay
depending on plug-in, also a fully
and sample analysis.
automatic data scan (AUDAS).
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To run and analyze an assay in Closed
To create, run, and analyze an assay
Mode a corresponding closed mode plug- in UDT Mode a corresponding UDT
in is required.
Mode plug-in is required.
Requirements for Rotor-Gene AssayManager software users
The following table covers the general level of competence and training necessary for
delivery, installation, routine use, maintenance, and servicing of the Rotor-Gene
AssayManager software.
Task
Personnel
Training and experience
Delivery
No special requirements
No special requirements
Installation
Laboratory technicians or
equivalent, IT personnel
Basic IT knowledge of
installing software
Routine use
Laboratory technicians or
equivalent
Professional users such as
technicians or physicians,
trained in molecular biology
techniques and the
functionalities of the RotorGene Q
Maintenance
Laboratory technicians or
equivalent, IT personnel
Professional users such as
technicians or physicians,
trained in molecular biology
techniques and the
functionalities of the RotorGene Q
Service
QIAGEN Technical or Field
Service Specialists only
Regularly trained personnel,
certified, and authorized by
QIAGEN
Training for Rotor-Gene AssayManager software users
To use the Rotor-Gene AssayManager software no additional special training is
required. The user has to read the accompanying documentation before using the
Rotor-Gene AssayManager software.
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1.4
1-17
Getting Started
This section of the user manual describes the system requirements for Rotor-Gene
AssayManager and how to install and configure Rotor-Gene AssayManager before
the software can be used.
1.4.1
Installing Rotor-Gene AssayManager
Rotor-Gene AssayManager and the corresponding plug-ins are available on DVDs.
The software cannot be downloaded from the internet. The data carrier provides
installation, update, and uninstall process for Rotor-Gene AssayManager, the RotorGene AssayManager database, and the Rotor-Gene AssayManager plug-ins (plug-ins
are delivered with different data carriers).
Note
Plug-ins cannot be uninstalled. In case you want to uninstall a plug-in, the core
application must be uninstalled together with the plug-in. See Uninstalling the
Rotor-Gene AssayManager for details.
Rotor-Gene AssayManager can be installed with 3 different configurations:
Task
Description
Install on standalone computer*
A user with local system administration privileges installs
the database (Microsoft® SQL Server Express) including
initial data, the Rotor-Gene AssayManager application,
and at least one Rotor-Gene AssayManager plug-in on a
computer.
The user is completely guided by the installation wizard
and will be prompted for input, if necessary.
Create new central
database and
install Rotor-Gene
AssayManager on
one or multiple
computers*
A user with all required database administration privileges
installs only the database (Microsoft SQL Server Express)
including initial data on a server.
The server is connected via local area network to the
computers of the application users.
Rotor-Gene AssayManager and at least one Rotor-Gene
AssayManager plug-in is installed on one or multiple
computers by a user with local administration privileges.
During installation the user is prompted for connection to
the database, which has to be provided by the database
administrator.
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Use existing
database server
and install RotorGene
AssayManager on
one or multiple
computers*
A user with all required database administration privileges
uses the installation wizard to install only a new database
instance including initial data on an existing database
server.
The database administrator is responsible to check whether
the database server fulfills the Rotor-Gene AssayManager
requirements. He is also responsible to perform all
database administration tasks necessary to back up the
system before installation. Furthermore, the database
administrator must guarantee the functionality of the
system after the successful installation or a failed
installation.
Rotor-Gene AssayManager and at least one Rotor-Gene
AssayManager plug-in is installed on one or multiple
computers by a user with local administration privileges.
During installation the user is prompted for connection to
the database, which has to be provided by the database
administrator.
* The term "computer" is used to describe a notebook or a PC, and not a server.
1.4.1.1
Requirements
The table below lists the computer requirements for Rotor-Gene AssayManager.
Description
Minimum requirements
Display
1024 x 768 pixel resolution or higher
Supported
operating systems
Microsoft Windows® XP Professional Service Pack 3,
Microsoft Windows 7
Disk space
250 GB
Processor
Intel® Core i3-380M Processor or higher
Memory
4 GB RAM recommended.
USB interface
4 USB 2.0 ports. If necessary, USB Hub can be ordered
through QIAGEN.
Contact www.qiagen.com for details.
DVD-ROM drive
1
Pointing device
Touchpad or mouse or equivalent is required.
Service packs
required
Microsoft Windows XP Professional: Service Pack 3
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Description
Minimum requirements
Bluetooth®
Must be switched off
PDF viewer or
similar
Must be installed, not part of the software installation
package
Power options
Never turn off hard disks, hibernate, or go to standby
1-19
Note
Any outstanding Windows update needs to be applied before installing Rotor-Gene
AssayManager. Otherwise the installation procedure might fail.
Note
The installation of Rotor-Gene AssayManager can only be performed with
administrator privileges.
Note
Only use original material, e.g., cables etc., supplied by QIAGEN.
1.4.1.2
Internationalization
The standard language on a notebook delivered by QIAGEN is set to English
(American). The language of the software itself is English. Rotor-Gene AssayManager
uses the computer language settings to display dates and decimal separators in the
corresponding format. To change the language settings of the computer, select
"Control Panel" from the windows start menu and select "Local language settings".
1.4.2
Installing Core Application and Plug-ins
The following chapters provide you with details about the installation of the software.
1.4.2.1
Installing the Core Application
For computer system requirements, refer to
Requirements.
Note
Rotor-Gene AssayManager uses several software packages provided by third
parties. If not already installed on the system, these software packages are
automatically installed at the beginning of the Rotor-Gene AssayManager software
setup. Depending on the installed software packages, a reboot of the system may
be required before proceeding with the setup.
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Note
The system must be virus and spyware free to install the Rotor-Gene AssayManager
software.
Rotor-Gene AssayManager requires an MS SQL Server 2008 R2 Express instance with
mixed mode authentication and tcp/ip network protocol activated for installation. The
installation process depends on whether MS SQL Server 2008 R2 Express already is
installed or should be installed on the local system or whether Rotor-Gene
AssayManager shall be installed with a remote connection to an existing SQL Server
on an external system:
If MS SQL Server 2008 R2 Express is already installed on the local system or a
remote connection to an existing SQL server or an external system, the installation
of MS SQL Server 2008 R2 Express is skipped and the installation continues with the
installation of Rotor-Gene AssayManager application.
If MS SQL Server 2008 R2 Express was not installed previously, the first step in the
installation process is the installation of MS SQL Server Express 2008 and then the
Rotor-Gene AssayManager application is installed.
Note
During installation process, click "Back" to go a step back in the installation process.
Click "Cancel" to stop and end the installation process.
Step-by-step procedure to install the Rotor-Gene AssayManager
1. Place the DVD in the computer's DVD drive.
The setup wizard automatically opens the "Rotor-Gene AssayManager Setup"
window.
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Note
If the setup wizard does not start automatically, double-click "My Computer" and
select the DVD drive. Double-click "setup.exe" to start Rotor-Gene AssayManager
installation.
2. The further installation process depends on whether SQL Server 2008 instance with
mixed mode authentication and tcp/ip network protocol is activated for
installation.
If the installation wizard could not detect an SQL Server installed on your system
and you want to install the SQL Server locally on your system, select Rotor-Gene
AssayManager application, prerequisites, and SQL Server Express and proceed
with step 4.
If the installation wizard detects an existing SQL Server on your system, a
corresponding message will be shown in the messages box below. The upper
option "Rotor-Gene AssayManager application, prerequisites, and SQL Server
Express" is disabled.
If you want to install Rotor-Gene AssayManager with a remote connection to an
existing SQL Server on an external system, select the option Rotor-Gene
AssayManager application and prerequisites.
3. Click "OK" to proceed.
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4. If applicable, the SQL Server will be installed. Click "Accept" to start the installation
of MS SQL Server 2008 R2 Express.
The installation progress windows is displayed:
5. The Rotor-Gene AssayManager Welcome screen will automatically be opened.
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6. Click "Next" to start the installation procedure.
7. The following windows security message may appear during the installation
process. Click "Install this driver software anyway".
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On a PC having Windows XP installed, click "Continue Anyway".
8. Depending on the software packages already installed on the system, different
license agreements for the required software packages will be displayed.
Accept the license agreements by checking "I accept the terms in the License
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Agreement" and click "Next".
9. The "Virus and spyware check" window is opened:
Confirm that the system is virus free by activating the "System is virus and spyware
free" option and click "Next".
10.The "Custom Setup" screen is displayed.
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11.Click "Disc Usage" to get an overview of the available and required disc space.
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Click "OK" to close the window.
12.Select the features to be installed.
Features "Database" and "Rotor-Gene AssayManager software" both
selected
For a stand-alone desktop scenario with application and database on one
computer, both features must stay selected.
Feature "Rotor-Gene AssayManager software" only selected
For the installation of the application accessing a central database server, the
“Database” feature must be deselected and the “Rotor-Gene Assay Manager
software” feature must stay selected.
Feature "Database" only selected
For installation of a central database server only, the “Rotor-Gene Assay
Manager software” feature must be deselected and the feature “Database” must
stay selected.
Note
For selection or deselection of features, use the drop-down menu.
The first 2 options displayed here are identical . Select the corresponding feature.
The third option deselects the corresponding feature.
13.Click "Next" to proceed with the installation of the selected features.
14.Optional: This step is necessary only if no SQL Server “RGAMINSTANCE” was
detected or if the “Database” feature has been deselected in step 12. Otherwise,
this screen will be skipped.
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Fill in the required parameters.
To check the database connection, click "Check database connection". If you
encounter problems during the connection process to the database server, contact
your local system administrator.
15.To proceed with the installation click "Next".
16.Click "Install" to start the installation.
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17.After the installation is completed click "Finish" to close the window.
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18.After the installation Rotor-Gene AssayManager can be started either from the
Windows start menu under QIAGEN/Rotor-Gene AssayManager or using the
desktop icon.
1.4.2.2
Installing Plug-ins
For the use of Rotor-Gene AssayManager at least one plug-in must be installed.
Note
The installation of the UDT basic plug-in is taken as an example for the installation
of any plug-in.
Step-by-step procedure to install a Rotor-Gene AssayManager plug-in
1. Place the DVD in the computer's DVD drive.
2. Double-click My Computer and select the DVD drive. Double-click UDTBasic.
Installation.msi to start the UDT basic plug-in setup wizard. Click "Next" to
proceed.
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3. Accept the license agreement by clicking the checkbox and click "Next".
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4. Confirm that your system is virus and spyware free by checking the corresponding
check box and click "Next".
5. Select the features to be installed.
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Features "UDT basic plug-in" and "Update database schema" selected
For a stand-alone desktop scenario with application and database on one
computer, both features must stay selected.
Feature "UDT basic plug-in" selected
This feature updates the Rotor-Gene AssayManager application with the UDT
basic plug-in. It is needed always if the Rotor-Gene AssayManager and its
database are installed on one system. The feature can be deselected only if a
database server without the Rotor-Gene AssayManager application is to be
updated.
Feature "Update database schema" selected
After the Rotor-Gene AssayManager installation, the database schema contains
unspecified Rotor-Gene AssayManager tables only. This feature adds the UDTspecific tables.
This feature is needed if the Rotor-Gene AssayManager and its database are
installed on one system. The feature can be deselected only if the database is
installed on a separate server and was updated by a prior UDT basic plug-in
installation.
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Note
For selection or deselection of features, use the drop-down menu.
The first 2 options displayed here are identical. Select the corresponding feature.
The third option deselects the corresponding feature.
6. Click "Disc Usage" to get an overview of the available and required disc space.
Click "OK" to close the window. Click "Next" to proceed with the installation of the
selected features.
7. Click "Install" to start the installation of the plug-in.
7. Wait until the installation process has finished.
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8. After the installation is completed click "Finish" to close the window.
9. After next restart of Rotor-Gene AssayManager the installed plug-in is available.
Related topics
Installing the core application
1.4.3
Uninstalling the Rotor-Gene AssayManager
Note
The uninstall process of the Rotor-Gene AssayManager software will remove the core
application as well as all installed plug-ins. It is not possible to uninstall only a plugin, as this will create inconsistencies in the database and ceases further access to
corresponding datasets.
Step-by-step procedure to uninstall Rotor-Gene AssayManager and all
installed plug-ins from your computer.
Note
If you want to uninstall Rotor-Gene AssayManager, close the application first.
Otherwise Rotor-Gene AssayManager might not be uninstalled completely.
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1. Select QIAGEN/Rotor-Gene AssayManager/Uninstall Rotor-Gene
AssayManager from the Windows Start Menu.
2. Confirm that you want to uninstall the product by clicking "Yes".
3. The windows installer program starts to uninstall the entire Rotor-Gene
AssayManager.
1.4.4
First Login
After successful installation of Rotor-Gene AssayManager, the system administrator
needs to log in for a first configuration of the software.
1. Enter user ID admin and password admin.
2. Select an appropriate mode (Closed Mode or User Defined Test Mode) and
confirm with "OK".
3. Change the default password to a new, secure password.
4. The "Settings" tab in the "Configuration" environment will be opened.
Note
All users without the "Administrator" role can ask the administrator to reset the
password. However, if the administrator forgets the administrator password, they
must contact QIAGEN Technical Services to reset the password, which requires an
on-site visit by a QIAGEN service engineer.
Note
It is strongly recommended to create at least one additional user account, without
an "Administrator" role, at first login. If a single user of Rotor-Gene AssayManager
aggregates different user roles including the "Administrator" role, there is a high risk
that the access to the software will be completely blocked if this user forgets the
password!
Note
The administrator after installation does not have the access rights for the "Setup
environment". This environment can be accessed for users with the role "Operator".
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Related topics
Logging in and logging out
User management
"Setup" environment
"Configuration" environment
1.4.5
First Configuration
Before Rotor-Gene AssayManager can be used, the creation of user profiles and the
registration of one or several Rotor-Gene Q cyclers in the "Configuration" environment
is essential. For details about these tasks refer to:
Managing users
Managing cyclers
1.5
Basic Concepts and General Software Usage
In the following chapter the concepts and the general software usage of Rotor-Gene
AssayManager are described.
1.5.1
Concepts
Rotor-Gene AssayManager uses multiple concepts to facilitate tasks and processes.
The following topics describe these concepts in detail:
Modes
User Management
Session Management
Rotor-Gene AssayManager and other QIAGEN products
Clarification of terms experiment and assay
1.5.1.1
Modes
Rotor-Gene AssayManager can be operated in 2 separate modes of operation with
individual characteristics:
Closed Mode
User Defined Test Mode (UDT Mode)
Closed Mode
User Defined Test Mode
(UDT Mode)
The Closed Mode is used for assays that
have been created and validated by
QIAGEN. These assays can only be
The User Defined Test Mode is used
for assays that have been created and
validated by a user of Rotor-Gene
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modified by QIAGEN.
Assay Manager with the user role
“UDT Mode Assay Developer".
In Closed Mode, assays are run and
analyzed without the permission to modify
the corresponding assay profiles.
In User Defined Test Mode, assays are
run and analyzed without the
permission to modify the
corresponding assay profiles.
The analysis in Closed Mode includes core The analysis in UDT mode includes
analysis, assay and sample analysis, an,d only the core analysis and the assay
depending on plug-in, also a fully
and sample analysis.
automatic data scan (AUDAS).
To run and analyze an assay in Closed
To create, run, and analyze an assay
Mode a corresponding closed mode plug- in UDT Mode a corresponding UDT
in is required.
Mode plug-in is required.
The mode is selected from the Rotor-Gene AssayManager login screen. The login
screen contains 2 fields to enter the user ID and the password, as well as an
additional drop-down menu to select the mode of operation.
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After the user has logged in, the selected mode is displayed in the status bar:
Closed Mode
1.5.1.2
UDT Mode
User Management
User interactions with the system must be assignable to an individual person.
Therefore, each user must log in before the Rotor-Gene AssayManager software can
be used. After finishing work the user should log out or lock the application.
A role must be assigned to every user. It is also possible to assign multiple roles to a
single user. The following properties are stored in the database for a user:
First name
Last name
User ID
Password
Role(s)
Related tasks
Creating a user profile
Changing user profile settings
Changing name/last name
Changing password
Changing role
Activating/deactivating a user profile
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Setting password policies and auto lock timer
1.5.1.2.1
User Roles
Different Rotor-Gene AssayManager functions can only be accessed by users with
certain roles. All available user roles and their permissions are listed in the following
table:
Role
Description
Administrator
The administrator has only permissions to
configure the system,
manage users,
create and edit report profiles,
manage archives.
Assay developer
The assay developer has all necessary permissions to create an
assay profile in UDT Mode.
Operator
The operator has all permissions necessary to
create a work list,
apply the work list,
view the analysis results.
The operator cannot approve or release assay results.
Approver
The approver is the only user with permissions to approve and
release assay results.
Super User
The super user has all available permissions of all available
rules as a convenient way to grant all permissions to one user, i.
e., Administrator, Assay Developer, Operator, and Approver.
The following actions can be performed by every role
Logging in and logging out
Locking and unlocking
Changing user profile settings
The following table gives an overview about permissions of the different user roles in
the different environments:
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Environment
"Setup"
"Approval"
"Archive"
"Service"
1-41
Ad
min
AD
Op
Ap
SU*
User can enter
the "Setup"
environment.
–
–
+
–
+
User can apply
runs in the
"Setup"
environment.
–
–
+
–
+
Access
"Approval"
environment
User can
access the
"Approval"
environment.
+
–
+
+
+
Approve test
results
Release of test
results
User can
approve the
test results in
the "Approval"
environment.
–
–
–
+
+
Create
support
package
User can
create support
packages in
the "Approval"
environment.
+
–
+
+
+
Access
"Archive"
environment
User can enter
the "Archive"
environment.
+
–
+
+
+
Create
support
package
User can
create support
packages in
the "Archive"
environment.
+
–
+
+
+
Access
"Service"
environment
User can enter
the "Service"
environment.
+
–
–
+
+
View audit
trail
User can
access the
Audit Trail tab
in the "Service"
environment.
+
–
–
+
+
Task
Description
Access "Setup"
environment
Apply runs
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Environment
Ad
min
AD
Op
Ap
SU*
User can enter
the "Config."
environment.
+
+
–
–
+
Configure
system
settings
User can
configure all
settings in the
"Config."
environment.
+
–
–
–
+
Manage
cyclers
User can
access the
"Cycler
Management"
tab in the
"Config."
environment.
+
–
–
–
+
User can
access the
"User
Management"
tab in the
"Config."
environment.
+
–
–
–
+
User can
access the
"Assay Profiles"
tab in the
"Config."
environment.
+
–
–
–
+
User can
access the
"Report
Profiles" tab in
the "Config."
environment.
+
+
–
–
+
User can enter
the
"Development"
environment.
–
+
–
–
+
Task
Description
Access
"Config."
environment
Manage users
"Configuration"
Manage
assay profiles
Manage
report profiles
"Development"
Access
"Development
" environment
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Environment
"Cycler"
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Ad
min
AD
Op
Ap
SU*
User can
develop assay
profiles in the
"Development"
environment.
–
+
–
–
+
Access
"Cycler"
environment
User can enter
the "Cycler"
environment.
+
–
+
–
+
Release
cyclers
User can add
a comment,
release a
cycler, stop a
process, and
close pop-ups
in the "Cycler"
environment.
–
–
+
–
+
Task
Description
Develop
assay profiles
* A dmin : Administrator; A D : Assay Developer; Op: Operator; A p: Approver; SU : Super User.
1.5.1.2.2
Password Policy
Unless otherwise defined the password must be between 8 and 40 characters long. An
administrator can also define, in the settings of the "Configuration" environment, if
using CLIA complaint password rules is mandatory. According to CLIA, a password
has to contain at least:
8 characters
2 upper case characters
2 lower case characters
2 numeric characters
2 special characters
An administrator can also define the password renewal interval. A user must renew his
password after the renewal interval has passed. Note that the last 10 passwords
cannot be reused.
Related topics
Setting password policies and auto-lock timer
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1.5.1.3
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Session Management
To start working with Rotor-Gene AssayManager, a user has to start a new session by
logging in. Logging in is possible from the login screen either after the application
was started or after a previous session was finished. Logging out is possible using the
command from the main menu or the logout button in the status bar.
Log out from
main menu
Log out from
status bar
To prevent misuse, a user can lock the application. Rotor-Gene AssayManager also
has an auto-lock timer that locks the application automatically after a predefined
time without user interaction (an administrator can customize the auto-lock feature,
see Setting up the auto-lock timer). If locked, the user can either continue working by
unlocking the application or alternatively another user can start a new session.
The automatic locking feature does not interrupt or impact the operation of the
cyclers.
Started runs are not interrupted or impacted if:
a user logs out,
another user starts a new session,
or the application is locked (automatically or manually).
The following graphic illustrates the session, locking concepts, and their
interdependencies:
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Behavior if unsaved data exist
If a user locks the application and unsaved data exist, a dialog is opened containing
a list of all environments with unsaved data:
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If another user wants to start a new session, a dialog is shown containing a warning
that unsaved data from the previous user exist, and the unsaved data are lost if the
new session is started.
Related topics
Logging in and logging out
Locking and unlocking
Setting password policies and auto-lock timer
1.5.1.4
Rotor-Gene AssayManager and other QIAGEN Products
Rotor-Gene AssayManager has different interfaces and data exchange features with
other QIAGEN products and external Laboratory Information Management Systems
(LIMS).
With Rotor-Gene AssayManager, up to 4 different Rotor-Gene Q instruments can be
controlled simultaneously. Each connected cycler can send raw acquisition data back
to Rotor-Gene AssayManager.
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Note
Rotor-Gene AssayManager and Rotor-Gene Q software may be installed on the
same computer in parallel. But only one of the programs can have an active
connection to a Rotor-Gene Q at a particular time.
Scenario 1:
In case the Rotor-Gene Q software is started prior to Rotor-Gene AssayManager and
connected to a cycler first, Rotor-Gene AssayManager is not able to set up a
connection to the cycler. Shut down the Rotor-Gene Q software. Restart Rotor-Gene
AssayManager to control the cycler with Rotor-Gene AssayManager.
Scenario 2:
In case Rotor-Gene AssayManager is started prior to the Rotor-Gene Q software and
connected to a cycler first, the Rotor-Gene Q software is not able to set up a
connection to the cycler. Shut down Rotor-Gene AssayManager. Restart the RotorGene Q software to control the cycler with the Rotor-Gene Q software.
Rotor-Gene template files (*.ret files) can be imported in Rotor-Gene AssayManager
to create assay profiles in UDT Mode. Result files from the QIAsymphony AS can be
used to generate work lists in Rotor-Gene AssayManager. All relevant sample and
assay related information are automatically set, and manual input during work list
setup is minimized.
Rotor-Gene AssayManager can be linked to a Laboratory Information Management
System (LIMS) directly or via a dedicated middleware solution (QIAlink™),* which
easily connects QIAGEN instruments with a LIMS. (Contact QIAGEN for availability of
QIAlink middleware.)
The following graphic illustrates the possible interactions between Rotor-Gene
AssayManager and the other compounds:
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Related topics
Importing a work list
Exporting a *.rex file
Setting up a run
1.5.1.5
Experiment vs. Assay
The terms "experiment" and "assay" are used with different meanings in Rotor-Gene
AssayManager. Rotor-Gene AssayManager allows multiple assays to run in one
experiment by creating a work list with multiple compatible assay profiles. All assays
within one run define an experiment.
Example
The following graphic gives an example. A work list is created consisting of 4 different
assays. The brighter colors represent test samples; the darker colors, non-test
samples, such as external controls. A 36-Well Rotor is used for the work list.
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After the run has finished, all individual assays of the experiment are listed in the
Approval environment. All test samples of an assay have to be approved and
released. An experiment is defined as fully released only if all test samples (and
external controls in case of UDT plug-in) of all assays of an experiment have been
released. The data are then transferred to the Archive environment, and the LIMS
output (optionally) and the report (optionally) are created.
Related topics
Creating/editing a work list
Starting a run
Finishing and releasing a run
1.5.2
General Software Usage
The following chapter describes the general software usage concept of Rotor-Gene
AssayManager.
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1.5.2.1
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Use of Color
For an optimal user interaction Rotor-Gene AssayManager has a specific color
concept for presenting information.
The following table provides an overview about the different colors used in the
software and their dedicated meaning:
Color
Description
Light blue
The field is interactive and clickable.
Dark blue
The field is selected or focused.
Gray
The field is read-only and can neither be selected nor
activated.
Yellow
The field requires input.
Example 1
The following dialog example gives an explanation of the color concept.
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Example 2
When creating a new work list in the "Setup" environment, there are 3 step buttons
("Assays", "Samples", and "Properties") for the different steps to complete. The coloring
concept of the step buttons is shown in the following graphic:
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1.5.2.2
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Displaying Errors and Warnings
Errors and warnings are essential information for the user. These messages point to a
problem or an erroneous situation. Rotor-Gene AssayManager differentiates between
4 different problem levels:
Priority
Name
1
Icon
Description of the
functionality
Action required by
user
System
error
A combination of not
acceptable incidents
User interaction
required
2
Validation
error
An error that occurs
due to a missing or
invalid user input
User interaction
required
3
Warning
Situation could be
optimized by further
input
User interaction
possible, but not
mandatory
4
Information
A message containing
additional information
about the current
situation
User interaction not
possible
All existing errors and warnings are displayed with the corresponding icon either in a
separate messages area or as a pop-up window. If applicable, the messages area
lists all currently existing errors and warnings sorted with descending priority.
"Messages" area
The following screenshot shows possible errors and warnings during work list creation
in the "Setup" environment. The messages are displayed with the corresponding icon,
the error text, and the error ID in brackets.
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Detailed view of the "Messages" area:
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Error messages pop-up window
Each error ID is unique. In case QIAGEN Technical Services needs to be contacted for
troubleshooting, have the error ID ready.
1.5.2.3
Entering Data
Shortcuts
The following hot keys are available in Rotor-Gene AssayManager:
"F1" to open the help file
Copy and paste operations ("CTRL"+"C" and "CTRL"+"V")
Navigation (tab key, cursor keys)
While entering data, the following keyboard shortcuts can be used:
"F2" to start editing
"Escape" to cancel the input
"Return" to commit an input
Identifying interactive fields
All interactive elements where a user can enter data are marked with a black triangle
symbol ( ) in their upper right corner.
The following example is taken from the work list creation step in the "Setup"
environment:
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Date picker: Entering date in date fields
Dates can either be entered manually into date fields using the keyboard or using an
interactive date picker in form of a pop-up calendar. A calendar icon ( ) is
positioned at the right of every date field.
Clicking the calendar icon ( A ) opens the pop-up calendar.
Change to the previous/next month by clicking the arrow icons B and C . Hovering
over the year label ( D ) displays additional control arrows, which are used to quickly
jump to the next (up arrow) respectively previous year (down arrow):
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Step-by-step procedure to enter a date using the date picker
1. Click the calendar icon
( A ) next to the date field.
The calendar pop-up is shown.
2. Continue using the following scheme:
To
Do this
Change the year
Hover the mouse over the year ( D ).
Date is displayed in blue. Additional control arrows are
shown.
Click the "up" arrow to change to the next year.
Click the "down" arrow to change to the previous year.
Change the month/
day
Click the "left" arrow ( B ) to change to the previous
month.
Click the "right" arrow ( C ) to change to the next month.
Click the date of the desired day.
The date picker disappears and the date field is populated with the selected date.
1.5.2.4
Working with Tables
Sorting tables
Some tables in Rotor-Gene AssayManager give the possibility to sort the contained
data by column. Sortable tables can be recognized by the Sort indicator icon ( ) in
one of the column headers. The data in the table are sorted according to this column.
Two different icons exist to visualize an ascending or descending sorting order:
Ascending sorting:
The table is sorted by the selected column is ascending order.
Descending sorting:
The table is sorted by the selected column in descending order.
To toggle the sorting order from ascending to descending or vice versa, click the
column header with the Sort indicator icon. To sort the data in the table according to
another column, click the column header of the respective column.
In the example below, the "Assay selection" table is sorted by the "Experiment" column
in ascending order.
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Selecting cells
A certain cell area can be selected by clicking in the first cell, holding down the left
mouse button, and dragging to the last cell of the area. Selected cells are highlighted
in dark blue color. To make multiple selection of non-adjacent cells, hold down the
"CTRL" key and click the cells to select.
Copying data from a table
Copying data from a table is possible by first selecting the cells to be copied and
then using "CTRL"+"C". The contents of the selected cells are copied to the clipboard.
The copied cells can easily be pasted to another area within Rotor-Gene
AssayManager or to another software for further processing using "CTRL"+"V".
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Context menu
Tables have context menus with varying commands. The context menu in Rotor-Gene
AssayManager is opened with a right-click on selected cells. In tables with a row
selector there is an additional context menu when first selecting rows by clicking the
row selector of the row and then clicking the right mouse button.
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Working with Graphs
Rotor-Gene AssayManager provides graph functions, such as zooming, panning, and
selecting samples to easily examine a graph in detail. The following topics describe
how to use these functionalities.
Tasks related to working with graphs
Zooming in
Zooming out
Panning
Selecting/deselecting samples
Sample information in graphs
1.5.2.5.1
Zooming in a Graph
Overview
For zooming in a graph in Rotor-Gene AssayManager, an individual zoom area can
be selected as in the following example of an amplification plot from the "Approval"
environment.
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Step-by-step procedure to zoom in a graph
1. Move the cursor over the graph's area. The cursor changes to cross hairs.
2.
a) Click and hold down the left mouse button. The mouse icon changes from
cross hairs to the cursor icon.
b) Drag the cursor until the end of the area to zoom in. A dark gray rectangle
visualizes the selected area, as long as the left mouse button is held down.
c) Release the left mouse button. The following menu pops up:
3. Left-click "Zoom". The graph will be zoomed to the selected area.
4. To scroll in the zoomed graph in vertical or horizontal direction just click right
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in the graph area, hold down the right mouse button, and move the mouse.
Example
Holding down the right mouse button and moving the mouse will change the
graph's display accordingly.
1.5.2.5.2
Zooming out a Graph
Step-by-step procedure to zoom out a graph
Double-click anywhere in a graph area to reset the zoom function to default-scale
and see the whole graph.
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Example
The graph shows a zoomed area of an amplification plot. Double-clicking anywhere
in the graph area will reset the zoom.
1.5.2.5.3
Selecting/Deselecting Samples
Overview
Rotor-Gene AssayManager provides 2 methods to select or deselect samples in an
amplification plot:
Using a graph
Using check boxes
Step-by-step procedure to select/deselect samples using a graph
1. Move the cursor over the graph area.
The mouse cursor icon changes to cross hairs.
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2.
a) Click and hold down the left mouse button. The mouse icon changes from
cross hairs to the cursor icon.
b) Drag the cursor until the end of the area to zoom in. A dark gray rectangle
visualizes the selected area, as long as the left mouse button is held down.
c) Release the left mouse button. The following menu pops up:
3. Left-click at the desired option
To
Select all samples within the selected
area
Deselect all samples within the selected
area
Cancel the process
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Select/deselect samples using check boxes
Samples are selected or deselected by activating or deactivating the corresponding
check boxes in the results table.
To
Do
Select all samples in the
table
Activate the check box in the column header ( A ).
Select a specific sample in
the table
Activate the check box in the corresponding sample
row ( B ).
Deselect all samples in the
table
Deactivate the check box in the column header ( A ).
Deselect a specific sample
in the table
Deactivate the check box in the corresponding
sample row ( B ).
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Note
The check box icon in the column header changes depending on the number of
selected samples.
Icon
Description
No sample is selected
One or more samples are selected
All samples are selected
1.5.2.5.4
Sample information in Graphs
To get sample information corresponding to a specific curve, hover the mouse over
the curve. The curve will be highlighted, and a tooltip containing the following
information will be displayed:
Tube number
ID
Assay type
Assay short name
1.5.3
Rotor-Gene AssayManager Workspace
Rotor-Gene AssayManager is divided into different environments. These environments
can be accessed by using the dedicated icons in the main toolbar. The following
environments are available:
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"Setup" environment
"Approval" environment
"Archive" environment
"Service" environment
"Configuration" environment
"Cycler" environment
Note
The "Development" environment is only available if a UDT mode plug-in is
installed.
The workspace of an environment consists of an environment-specific working area
and of the following general elements:
Menu
Main toolbar
Working area
"Messages" area
Button bar
Status bar
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General Elements
The following general user interface elements are described in this section:
Menu
Main toolbar
"Messages" area
Button bar
Status bar
1.5.4.1
Menu
File menu
Log in
Select "Log in" to log in to Rotor-Gene AssayManager. This option is grayed out if a
user is already logged in.
Log out
This enables the current user to log out. If there are unsaved data, the following
warning is shown with a list of environments where unsaved data exist.
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If there are no unsaved data, the following dialog is shown:
Lock
This locks the current session. To unlock, the logged in user has to enter the password.
Change password
This opens a dialog to change the password. The old password has to be entered,
followed by the new password and a confirmation of the new password.
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Service login
This option is for login of a QIAGEN Field Service Engineer. This field is grayed out if
a user is already logged in.
Exit
Closes Rotor-Gene AssayManager. If there are unsaved data, a warning will appear.
Help menu
Open Rotor-Gene AssayManager help file
This opens the help file for Rotor-Gene AssayManager core application.
Open UDT basic Plug-in help file
This opens the help file dedicated for functions related to the UDT basic plug-in. If
other plug-ins are installed, there will be more help files available.
About
The “About Rotor-Gene AssayManager” dialog box appears and displays
information about the Rotor-Gene AssayManager and the loaded plug-ins including
the version numbers.
1.5.4.2
Main Toolbar
The main toolbar contains 2 areas:
Environment icons
Cycler icons
Environment icons
The environment icons are used to change to the corresponding environment. The
currently active environment is highlighted.
Rotor-Gene AssayManager has 6 different environments. To get detailed information
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about a specific environment, click its name in the list.
"Setup" environment
"Approval" environment
"Archive" environment
"Service" environment
"Configuration" environment
The "Development" environment is only available if a plug-in for UDT mode is
installed.
Cycler icons
The cycler icons visualize the up to 4 registered cyclers managed by Rotor-Gene
AssayManager. Clicking a cycler icon changes to the corresponding cycler screen.
For details, see
1.5.4.3
"Cycler" environment.
Messages Area
Depending on the selected environment and the corresponding dialog within the
environment, there is a "Messages" area containing all warnings, errors, and
information related to the current operation.
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Example: "Messages" area in the "Setup" environment
Related topics
Using colors
Displaying errors and warnings
1.5.4.4
Button Bar
The button bar is placed at the bottom of the screen. It contains buttons specific for
the selected environment.
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Status Bar
The status bar is always visible and gives an overview about the session status.
Status bar element
Explanation
Mode indicator
Indicates the current user mode, i.e., Closed Mode or User
Defined Test Mode (UDT Mode).
If the user is logged in in Closed Mode, the label "Closed
Mode" and the corresponding icon is shown:
If the user is logged in in User Defined Test Mode, the label
"User Defined Test Mode" and the corresponding icon is
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shown:
Date
Shows the current date.
User name
Shows first and last name of the user currently logged in.
Log out button
Logs out the current user. If there are unsaved data, a
warning will appear.
Related topics
The two different modes in Rotor-Gene AssayManager
Logging in and logging out
1.5.5
Environments
Rotor-Gene AssayManager contains 6 different environments.
An overview of access rights for different user roles can be found under User roles.
You can switch to another environment by clicking the appropriate button. The icon of
the currently active environment is highlighted with white font and a blue gradient
background color.
Environment
Description
Used for creation, management and application of work lists.
Used to search for unreleased or partially released assays and
for the approval of dedicated samples. Experiment reports are
created on release of a sample.
Used to search for fully released experiments and to generate
experiment reports using predefined report profiles.
Used to adjust the settings of Rotor-Gene AssayManager.
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Used to develop new assay profiles in User Defined Test Mode.
Used to stop or finish a run and to release a cycler after a run is
finished.
1.5.5.1
Setup Environment
Overview
The "Setup" environment is one of the core parts of the Rotor-Gene AssayManager
application. It automatically appears after a user with the assigned role of an
Operator successfully logs in to Rotor-Gene AssayManager. The "Setup" environment
consists of 3 different screens where tasks can be assigned:
Screen
"Available work lists"
"Create new work list"
"Assays" step
"Samples" step
"Properties" step
"Apply work list"
1.5.5.1.1
Assigned tasks
Creating a new work list
Importing a work list
Editing a work list
Duplicating a work list
Exporting a work list
Deleting a work list
Applying a work list
Create a new work list:
Appears after clicking "New work list"
Starts the process to create a new work list
Setup run and apply a work list
Available Work Lists View
The "Available work lists" view contains 2 areas:
A table with available work lists (stored in the internal database).
The button bar at the bottom of the screen
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The "Available Work Lists" Table
The "Available work lists" table displays the following information for all currently
available work lists:
Status icon
Work list name
Number of samples
Assay profiles
Rotor type
Reaction volume
Author
Creation date
Last applied
The data in the table is sortable. By clicking at the column header, the table's data is
sorted in ascending order. By clicking at the column header again, the table's data is
sorting in descending order.
A status icon is displayed in the very left column of a work list in case of existing
warnings or errors. Possible icons are:
Icon
Description
Deactivated assay profile or expired kit
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Message: "This work list contains invalid samples"
A work list contains invalid samples. This message is used only for imported
work lists.
The work list is currently locked.
Note
Moving the mouse over the icon reveals a tooltip with detailed information about
the problem.
In the very right columns of a work list, the Action buttons and the Apply button can be
found.
Type
Icon Label/
Title
"Edit work
list"
Description
Link to
Editing a work list means modifying
its parameters in the "Edit work list"
view. The parameters of the work list
can be modified using the "Edit work
list" view.
Creating/
editing a work
list
Note: This button is only enabled if
the option "is editable" was set
during work list setup and the work
list is not locked. Work lists imported
from QIAsymphony or LIMS to the
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software cannot be edited.
"Duplicat
e work
list"
Creates a copy of the selected work
Creating/
list. A copy of the selected work list is editing a work
created. This copy can subsequently list
be edited in the "Edit work list" view.
Note: All modifications are
temporary until the new work list is
saved.
Note: This icon is disabled for work
lists imported from QIAsymphony or
LIMS.
"Apply"
button
"Export
work list"
Exports the work list as *.iwl file.
–
The intended use of this function is to
exchange work lists between
different Rotor-Gene AssayManager
installations using the import/export
function.
"Remove
work list"
Removes the work list from the
system. A warning must be
confirmed before the work list is
deleted.
–
"Apply
work list"
The work list is applied (i.e., the run
is performed) and further details
have to be entered in the "Run work
list" view.
Apply work list
view
Note: This button is enabled if the
work list is set as "ready to be
applied" and the work list is not
locked.
If not
Displays all work lists,
activated: regardless if they
already have been
applied or not.
If
Displays only work lists
activated: which have not been
applied yet.
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Note
The "Available work lists table" might become very long and confusing: this table
might contain a number of work lists that you do not need anymore.
Remove the work lists you do not need anymore at regular periods:
1. Click the "Remove work list" button ( ).
2. Confirm the warning "Work List Removal" by clicking "OK". The deleted work list
disappears from the "Available work lists table".
3. Repeat these steps for any other work list you want to remove.
The Button Bar
The button bar is arranged at the bottom of the screen:
Label/Title
Description
A
"New work
list"
Create a new work list. This button links to the "Create new
work list" screen.
B
"Import"
Import a work list from a file. A file selection dialog is opened
where the work list to be imported can be selected. The source
type is determined by the item selected in the drop-down
menu C .
C
"Import
type"
Drop-down menu to select the import source file type for the
import work list command. Rotor-Gene AssayManager can
import work lists from QIAlink/LIMS, QIAsymphony, and other
Rotor-Gene AssayManager installations.
Possible values:
The entries in this menu depend on the import settings in the
"Configuration" environment.
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The group box "Default data source directories" in the
"Settings" tab of the "Configuration" environment defines
whether the import of external work lists (from Rotor-Gene
AssayManager, QIAsymphony, or a LIMS) is possible and
determines the source directory.
A check box in front of the 3 import settings determines if the
corresponding import setting is activated or not. If the check
box is activated, the import of this specific work list is enabled.
The "Import type" drop-down menu in the "Setup" environment
is populated with this import option.
Example:
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The "Import QIAsymphony work lists" option is deactivated in
the example above. The QIAsymphony import option is
removed from the "Import type" menu.
Tasks related to the "Available work lists" view
Creating a new work list
Editing/modifying a work list
Exporting a work list
Importing a work list
Applying a work list
1.5.5.1.2
Apply Work List View
Selecting the "Apply" button either in the "Available work lists" view or in the "Create
New/Edit work list" view links to the "Apply work list" view.
In the "Apply work list view" the following tasks can be accomplished to start a run:
Define an experiment name
View sample details
Print a work list
Select a cycler
Confirm that the locking ring has been attached to the rotor
Start the run
Furthermore detailed information about the work list and the cycler are displayed:
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Work list information
Work list name
Creation date
Last modification date
Last application date
Rotor type
Number of free positions
Reaction volume
Assays used in the work list
• Assay name
• Number of samples
• Material number
• Kit expiry date
• Lot number
Cycler information
Position
Name
Next verification date
Cycler status
Serial number
Optical configuration
Summary area
The "Summary" area is intended to enter a mandatory experiment name. The
"Summary" area also provides detailed information about the work list and its
incorporated assay(s). Sample details can be displayed in a secondary table.
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Label/Title
Description
A
"Experiment
name"
Input box to enter a mandatory experiment name. The
experiment name must fulfill 2 requirements:
The experiment name must not exceed 80 characters.
The experiment name must be unique.
B
"Default name"
button
A default name is entered automatically in the experiment
name input box using the name pattern defined in the
"Configuration" environment.
Further information can be found under "Configuration"
environment - "Settings"
C
Data field:
"Free positions"
"Reaction
Shows the following data:
Number of free positions
Reaction volume
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volume"
D
Data field:
"Work list
name"
"Created"
"Last modified"
"Last applied"
Shows the following data:
Work list name
Creation date
Last modification date
Last application date
E
"Assays" table
Table with a list of all assays incorporated in the work list.
For every assay the following data is shown:
Assay name
Number of samples
Material number
Kit expiry date
Lot number
F
"View sample
details..."
Overview of the samples in the work list in form of a table.
This table can be printed by clicking "Print work list..." ( G
).
Note
The printout can be used as a pipetting scheme.
"Cycler selection" area
The "Cycler selection" area mainly consists of the "Cycler selection" table, which lists
all available and usable cyclers with the following data:
Position of cycler
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Name of cycler
Next temperature verification date (residual days in brackets)
Status of cycler
The "Cycler details" table below displays the "Serial number" and the "Optical
configuration" of the selected cycler.
The "Cycler selection" table has 4 rows, representing the maximum of 4 cyclers that
can be operated by Rotor-Gene AssayManager. If fewer than 4 cyclers are configured,
residual table rows will be disabled.
All compatible cyclers with the status "Ready" can be selected for the work list to be
applied using the "Select" radio button. After successful cycler selection, the dedicated
"Ring attached" check box will become active. Confirm that the locking ring is
attached to the rotor by activating the "Ring attached" check box to start the cycler.
Note
A successful cycler selection requires at least that the optical configuration of a
cycler matches the configuration defined by the assay profiles referenced in the work
list.
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Button bar
The button bar contains 3 interactive buttons:
A
Label/Title
Description
"Print work list..."
Generation of a work list report in *.pdf format with the
following structure:
Work list name
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Creation date and time, user name
Rotor information
Rotor type
Volume
Assays
Assay profile
name
Version
Sample details
Position
Sample ID
Target(s)
Type
Assay
Comment
Kit
information:
• Material
number
• Expiry date
• Lot
number
Note
The work list can also be printed by clicking the "View
sample details..." button; see Printing work list using
view sample details button.
Note
The printout can be used as a pipetting scheme.
B
"Cancel"
C
"Start run"
The application process is canceled.
The "Apply work list" screen is closed without saving any
changes.
The "Available work lists" screen is shown.
After the start of the cycling process, the cycler screen of
the selected cycler is displayed.
Note: The "Start run" button is disabled by default. This
button is activated if the user has selected a cycler in the
"Cycler selection" table and has confirmed that the locking
ring has been attached.
When the user clicks the "Start run" button, the following
actions are performed:
The experiment is saved in the database.
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The run is started.
Rotor-Gene AssayManager switches to the "Cycler"
environment of the selected cycler.
Tasks related to the "Run work list" view
Starting a run
Managing cyclers
Setting work list naming options
1.5.5.1.3
Create New/Edit Work List View
The "Create new work list" view and the "Edit work list" view share the same design therefore the description below is valid for both tasks, creating and editing a work
list.
The task of creating a new work list/editing a work list is subdivided into 3 steps:
"Assays"
"Samples"
"Properties"
The screen layout for these steps have 2 static elements in common: the step marker
and the button bar. These elements remain unchanged if the user changes from one
step to another - with the exception that the "Properties" step contains an additional
"Apply" button. The main screen area varies according to the current step. The step
marker is used to change between these 3 steps.
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Step marker
The step marker is used to change between the 3 different steps.
Note
It is not necessary to follow the 3 steps one after another. The steps can be
accessed arbitrarily. Unsaved changes are maintained if the user changes to
another step.
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The coloring of the step marker changes, depending on whether errors occur and if
the step is currently active or not.
Status
Coloring
Disabled step
Grayed out
Currently active step without
error
Gray background
white font
Currently active step with
error
Brown background
yellow font
Currently not active step
without error
Blue background
dark blue font
Currently not active step
with error
Yellow background
dark brown font
Example
Button bar
The button bar is arranged at the bottom of the screen.
Label/Title
Description
Note: Button is only enabled if the work list is valid and
contains no errors.
Task: Generate a work list report in *.pdf format.
In case unsaved changes are present, the following warning
must be confirmed before the *.pdf file can be generated. A
work list must be saved in the database before it can be
printed.
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The generated *.pdf has the following structure:
Work list name
Creation date and time, user name
Rotor information
Rotor type
Volume
Assays
Assay profile
name
Version
Sample details
table
Position
Sample ID
Target(s)
Assay type
Comment
Kit information:
Material
number
Expiry date
Lot number
Note: Button is enabled if at least the work list name is valid.
Task: Export the work list as *.iwl file.
The *.iwl file can be imported to other Rotor-Gene
AssayManager installations (exchange functionality). If
unsaved changes are present, the following warning must be
confirmed.
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Task: Save the current progress and return to the available
work lists table.
Task: Reset the current creation process.
If a new work list was created, all fields are reset to their
default value. If an existing work list was edited, unsaved
changes of the work list are discarded. After clicking "Reset",
the following warning must be confirmed.
Note: Button is only enabled if unsaved changes exist and a
valid work list name has been entered.
Task: Save the work list.
The current work list is saved to the database under the work
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list name entered in the "Properties" step. The work list is
subsequently available in the "Available work lists" table.
If a work list was edited, the "Last modified" field is set to the
current date, time, and user.
If a new work list was created, the "Created" field is set to the
current date, time, and user.
Clicking "Save" if the work list is still incomplete opens the
following dialog:
Note: An incomplete work list can be saved if at least a valid
work list name was entered. If an incomplete work list is saved,
Rotor-Gene AssayManager displays a warning that has to be
confirmed.
Task: Cancel the creation process.
All entries are deleted and the "Available work lists" table is
shown. After clicking "Cancel", the user must confirm that
unsaved data will be discarded.
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Task: Applies the work list.
Further information can be found under Apply work list view.
Assays step
In this step, the user assembles a work list by adding assay profiles to the work list. In
its simplest form, only one assay profile is added to the work list. It is also possible to
add multiple, compatible assay profiles.
The following requirements must be fulfilled when assay profiles are combined:
The assay profiles must be compatible (compatibility of assay profiles is defined in
the Assay profile editor).
The maximum number of tubes for the selected rotor is not exceeded.
The assays step consists of 4 areas:
"Available assay profiles" table
"Selected assay profiles" table
"Messages" area
Transfer buttons
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Select and edit assay profiles:
Select one assay profile for the work list from the "Available assay profiles" table
and add it; in case the work list contains multiple assay profiles, select a
compatible assay profile and add it.
Select the rotor type and the reaction volume.
Transfer the assay(s) to the "Selected assay profiles" table.
Depending on the settings in the "Configuration" environment, the following data
might have to be entered in the selected assay profiles table for every selected assay:
Number of samples
Material number
Kit expiry date
Lot number
Note
These data (except the number of samples) can either be entered manually in the
individual boxes or by using a bar code scanner.
To activate the bar code scanning function, click the bar code symbol in the very
right column. The "Scan QIAGEN Kit Bar code" dialog opens. The bar code of the
dedicated QIAGEN kit can be scanned. The values for material number, kit expiry
date, and kit lot number will be automatically populated with the values from the
scan. Only the number of samples has to be entered manually.
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Note
For a description of how to install and use a handheld bar code scanner, please
refer to the corresponding device manual.
We recommend the bar code scanner delivered with QIAsymphony instruments,
which can be ordered separately from QIAGEN (Handscanner Touch 65-PRO m.
CAB-412/USB A, cat. no. 9241227).
Transfer buttons
The transfer buttons are used to add and remove assay profiles to/from the selected
assay profiles table.
Icon
Description
Transfer the selected assay profile from the "Available assay profiles" table
to the "Selected assay profiles" table.
This button is enabled if:
An assay profile is selected in the "Available assay profiles" table.
Sufficient free wells are available on the selected rotor.
The selected assay profile is compatible with assay profiles already in the
"Selected assay profiles" table.
Remove the selected assay profile from the "Selected assay profiles" table.
This button is enabled if an entry is selected in the "Selected assay profiles"
table.
"Available assay profiles" table
List with all available assay profile names, sorted alphabetically in ascending order.
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A
Label/Title
Description
"Available
assay
profiles" table
Table of all available assay profiles with the following
columns:
Name of assay profile
Version number
Number of external controls used by the corresponding
assay.
B
"Rotor type"
selection
menu
Drop-down menu with predefined rotor types.
Select one rotor type for the new work list.
The "Rotor type" selection menu displays the selected
value. This menu becomes disabled after an assay profile
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has been transferred from the "Available assay profiles"
table to the "Selected assay profiles" table.
To re-enable this menu, all assay profiles have to be
removed from the "Selected assay profiles" using the
transfer button <.
C
"Free
Info about the number of free positions on the rotor.
positions" info
field
The value in this read-only field depends on the selected
rotor. This value is calculated by subtracting the
mandatory assay positions (i.e., external controls) and the
number of samples from the number of rotor wells.
Example:
The assay requires 1 NTC (no template control) and 4
quantitation standards. 12 samples shall be processed in
a 72-well rotor.
1 NTC + 4 standards = 5 required positions
5 required positions + 12 samples = 17 reserved
positions
72 wells – 17 reserved positions = 55 free positions
The example above is valid for assays where one sample
is applied into one tube. In case of tube splitting, i. e., one
sample is split to multiple tubes, the number of test
samples has to be multiplied by the number of necessary
tubes.
For example, if a samples is split to 5 tubes, then the
number of necessary test samples is determined by
multiplying the number of test samples by 5.
D
"Volume
selection"
menu
Drop-down menu with predefined reaction volumes for
the new work list. Select the appropriate reaction volume
from the drop-down menu.
Note
The screenshot above is an example. The available
reaction volumes are defined by the assay profile.
The "Volume selection" menu displays the selected value.
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This menu becomes disabled after an assay profile has
been transferred from the "Available assay profiles" table
to the "Selected assay profiles" table.
To re-enable this menu, all assay profiles have to be
removed from the "Selected assay profiles" using the
transfer button "<".
E
"Compatible
assay
profiles"
check box
If not
activated:
If activated:
List all available assay profiles.
Incompatible assay profiles are grayed
out.
If an assay profile has already been
added to the "Selected assay profiles"
table, only compatible assay profiles will
be listed.
Note
Multiple assay profiles are defined as being compatible if all of the following
requirements are fulfilled:
The thermal cycling profiles are identical.
The auto-gain settings are identical.
They share at least one rotor type.
They share at least one reaction volume.
The optical configuration restrictions allow the usage of at least one cycler type,
and they share at least one optical configuration.
They are generally allowed to run with other assays.
They share the same cycling group, or they are not part of a cycling group at all.
"Selected assay profiles" table
Assay profiles added to the work list (one or multiple) are listed in the "Selected assay
profiles" table. This table is not sortable.
This table contains data given by the respective assay profile and data that has to be
entered manually or with a bar code scanner. The following table shows the source
for every column:
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Source for column data
"Assay
profile
name"
"Short name"
Values given by the assay profile
"Version"
"# controls"
"# samples"
Manual input required
"Material
number"
"Kit expiry
date"
Input required either manually or by using a bar code scanner
"Lot number"
"Scan"
Values are entered either manually or via scanning the bar
code of the respective QIAGEN kit. Click
in the very right
column to open the following "Scan QIAGEN kit bar code"
dialog:
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Column
Source for column data
Using the bar code dialog facilitates the tedious task of
manually entering the material number, expiry date, and lot
number of the kit. The bar codes of QIAGEN kits contain the
information as bar code itself and as a sequence of digits. The
user can either scan the bar code using a bar code scanner or
enter the bar code digits into the "Kit bar code" field.
Note
The setting, whether a valid product number, etc., is required, is set in the "Settings"
screen of the "Configuration" environment.
These requirements can be set independently for the Closed Mode and the UDT
Mode.
If the setting is set to be "required" for one of the three options (check box is
activated), then the operator must provide the information.
It is not possible to leave void the respective input fields in that case.
Further details can be found in the description of the
under "Settings".
"Configuration" environment
"Assay position" control buttons
The "Assay position" control buttons are placed below the "Selected assay profiles"
table.
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Two arrow buttons are used to change the position of the "Selected assay profiles" in
the table. Click the up arrow to move an assay profile up. Click the down arrow to
move it down. This will also affect the assay position on the rotor.
"Samples" step
The "Samples" step shows the sample details in tabular form. All sample types from
all selected assay profiles are displayed here. In case multiple assay profiles were
added, they are listed subsequently.
Note
The order of the samples within one specific assay profile is determined by the order
specified during the creation of the assay profile. The order of multiple assay
profiles is defined by their order in the "Assays" step.
The number of displayed samples depends on:
The number of test samples entered in the "Assays" step
Required samples given by the assay profile
The number of assay profiles added in the "Assays" step
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The editable columns of the samples details table (line color, line style, ID, and
comment) have a pop-up menu, which can be accessed by a right click in the
respective column. The columns are described in the following table:
Column
Description
Row selector
The row selector is intended to select single or multiple rows.
If a row is selected, the column will be marked in blue and the
row selector icon will change:
Unselected row
Selected row
To select several consecutive rows, click the first row selector,
hold down the left mouse button, and drag the cursor to the
last desired row. To add a single row to a selection, hold
down the Control button and click the row selector.
Pop-up menu:
Note: A row must be selected using the row selector before
the corresponding pop-up menu can be opened.
If a single row is selected, the "Assign IDs" menu entry is
disabled. This entry is only activated if multiple rows are
selected.
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Open the pop-up menu by right clicking in any area of a
selected row.
Pop-up menu for a
single row selection
Pop-up menu for multiple row
selection
Label/Title
"Assign ID"
Description
"Assign same
IDs"
Assigns the ID value from the
first cell of the selection to all
other selected cells.
"Assign unique Based on the ID of the first
IDs"
selected cell, an incremental
number is added to all
selected cells.
Example: If first cell has the
ID Sample, the generated
values are Sample 1, Sample
2, Sample 3, etc.
If the first selected cell is
empty, an incremental
number is added to all
selected cells.
Example: If the first cell is
empty, the generated values
are 1, 2, 3, etc.
"Color"
Open a color palette where
the user can select a specific
color for the amplification
curve of the selected samples.
"Line Style"
Open a style palette where
the user can select a specific
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line style for the amplification
curve of the selected samples.
"Pos."
Displays the position of the sample in the rotor. The position
of a sample is determined by the assay profile and the order
of the assay profiles in the "Assays" step (in case the work list
consists of multiple assay profiles).
The maximum position number is restricted by the selected
rotor type.
Line color
The color of a sample's amplification curve in the PCR plot
can be set by opening the color palette and selecting one out
of 20 predefined colors.
Pop-up menu:
It is possible to select multiple samples and assign them the
same line color using this pop-up menu.
"Style"
The line style of a sample's amplification curve in the PCR
plot can be set by opening the line style palette and selecting
one out of 6 predefined styles.
Pop-up menu:
It is possible to select multiple samples and assign them the
same line color using this pop-up menu.
"Sample ID"
The sample ID must not be empty and must have 1 to 40
characters.
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Pop-up menu:
The sample ID pop-up menu depends on whether a single or
multiple cells are selected.
Pop-up menu for a single Pop-up menu for multiple ID cells
ID cell selection
selection
"Status"
Label/Title
Description
"Copy"
Copy the content of the selected ID
cells - single or multiple - to the
clipboard.
"Paste"
Paste the content of the clipboard to
the selected cell. A warning is
displayed before data is overwritten.
"Assign same
IDs"
Assign the ID value from the first cell of
the selection to all other selected cells.
Note: For some assay profiles it is not
allowed to have the same ID for
different samples. In this case "Assign
same IDs" entry is disabled in the
context menu.
"Assign unique
IDs"
Based on the ID of the first selected cell,
an incremental number is added to all
selected cells.
Example: If first cell has the ID Sample,
the generated values are Sample 1,
Sample 2, Sample 3, etc.
"Cancel"
Close the pop-up menu.
Note: This column is used only if a QIAsymphony work list is
imported.
Possible statuses of samples from a QIAsymphony work list
are:
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Valid
Invalid
Unclear
None (empty field) is the status if QIAsymphony has not
been used.
"Sample type"
The sample type is listed in this field.
Possible values are:
Test
NTC
PC
EC+
ECQS
Test sample
No template control
Positive control
Positive extraction control
Negative extraction control
Quantitation standard
"Targets"
Acquisition target given by assay profile
"Assay profile
name"
Short assay profile name given by assay profile. Hovering
over the short assay profile name shows a tooltip with the full
assay profile name.
"Comment"
The comment column may be empty. If a comment is filled
in, it must contain no more than 256 characters.
"Properties" step
The properties step is used to assign the new work list a name, either by entering the
name manually or by using a generated default name. Furthermore, 2 options may
be set (work list "is editable" and "is applicable").
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A
Label/Title
Description
"Work list
name"
Text field to enter a name for the new work list.
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Note
Maximum length for the name is 40 characters. The entered
name must be unique (in case a new work list is created).
B
"Default
name"
Automatically generate a name for the work list. The pattern
for the generated name is defined in the "Configuration"
environment under "Settings".
C
"Is editable"
check box
Determines whether a work list can be modified later. This
check box is disabled by default. It is enabled when the "work
list is ready to be applied" check box is activated.
If not
activated:
Work list cannot be modified later.
The "Edit work list" icon in the action bar is
deactivated:
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If activated:
Work list can be modified later.
The "Edit work list" icon in the action bar is
activated:
D
"Is
applicable"
check box
Determines whether a work list can be applied:
If not activated:
Work list cannot be applied.
If activated:
Work list can be applied.
When this check box is activated, the (disabled) "Apply" button
in the button bar and the "Is editable" check box get activated:
"Is applicable" unchecked
"Is applicable" checked
"Apply" button in button bar "Apply" button in button bar is
is disabled.
disabled.
"Is editable" check box is
disabled.
"Is editable" check box is
enabled.
E
"Created"
info field
Displays who created the work list and when (field is
populated upon saving).
F
"Last
modified"
info field
Displays who modified the work list and when (field is
populated upon saving).
G
"Last
applied"
info field
Displays when the work list was last applied.
H
"External
order ID"
Optional field that can be used for work lists imported from a
LIMS. The order ID will also be written to the LIMS output so
that the LIMS can map the results to the initial order. Check
whether your LIMS supports this kind of order IDs.
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Cycler Environment
The "Cycler" environment is used for the cyclers and gives an overview about all RotorGene Q instruments accessible by Rotor-Gene AssayManager. Up to 4 different RotorGene Q cyclers can be registered and subsequently controlled by Rotor-Gene
AssayManager in parallel. The different cyclers are represented by individual "Cycler"
icons, which are always displayed at the very top right of the Rotor-Gene
AssayManager screen.
The content of the "Cycler" environment depends on whether a cycler is currently idle,
in operation, or whether a run has been stopped but not yet released. The visual
appearance of the cycler icon indicates the current state of the cycler.
"Cycler" icon
The "Cycler" icon changes its appearance depending on the progress and the result of
the run.
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Cycler idle
Cycler working
The progress indicator
visualizes the run progress.
Run finished
Run stopped
successfully (either by clicking "Stop
Process" or an error
occurred).
Further cycler icons are listed below:
Cycler offline
Cycler activated
Invalid
verification
Run stopped and
cycler offline
"Idle Cycler" screen
In case a cycler is idle, clicking the corresponding icon displays the following screen:
There are two alternatives to start a run on an idle cycler:
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Apply an existing work list from the "Available Work Lists" table.
Create a new work list and apply it.
"Active Cycler" screen
If a cycler is active, a run has been finished or stopped manually and has not yet been
released, a plug-in specific screen will be displayed.
The amplification of the samples is displayed in real time in the plot area. After the
run process has finished, the run is released and the sample results can be approved.
It is possible to stop the process before it is finished. If the "Stop process" button is
clicked during the run, a confirmation dialog with the message “The run will be
stopped." appears. Click "OK". The run is stopped as soon as the device has finished a
profile step. This can take up to 60 seconds. The experiment is stored on the database
with the result status "Run stopped". Afterwards, the "Finish run" button is enabled and
the "Stop process" button is disabled.
The cycler screen consists of 4 areas:
Information panel
"Sample information" area
Plot area
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"Cycler" icon
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Information panel
Label
Explanation
Collapse icon
The collapse icon is used to collapse the Information panel to a
single row to gain screen space to enlarge the "Sample
information" area. If the area is collapsed, only the experiment
name is shown.
Experiment name Experiment name as defined during work list setup.
A
Name of the cycler
B
Comment field, maximum 256 characters are allowed
C
Operator name
"Sample information" area
The "Sample information" area lists all samples of the run in a table with the following
columns:
Line color (derived from the work list)
Sample position on rotor
Sample ID
Sample type:
Test
NTC
PC
EC+
ECQS
Test sample
No template control
Positive control
Positive extraction control
Negative extraction control
Quantitation standard
Assay short name
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The number of rows is equal to the number of wells on the rotor. If the number of
samples used is less than the number of wells on the rotor, the sample type "Empty" is
assigned to unused rotor positions.
Multiple assays
In case multiple assays were used to set up an experiment, the assays are arranged
one after the other.
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Behavior of the "Sample information" area
The acquisition plots for specific samples can be hidden or shown in the plot area.
Click in the row of the designated sample. By default, all samples used are shown and
hence highlighted in a dark blue color. Rows of disabled samples (i.e., hidden
acquisition plot) are colored in brighter blue.
Acquisition plots are enabled by
default for all samples. The row is
colored in dark blue.
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In the example above, the
amplification curves of tubes 2, 3,
and 5 have been disabled. These
rows are colored in brighter blue.
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Plot area
The plot area displays the amplification curves for a selected acquisition of the
different samples recorded by the Rotor-Gene Q in real time.
Label
Explanation
A
Coordinates
Shows the coordinates of the current mouse position. If
the mouse cursor is within the plot area, the mouse
cursor changes to cross hairs ( ). The current
coordinates are displayed in this field.
The coordinates are shown as "Fluorescence" and
"Cycles" values.
B
Target selection
menu
Selects the acquisition target used for the plots.
C
Graph options
Displays options to modify the scaling of the plot.
The plot is scaled to 100%. The whole plot is
displayed fitted in the graph area. The scale is
reset to display from 0 to 100 fluorescence
units. The x-axis is set to a maximum value
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equal to the number of cycles in the run
profile, and the y-axis is set to 100.
The auto scale button fits the scale to the
maximum and minimum readings in the
data.
The y-axis range is restricted to the lowest and
highest measured fluorescence value. The xaxis is set to a maximum value equal to the
number of cycles in the run profile.
D
Zoom factors
Displays zoom factors separately for the x-axis and the
y-axis.
E
"Start time"
Displays the start time of the run.
F
Progress indicator
bar
Displays the progress of the experiment. The indicator
bar visualizes the acquisition progress: the dark blue
colored part of the bar visualizes the elapsed time; the
brighter blue colored part, the remaining time of the
experiment.
The text over the progress indicator changes
depending on the current status of the run:
Text
Explanation
"Remaining
time"
Ongoing experiment
"Analyzing"
Experiment was finished, analysis
has started
"Ready"
Experiment analysis finished
G
"Remaining time"
estimation
Displays the estimated remaining time.
H
"Stop process"
Stops the run.
After clicking the "Stop process" button, a warning
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dialog must be confirmed to stop the run. The run will
be stopped as soon as the device has finished a profile
step. This can take up to 60 seconds.
The status "Run stopped" is assigned to the experiment
in the internal database.
I
"Finish run"
Finish the run.
The following dialog is opened:
The behavior of this dialog depends on the "Finish run"
setting defined in the "Configuration" environment. The
administrator can set the option that a run has to be
released before it can be approved. If this option is
activated, the administrator can further define that the
release must be signed:
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If this setting is deactivated, the run can be approved in
the "Approval" environment without releasing the run.
For further information, see
environment.
"Configuration"
Behavior of the Plot area
The plot area has interactive functionalities:
Context menu:
An area of the amplification plot can be selected. Click and hold the left mouse
button and drag the mouse pointer. A context menu appears with the options to
zoom, select, or deselect corresponding samples.
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Zoom:
Clicking "Zoom" in the context menu zooms the amplification plot to the selected
area. By right-clicking and holding down the mouse button, the cursor changes to a
hand symbol ( ). The amplification plot area can be scrolled in all directions by
moving the mouse. Double-click anywhere in the amplification plot area to reset the
zoom to 100%.
Identification of amplification curves:
Hovering the mouse over an individual amplification curve highlights the curve in
the amplification plot and displays a tooltip with the following data:
- Tube number
- Sample type
- Sample ID
- Assay type
The corresponding sample in the "Sample information" table is highlighted in darker
blue to visualize its position in the table.
Tasks related to the "Cycler" view
Managing cyclers
Finishing and releasing a run
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Approval Environment
The "Approval" environment is used to search for unreleased or partially released
assays and to approve and release every single test sample of the assay. The
"Approval" environment mainly consists of 2 different screens:
"Filter" screen: Used for filtering and selecting specific assays for the approval and
release process
"Approval" screen: Used for checking the assay result and approving and releasing
every individual test sample
Note
All functions of the "Approval" environment can be used by users with the user role
"Approver". A user with the user role "Operator" can also access this environment,
but without rights to approve or release data.
Assays intended to be approved can be filtered by defining search criteria. After
applying the filter options, the corresponding assays are displayed in the table next to
the filter options section. To start the approval and release process, the assays to be
approved are selected by checking the corresponding check box and clicking "Start
approval".
The results of every individual test sample and, depending on the plug-in, even the
external controls have to be checked and approved separately. Depending on the
status of the individual samples, the status of the experiment will change accordingly.
Possible sample status
Undefined
Accepted
Rejected
Possible assay status
Unreleased
Partially released
Fully released
Dependency between sample status and assay status:
All samples undefined
Experiment unreleased
Samples sporadically
accepted or rejected
Experiment partially released
All samples accepted or
rejected
Experiment fully released
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1.5.5.3.1
Filter Screen
The "Filter" screen is intended to
Filter for not yet released or partially released assays
Select assays to start the approval process
It consists of 2 parts:
"Filter options" area at the left hand side of the screen
"Assay selection" area at the right hand side of the screen
Initially, the "Assay selection" area is empty. Specific criteria in the filter options have
to be defined and applied to search for specific assays. All assays matching these
criteria will be listed in the "Assay selection" area. Using the check boxes, the user
selects one or multiple assays to be approved. By clicking the "Start approval" button
the "Approval" screen appears.
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"Filter options" area
By default the filter options are set to search for assays of the last month. All other filter
options are disabled. To enable the advanced filter options, the check box "Use
advanced filter options" ( A ) must be checked.
Note
Filtering for text is not case sensitive. For example, if sample01 is entered in the
"Filter contained sample IDs" box, samples with IDs Sample01 and SAMPLE01 are
also considered as matching samples.
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Label/Title
Description
Date filter
options
Enter a start date and an end date in the corresponding fields
to filter for assays with a run start date in the defined date
interval.
Dates can either be manually entered or using the date
picker.
Restrictions:
Wildcard characters are not allowed.
Dates must be entered completely.
A
"Use
advanced
filter
options"
check box
Click in the check box next to "Use advanced filter options" to
activate the advanced filter options.
Filter Criterion
Explanation
"Filter assays"
To filter for specific assays, activate
the "Filter assays" check box. All assays
are displayed in a list. A check box in
front of every assay row allows to
select individual assays.
Multiple assay selections are possible
to search simultaneously for different
assays.
"Assay status"
Filter for the assay status using the
radio buttons. Possible values are:
Successful
Failed
Both
"Release status"
Filter for the release status using the
radio buttons. Possible values are:
Unreleased
Partially
Both
"Filter experiment
Filter for the experiment name by
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name"
activating the check box and entering
an experiment name.
"Filter contained
sample IDs"
Filter for specific sample IDs by
activating the check box and entering
one or multiple sample IDs.
Multiple sample IDs have to be
entered in individual rows without any
separators.
"Filter operator"
Filter for a specific operator by
activating the check box and selecting
an operator from the list.
"Filter cycler serial
number"
Filter for a cycler serial number by
activating the check box and entering
a cycler serial number (only digits).
B
"Reset filter"
button
Resets all filter options to the default values.
C
"Apply filter"
button
Starts the filter process.
All experiments matching the filter criteria will be listed in the
"Assay selection" area.
"Assay selection" area
The "Assay selection" area consists of a table containing experiments. These
experiments meet the search criteria defined in the "Filter options" area.
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Column
Explanation
Row
selector
The row selector is a tool to select and deselect assays in
the assay selection table.
Single assays are selected by activating the check box ( ) of
the corresponding experiment. Use multiple check boxes to
select multiple assays.
Clicking the row selector highlights the current row in dark
blue. The row selector icon changes:
Deactivated
row selector
Activated
row selector
To highlight adjacent rows, click the first element's row
selector, hold down the left mouse button, and move the
cursor to the last element to be highlighted. All rows in
between are highlighted. Use the Control key to make
multiple selections of non-adjacent rows.
Context menu
The context menu of the row selector is used to select or
deselect the highlighted assay:
Label/Title
Description
"Select"
Activates the check box for all
highlighted assays.
"Deselect"
Deactivates the check box for all
highlighted assays.
"Invert
selection"
Inverts the status of the check box for all
highlighted assays, i.e., selected assays
are unselected and vice versa.
"Cancel"
Closes the context menu.
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Assays
selector
check box
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The assay selector check box is used to select the assays to
be approved. To select all assays for the approval process,
activate the check box in the column header ( A ).
The column select icon ( A ) changes according to the
number of selected assays.
No assay selected
One or more assay selected, but not all
All assays selected
"Experiment"
Experiment name defined before starting the run
Assay
validity
Shows the assay's validity status:
If the assay is valid, this field is empty.
In case an assay is invalid, this is indicated by a warning
icon:
The reason for invalidity is shown in a tooltip. Possible
reasons are:
Run failed
A problem with the cycler or the
cycler connection.
Run stopped
A run was stopped manually.
Assay invalid
Invalid external controls can lead to
an invalid assay. For details refer to
the detailed analysis.
Analysis failed Various reasons. Contact QIAGEN
Technical Services.
"Assay"
Full name of the assay(s) used for this experiment
"# samples"
Number of samples
"Operator"
Name of the operator
"Run date"
Run date of the experiment
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"Status"
Release status of the assay
If this field is empty, no samples from this assay have been
released yet.
If not all samples have been released, this assay has the
status "Partially released". This is indicated by the icon.
If an assay is locked, the column shows a lock icon .
"Start approval"
button
Starts the approval process of the selected assays. This
button is enabled if at least one assay is selected.
By clicking this button, the "Approval" screen is displayed. All
selected assays get the status "Locked".
1.5.5.3.2
Approval Screen
Note
The approval procedure and appearance of the approval screen may be different
depending on the plug-in of the assay used. For details regarding different approval
procedures, refer to the corresponding Rotor-Gene AssayManager plug-in user
manuals. In this manual, example screens and procedures for the UDT basic plug-in
are shown.
The "Approval" screen is used to:
Check the result of an assay
Approve (accept or reject) the result of every sample
Release individual sample results and whole assays
Create a support package to facilitate support in case of problems
The results of the samples of the previously selected assay can be checked and have
to be accepted or rejected and finally released. Assays where not all sample results
have been released are saved as partially released assays. Only if all sample results
have been released and no test sample has the status "undefined", the assay is
defined as "fully released". A fully released assay will no longer be available in the
"Approval" environment. This assay will be moved to the "Archive" environment.
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The "Approval" screen consists of the following 4 areas:
Area
Functionality/Tasks
Tab list
All assays selected in the previous step are displayed in the tab
list. This allows the user to work on multiple assays
simultaneously.
In case the screen space is insufficient to fit all assays,
navigation arrows are added to the tab list.
"Plots and
information" area
This area contains various data about an experiment.
This area is subdivided in up to 6 separate tabs (depending on
the selected assay and the currently used plug-in).
"Results" area
This area contains details about the samples and radio
buttons to approve or reject individual sample results.
Button bar
This area contains buttons to save, close, reset, and finally
release the selected sample results of the assay.
Tab list
All assays chosen for approval in the previous "Assay selection" step are listed in the
tab list. Every selected assay is displayed as a tab with the experiment name and the
assay name in the tab header. The currently active tab is highlighted gray. The
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inactive tab(s) are light blue. If an experiment contains unsaved modifications, this will
be indicated by a symbol beside the experiment name.
A tab is closed by clicking the "Close" button in the button bar. The red close button at
the very right of the tab list is used to close all tabs. In case the screen size is not
sufficient to display all assay tabs, a left and right arrow symbol is displayed to
navigate between the tabs.
"Plots and information" area
The "Plots and information" area is subdivided into 6 sub tabs:
1.
"Raw data"
2.
"Processed data"
3.
"Standard curve"
4.
"Experiment"
5.
"Assay"
6.
"Audit Trail"
Graphic focused:
Shows amplification plots of raw and processed
data as well as the standard curve, respectively
(depending on the selected assay and the
currently used plug-in).
Data focused:
Shows detailed data about the experiment and
the assay.
Shows all actions that are recorded in the audit
trail.
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Note
The collapse icon ( ) is used to collapse the "Plots and information" or the "Results"
area to gain screen space for the other area. If an area is collapsed to a single row,
the icon changes to
for expanding the area back to the default size.
"Raw data" sub tab
The "Raw data" sub tab displays a plot of the fluorescence measured during the assay
run. The line styles and colors used in the plots are defined during the creation of the
corresponding assay profile. The availability of raw data depends on the currently
used plug-in.
Label/Title
Icon
Description
Collapse icon
Collapses the "Plots and information" or the "Results area"
to gain screen space for the other area.
Target selection
menu
Selects the target source used for the corresponding plot.
This button resets the scale of the y-axis (visualization of
the fluorescence) from 0 to 100 fluorescence units. The xaxis is set to a maximum value equal to the number of
cycles in the run profile.
Graph
options
The auto-scale button attempts to fit the scale of the y-axis
to the maximum and minimum readings in the data. The
x-axis is set to a maximum value equal to the number of
cycles in the run profile.
Disabled in "Raw data" tab.
Disabled in "Raw data" tab.
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Clicking the "Full screen" button enlarges the amplification
plot to maximum size. Clicking it again will scale down the
amplification plot back to normal size.
Coordinates
Shows the coordinates of the mouse pointer (cross hairs) in
the amplification plot area in the amplification plot. First,
the fluorescence value on the y-axis is displayed, followed
by the cycle value on the x-axis.
Coordinates are displayed only if the cursor is over the
amplification plot. Otherwise the coordinate values are set
to 0.
Behavior of the plot area
When the mouse is hovered over the amplification plot, the cursor changes to cross
hairs ( ).
The current position of the mouse cursor over the amplification plot is displayed in
real time in the coordinates field.
Hovering with the mouse over the amplification curve of a specific sample opens a
tooltip displaying the following information:
Tube
number
Sample
ID
Sample
type
Assay
name
(long)
An area of the amplification plot can be selected by clicking and holding the left
mouse button and dragging the mouse pointer. A context menu with several options
appears.
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Description of the context menu's functions:
Note
Navigation in a zoomed amplification plot
By right-clicking and holding down the mouse button the cursor changes to a hand
symbol (
). The plot area can be scrolled in all directions by moving the mouse.
Double-click anywhere in the amplification plot area to reset the zoom to 100%.
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Processed Data
The availability of processed data depends on the currently used plug-in. The
"Processed data" sub tab has the same elements and the same behavior as the "Raw
data" sub tab with only a few differences:
1. The raw fluorescence data are normalized using the internal algorithm of RotorGene AssayManager according to the settings of the corresponding assay profile.
2. The graph options are partially different. The following table describes only the
differences to the raw data tab:
Disabled in "Processed data" tab
Graph
options
By clicking the "Linear scale" button, the amplification plot
is displayed using a linear scale. If this option is selected,
the "Linear scale" button is highlighted in dark blue color.
By clicking the "Logarithmic scale" button, the
amplification plot is displayed using a logarithmic scale.
If this option is selected, the "Logarithmic scale" button is
highlighted in dark blue.
Standard Curve
The standard curve sub tab displays the standard curve as a result of plotting the CT
values of the quantitation standards on the y-axis against their concentration on the xaxis. For easy identification the color of the data points corresponds with the style for
the individual samples selected in the assay profile. Additionally, hovering with the
mouse over the data point of a specific sample opens a tooltip displaying the
following information:
Tube number
Sample ID
Sample type
Assay name (long)
Note
The standard curve is only available for quantitative assays and certain plug-ins.
The "Plots and information" area consists of a standard curve plot area where the
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curve is displayed, and an information panel with statistical information about the
curve.
Standard curve plot area
The layout is similar to the "Raw data" and "Processed data" sub tabs:
A drop-down menu to select the target
Graph option buttons to manage the plot
A coordinates field, displaying CT and concentration values of the current cursor
position in the plot
Information panel
The informational panel provides information about the acquisition channel and
statistical parameters describing the parameter values of the regression analysis:
The statistical regression parameters are:
Parameter
Explanation
R
Root extracted from R2
R2
The correlations coefficient R2 is a statistical parameter to measure
the fit of the data points to the regressed line. In general, the
standard curve should have an R2 value = 0.990. However, the
individual limit for this value can be set during assay profile
creation.
M
Curve slope
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B
Curve offset
Efficiency
Describes the amplification efficiency in a PCR
Experiment
The "Experiment" sub tab provides detailed information about the experiment.
Assay
The "Assay" sub tab provides detailed information about the selected assay.
Audit Trail
The "Audit trail" sub tab contains detailed information about any substantial events of
the experiment in adjacent order.
Example:
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"Results" table
All samples and external controls are listed in separate rows of the results table. If a
sample has multiple targets, the row is further split and the results of every individual
target are displayed. Any test sample results provided by Rotor-Gene AssayManager
must be investigated as being correct or incorrect and must be approved (accepted
or rejected) accordingly. Accepted or rejected samples must be released as a final
step.
Note
The approval procedure may be different depending on the plug-in currently used.
For details regarding the approval procedure, refer to the corresponding RotorGene AssayManager plug-in user manual.
Assays with at least one undefined test sample get the status "Partially released". If all
test samples of an experiment have been released, the experiment status is set to
"Fully released". The experiment is transferred to the "Archive" environment. Future
access to the data of the experiment is possible from the "Archive" environment.
Results table
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The results table contains the following columns:
Column
Explanation
Row
selector
The row selector enables the user to select and deselect samples
in the results table and to approve the status of multiple test
samples simultaneously.
Selecting single assays is simply done by activating the check
box ( ) of the corresponding sample. Use the row selector to
select multiple samples.
Clicking the row selector highlights the current row. The row
selector icon changes. The highlighted row will be colored in
dark blue.
Deactivated
row selector
Activated
row selector
To highlight adjacent rows, click the first element's row selector,
hold down the left mouse button, and move the cursor to last
element to be highlighted. All rows in between are highlighted.
Use the "Control" key to make multiple selections of nonadjacent rows.
Context menu
The context menu of the row selector is used to select/deselect
the highlighted sample experiment:
Label/title
Description
"Copy"
Copies the content of the selected rows to
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the clipboard (the individual cells are
separated by tab characters, the row start is
characterized with a carriage return)
Graph
selector
check box
"Show curves"
Shows the curves of the selected samples in
the amplification plot
"Hide curves"
Hides the curves of the selected samples in
the amplification plot
"Invert
selection"
Inverts the row selection
"Accept"
Sets the approval status of the selected
samples to "Accept"
"Reject"
Sets the approval status of the selected
samples to "Reject"
"Reset to
undefined"
Resets the approval status of the selected
samples to "Undefined". This is only
possible if the sample result is not released
yet.
"Cancel"
Closes the context menu
The graph selector check box is used to show or hide the
amplification curve of the selected sample.
Hide the amplification curve of the sample
Show the amplification curve of the sample
The column select icon in the table header changes according to
the number of selected samples.
No sample selected
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Samples selected sporadically
All samples selected
Click the column select icon to easily select or deselect all
samples.
Line color
Line color of the amplification curve used for the sample
Line style
Line style of the PCR amplification curve used for the sample
Sample ID
Sample ID of the sample (as defined during work list setup)
Status
Upstream status of the sample.
Possible values are:
QIAsymphony sample status valid
QIAsymphony sample status unclear
QIAsymphony sample status invalid
Target
Display all targets related to the sample. The sample row is
split, and every target is displayed in a separate row.
CT
Calculated CT value for the target
Results
Rotor-Gene AssayManager sample evaluation result. Possible
results are:
Concentration value including a concentration unit
Signal detected
No signal
Invalid
Flags
Exceptions identified by Rotor-Gene AssayManager analysis.
Possible flags are listed in the corresponding Rotor-Gene
AssayManager plug-in user manual.
Sample
comment
For every sample a comment can be entered. Maximum 256
characters are allowed. Comments already entered during work
list setup are shown.
Approval status
The last 3 columns are reserved for the approval buttons. Here
the approval status of the test samples has to be defined using
three radio buttons.
Note: The approval procedure may be different depending on
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the plug-in currently used. For details regarding the approval
procedure, refer to the corresponding Rotor-Gene
AssayManager plug-in user manual.
Initially, the approval status of all test samples is set to
"undefined". This means that the undefined radio button is
activated and the background color of all 3 approval buttons is
set to yellow.
When the result of a test sample is set to "Accepted" by clicking
the "Accept" button, the background changes to green and the
background color of the 2 other buttons changes to blue.
When the result of a test sample is set to "Rejected" by clicking
the "Reject" button, the background changes to red and the
background color of the 2 other buttons is set to blue.
Results table options
Note
The results table options differ from plug-in to plug-in. Refer to the relevant plug-in
manual for details.
Button bar
Title/label
Explanation
Saves all changes and closes the current assay. No test
results will be released.
Discards all unsaved changes.
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Note: Visualization options, such as "Show IC", check boxes
of samples, etc., are not changed.
Saves all changes; remains in this dialog. No test results
will be released.
Closes the selected experiment. If there are unsaved
changes, a warning will be displayed.
Opens a dialog to release test results and optionally create
a report using a report profile selected from the "Report
profile" drop-down menu.
The status of the assay is set to:
"Fully released" if all test samples were released and no
test sample has the status "Undefined".
"Partially released" if at least one test sample is approved
and released while at least one test sample still is not yet
released.
The *.pdf report file is saved in the folder defined in the
"Configuration" environment, under
Settings
folder.
Local Settings
Folders for exporting
Report
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Archive Environment
The "Archive" environment is used to search for released assays and to generate
experiment reports using predefined report profiles. Note that filtering in the "Archive"
environment is limited to the currently active archives. Inactivated archives are not
included in the filtering. Different archives can be activated or deactivated using the
"Archive Management" tab in the "Configuration" environment.
The "Archive" and the "Approval" environments have a very similar layout.
Note
After finishing, an assay can have one of the following statuses:
Unreleased
No sample has been released yet.
Partially released
At least one, but not all test samples have been released.
Fully released
All test samples have been released.
Unreleased experiments can be accessed in the "Approval" environment; fully
released experiments in the "Archive" environment. Partially released experiments
can be accessed in both environments.
The main tasks (searching and reporting data) are carried out in 2 different screens:
Filter options and assay selection screen
Showing assays screen
1.5.5.4.1
Filter Screen
The Filter screen is used to search for and select partially or fully released
experiments. The layout and behavior is identical to the Filter screen of the
"Approval" environment. The only differences are:
Only experiments with either status "partially released" ( A ) or "fully released" ( B )
are shown.
The "Show assays" button ( C ) is shown instead of the "Start approval" button.
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For details about the functionality of the Filter screen, see
1.5.5.4.2
"Approval" environment.
Show Assays Screen
The Show Assays screen of the "Archive" environment is used for the following tasks:
Check experiment data of partially or fully released experiments
Create a support package to facilitate support in case of problems
Print reports as *.pdf file using report profiles
The layout of this screen is very similar to the "Approval" screen in the "Approval"
environment. Some functions are disabled here, for example the approval buttons in
the results table as well as the assay comment field. Released assays cannot be
modified.
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A
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Label/Title
Description
"Create
support
package..."
Rotor-Gene AssayManager has a built-in support function. In
case problems with a specific experiment occur a support
package can be generated. This file can be sent via email to
QIAGEN Technical Services.
The name of the generated support package has the format:
<Experiment name>_<Assay name>_<Timestamp>.
zip
Upon clicking "Create support package..." ( A ), the support
package will be generated. A save file dialog is opened to
select the target directory for the support package.
The default directory for saving the support package file is set
in the "Configuration" environment under the "Settings" tab
in the support packages option.
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1.5.5.5
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B
"Export *.rex
file..."
Exports raw data of all assays from an experiment to a *.rex
file.
This button is only enabled if all assays of the experiment are
completely released.
C
"Report
data..."
Creates a report of the experiment as *.pdf file. The report is
generated using the report profile selected from the "Report
Profile" menu.
D
"Close"
Closes the "Show Assays" screen and returns to the Filter
screen of the "Archive" environment.
Service Environment
The "Service" environment contains the "Audit Trail" tab.
"Audit Trail" tab
The audit trail is a record of all user actions. All actions are traced in the audit trail
and can be filtered and printed out. The Rotor-Gene AssayManager audit trail is
designed based on guidelines in FDA CFR Title 21, Part 11 Electronic Records,
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Electronic Signatures.
All activities of a user are logged in an audit trail categorized in 8 different contexts:
Installation
User
Session
Profile
Settings
Cycler
Work list
Experiment
The content of the audit trail can be accessed using the "Service" environment. Here,
various filter criteria can be selected and applied. The "Audit Trail" tab contains 2
areas:
"Filter" area
"Results" table
"Print to PDF" button
The user defines filter criteria in the "Filter" area and applies the filter. All entries in the
audit trail matching the filter criteria will be listed in the "Results" table.
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The content of the matching entries in the "Results" table are not editable, the table
cannot be sorted. It is possible to select a row and copy the content to the clipboard
using the "CTRL" + "C" shortcut. A *.pdf report file of the matching entries can be
generated by clicking the "Print to PDF" button.
Filter area
Explanation
A
Filter for date and time
Enter a date in the "Date from" and "Date to" fields either manually or using
the date picker. Enter a time in the "Time from" and "Time to" fields.
B
Filter for a user name
C
To
Do this
Filter for all users
Activate "All users".
Filter for the current user
Activate "This user".
Filter for a specific user
Activate "Specific" and enter a user ID in the
"User ID" field.
Filter for an experiment name
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D
To
Do this
Filter for all experiments
Activate "All".
Filter for a specific
experiment
Activate "Specific" and enter an experiment
name in the "Experiment name" field.
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Filter for a specific context
Select a context to filter for from the "Context" menu by activating the
corresponding check box. Multiple selections are possible. By default all
check boxes are activated.
E
F
Filter for a computer
If Rotor-Gene AssayManager is installed in a network on multiple
computers, this setting allows to filter for a specific computer name. In a
single computer installation environment, this setting is less useful.
To
Do this
Filter for the computer
in use
Activate "This computer".
Filter for all computers
Activate "All computers".
Filter for signed actions
The administrator can define in the "Settings" tab of the "Configuration"
environment that the release of a run and the release of test results have to
be signed: see Signing release of a run option, Signing release of test
results option. This filter option is used to filter for signed actions only.
To
Do this
Filter for all actions
Activate "All actions".
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G
To
Do this
Filter for signed actions
only
Activate "Signed only".
Filter for messages
To
Do this
Filter for all messages
Activate "All".
Filter for a specific
message
Activate "Specific" and enter a message ID in
the "Message ID" field.
H
Select a language.
I
Reset the "Filter" settings to the default values.
The default values and selection of control are as follows:
"Date & time"
J
Date from:
Current date
Date to:
Current date
Time from: 00:00:00
Time to: 23:59:59
"User"
All users activated
"Computer"
All activated
"Signed actions"
All actions activated
"Message ID"
All activated
"Experiment"
All activated
"Context"
All check boxes are selected.
Apply the selected filter criteria. All entries in the audit trail matching the
filter criteria are listed in the results table.
Results table
The results table lists all entries in the audit trail matching the filter criteria.
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The contents of the matching entries in the "Results" table are not editable, and the
table cannot be sorted. It is possible to select a row and copy the content to the
clipboard using "CTRL" + "C".
Column
Description
"Context"
Context of the entry. Possible values are:
Installation
User
Session
Profile
Settings
Cycler
Work list
Experiment
"Date & Time"
Date and time
"User"
Name of the user logged in the audit trail
"Experiment"
Name of the experiment logged in the audit trail
"Message ID"
ID of the message
"Text"
Text of the audit trail message
"Signed"
Indication if the audit trail entry is signed or not
"Print to PDF" button
Print the audit trail messages to a *.pdf file.
Tasks related to the "Service" environment
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Working with audit trails
1.5.5.6
Configuration Environment
In the "Configuration" environment, the settings of Rotor-Gene AssayManager can be
adjusted. Furthermore, different users, cyclers, archives, assay profiles, and report
profiles can be managed.
Note
Only users with the role "Administrator" can access this environment.
The "Configuration" environment is organized in 6 different tabs.
The following table shows the tabs and their assigned tasks.
Tab
Assigned tasks
"Settings"
Define global settings
Define local settings
"User Management"
Add user
Edit user data
Modify user roles
Change password
Activate/deactivate user
"Cycler Management"
Set up new cyclers
Remove cyclers
Enter next verification date
"Archive Management"
Activate/deactivate archives
"Assay Profiles"
Activate/deactivate assay profiles
Import assay profiles
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Create or adapt report profiles
Import report profiles
Export report profiles
Delete report profiles
Select content sections
Tasks related to the "Configuration" environment
Administrative tasks
1.5.5.6.1
Settings
The "Settings" tab is divided in 2 sections:
"Global Settings": Global settings are stored in the database. They are "global" for
all clients connected to the database.
"Local Settings": Local settings are only applied to the currently used computer.
Note
Thematically associated settings are bundled in group boxes. Every group box has a
title.
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Global settings
Miscellaneous settings are defined in the global settings. These are bundled in 7
group boxes.
A
Group box "Experiment"
B
Group box "Finish run"
C
Group box "Reporting"
D
Group box "Work list"
E
Group box "Analysis/Approval"
F
Group box "Cycler verification management"
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Group box "User management"
Group box "Experiment"
The settings in the "Experiment" group box define the default naming scheme for
experiments. To apply a work list, an experiment name must be entered. The user can
either enter an arbitrary name in the "Experiment name" field ( 1 ) or let Rotor-Gene
AssayManager automatically generate a default name by clicking "Default name" ( 2
). This default name can be configured in the "Experiment" group box.
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Explanation
A-1
Activate "Use work list name" to use the same name as given to the work
list that is applied.
A-2
Activate "Select pattern" to define a specific naming scheme.
A-3
Display the current work list name definition. This field is empty if "Use
work list name" is selected. If "Select pattern" is selected, the resulting
experiment name is shown.
Example:
The experiment name is set to be the
same as the work list name, hence the
field is empty.
A-4
The resulting experiment name is
displayed.
The scheme for the default name consists of 5 options:
"User-definable section"
"Assay profile short names"
"Date"
"Time"
"Operator"
Activating the check box in front of the last 4 options includes these
information in the experiment name. The options are separated by a "_"
character in the experiment name. A user definable section with a
maximum of 15 characters is entered directly in the corresponding field.
The order of the individual information cannot be changed. If a user
definable section is defined, the resulting experiment name will always
start with this section.
Rotor-Gene AssayManager is delivered with the following default
settings:
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The text in the field "Format of generated experiment names", here
Exp_AS1_AS2_AS3_20120327_1359, results from the input in the "Userdefinable section" Exp, the "Assay profile short names" AS1_AS2_AS3, the
current date 20120327, and the current time 1359.
Group box "Finish run"
Option to set
If a user must release a run before the approval can be started.
If a user must sign the run release by entering the password.
Explanation
B-1
If activated, the user must click "Release" (or "Release and go to
approval") after a run has finished to transfer the experiment to the
"Approval" environment. As long as an experiment is not released this
way, it will not be listed in the "Approval" environment and cannot be
approved.
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B-2
This option is available only if B-1 was activated before.
If this option is activated, the "Release" and "Release and go to approval"
buttons are disabled after the run has finished. The user must sign the
release by entering his password in the "Password" field. Only if the
correct password is entered, then the "Release" and "Release and go to
approval" buttons are enabled. The user can then release the experiment
to the "Approval" environment.
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Group box "Reporting"
The "Reporting" group box is used to customize the layout of reports using images.
Rotor-Gene AssayManager provides 2 different options:
Image in the header of every report page
Image at the last page of the report
The following graphic illustrates these options:
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The images must have one of the following formats:
*.bmp
*.jpg
*.png
Explanation
C-1
Displays a preview of the selected header image. If no image is
selected, the message "No image configured" is shown.
C-2
Use to select a header image. The size of the header image must not
exceed 1900 x 300 pixels.
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Step-by-step procedure to select a header image
1. Click the pencil icon ( C-2 ).
The file dialog opens.
2. Navigate to the directory with the image file and select it.
3. Click "OK".
The selected image is loaded and displayed in C-1 . All generated
reports will contain the selected image in its header.
Note
Select the appropriate image type in the file open dialog using the "
File type" drop-down menu.
C-3
Remove a previously selected header image. After confirming a warning,
the image preview will be removed from field C-1 . The text "No image
configured" is displayed.
C-4
Displays a preview of the selected finishing image. If no image is
selected, the message "No image configured" is shown.
C-5
Use to select a finishing image.
Used to select a finishing image. The size of the finishing image must not
exceed 1900 x 828 pixels.
Step-by-step procedure to select a finishing image
1. Click the pencil icon ( C-5 ).
The file dialog opens.
2. Navigate to the directory with the image file and select it.
3. Click "OK".
The selected image is loaded and displayed in ( C-4 ). All generated
reports will contain the selected image on its last page.
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Note
Select the appropriate image type in the file open dialog using the
"File type" drop-down menu.
C-6
Remove a previously selected finishing image. After confirming a
warning, the image preview will be removed from field C-4 . The text
"No image configured" is displayed.
Group box "Work list"
The "Work list" group box bundles various options concerning work lists, e.g., the
naming scheme for default names, requirements for material numbers, etc.
Explanation
D-1
Displays the current default work list name definition, as it results from
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the selected options in D-2 .
D-2
When the user manually creates a new work list in the "Setup"
environment, a work list name must be entered in the "Properties" step.
The user can either enter an arbitrary name in the "Work list name" field (
1 ) or let the Rotor-Gene AssayManager automatically generate a
default name by clicking the "Default name" ( 2 ) button.
The scheme for the default name can consist of up to 4 options:
"User-definable section"
"Date"
"Time"
"Operator"
Activating the check box in front of the last 3 options includes these
information in the work list name. The options are separated by a "_"
character in the work list name. A user definable section with a maximum
of 15 characters is entered directly in the corresponding field. The order
of the individual information cannot be changed. If a user definable
section is defined, the resulting work list name will always start with this
section.
Rotor-Gene AssayManager is delivered with the following default
settings:
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The text in the field "Format of generated work list names", here
WL_20120327_1319, results from the input in the user-definable
section WL, the current date 20120327, and the current time 1319.
D-3
If this check box is activated, samples flagged as "unclear" during
sample preparation or assay setup by QIAsymphony will be handled as
valid. An "UNCLEAR" flag is assigned to the valid sample result as a
warning.
If the check box is not activated, unclear samples will be handled as
"invalid" samples and no usable results are assigned by Rotor-Gene
AssayManager after the run is finished. Affected samples will get an
"INVALID" flag as result.
Note
The QIAsymphony sample flag "unclear" implies that there was a
problem during sample preparation or assay setup (e.g., cooling
temperature was not reached or the run was paused). Enabling the
processing of unclear samples may cause doubtful sample results.
D-4
If activated, the checksum algorithm is applied for work list import from
a LIMS. If not activated, Rotor-Gene AssayManager does not verify the
checksum of a work list to be imported from a LIMS.
D-5
The options in D-5 and D-6 refer to the creation of a new work list. In
this first step of the work list creation process, the user enters the number
of test samples. Optionally, the user can enter the material number, kit
expiry date, and the lot number.
If the check boxes in front of the options in the work list group box are
activated, the associated entries are mandatory during work list setup. If
the check boxes are not activated, the associated entries are optional.
D-6
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These options can be set independently for work list setup in Closed
Mode (options in D-5 ) and UDT Mode (options in D-6 ).
Group box "Analysis/approval"
These settings influence the "Approval" environment.
Explanation
E-1
By checking the check box "Enable to set assay to valid (UDT Mode)", the
"Set assay to be valid" check box in the "Approval" environment of the UDT
Mode (which is deactivated by default) can be activated.
The "Set assay to be valid" check box has the following functionality:
If an assay in UDT Mode is invalid, it can be manually set to be valid by
checking the "Set assay to be valid" check box. Using this functionality,
individual external controls that were evaluated as invalid by RotorGene AssayManager are excluded from the analysis. The test sample
results are set to valid. Invalid quantitation standards will be excluded
from standard curve calculation.
If the "Set assay to be valid" check box is used for assay approval, this
will be mentioned on the result report.
E-2
If the check box is activated, the release of test results in the "Approval"
environment has to be signed with the approver's password.
The following table illustrates this behavior by comparing the
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deactivated/activated check box and the resulting dialog in the release
step of the "Approval" environment.
User releases test samples simply The approver's password must be
by clicking "OK".
entered before test samples are
released. The "OK" button is disabled
by default and will be activated once
the correct password is entered.
Group box "Cycler verification management"
Explanation
F -1
Rotor-Gene AssayManager continuously checks the status of connected
cyclers concerning verification.
The option F -1 determines if cyclers with a verification status past due are
automatically disabled or not.
Activated
If the verification of a cycler is already
expired, the cycler's status is set to “Needs
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verification”. This cycler is no longer
available for experiments.
To enable a cycler again, a temperature
verification needs to be performed. An
administrator needs to enter a valid, future
“Next verification” date in the "Edit cycler"
dialog.
Deactivated
If the check box is deactivated, cyclers can be
used for experiments even if the verification is
already expired.
Group box "User management"
The settings in this group box influence the password renewal interval, password rules,
and the auto-lock timer.
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Explanation
G -1
Defines the time interval for a renewal of user passwords. The value must
be in the range of 0–999 days.
Note: If the value is set to 0, the password never expires.
G -2
If activated
Users must use CLIA compliant passwords. This means a
password has to contain at least 2 upper case
characters, 2 lower case characters, 2 numerical
characters, and 2 special characters.
If deactivated Password must have at least 8 and no more than 40
characters.
G -3
If there is no user interaction, the application will be locked automatically
after the time defined here. The value must be in the range of 0–60
minutes.
Note: If the value is set to 0, the auto-lock is deactivated and the
application will never be locked automatically.
Local settings
The user defines export directories and source directories for the local installation.
These defined settings are applicable only to the local computer. The user can define
a specific directory by clicking
and selecting the specific export/source
directory.
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Explanation
A
Target directory where reports generated in the "Approval" or "Archive"
environment are saved.
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B
Target directory where export data for a LIMS are saved. Initially, this option
is disabled. To enable this option, the check box "Export results to LIMS" must
be activated:
If this check box is activated, results released in the "Approval" environment
are exported in a LIMS compatible file to the specified directory. The target
LIMS system must be configured in a way that it searches for new files in the
same directory as specified here.
C
Source directory for assay profiles for development in UDT mode.
D
Source directory for assay profiles to be imported into the Rotor-Gene
AssayManager database via the "Assay Profiles" tab in the "Configuration"
environment.
E
Source directory for Rotor-Gene experiment template files (*.ret) used in the
"Development" environment of the UDT mode.
F
Source directory for Rotor-Gene quantitation template files (*.qut) used in the
"Development" environment of the UDT mode.
G
H
I
Rotor-Gene AssayManager can import
work lists from other Rotor-Gene
AssayManager installations,
QIAsymphony, and LIMS. The user can
select which of these 3 import options
shall be available by activating the
check boxes G – I .
The import type menu in the "Setup"
environment will be populated with
the selected import options
accordingly.
J
Destination for *.rex-files exported from the "Archive" environment.
K
Directory for importing and exporting report profiles
L
Destination for support packages created from the "Approval" or "Archive"
environment.
M
Source directory for Rotor-Gene experiments (*rex-files) to be tested in the
"Development" environment of the UDT mode.
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Tasks related to the "Settings" environment
Managing cyclers
Managing report profiles
Creating/editing a work list
Finishing and releasing a run
Managing users
1.5.5.6.2
User Management
The "User Management" tab provides an overview of all configured user profiles and
the possibility to manage these user profiles. For details about users and their roles
refer to Concepts - user management.
The "User Management" tab consists of 2 parts:
"Registered users" table
Button bar
"Registered users" table
The "Registered users" table lists all user profiles already configured in Rotor-Gene
AssayManager. A user profile can be activated or deactivated. To display a
deactivated user profile in the table, the "Show only activated user profiles" check box
must be deactivated. The activation status of a user profile is displayed in the first
column of the table.
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Column
Explanation
User status
Status of the user profile. A user profile can be deactivated or
activated. The activation status is displayed by the icon in the
first column of the table.
User is activated.
User is deactivated.
Note
Deactivated user profiles will only be shown in the table if the
"Show only activated user profiles" checkbox is deactivated.
If the checkbox is activated, only activated users profiles will be
shown.
"User ID"
Shows the user ID
"First name"
Shows the user's first name
"Last name"
Shows the user's last name
"Roles"
Shows the user's roles. In case multiple roles are assigned to a
user, all roles are listed sequentially and separated by comma.
Example
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"Edit user"
button
The "Edit user" button opens the "Edit User" dialog where
properties and settings can be modified for a user.
Label/Title Description
A
"First
Maximum 50 characters
name" field
B
"Last
Maximum 50 characters
name" field
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C
"User ID"
field
ID must be unique and may not exceed a
maximum of 40 characters.
User IDs containing the words QIAGEN,
Service, and User in combination are not
allowed.
D
"Password"
fields
Sets a new password for the user
The password must be in the range of 8–
40 characters. If CLIA complaint password
rules are activated in the "Settings" tab, the
password has to contain at least 2 upper
case characters, 2 lower case characters, 2
numerical characters, and 2 special
characters.
The password must be re-entered exactly in
the "Confirm password" field.
E
"Activate
user" check
box
Activates or deactivates a user profile by
clicking this check box
User profile is
activated.
User profile is
deactivated.
F
"Messages"
box
Displays information, warnings, and errors.
G
"Roles"
selection
list
Assigns roles to a user profile. Activate the
check box in front of a role to assign this
role to the current user profile.
It is possible to assign multiple roles to a
user profile. For details see User roles.
H
"OK"
button
Confirms the current settings, closes the
dialog, and goes back to the "User
Management" tab.
I
"Cancel"
button
Cancels the current settings, closes the
dialog, and goes back to the "User
Management" tab.
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Button bar
Label/Title
Description
A
"Refresh list"
This button is always enabled.
Updates the "Registered users" table by retrieving the list of
users from the internal database.
B
"New user..."
This button is always enabled.
Creates a new user profile. The following "Add user" dialog is
opened:
Characteristics upon opening the dialog:
All fields are initially empty
The following mandatory fields are colored in yellow:
• "First name"
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• "Last name"
• "User ID""
• "Password
The
check box is activated
No role is selected
"OK" button is deactivated
All elements in this dialog are equal to the dialog described
in the table above.
Confirm all entries with "OK" to go back to the "User
Management" tab.
Activated ( )
The new user profile is added to the
"Registered users" table and is
selected.
Deactivated ( )
The new user profile is added to the
internal database but not shown in
the "Registered users" table.
Tasks related to the "User Management" tab
Creating a user profile
Changing user profile settings
Activate/deactivate a user profile
1.5.5.6.3
Cycler Management
The "Cycler Management" tab gives an overview of the configured cyclers, their
properties, and their current status.
The "Cycler Management" tab mainly consists of 2 parts:
"Registered Cyclers" table with 2 buttons for every cycler
• "Edit cycler" button
• "Delete cycler" button
"Verification comment for selected cycler" area
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"Registered Cyclers" table
The "Registered Cyclers" table consists of 4 rows. Every row represents one of the up to
4 configurable cyclers. If no cyclers are configured yet, all columns except the position
column are empty. The following graphic shows an example configuration with
cyclers registered in positions 2 and 4. Positions 1 and 3 do not contain any data.
Column
Explanation
"Position"
A graphical illustration represents the configurable cyclers. The
current cycler position is indicated by a black square.
Example:
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In the illustration above, the first and third cycler positions are not
registered. Their icons are inactive.
"Name"
Name of a registered cycler.
Characteristics
Must not be empty
Must have 1–8 characters
Must be unique within a Rotor-Gene AssayManager installation
"Serial number"
Serial number of a registered cycler.
Characteristics
Must not be empty
Must be unique within a Rotor-Gene AssayManager installation
Must match a connected cycler that is switched on
After entering the serial number of a connected cycler, its optical
configuration is automatically checked by the Rotor-Gene
AssayManager and displayed in the "Optical configuration" box.
This box remains empty if no cycler with the entered serial number
is connected.
"Optical
configuration"
Optical configuration of a registered cycler.
"Next
verification"
Next temperature verification date and remaining days until that
date.
Characteristics
This field can be empty.
If it is set to empty, the “Verification comment” text box is
disabled and its content is cleared.
If the date is expired, the "Verification comment" text box is
disabled.
If a date is set, the date must be in the future.
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"Cycler status"
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Shows the current status of a registered cycler. Possible values are:
Offline
Cycler is not connected or connected
but not switched on.
Ready
Cycler is ready.
Needs verification
Verification has expired.
Loaded
The cycler is loaded and ready to be
run.
Running
Cycler is currently running.
Run stopped
User has stopped a run while the cycler
was running.
Run complete
Run has finished successfully.
Run failed
Error occurred during the run.
Run stopped, cycler Cycler was disconnected when it had the
disconnected
status "Run stopped".
"Actions"
Run complete,
cycler disconnected
Cycler was disconnected when it had the
status "Run complete".
Run failed, cycler
disconnected
Cycler was disconnected during a run or
when it had the status "Run failed".
The actions column contains 2 buttons for:
Editing the cycler's properties
Removing a cycler
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"Remove cycler" button
If the "Remove cycler" button is clicked, the following dialog will
be displayed and has to be confirmed with "OK" to remove a
cycler finally:
"Edit cycler" button
If the "Edit cycler" button is clicked, the "Edit cycler" dialog will be
displayed.
Explanation
A
A graphical illustration representing the up to 4
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configurable cyclers. The current cycler position is
indicated by a black square.
B
Name of the cycler. The field can be edited.
C
Serial number of the cycler. The field can be edited.
D
Optical configuration of the cycler. The field cannot be
edited; it is read-only.
E
Next verification date. The date can either be entered
manually or using the date picker ( ).
F
Displays the number of remaining days until the
verification date. The field cannot be edited.
G
Text field to enter an optional verification comment.
Tasks related to the "Cycler Management" tab
Adding a cycler
Editing cycler settings
Removing a cycler
1.5.5.6.4
Archive Management
In the "Archive Management" tab, it can be defined which archives are browsed for
experiment data during assay selection in the "Archive" environment.
Background information
After finishing a run, all experiment data and audit trails are stored in the main
database until all sample results of the experiment are released in the "Approval"
environment. After release of the sample results the experiment data are accessible
via the "Archive" environment.
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Characteristics of an archive database
An archive database covers a certain time span that is defined by the date of the
first and the last audit trail message stored in the database.
An archive database has a size of 10 GB. If a database is close to its maximum
capacity, the database is marked as "closed" and a new archive database is
created automatically.
All these processes concerning the creation and management of archive databases
are automatically performed in the background. The main database only contains
data from current, non-released, or not fully released experiments.
Tasks related to the "Archive Management" tab
The "Archive Management" tab consists of 2 parts:
"Archive Management" table
Button bar
"Archive Management" table
The "Archive Management" table lists all currently existing archive databases.
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Column
Explanation
Check box
A check box column indicates if an archive database is currently
active or inactive. Only active archive databases will be browsed
for experiment data searched from the "Archive" environment.
Deactivated databases will not be included in a search. In addition,
audit trail messages related to the archived experiments will not be
shown in the "Service" environment if the dedicated archive
database is deactivated.
Activated ( )
The corresponding archive database will be
browsed for experiment data when searched
from the "Archive" environment.
Audit trail messages related to the
experiments stored in the corresponding
archive database can be found in the
"Service" environment.
Deactivated ( )
The corresponding archive database will
not be browsed for experiment data when
searched from the "Archive" environment.
Audit trail messages related to the
experiments stored in this database and
other audit trail messages in the time span
of the database cannot be found in the
"Service" environment.
"Name"
Name of the archive database.
"Time period"
Time period covering all experiments in the archive.
Start date
Creation date of the first audit trail entry in the
database.
End date
Creation date of the latest audit trail entry in the
database.
The end date of the active archive is empty.
Button bar
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Label/Title
Description
A
"Refresh list"
Unsaved modifications are discarded.
B
"Save"
Saves all modifications.
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Tasks related to the "Archive Management" tab
Managing archives
1.5.5.6.5
Assay Profiles
The "Assay Profiles" tab in the "Configuration" environment is used to manage assay
profiles, i.e., importing, exporting, activating, and deactivating assay profiles. Assay
profiles cannot be edited in this tab.
Assay profiles can clearly be identified by their name and a version number. It is
possible to have several assay profiles with the same name but different version
numbers - but only one can be active. All other assay profiles with this name are
automatically deactivated.
Example:
The following screenshot shows an example where an assay profile "Rotor-Gene SYBR
Green PCR Demo Kit" exists in two different versions, 3.0.0 and 5.0.0. Only one
version can be active. Version 3.0.0 is deactivated (icon ), and version 5.0.0 is
activated (icon ).
The "Assay Profiles" tab consists of 2 parts:
"Assay profiles management" table
Button bar
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"Assay profiles management" table
The "Assay profile management" table lists all available assay profiles, i.e., all assay
profiles stored in the current Rotor-Gene AssayManager installation. Every assay
profile is displayed in a separate row. The table is sortable: Clicking the
corresponding column header will sort the table according to the selected column. A
row in the header of the corresponding column indicates the sorting column ( icon
for ascending order, icon for descending order).
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Note
With the check box "Show only active profile versions" it can be determined if
deactivated assay profiles are shown in the table or not.
If activated
Only activated assay profiles are shown; deactivated assay
profiles are hidden.
If deactivated
Both activated and deactivated assay profiles are shown.
Column
Explanation
Status
Status of the assay profile.
Deactivated assay profile
Activated assay profile
"Name"
Name of the assay profile.
"Version"
Version number of the assay profile.
"Short name"
Short name of the assay profile.
"Plug-in type
and version"
Plug-in type and version the assay profile was created with.
"Creation date"
Creation date of the assay profile.
Button bar
A
Label/Title
Description
"Refresh list"
Updates the list of all available assay profiles.
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B
"Deactivate"
Deactivates the selected assay profile. A confirmation dialog
must be confirmed by clicking "OK" before the selected assay
profile is deactivated.
If the check box "Show only active profile versions" is
deactivated, the deactivated assay profile is listed in the
table with an icon in its status column.
If the check box is activated, the deactivated assay profile is
not listed in the table anymore.
C
"Activate"
Activates the selected assay profile. A confirmation dialog
must be confirmed by clicking "OK" before the selected assay
profile is activated.
The icon of the assay profile changes from deactivated ( ) to
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activated ( ).
The check box "Show only active profile versions" must be
deactivated to list activated and deactivated assay profiles in
parallel in the table.
If another version of the assay profile is active, the following
dialog is displayed.
Confirm with "OK" to disable the other version.
D
"Export..."
Exports an assay profile (file extension *.iap). A dialog is
opened to select the destination directory and a file name.
The selected assay profile will be exported accordingly.
E
"Import..."
Imports an assay profile. A dialog is opened to select the
assay profile (file extension *.iap). The selected assay profile
will be imported to the assay profile management table.
Explanation: Relationship between deactivating assay profiles in the "Configuration"
environment and work lists in the "Setup" environment.
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If an assay profile is deactivated in the "Configuration" environment, work lists in the
"Setup" environment containing this assay profile cannot be applied anymore.
Tasks related to the "Assay Profiles" tab
Activating/deactivating an assay profile
Importing/exporting an assay profile
1.5.5.6.6
Report Profiles
A report containing various data about an experiment can be generated by RotorGene AssayManager in a *.pdf file format. Depending on the individual needs, it is
not always useful to include all available experiment information in a report.
Therefore the content of a report can be tailored by configuring and applying
different report profiles. In the "Report Profiles" tab different report profiles can be
configured. This is done by selecting the useful information from 8 main categories
and its subordinated content options. By applying the configured report profiles in the
"Approval" or "Archive" environment, reports are created containing only the desired
experiment information.
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Report profiles are stored in the internal database. Report profiles can be exported to
and imported from other Rotor-Gene AssayManager installations. The default export
and import directories for report profiles can be configured in the "Settings" tab of the
"Configuration" environment.
Note
QIAGEN specific report profiles cannot be copied or exported.
The "Report Profiles" screen consists of 3 elements:
"Report profiles" menu
Button bar
"Content selection" area
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"Report profile" menu
The "Report profile" drop-down menu contains all configured report profiles. The
currently selected report profile is displayed in the menu. Clicking the menu arrow ( )
shows a full listing of all currently available report profiles.
Button bar
Label/Title
Description
A
"New profile" Creates a new report profile. All content selection options are
activated by default for a new report profile.
B
"Import..."
Imports a report profile file (file extension *.irp). An import file
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dialog is shown where the report profile file to be imported
can be selected.
C
"Export..."
Exports the currently selected report profile (file extension *.
irp). An export file dialog is shown where the destination
directory and file name for the report profile to be exported
can be specified.
D
"Delete"
Deletes the currently selected report profile. A confirmation
dialog must be approved.
Clicking "OK" removes the report profile from the internal
database.
E
"Save as..."
Saves the configured report profile. The following dialog is
opened:
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E-1
Field to enter a name for the report profile file.
E-2
Saves the report file in the internal database
using the name entered in field E-1 .
E-3
Cancels the process and closes this dialog.
"Content selection" area
In the "Content selection" area, different experiment information can be selected to be
included in a report profile by activating or deactivating the respective check boxes
and radio buttons.
All available content options are grouped in 8 major categories:
"Assay Information"
"Experiment Information"
"Graphics"
"External Controls - Overview"
"External Controls - Details"
"Test Results - Overview"
"Test Results - Details"
"Audit Trail"
Clicking one of these major content categories opens the corresponding detailed
content options. These are minor content options that allow a finer adjustment of the
resulting report contents.
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The ID of external controls and test samples are mandatory fields and cannot be
deselected. The ID is always activated. Even all content options in the "Audit trail"
major category are also mandatory and cannot be deselected.
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Tasks related to the report profiles tab
Creating a new report profile
Importing/exporting a report profile
Deleting a report profile
1.5.6
General Work Flow
The following graphic summarizes the work flow in Rotor-Gene AssayManager.
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Plug-in Concept
Rotor-Gene AssayManager is a versatile application. The number of assay types that
can be processed can even be expanded with its plug-in architecture.
The general work flow is provided by the core application and its frame work. The
work flow for specific assays - including analysis - is provided by plug-ins. Plug-ins
cover the control of the following tasks:
Processing of acquired data
Analysis algorithms
Presentation of results (GUI layout of the approval work flow)
Layout and structure of report contents
Output to LIMS
The following graphic illustrates the plug-in concept:
1.6
Using Rotor-Gene AssayManager
The work flow in Rotor-Gene AssayManager can be divided in 2 sections:
Standard tasks
Administrative tasks
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Standard tasks are tasks that are performed on a daily basis.
Administrative tasks are tasks performed to manage and configure the work flow.
1.6.1
Standard Tasks
The following tasks are performed by users who are involved in the routine work of a
lab, i.e., running experiments and analyzing data.
Logging in and logging out
Locking and unlocking
Setting up a run
Starting a run
Finishing and releasing a run
Approving a run
Working with reports
Working with audit trails
The following graphic gives an overview of the work flow in Rotor-Gene
AssayManager:
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Logging In and Logging Out
All user interactions in Rotor-Gene AssayManager are assigned to a specific user.
Therefore, every user must be authenticated using a specific user ID and password.
Before leaving the computer, a user is advised to lock the application or to log out.
Step-by-step procedure to log in to Rotor-Gene AssayManager
1. Launch Rotor-Gene AssayManager,
or
if a user has logged out from a previously launched session, select "Log in" ( A )
from the main menu.
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The login screen is shown.
2.
3.
4.
5.
Enter the user ID in "User ID" field ( B ).
Enter the password in the "Password" field ( C ).
Select Closed or User Defined Test from the "Mode" menu ( D ).
Click "OK" ( E ).
Note
Closed mode plug-ins may not be available in all countries. If no Closed mode
plug-ins are installed, a log in in Closed mode will give you only very limited access
to adminstrative tasks, but you can neither perform experiments nor any analysis.
The user is logged in and forwarded to the default screen that matches their role as
listed in the table below. Users with multiple roles are forwarded to the default screen
of their first matching role. For example, a user with the role Administrator is
forwarded to the "Settings" tab in the "Configuration" environment. A user with roles
Operator and Approver will be forwarded to the "Setup" environment.
Role
Environment
Screen/tab
Operator
"Setup" environment
"Available work
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lists" screen
Approver
"Approval" environment
Filter assays
screen
Assay developer (if Closed Mode is "Configuration"
selected)
environment
"Report Profiles"
tab
Assay developer
(if UDT Mode is selected)
"Development"
environment
Assay profile
step
Administrator
"Configuration"
environment
"Settings" tab
SuperUser
"Configuration"
environment
"Settings" tab
The selected mode is indicated at the bottom left of the screen:
or
Step-by-step procedure for logging out of Rotor-Gene AssayManager
The user can choose between 2 alternative methods to log out: The user can either
use the log out command in the main menu or the log out button in the status bar.
1. Click "Log out" ( A ) in the main menu,
or
click "Log out" ( B ) in the status bar.
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2. A confirmation dialog is shown. If unsaved data exist, an "Unsaved Data" dialog is
shown with a list of all environments containing unsaved data:
Otherwise a standard confirmation log out dialog is shown:
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3. Click "OK" (clicking "Cancel" cancels the log out and closes the dialog).
The user is logged out and the login screen is shown.
Note
If a user logs out, active cyclers will continue.
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Related topics
Managing users
Modes in Rotor-Gene AssayManager
Session management
Main toolbar
Status bar
1.6.1.2
Locking and Unlocking
The application can be locked to restrict access. The locked application can be either
unlocked by the user who has locked it, or a new session can be started.
Step-by-step procedure to lock Rotor-Gene AssayManager
1. Click "Lock" in the main menu.
If no unsaved data exist, the application is locked and the following dialog is
displayed:
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If unsaved data exist, an "Unsaved Data" dialog is shown with a list of all
environments containing unsaved data.
2. Confirming by clicking "OK" locks the application. The dialog above is shown.
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Step-by-step procedure to unlock Rotor-Gene AssayManager
Precondition is that the application was locked before. The following screen is shown:
1. Click "Unlock".
The following dialog is opened. Note that the user name in the login field is set to
the user who locked the application prior. Only this user is allowed to unlock the
application.
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2. Enter the password in the "Password" field.
3. Click "OK".
The application is unlocked.
It is possible to start a new session if the application is locked by another user by
clicking "New session". If the previously logged in user did not save all data, the
following dialog is shown:
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Related topics
Managing users
Session management
1.6.1.3
Setting up a Run
Overview
A work list is used to define an experiment, i.e., which assays shall be applied, their
order, the number of samples, etc.
All tasks related to work lists are carried out in the "Setup" environment.
Tasks related to work lists
Creating/editing a work list
Importing a work list
Duplicating a work list
Exporting a work list
Deleting a work list
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Note
Use only assay kits with the same lot number for setting up an assay.
1.6.1.3.1
Creating/Editing a Work List
Overview
Work lists combine one or more assay profiles that are intended to run in an
experiment. The user creates a work list by first selecting one or multiple compatible
assay profiles. Optionally the user can adjust the material number, the kit expiration
date, and the lot number. After defining the number of samples for the work list, each
individual sample has to get an ID. Finally, the user defines the name of the work list,
sets its properties, and saves the work list. The user can save an unfinished work list at
any time and continue with the definition later.
A work list is created in the "Setup" environment ( A ). This environment automatically
appears on login for users with the role of an operator. Initially, the "Available work
lists" screen is shown with a list of all currently available work lists on the system.
Clicking the "New" button ( B ) at the bottom right of the screen changes to the "Create
new work list" screen where the new work list is set up.
The "Create new work list" screen comprises 3 different steps:
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A
Name
Description
"Assays"
Select or enter the following data:
One (or multiple, compatible) assay profile(s)
Rotor type
Reaction volumes
Number of samples
Material number
Kit expiration date
Lot number
B
"Samples" The assay setup is displayed as defined in the assay profile.
Enter IDs for each test sample. Optionally add a comment.
Line colors and line styles for amplification curves can be
adapted.
The order of the samples cannot be changed. The order is
defined by the assay profile and the order of different assay
profiles selected in the "Assays" step, if applicable.
C
"Propertie
s"
The creation of a work list process is finalized by activating 2
different options:
"Work list is editable"
"Is applicable"
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Note
Unsaved changes will not be lost if the user changes to another environment.
The "Setup" environment is not a wizard, i.e., the steps do not need to be followed
in a specific order.
A new work list can be saved in an uncompleted state. It is sufficient that at least a
valid work list name is provided.
Step-by-step procedure to create a new work list
Creating a new work list comprises 5 steps:
1. Create a new, empty work list.
2. Add one (or multiple) assay profile(s) to the work list ("Assays" step).
3. Assign sample IDs ("Samples" step).
4. Define the properties of the work list ("Properties" step).
5. Save the work list.
Step 1: Create a new, empty work list
a) If it is not active yet, change to the "Setup" environment by clicking the "Setup" icon
in the main toolbar ( A ).
b) Click the "New work list" button ( B ) at the bottom right of the screen.
The "Create work list" screen is opened. The "Assays" step marker is activated,
as indicated in dark yellow.
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Step 2: Add one (or multiple) assay profile(s) to the work list ("Assays"
step)
In this step, the user adds one or multiple compatible assays to the work list. Multiple
assay profiles can only be added if enough positions are available on the rotor. The
"Assays" step lists all available assay profiles in the "Available assay profiles" table at
the left in alphabetical order. The selected assays will be added and shown in the
"Selected assay profiles" table at the right.
The order in which assays are added defines their order on the rotor. The order can
be changed by using the assay position arrows below the right table, i.e., the assays
can be moved up and down in the table.
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a) In the "Available assay profiles" table ( D ) click the assay you want to be included.
Only one entry can be selected at a time. If an entry is selected, the corresponding
row is highlighted blue. Depending on the assay profile the "Rotor type" ( F ) and "
Volume" ( G ) drop-down menus may be colored in yellow to indicate a
mandatory entry.
Note
The check box "Show only compatible assay profiles" ( H ) determines the
behavior of the "Available assay profiles" table:
If not activated:
If activated:
All available assay profiles are listed. Incompatible assay
profiles are grayed out.
If an assay profile has been added to the "Selected assay
profiles" table, only compatible assay profiles will be listed.
b) Click the "Rotor type" drop-down menu ( F ) to select the rotor type that will be
used.
Note
Assay profiles that require more tube positions than available on the selected
rotor are grayed out in the table.
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c) Click the "Volume" drop-down menu ( G ) to select the reaction volume that will
be used.
The "Add assay to work list" ( I ) button is set to active.
d) Click the "Add assay to work list" ( I ) button to transfer the selected assay to the "
Selected assay profiles" table at the right.
The first 4 columns in the "Selected assay profiles" table ("Assay profile name",
"Short name", "Version", "# controls") are populated with data from the assay
profile. The "# samples", "Material number", "Kit expiry date", and "Lot number"
columns must be entered manually.
e) Enter the number of test samples in the "# samples" column.
Note
Enter the number of different sample IDs. If the selected assay profile analyzes
each sample ID for x different targets in individual rotor positions, x rotor
positions will automatically be grouped per sample ID. Replicates are classified
as individual sample IDs.
The sample IDs themselves have to be entered in the following "Samples" step.
f) The material number, kit expiration date, and the lot number can either be entered
manually or scanned.
Alternative 1: Manual entry of material number, kit expiration date, and
lot number
Enter the material number, the kit expiration date, and the lot number manually.
Use the date picker ( ) to enter the date using an interactive calendar.
Alternative 2 (for QIAGEN kits only): Automatic entry of material
number, kit expiration date, and lot number by scanning the kit bar
code
Click the "bar code" icon in the scan column.
The "Scan QIAGEN kit bar code" window opens.
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Either scan the bar code with a scanner or type in the kit bar code into the "Kit bar
code" field. Material number, kit expiration date, and kit lot number will
automatically be populated.
Note
Use only assay kits with the same lot number for setting up an assay.
Repeat steps a–f for all other assay profiles you want to be included in
the work list.
Note
Incompatible assay profiles cannot be selected. These are disabled and grayed
out by Rotor-Gene AssayManager.
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Hint
To remove an assay profile from the work list:
1. Click the assay profile in the "Selected assay profiles" table.
The name is marked and the "Remove selected assay from work list" button
is activated.
2. Click the "Remove selected assay from work list" button.
The following confirmation dialog is displayed:
3. Click "OK" to remove the assay profile from the work list. Click "Cancel" to close
the dialog without removing the assay profile from the work list.
Step 3: Assign sample IDs to assay profiles ("Samples" step)
In the previous step ("Assays") one or multiple, compatible assays were added to the
work list. The number of test samples was defined in the "# samples" field of the
selected assay profiles table. The position and quantity of external controls, such as
quantitation standards and NTC, are derived from the assay profile.
The main purpose in the "Samples" step is to assign IDs to the test samples, select line
styles and line colors for samples, and (optionally) enter a comment. The "Sample
details" table lists all test samples and non-test samples. In case multiple assay
profiles were added, the order of the assay profiles is determined by their order
defined in the "Assays" step.
a) Change to the "Samples" step by clicking "Samples" ( J ) in the step bar.
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The "Sample details" table is displayed with a visualization of the current assay
design. The ID field of the test samples is colored yellow because these entries are
mandatory.
b) If supported by the plug-in currently used, a color for the respective amplification
curve can be selected. To select a color for an amplification curve, right-click the
color icon of the corresponding row ( L ). A color palette is opened.
Click a color to select it.
c) If supported by the plug-in currently used, a line style for the respective
amplification curve can be selected. To select a line style for an amplification
curve, right-click the line style icon of the corresponding row ( M ). A line style
palette is opened.
Click a style to select it.
d) Enter an ID into the ID field ( N ) for every test sample. The ID must be between 1
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and 40 characters long. The sample IDs can either be identical or unique.
However, some assay profiles restrict the use of the same IDs.
e) Optional: Enter a comment in the "Comment" field ( O ). The comment must not
exceed 256 characters.
Step 4: Define the properties of the work list ("Properties" step).
This screen is intended to enter the work list name and to review information about
when it was created, modified, and last applied. The user can also specify if a work
list can be edited or applied.
a) Change to the "Properties" step by clicking the "Properties" step marker ( P ).
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Gene AssayManager automatically generate a work list name, click "Default name"
( R ). Rotor-Gene AssayManager automatically creates a default name using a
user-defined pattern (see Settings) and populates the field.
c) Activate the desired options:
To
Do this
Explanation
Define a work list as being
editable
Activate check
box S
The work list can be
edited, i.e., modified,
later. If this option is
deactivated, the work list
cannot be changed.
Mark a work list as being
applicable
Activate check
box T
If the "is applicable"
option is deactivated, the
work list cannot be
applied. To start a run,
this option must be
activated.
Note
The field "External order ID" is optional.
Step 5: Finish creating the work list
Finish creating a work list by clicking one of the buttons in the button bar:
To
Print the work list to PDF after having saved the work list
Export the work list to a folder after having saved the
work list
Save the work list and go back to the start screen of the
"Setup" environment.
Cancel your entries and set properties to default
Save the work list
Cancel your entries
Apply your work list
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Related topics
Managing assay profiles
Managing cyclers
Entering data
Using colors
"Setup" environment
1.6.1.3.2
Importing a Work List
Importing a work list is a function used either to exchange work lists between different
Rotor-Gene AssayManager installations or to import work lists from an upstream
laboratory device (for example a LIMS or QIAsymphony).
The import command is placed in the "Setup" environment ( A ) and consists of 2
elements:
A drop-down menu ( B ) to select the source of the file
The "Import" button ( C )
A work list can be imported from the following sources (entries from the drop-down
menu B ):
Source
Rotor-Gene
AssayManager
File
extension
*.iwl
Description
Exported Rotor-Gene AssayManager
work list
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Source
File
extension
Description
QIAsymphony
*.xml
Result file from QIAsymphony AS
QIAlink/LIMS
*.lwl
Work lists from QIAlink or a LIMS
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After a work list to be imported has been selected, Rotor-Gene AssayManager
internally checks its syntax and signature. If the check is successful, the work list will be
imported and added to the "Available work lists" table. Otherwise the work list will
be rejected with a corresponding error message.
Note
The entries in the import drop-down menu ( B ) depend on the settings set in the
"Settings" tab of the "Configuration" environment. An administrator can activate/
deactivate each of the 3 possible import options.
Step-by-step procedure to import a work list
1. If it is not active yet, change to the "Setup" environment by clicking the "Setup" icon
in the main toolbar ( A ).
2. Select the source for the work list to be imported from the "Import type" drop-down
menu ( B ). If the menu is disabled or necessary entries are missing, these can be
customized in the "Configuration" environment in the "Settings" tab. If necessary,
save the changes in the settings.
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3. Click "Import" ( C ).
The "Select file" dialog opens. By default, the directory set for this import type in
the "Configuration" environment is shown.
4. Change to the directory where the file to be imported is located. Select it and click
"Open".
Rotor-Gene AssayManager internally checks the signature and the syntax of the
work list.
5. The work list is imported and added to the list of available work lists.
Note
The name of work lists imported from QIAsymphony is automatically created with
the following information separated by an underscore:
“QS” as identifier for work lists imported from QIAsymphony
Batch ID of the QIAsymphony AS run
“S” + slot number of QIAsymphony AS, where the assay was set up
Rack ID of QIAsymphony AS run
Start date of QIAsymphony AS run in format “YYYYMMDD”
Start time of QIAsymphony AS run in format “HHMMSS”
In case that the QIAsymphony AS result file contains information about several
batches, this information will be separated in different work lists.
Related topics
Settings
Setting up work list name options
Rotor-Gene AssayManager and other QIAGEN products
Available work lists view
1.6.1.3.3
Duplicating a Work List
General
A specific work list is duplicated from the "Setup" environment ( A ) by clicking the
"Duplicate work list" button ( B ) in the "Actions" bar ( C ) of the corresponding work
list.
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The "Duplicate work list" button is always enabled. Clicking this button creates a copy
of the selected work list. The "Work list modification" screen is displayed. This screen is
analog to the "Creating a work list" dialog. The copy is not saved to the database
until "Save" is clicked.
The duplicated work list has the following properties:
The fields "# samples", "Material number", "Kit expiry date", and "Lot number" are
editable.
The "is editable" check box is enabled. The "is applicable" check box of duplicated
work lists is not activated.
The "Last applied" and "Last modified" fields are empty and will be set when the
work list is saved for the first time.
Step-by-step procedure to duplicate a work list
1. If it is not active yet, change to the "Setup" environment by clicking the "Setup" icon
in the main toolbar ( A ).
All available work lists are displayed in the table.
2. Locate the work list you want to duplicate, and click the corresponding "Duplicate
work list" button ( B ) in the "Actions" bar ( C ).
The "Edit duplicated work list" screen is shown.
3. Modify those parameters you need to change according to the steps described in
steps 2 to 5 of the procedure Creating/editing a work list.
Related topic
Available work lists view
1.6.1.3.4
Exporting a Work List
Exporting a work list is used to exchange work lists between different Rotor-Gene
AssayManager installations that are using different databases.
The export functionality can be found in the "Setup" environment ( A ). The "Actions"
bar ( C ) in the "Available work lists" table includes the "Export work list" button ( B ).
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Step-by-step procedure to export a work list
1. If it is not active yet, change to the "Setup" environment by clicking the "Setup" icon
in the main toolbar ( A ).
2. Move the mouse cursor to the "Actions" bar ( C ) of the work list you want to export.
3. Click the "Export work list" button ( B ).
A dialog opens to select the target directory and the file name. By default, the
directory set in the "Configuration" environment is preselected.
4. Browse to the designated directory.
5. Enter a file name for the exported work list.
6. Click "OK".
The work list will be saved under the entered file name and with the extension *.iwl.
Related topic
Available work lists view
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Deleting a Work List
Step-by-step procedure to delete a work list
1. If it is not active yet, change to the "Setup" environment by clicking the "Setup" icon
in the main toolbar ( A ).
All available work lists are displayed in the table.
2. Locate the work list you want to delete, and click the corresponding "Delete work
list" ( B ) button in the "Actions" bar ( C ) of the appropriate row of the table. The
following confirmation dialog is shown:
3. Click the appropriate button:
To
Delete a work list and return to
the "Setup" start screen.
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Click
The selected work list entry will be
deleted from the database and
then disappears from the work list
table.
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To
Cancel the delete process and
return to the "Setup" start screen
Click
The selected work list entry will
remain as before.
Related topic
Available work lists view
1.6.1.4
Starting a Run
A run can be started from the "Available work lists" table in the "Setup" environment (
A ) by clicking the "Apply" button ( B ) in the button bar of the appropriate work list
entry. An alternative is to start a run after a new work list has been successfully
created. Details can be found under Creating/editing a work list.
After the run is triggered, the "Apply work list" screen is opened. The user must enter an
experiment name and select a cycler. Furthermore, an overview of the samples can be
displayed and printed to a *.pdf file (command "View sample details", then "Print work
list"). This printout can be used as a pipetting scheme.
Note
An experiment name must be entered.
The length of the experiment name is limited to 80 characters.
The experiment name must be unique in the database.
The default name is defined under "Settings" in the "Configuration" environment.
Upon delivery, the default name for the experiment name is defined as follows:
<Assay profile short names>_<YYYYMMDD>_<HHMM>, e.g.,
AS1_AS2_AS3_20120327_1359.
It may happen that the default name exceeds 80 characters. In this case you have to
shorten the name manually to meet the requirements.
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Step-by-step procedure to apply a work list
1. If it is not active yet, change to the "Setup" environment by clicking the "Setup" icon
in the main toolbar ( A ).
The "Setup" environment is opened. All available work lists are displayed.
2. Select the work list you want to apply. Click "Apply work list" in the last column of
the row ( B ).
The "Apply work list" screen is shown. It consists of 3 areas: "Summary", "Cycler
selection", and the "Messages" section.
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3. Enter the name of the experiment in the "Experiment name" field ( C ), or click
"Default name" ( D ) to generate a name automatically.
4. Click the "Select" radio button ( E ) to select a cycler with the status "Ready".
5. Activate the "Ring attached" check box ( F ) to confirm you have attached the
locking ring.
The "Start run" button ( G ) is now activated.
6. Click the green "Start run" button ( G ) to start and apply the run. Click "Cancel" to
abandon the preparation of the run. In this case this screen will be closed and the
"Available work lists" screen is shown.
After clicking the "Start run" button, the following happens:
The experiment is saved to the database.
The run is started.
The application switches to the cycler environment of the cycler selected for the
run.
Optional Step
The user can get detailed information about the samples using the "View sample
details..." ( H ) and "Print work list..." buttons ( I ).
Clicking "View sample details..." opens a scrollable list with detailed information
about the samples:
A *.pdf file with this data can be generated either by clicking "Print work list..."
from this screen or from the "Apply work list" screen. This file can be used as a
pipetting scheme.
Related topics
Creating a work list
Managing cyclers
Settings
Available work lists view
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Finishing and Releasing a Run
During a run:
After a run is started, the environment of the selected cycler is displayed. This screen
mainly consists of the sample information at the left and the plot area at the right.
During the run process and depending on the currently used plug-in, the amplification
curves will be displayed and updated in real time. A progress indicator at the bottom
left and a progress indicator placed underneath the cycler's icon show the run
progress. It is possible to stop the run by clicking "Stop process".
Both sample information and plot area provide interactive functionalities to check the
amplification curves of single (or multiple) samples.
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Note
Upon starting the run, all samples are selected and marked blue and all
amplification curves are shown.
Click a single sample row in the sample information table to select/deselect a
sample. To make multiple selections, move to the first sample to be selected, hold
down the left mouse button, and drag the mouse to the last sample. The status of the
first selected sample defines whether these samples are selected or deselected: if the
first sample was initially selected, all samples will be deselected and vice versa.
Finishing a run:
When the run has finished, the cycler icon will change. The stop process button will
change its label to finish run. The following table gives an overview how the button
label and cycler icons change from start to the end of a run.
Cycler idle
Run started
Run finished
Cycler
Icon
Progress
Indicator
–
Label of
button
–
The operator must click "Finish run" to finalize the run.
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Note
If "Stop Process" is clicked during the run or an error occurs, the run is stopped and
the cycler icon changes to:
For further details, see
"Cycler" environment
Step-by-step procedure to finish a run
1. If it is not open yet, change to the corresponding "Cycler" screen by clicking its icon
in the main toolbar.
The "Cycler" screen is displayed.
2. To finish a run, click "Finish run".
The "Finish run" dialog is opened. It provides details about the position and the
name of the cycler, the run status, the experiment name, errors during run, and a
comment. Depending on the run properties, some of the fields may be empty.
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3. Select the desired option:
To
Click
Release the cycler
Release the cycler and change to the
"Approval" environment
Cancel the release process and change to
the "Cycler" view
When the user releases the cycler, the following processes are triggered:
The cycler is released and ready for a new run.
The run is stored in the internal database with all experiment data (sample
information, etc.).
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Difference if release of run has to be signed
The administrator can determine that the release of a run must be signed. This option
is set in the "General settings" tab of the "Configuration" environment.
If the option was set, the run has to be signed with a password (user profile password).
The buttons "Release" and "Release and go to approval" are initially disabled. These
buttons are enabled only if a valid password is entered in the "Password" field.
Note
After a run is finished and the cycler is released, open the lid, remove the rotor, and
discard the samples immediately.
Related topics
Making a release mandatory
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"Cycler" environment
1.6.1.6
Approving a Run
Overview
After a run has finished and the cycler has been released, the experiment will be
stored in the internal database. The analysis of the acquired data is performed
automatically depending on the plug-in corresponding to the assay profile and the
rules and parameter values defined by the assay profile.
Rotor-Gene AssayManager provides test results that must be approved and released
by a user with the role of an approver. Depending on which Rotor-Gene
AssayManager plug-in is currently used, the individual approval process may differ.
In this section only the general functions are described. For details about the
individual approval process, refer to the corresponding plug-in user manual.
1.6.1.6.1
Filtering Experiments
The first step in the approval process is to filter the assay to be approved. This is done
by using filter criteria in the "Approval" environment.
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This environment mainly consists of 2 parts: the "Filter options" at the left and the
"Assay selection" table at the right. The filter criteria are defined in the "Filter options"
area. All assays matching the criteria will be listed in the "Assay selection" table at the
right.
The most simple filter is the search for assays within a certain date range. Advanced
filter options allow to define further filter criteria.
The following table provides an explanation of the filter criteria:
Filter Criteria
Comment
Date range
Enter a start date and an end date in the
corresponding fields to filter for assays with a run start
date in the defined date interval.
Dates can either be manually entered or using the
date picker.
Restrictions:
Wildcard characters are not allowed.
Dates must be entered completely.
"Filter assays"
To filter for specific assays, activate the "Filter assays"
check box. All assays are displayed in a list. A check
box in front of every assay row allows to select for
individual assays.
Multiple assay selections are possible to search
simultaneously for different assays.
"Assay status"
Filter for the assay status using the radio buttons.
Possible values are:
Successful
Failed
Both
"Release status"
Filter for the release status using the radio buttons.
Possible values are:
Unreleased
Partially
Both
"Filter experiment
name"
Filter for certain assays by activating the check box
and entering an experiment name.
"Filter contained
sample IDs"
Filter for specific sample IDs by activating the check
box and entering one or multiple sample IDs.
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Multiple sample IDs must be entered in individual
rows without any separators.
"Filter operator"
Filter for a specific operator by activating the check
box and selecting an operator from the list.
"Filter cycler serial
number"
Filter for a cycler serial number by activating the
check box and entering a cycler serial number (only
digits).
Step-by-step procedure to filter assays
1. If it is not active yet, change to the "Approval" environment by clicking the
"Approval" ( A ) icon in the main toolbar.
2. In the "Filter options" section in the left part of the screen, select the appropriate
filter criteria.
3. Enter a start and an end date in the "Start date" ( B ) and "End date" ( C ) fields
either manually or using the date picker.
To use advanced search criteria:
4. Activate the "Use advanced filter options" ( D ) check box.
5. Select the appropriate filter options. Multiple selections are possible.
6. Click "Apply filter" ( E ) to search the internal database for experiments meeting the
criteria defined in the previous step.
All assays meeting the filter criteria will be listed in the "Assay selection" table ( F )
in the right half of the "Approval" environment.
7. Activate the check box in front of the assay to approve. It is possible to select
multiple assays.
The "Start approval" button is activated when at least one assay is selected:
8. Click "Start approval".
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Note
Click "Reset filter" ( G ) to reset the selected filter options to the default values, i.e.,
start date set to one month ago, end date set to today, advanced filter options
deactivated.
1.6.1.6.2
Approving Samples
Depending on which Rotor-Gene AssayManager plug-in is currently used, the
individual approval process may differ. For details about the individual approval
process, refer to the corresponding plug-in user manual.
1.6.1.6.3
Releasing Data
After the approval of sample results, the data must be released. If a sample result is
released, its approval status and the comment cannot be changed anymore.
Step-by-step procedure to release data
1. After approving the sample results, click "Release/report data" in the button bar.
The following dialog will be opened:
2. To create a report, activate the "Create report" option ( A ) and select a report
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profile from the drop-down list ( B ).
3. If the release must be signed, enter the Rotor-Gene AssayManager login password
in the "Password" field ( C ). This option is set by the administrator in the
"Configuration" environment.
4. To release the data, click "OK" ( D ). Click "Cancel" ( E ) to cancel and go back to
the "Results" table.
All approved sample results with the status "Accepted" or "Rejected" that have not
been released before will now be released. The data will be stored in the internal
database of Rotor-Gene AssayManager. If at least one sample result has not been
approved and still has the status "Undefined", the experiment will be marked as
"Partially released". If all sample results have been approved, the status "Fully
released" is assigned to the assay. As a result, the assay will no longer be available
in the "Approval" environment but can be accessed from the "Archive" environment.
Note
LIMS output is generated during release if configured.
1.6.1.7
Working with Reports
A report can be generated either during the release of sample results in the
"Approval" environment (see Approving a run) or for already released experiments
from the "Archive" environment. The content of a report is defined by individual report
profiles that can be configured in the "Report profiles" tab of the "Configuration"
environment.
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Note
The target directory to save the generated report and the source directory for report
profiles are defined in the "Settings" tab of the "Configuration" environment.
Step-by-step procedure to create a report in the Archive environment
1. Click "Archive" ( A ) in the main toolbar to change to the "Archive" environment.
The "Assay selection" screen is displayed.
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2. Select the appropriate filter options and click "Apply filter" ( B ).
A list with assays matching the filter options is displayed.
3. Select one or multiple assays by activating the corresponding check boxes ( C ).
4. Click "Show assays" ( D ).
5. Click "Report data..." ( E ) in the button bar.
The "Report Data" dialog is opened.
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6. Select a report profile from the "Report Profile" drop-down menu ( F ) .
7. Click "OK" to create the report. Click "Cancel" to cancel and return to the approval
screen.
A report of the selected experiment is generated as a *.pdf file using the selected
report profile and saved in the report folder defined in the "Configuration"
environment.
Related topics
Managing report profiles
Setting target directory for report profiles
"Archive" environment
"Approval" environment
1.6.1.8
Working with Audit Trails
The audit trail logs all actions performed in Rotor-Gene AssayManager. In the
"Service" environment, various filter criteria can be selected to filter the audit trail
entries. All entries matching the filter criteria are listed in the "Results" table.
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Step-by-step procedure to filter for audit trail entries
1. Click "Service" ( A ) in the main toolbar.
The "Service" environment contains an "Audit trail" tab containing a "Filter area" to
apply various filter criteria and a results table where matching audit trail entries
are listed.
2. Select filter criteria from the group boxes in the "Filter criteria" area ( B ). Different
filter criteria can be combined. The following filtering options can be used:
Date
User
Experiment
Context
Computer location
Signed actions
Message ID
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3. Click "Apply filter" ( C ). All entries in the audit trail matching the filter criteria are
listed in the "Results" table. Click "Reset filter settings" ( E ) to set default filter
options.
4. Click "Print to PDF" ( D ) to create a *.pdf file containing the filter criteria and the
dedicated audit trail entries. This *.pdf file has to be saved manually, if necessary.
Note
If the number of entries matching the filter criteria exceeds 1200 entries, an error
message is shown. Adjust the filter settings.
Related topics
"Service" environment
1.6.2
Administrative Tasks
The following administrative tasks can be performed by those users logged in as
administrators.
Warning
Rotor-Gene AssayManager shall not be used with the admin account of Microsoft
Windows operating system.
Managing assay profiles
Customizing reports using report profiles
Managing cyclers
Managing users
Managing archives
Working with audit trails
Customizing settings
1.6.2.1
Managing Assay Profiles
Overview
Assay profiles can be managed in the "Assay Profiles" tab of the "Configuration"
environment. All previously imported assay profiles are listed in a table. A button bar
at the bottom of the screen contains all commands to manage assay profiles. Assay
profiles can be activated, deactivated, imported, and exported.
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Tasks related to managing assay profiles
Importing/exporting an assay profile
Activating/deactivating an assay profile
1.6.2.1.1
Importing/Exporting an Assay Profile
Rotor-Gene AssayManager provides an import/export feature for assay profiles to
exchange assay profiles between different Rotor-Gene AssayManager installations. An
imported assay profile will be added to the list of "Available work lists" in the "Setup"
environments. The imported assay profile is available for the creation of new work
lists. This is done in the "Setup" environment. Newly developed assay profiles have to
be imported before they can be used in Rotor-Gene AssayManager.
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Step-by-step procedure to export an assay profile
1. Change to the "Assay profiles management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click "Assay Profiles" ( B ) tab.
2. Select the assay profile to export by clicking in the corresponding table row.
The selected row is marked blue.
3. Click "Export" ( C ).
The file dialog is opened.
4. Select the target directory, enter a file name for the assay profile, and click "OK".
The selected assay profile is saved to the selected directory. The file extensions is *.
iap.
Step-by-step procedure to import an assay profile
1. Change to the "Assay profiles management" screen:
b) Click "Configuration" ( A ) in the main toolbar.
c) Click "Assay Profiles" ( B ) tab.
2. Click "Import" ( D ).
The select file dialog is opened.
3. Change to the directory containing the assay profile you want to import. Select it,
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and click "Open".
The selected assay profile is loaded and added to the list of available assay
profiles.
Note
The same version of an assay profile cannot be imported twice.
Related topics
Configuration - assay profiles
Setting up a run
"Setup" environment
1.6.2.1.2
Activating/Deactivating an Assay Profile
Assay profiles can be activated and deactivated. Only activated assay profiles are
available for creating and applying work lists in the "Setup" environment. Deactivated
assay profiles cannot be used but can be reactivated by an administrator if required.
Existing work lists containing a deactivated assay profile cannot be applied anymore,
which is indicated in the status column of the "Setup" environment.
By default the "Show only active profile versions" check box at the bottom left of the
screen is activated. To see activated and deactivated assay profiles in parallel in the
list, deactivate the check box. Activated and deactivated assay profiles can be
differentiated by the following icons:
Icon
Assay profile status
Activated
Deactivated
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Step-by-step procedure to deactivate an assay profile
1. Change to the "Assay profiles management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click "Assay Profiles" ( B ) tab.
2. Select the assay profile to be deactivated by clicking in the corresponding table
row.
The selected row is marked blue.
3. Click "Deactivate" ( C ).
The following confirmation dialog is opened:
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4. Click "OK".
The selected assay profile will be deactivated. The icon of the assay profile
changes from
to
in the assay profiles table.
Step-by-step procedure to activate an assay profile
1. Change to the "Assay profiles management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click "Assay Profiles" ( B ) tab.
2. Ensure that the "Show only active profile versions" check box is deactivated.
Otherwise deactivated assay profiles are not shown and cannot be activated.
3. Select the assay profile to activate by clicking in the corresponding table row.
The selected row is marked blue.
4. Click "Activate" ( D ).
The following confirmation dialog is opened:
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5. Click "OK".
The selected assay profile will be activated. The icon of activated assay profile
changes from
to
in the assay profiles table.
Note
Only one version of an assay profile can be active. If another version of an active
assay profile is activated, the previous one is automatically deactivated.
Related topics
Configuration - assay profiles
1.6.2.2
Managing Report Profiles
Report profiles define which experiment data will be included in a report. Before
creating a report, a specific report profile has to be selected from a list of all
available report profiles. Depending on the individual needs, different report profiles
can be configured in the "Report Profiles" tab of the "Configuration" environment.
Note
Some plug-ins contain a specific report profile that is mandatory.
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All available report profiles are listed in the "Report profile" drop-down menu. The
content to be included in a report when using a specific report profile can be selected
in the content selection area. A button bar at the top of the screen contains all
commands to manage report profiles.
Tasks related to managing report profiles
Creating a new report profile
Importing/exporting a report profile
Deleting a report profile
1.6.2.2.1
Creating a New Report Profile
Step-by-step procedure to create a new report profile
1. Change to the "Report Profiles" management screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Report Profiles" ( B ) tab.
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2. By default a new report profile template is selected in the "Report profile" dropdown menu ( C ) called *NewReportProfile with all content selection options
activated. If another report profile was selected before, a new report profile can be
generated by clicking "New profile" ( D ).
3. Deactivate the check box of an item in the content selection or options area to
exclude it from the report file. Only items with activated check box will be included
in the report.
Note
The option "Sample result" is only useful for experiments where Rotor-Gene
AssayManager has to evaluate a result for a certain sample ID over different
assays in several rotor positions.
For standard or multiplex assays with one rotor position per sample ID, select the
"Show target result only" radio button in the "External Controls - Overview"
and "Test Results - Overview" sections and deselect the "Sample result" check
box in the "External Contorols - Details" and "Test Results - Details" sections.
Otherwise the report will contain a "Sample result not supported" warning for
every single sample.
4. Click "Save as..." ( G ) to save the report profile.
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5. The "Save report profile as..." dialog is displayed:
6. Enter a name for the new profile in the "Report profile name" field ( H ).
7. Click "OK".
8. The report profile is created and listed in the report profiles list ( C ).
Note
Report profiles delivered by QIAGEN are read-only, i.e., they can only be
imported or deleted.
1.6.2.2.2
Importing/Exporting a Report Profile
Report profiles can be exchanged between different Rotor-Gene AssayManager
installations using the report profile import and export function.
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Note
The default directory for report profile import and export is set in the
of the "Configuration" environment.
Step-by-step procedure to import a report profile
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1. Change to the "Report Profiles" management screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Report Profiles" ( B ) tab.
2. Click "Import" ( E ).
The file dialog is opened.
3. Change to the directory containing the report profile you want to import. Select the
report profile and click "Open".
The selected report profile is loaded and added to the list of available report
profiles in the drop-down menu ( C ).
Note
The maximum path length including the report file name must not exceed 256
characters.
Step-by-step procedure to export a report profile
1. Change to the "Report profiles" management screen:
b) Click "Configuration" ( A ) in the main toolbar.
c) Click "Report Profiles" ( B ) tab.
2. Select the report profile to be exported from the "Report profile" drop-down menu (
C ).
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3. Click "Export" ( D ).
The file dialog is opened.
4. Change to the target directory, and click "OK".
The report profile is saved to the selected directory. The file extensions is *.irp.
Note
Report profiles delivered by QIAGEN are read-only and cannot be exported.
1.6.2.2.3
Deleting a Report Profile
Obsolete report profiles can be removed using the delete function.
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Step-by-step procedure to delete a report profile
1. Change to the "Report Profiles" management screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Report Profiles" ( B ) tab.
2. Select the report profile to be exported from the report profile menu ( C ).
3. Click "Delete" ( D ).
The following confirmation dialog is opened:
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4. Click "OK".
The selected report profile is deleted and removed from the report profile dropdown menu ( C ).
1.6.2.3
Managing Cyclers
Rotor-Gene AssayManager can manage and operate up to 4 different Rotor-Gene Q
instruments in parallel. The cyclers can be configured and managed in the "Cycler
Management" tab of the "Configuration" environment.
Tasks related to managing cyclers
Adding a cycler
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Tasks related to managing cyclers
Editing cycler settings
Removing a cycler
Possible cycler states are:
1.6.2.3.1
Status
Description
Offline
The cycler is either connected or not connected but not turned
on.
Ready
The cycler is activated and ready.
Loaded
The cycler is loaded.
Needs verification
The cycler needs to be verified.
Running
The cycler is performing a run.
Run stopped
The cycler was stopped, but has not been released yet.
Run complete
The run finished successfully.
Run failed
An error occurred during the run.
Run stopped, cycler
disconnected
The cycler has been disconnected after the run has been
stopped but has not been released yet.
Run complete,
cycler disconnected
The cycler was disconnected after the run had been
completed.
Run failed, cycler
disconnected
The cycler was disconnected after the run had failed.
Adding a Cycler
Step-by-step procedure to add a cycler
1. Connect the USB cable supplied to a USB port of the computer.
2. Connect the USB cable to the back of the Rotor-Gene Q.
3. Connect the Rotor-Gene Q to the power supply. Connect one end of the AC power
cord to the socket located at the rear of the Rotor-Gene Q and the other end to the
AC power outlet.
4. If not already done, install Rotor-Gene Q software version 2.1, or higher. The
driver is installed automatically with the software.
5. Once the software has been installed, switch on the Rotor-Gene Q by moving the
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switch, located at the back on the right hand side, to the "On" position.
Note
For details about hardware installation and the installation of the Rotor-Gene Q
software, refer to the Rotor-Gene Q user manual.
6. Open Rotor-Gene AssayManager.
7. Change to the "Cycler Management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Cycler Management" ( B ) tab.
Note
The cycler must be connected to the computer and switched on before it can be
registered in Rotor-Gene AssayManager.
6. Click the "Edit cycler" icon ( C ) of an empty row.
7. The "Edit cycler" dialog is shown:
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8. Enter a name with up to eight characters in the "Name" field ( D ) and the serial
number of the connected Rotor-Gene Q in the
"Serial number" field ( E ). The
optical configuration of the cycler will automatically be recognized by the RotorGene AssayManager once the name and serial number are entered.
9. Optional: Enter a date when the cycler needs next verification in the "Next
verification" field ( F ) and a verification comment. The comment field can be used
to specify what kind of verification shall be performed at the defined date.
10.Click "OK" to add the Rotor-Gene Q to the "Registered cyclers" table.
Note
If more than one cycler is registered in Rotor-Gene AssayManager, we highly
recommend labeling each cycler prominently on the front instrument housing with
the specific name given during registration. This eases identification of cyclers when
loading or when several cylers are running in parallel and omits to refer back each
time to the serial number on the type plate.
Related topics
Setting up a run
"Cycler" environment
1.6.2.3.2
Editing Cycler Settings
Step-by-step procedure to modify a cycler's settings
1. Change to the "Cycler Management" screen:
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a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Cycler Management" ( B ) tab.
2. Click the "Edit cycler" icon ( C ) of an already registered cycler.
3. The "Edit cycler" dialog is shown.
4. The cycler name, the next verification date, and the verification comment may be
edited.
5. Click "OK" to update the cycler configuration.
Related topics
Setting up a run
"Cycler" environment
1.6.2.3.3
Removing a Cycler
Note
Cyclers can only be removed if they are offline, ready, or in status "needs
verification".
Step-by-step procedure to remove a cycler
1. Change to the "Cycler Management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Cycler Management" ( B ) tab.
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2. Move the mouse to the row containing the cycler to be removed from the
"Registered cyclers" table.
3. Click the "Remove cycler" button ( C ).
The following confirmation dialog is opened.
4. Click "OK". The selected cycler is removed from the "Registered cyclers" table and
cannot be used anymore.
Related topics
Setting up a run
"Cycler" environment
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1.6.2.4
Managing Users
A user with the assigned role "Administrator" can add new user profiles or activate,
deactivate, and modify existing user profiles. User profiles cannot be deleted but only
deactivated, if necessary.
Users are managed in the "User Management" tab of the "Configuration"
environment.
Tasks related to managing users
Creating a user profile
Changing user profile settings
Activating/deactivating a user profile
Setting password policies and auto-lock timer
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Creating a User Profile
Step-by-step procedure to create a user profile
1. Change to the "User Management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "User Management" ( B ) tab.
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2. Click "New user..." ( C ).
3. The "Add user" dialog is shown:
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4. Enter the first name, the last name, and a user ID in the corresponding fields D ,
E , and F .
5. Enter a password in the "Password" field ( G ), and enter it again in the "Confirm
password" field ( H ).
Note
The password must be in the range of 8–40 characters. If CLIA complaint
password rules are activated in the "Settings" tab of the Configuration
environment, the password has to contain at least 2 upper case characters, 2
lower case characters, 2 numerical characters, and 2 special characters.
6. The "Activate user" check box ( I ) is activated by default. To create a deactivated
user profile, deactivate this check box.
7. Activate the check boxes of the role in the "Roles" table that will be assigned to the
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user ( J ). It is possible to assign multiple roles to a user.
8. Click "OK".
The new user profile is added to the "Registered users" table.
Note
The user must change the password at the first login.
Password rules can be set up in the "Configuration" environment in the
"Settings" tab.
Related topics
Configuration - managing users
User roles
1.6.2.4.2
Changing User Profile Settings
Note
A user ID can never be edited or removed. However, the following data can be
modified:
First name
Last name
Password
Roles
Step-by-step to modify user settings
1. Change to the "User Management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "User Management" ( B ) tab.
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2. Click the "Edit User" icon ( C ) of a user profile.
3. The "Edit User" dialog is shown:
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4. If applicable, modify the name of the user in the fields D and E .
5. If applicable, enter a new password in the "Password" field ( F ), and enter it again
in the "Confirm password" field ( G ).
6. Toggle the "Activate user" check box ( H ) to change the activation status of the
user.
7. If applicable, modify the check boxes in the "Roles" table ( I ) according to the
needs. It is possible to assign multiple roles to a user.
8. Click "OK". The user profile will be updated according to the modifications made.
Note
The user must change the password at the next login.
Related topics
Configuration - managing users
User roles
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Activating/Deactivating a User Profile
A user profile can never be deleted but only deactivated. This ensures that actions in
the audit trails can always be tracked back to a specific user.
Note
Only the status of a user who is currently not logged in can be changed.
Note
To make deactivated user profiles visible under "Registered users", deselect "Show
only activated user profiles".
Step-by-step to deactivate a user
1. Change to the "User Management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "User Management" ( B ) tab.
2. Click the "Edit User" icon ( C ) of a user profile.
3. The "Edit User" dialog is shown:
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4. Uncheck the "Activate user" check box ( D ) to deactivate the user profile.
5. Click "OK".
The user profile is deactivated. Its status icon in the "Registered users" table
changes from
to .
Step-by-step to activate a user
1. Change to the "User Management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "User Management" ( B ) tab.
2. Ensure that the check box "Show only activated user profiles" is unchecked to make
deactivated user profiles visible.
3. Click the "Edit user" icon ( C ) of a deactivated user profile.
4. The "Edit User" dialog is shown:
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a) Activate the "Activate user" check box ( D ) to activate the user profile.
b) Click "OK". The status icon in the "Registered users" table changes from
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to
Setting Password Policies and Auto Lock Timer
A user with assigned role "Administrator" can set up password policies and the autolock timer in the "Settings" tab of the "Configuration" environment.
Passwords for user profiles have to be changed after the specified number of days.
The administrator can also define that CLIA compliant password rules must be
applied for password creation.
The auto-lock timer locks the application after a certain time without user interaction.
Step-by-step to set the password renewal interval
1. Change to the "Settings" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Setting" ( B ) tab.
2. Go to the "User management" group box. Enter the number of days in the
"Password renewal interval" field ( C ) after which the password for user profiles
should expire.
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Note
Entering a value of 0 means the password will never expire.
Step-by-step to activate CLIA compliant password rules
1. Change to the "Settings" screen:
b) Click "Configuration" ( A ) in the main toolbar.
c) Click the "Setting" ( B ) tab.
2. Go to the "User management" group box, and activate the check box "Use CLIA
compliant password rules" ( D ).
The user is required to use CLIA compliant passwords.
Further information on password rules can be found under Password policy.
Step-by-step to set up the auto-lock timer
1. Change to the "Settings" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Setting" ( B ) tab.
2. Go to the "User management" group box, and enter the number of minutes after
which the application will be locked in the "Auto-lock timer" field ( E ). After the
specified time without user interaction, the application will be locked.
Note
Entering a value of 0 means the auto-lock timer is deactivated and the user is
never logged out automatically.
Related topics
Configuration - managing users
User roles
1.6.2.5
Managing Archives
Rotor-Gene AssayManager creates archives to save and archive experiment data with
a size of up to 10 GB each. A new archive is created automatically when the archive
currently used is full.
When filtering for specific experiments in the "Archive" environment, only activated
archives will be browsed. By default this is the archive currently in use. If searching
becomes too slow due to increasing data sizes, archives can be deactivated. It is
possible to include deactivated archives in the browsing process by reactivating them
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in the "Archive Management" tab of the "Configuration" environment.
Note
Browsing in several archives will slow down the search time of Rotor-Gene
AssayManager.
Step-by-step procedure to activate or deactivate an archive
1. Change to the "Archive Management" screen:
a) Click "Configuration" ( A ) in the main toolbar.
b) Click the "Archive Management" ( B ) tab.
The "Archive Management" screen contains a table listing all existing archives. A
check box at the beginning of every row ( C ) indicates if an archive is activated or
deactivated.
If check box is...
Archive is...
Checked
Activated
Unchecked
Deactivated
2. Check the check box of archives to be activated. Uncheck the check boxes of
archives to be deactivated.
3. Click "Save" ( D ).
Related topics
Configuration - managing archives
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Filtering for experiments
1.6.2.6
Customizing Settings
A user with the assigned role "Administrator" can customize the settings in the
"Configuration" environment. The settings are divided into two sections, "Global
settings" and "Local settings":
"Global settings": Global settings are stored in the database and affect all clients
using the database.
"Local settings": Local settings affect only the specific computer.
For details, see
1.7
Settings.
Maintenance
Both the Rotor-Gene Q cycler and the computer running the Rotor-Gene
AssayManager need to be maintained. Details can be found in the relevant
manuals.
Rotor-Gene AssayManager is a software and does not need to be maintained in
general. However, the database may need to be maintained.
Maintaining the database
Important
It is important to back up the database: in case of a computer failure you are able
to recover your data from your last backup.
It is not possible to back up the content of the computer’s hard disc directly to get
a backup of the database.
Precondition
A special software tool is needed for creating a backup of the Rotor-Gene
AssayManager database. The Microsoft SQL Server 2008 Management Studio
Express (SSMSE) is a graphical management tool for SQL Server 2008 R2 Express
used as database in Rotor-Gene AssayManager. See http://www.microsoft.com for
instruction on how to download and install the SSMSE.
Note
Select for download a Microsoft SQL Server 2008 Management Studio Express
version for 32-bit computer systems. These are typically denoted with “x86” in the
file name.
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Note
You must have administration privileges for installing the SSMSE.
First start
Note
You must have appropriate rights for working with the SSMSE.
When starting SSMSE you must authenticate yourself. The name of the server is
RGAMINSTANCE.
Hints for backing up a database
Before backing up the database, close Rotor-Gene AssayManager.
Make sure no runs are active.
Make sure all changes are saved.
Make sure all remotely connected Rotor-Gene AssayManager instances are shut
down.
Back up the following databases:
aspnetdb
Rotor-Gene AssayManager
All databases starting with “IdentArchive”
To access the backup option dialog, select the context menu entry for the desired
database:
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Further information can be obtained from the "Help-function" of the SSMSE or http://
www.microsoft.com for setting up the backup of the database according to your
demands.
1.8
Troubleshooting
This section provides information about what to do if an error occurs when using
Rotor-Gene AssayManager.
Resolving error messages and warnings
Error messages and warnings are displayed when a problem occurs during the
operation of Rotor-Gene AssayManager. All messages have an error ID, which is
displayed at the end of the error message. It is possible that several errors are
combined in only one message. Refer to the error IDs listed in this section if an error
message or warning appears. If error messages or warnings appear that are not
listed here or if the error cannot be resolved, note the error ID, the error text, and the
steps leading to the error. Then contact QIAGEN Technical Services.
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Note
If QIAGEN Technical Services needs to be consulted for troubleshooting of an error,
note the steps leading to the error and the information from any dialog boxes that
appear (or at least the error IDs). This will help the QIAGEN Technical Service
Specialist to resolve the error.
If there are problems with a specific experiment, create a support package and send it
to QIAGEN Technical Services.
Creating a support package
Rotor-Gene AssayManager provides the possibility to create support packages
containing all relevant information about a specific experiment. Depending on the
approval status of the erroneous experiment, either go to the "Approval" or "Archive"
environment, select the correct experiment, and start the approval process or let the
assay data be displayed, respectively. Click "Create support package..." at the bottom
left of the screen to create a support package for the selected experiment.
A dialog opens for selecting a file name and the directory where the support package
will be saved. The default support package file name contains the experiment name
followed by the assay profile name, the current date, and time.
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The support package will be saved as a single file containing all relevant information
about the experiment. This file can be attached to an email and sent to QIAGEN
Technical Services for troubleshooting.
Note for laboratories using several installations of Rotor-Gene
AssayManager
A support package should always be created at the computer that was connected
to the Rotor-Gene Q during processing the erroneous experiment to ensure that all
relevant information are included.
1.8.1
System Setup
This section contains information about potential errors during system setup.
Error description
Comments and suggestions
Computer or Rotor-Gene Q
does not turn on
Check the power connection. The power cable
might be loose or faulty. Reconnect or replace the
cable.
Rotor-Gene AssayManager
cannot communicate with the
cycler
Check the cable connection between Rotor-Gene
Q and the computer. The USB cable might be
loose or faulty. Reconnect or replace the cable.
Only use cables and accessories supplied by
QIAGEN that are dedicated for connecting the
Rotor-Gene Q. Switch off the Rotor-Gene Q and
switch it back on again. Close the Rotor-Gene
Software, if applicable. Restart Rotor-Gene
AssayManager.
Rotor-Gene AssayManager
does not start
a) Rotor-Gene AssayManager
is not installed
Install Rotor-Gene AssayManager.
b) Old version of Microsoft
Windows
Rotor-Gene AssayManager can only be operated
with Windows XP or Windows 7.
c) No plug-in installed
Rotor-Gene AssayManager consists of the core
software and plug-ins with application specific
components. Besides the core software, at least
one plug-in must be installed to be able to use
Rotor-Gene AssayManager.
d) Different versions of core
application/plug-in
All Rotor-Gene AssayManager installations that
use the same database must have installed:
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the same plug-in versions
the same core version.
Note: "Same version" means all 3 parts of the
version number must be the same. Even
maintenance upgrades must be executed
simultaneously on all machines.
Rotor-Gene AssayManager
does not work properly and
freezes before the user can
log-in
1.8.2
Rotor-Gene AssayManager is only compatible with
32-bit versions of Windows XP or Windows 7.
Windows Vista may cause severe problems when
using Rotor-Gene AssayManager. Update your
computer to Windows 7 or install Rotor-Gene
AssayManager on another computer with a
compatible Windows version.
Operation
This section contains information about potential errors during operation of RotorGene AssayManager.
Instrument-related errors
Error description
Comments and suggestions
No or weak fluorescence signal
detected
Open the lid of the Rotor-Gene Q and
ensure that the lenses, located at both
the emission and the detection source,
are clean. This is achieved by gently
wiping a cotton tip applicator,
moistened with ethanol, over the lenses.
For details see the Maintenance section
of the Rotor-Gene Q user manual.
Erroneous instrument performance
Keep the work bench area clean and
free from dust and sheets of paper. The
air inlet of the Rotor-Gene Q is at the
bottom. Loose material such as paper or
dust may compromise performance.
Run cannot be started
Close the lid of the Rotor-Gene Q before
starting a run.
Software-related errors
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Error description
Comments and suggestions
Second Rotor-Gene AssayManager
installation cannot access data from
another installation
If several Rotor-Gene AssayManager
installations are used, ensure that core
software and plug-ins of all installations
have exactly the same version. Software
upgrades have to be applied
simultaneously to all computers sharing
Rotor-Gene AssayManager data.
QIAsymphony AS result file cannot be
imported to Rotor-Gene AssayManager
Rotor-Gene AssayManager is only
compatible with QIAsymphony software
version 4.0 or higher. Update your
QIAsymphony system to the latest
software version.
Furthermore the QIAsymphony AS result
file has to match an assay profile in the
Rotor-Gene AssayManager database.
The background in plots is printed in
black
Some printer drivers are configured in a
way that transparent background colors,
which are used in the Rotor-Gene Assay
Manager plots, are printed in black.
Check the manual of your printer how to
change this configuration.
Technical background: To ensure that
the displayed results of the plots are
exactly the same as the printed
reports, the background colors need to
be transparent.
General errors
Error description
Comments and suggestions
Incorrect rotor loading
Load tubes and Rotor-Discs in the correct
orientation into the rotor ensuring that
each tube sits correctly in place.
Samples will not optimally be aligned
over the detection system if not placed
correctly in the rotor. This could result in
a reduction of the acquired fluorescence
signal and the detection sensitivity.
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Missing locking ring
Always attach the dedicated locking ring
to the rotor before starting a run. The
locking ring ensures that caps remain on
tubes during a run and that tubes or
Rotor-Discs sit correctly in place.
Rotor not completely filled
To achieve maximum temperature
uniformity, each position in the rotor
must contain a tube. Filling all positions
in the rotor ensures even airflow to every
tube. Keep a set of empty capped tubes
available that can be used to fill any
unused positions.
The bar code of a QIAGEN kit cannot
be read using the handheld bar code
scanner
Make sure that the handheld bar code
scanner is correctly connected to the
computer and configured properly, e.g.,
data will be sent after pressing "Enter".
Try to read other bar codes with the
scanner. Ensure that all bar codes can
be easily read.
Login error
Check whether the user name is correct.
Make sure to enter the correct password.
Note that after 3 unsuccessful log-in
attempts the user profile will be locked.
In that case another registered user with
the role of an administrator has to reactivated the user profile.
Sample position is incorrect
When setting up an experiment be sure
to place the reaction tubes in the correct
positions of the rotor. During work list
setup, the sample details and their
respective positions can be displayed or
printed using the "View sample details..."
or the "Print work list..." button,
respectively. If using strip tubes, 0.1 ml,
be sure not to invert the strip tubes
during transfer from assay setup to the
rotor.
Error Messages and Error Codes
The source of a message is indicated in the error ID. The general structure of an error
ID is:
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The following list provides all error messages that might occur during operation of
Rotor-Gene AssayManager. In case QIAGEN Technical Services needs to be
contacted, provide the service specialist with the following information:
Actions performed before the error message occurred
Error ID
Note
The error ID is unique and helps QIAGEN Technical Services to clearly identify the
error message.
Error ID
30007
30008
30009
30011
30013
30014
30017
Error Text
Assign at least one role to user {0}.
The following roles in the database are obsolete: {0}. Contact QIAGEN
Technical Services.
Could not find the following role '{0}' in the database. Contact
QIAGEN Technical Services.
The database connection is lost. The session has to be closed. Unsaved
data are discarded. Contact your system administrator to fix the
problem and log in again. Running experiments will continue; they will
be saved automatically into the database as soon as the connection is
restored.
The application initialization failed because the database connection is
not available. The application will exit now. Contact your local
administrator.
Could not log-in to the application. The database connection is lost.
Contact your local administrator.
Rotor-Gene AssayManager is already started on this computer
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Error ID
110000
110005
110006
110007
110008
110009
110010
110019
110036
110038
110039
110040
110044
110048
110049
110055
110056
110057
110058
110059
110060
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Error Text
The new assay profile failed. Check the assay profile content and load
again.
Assay profile could not be loaded.
The assay profile could not be saved. The system could not write to file
system. Contact your local administrator.
The required plug-in {0}, version {1}, for the selected assay profile is
not available. Ask your software administrator to install the plug-in.
In Closed Mode only assay profiles distributed by QIAGEN can be
loaded. The selected file is not a QIAGEN original file. Switch to User
Defined Test Mode to open the selected assay profile.
In User Defined Test Mode (UDT Mode), you cannot load profiles
distributed by QIAGEN for Closed Mode. The file will not be loaded.
Log in in Closed Mode to load this file.
The signature of the file is invalid. It will not be loaded. Provide a valid
signature.
The selected assay profile contains an unknown rotor type. Select a
different assay profile.
The selected run template cannot be used with the selected plug-in "{0}
{1} {2}".
The run profile could not be loaded. The optical configuration does not
match any of the cyclers currently available.
The run profile could not be loaded.
The optical configuration is unknown.
The run template of the current assay profile does not match the run
settings of the .rex-file.
One or more steps in the assay profile editor are invalid. Correct these
invalid steps to start the assay profile tester.
The .rex file at {0} cannot be accessed. Check if the .rex file path is
correct.
The color channels of the run profile of the current assay profile do not
match the .rex file color channel {0}. Select another assay profile or .rex
file.
The samples of an assay must be arranged without gaps. At .rex file
tube position {0} on page {1} a sample is positioned after a gap.
Based on the assay profile, a {0} sample is expected in .rex file tube
{1} but the .rex file contains a {2} sample. Adjust the assay profile or
select another .rex file.
There is no plug-in available with name {0}, version {1} and
application mode {2}.
The signature of .rex file {0} is invalid. It cannot be loaded. Select
another .rex file.
The samples of an assay must be arranged without gaps. The .rex file
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Error ID
110061
110072
110073
110088
110092
110093
150001
150006
150007
150008
150029
150030
150032
150033
150034
150035
150036
150037
150038
150043
150113
150114
150115
Error Text
page {0} contains empty tubes that do not reach the end of the file.
Not all control samples of the current assay profile are specified in .rex
file. Adjust the assay profile or select another .rex file.
A .rex file was loaded, but the analysis cannot be started. Reasons:
The selected .rex file could not be loaded. Reasons:
Assay profile version '{0}' does not match with the current Rotor-Gene
AssayManager version.
This assay profile was created with plug-in {0} version {1} and
application version '{2}' and cannot be upgraded.
The assay profile could not be mapped to the .rex file. Adjust the assay
profile or select another .rex file.
There is already a profile in the database with the same name and
version. The file you selected will not be imported.
File {0} does not exist.
The signature of the file is invalid. The file will not be imported. Provide
a valid signature.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
The file contains an incomplete or invalid assay profile. The file will not
be imported.
Enter a valid assay profile path.
The file cannot be read. It will not be imported.
The signature of the file is invalid. The file will not be imported. Provide
a valid signature.
The plug-in required by the selected assay profile is not installed. Install
the required plug-in and repeat the import of the assay profile.
In Closed Mode, you can only import profiles distributed by QIAGEN.
The file you selected will not be imported. Log in in User Defined Test
Mode to import this file.
In User Defined Test Mode, you cannot import profiles distributed by
QIAGEN for the Closed Mode. The file you selected will not be
imported. Log in in Closed Mode to import this file.
Assay profile could not be loaded.{0}
The selected assay profile contains an unknown rotor type. Select a
different assay profile.
Assay Profile could not be imported.
{0} could not be loaded. The file reading failed. Select a different
image file.
The assay profile could not be activated. It refers to assay parameter set
names already present in the following active assay profile(s): {0}
The assay profile could not be imported. It refers to assay parameter set
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Error ID
150120
150134
150138
190000
190001
190002
190015
190019
190021
190023
190024
190026
190027
190031
190032
190034
190035
190036
190037
190038
190039
190040
190041
190044
190045
190046
190047
190048
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Error Text
name and volume pair combinations already present in the following
active assay profile(s): {0}.
The assay profile is not finalized. Finalize the assay profile.
The Assay profile was created with RotorGene AssayManager version
{0}, which is not compatible to the currently installed version {1}.
Assay Profile export failed because: {0}
The unique application ID is not stored in the registry. Contact your
local administrator.
Cannot read the unique application ID that is stored in the registry.
Contact your local administrator.
Cannot write Rotor-Gene AssayManager unique application ID to the
registry. Start the application again with administration rights.
File {0} does not exist.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
Rex channel reference key not found.
Rex file export failed. Reason: {0}
Experiment validation failed. Reason: {0}
The experiment validity check failed.
Failure to get acquisition channel reference.
The .rex file import created an invalid experiment: {0}. Retry or select
another .rex file.
The .rex file specifies a rotor which is unknown to the system. Select
another .rex file.
Signature could not be validated.
Failed reading the file
Signature could not be validated.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
The access to the selected file or folder is denied. Select a different file
or folder.
Unexpected I/O error with file {0}. Contact QIAGEN Technical Services.
A unsupported operation was called on the file-system or memory
resources. Contact QIAGEN Technical Services.
The directory path to the file {0} does not exist. Select another path.
The file {0} is already used.
File {0} does not exist.
File {0} does not exist at the path {1}.
Invalid argument used.
Path must not contain /.":|?><\ and leading white spaces.
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Error ID
190049
190050
190051
190052
190053
190054
190055
190056
190057
190061
190062
190063
190064
190065
190066
190067
190069
190070
190071
190072
190073
190074
190080
190081
190121
Error Text
The provided file path is invalid. Enter a valid path.
Invalid path {0} accessed. Access a valid path.
XML signature invalid.
Not supported operation called on the file-system or memory
resources.
Path too long. : {0}
The resource has an invalid document format. Contact QIAGEN
Technical Services.
The access to the selected file or folder is denied. Select a different file
or folder.
Unexpected I/O error with file {0}. Contact QIAGEN Technical Services.
A unsupported operation was called on the file-system or memory
resources. Contact QIAGEN Technical Services.
A Rotor-Gene AssayManager work list from file {0} cannot be imported.
The work list was exported with a different application mode. Make sure
the application modes are the same.
The Rotor-Gene AssayManager work list from file '{0}' cannot be
imported. It contains assay profiles which are not available. Select
another file.
The Rotor-Gene AssayManager work list from file {0} cannot be
imported. It contains assay profiles which are either not installed or
deactivated.
The Rotor-Gene AssayManager Work List from file '{0}' cannot be
imported, because it contains a rotor type that is not available.
The Rotor-Gene AssayManager Work List from file '{0}' cannot be
imported. The following error occurred: {1}
The Rotor-Gene AssayManager Work List '{0}' cannot be exported. The
following error occurred: {1}
The file was created using Rotor-Gene AssayManager {0}, it cannot be
opened. Make sure the versions are the same.
Schema validation failed: {0}
Failed reading the file.
XML signature invalid.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
Signature could not be validated.
The optical configuration is unknown. Select a compatible run profile.
This work list cannot be used in {0} mode.
One of the run profiles contains a run profile entry of an unsupported
type. Select another run profile.
The file '{0}' does not match the QIAsymphony AS result file
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Core Application User Manual - October 2012
Error ID
190123
190124
190125
190126
190127
190128
190129
190131
190132
190134
190135
190136
190137
190138
190139
190140
190141
190142
190143
190144
190145
1-289
Error Text
specification. The file cannot be imported.
No active assay profile matches the APS '{0}', the QIAGEN original
setting 'not required' and the volume pair '{1} µl, {2} µl' explicitly.
No active assay profile matches the APS '{0}', the QIAGEN original
setting 'required' and the volume pair '{1} µl, {2} µl' explicitly.
The referenced assay profiles ‘{0}’ are not compatible to each other.
Reasons:
The assay kit information check of APS '{0}' produced the following
errors:
The number of assay points is '{0}'. This number exceeds the number of
tubes on the rotor of the referenced assay profiles '{1}’.
The assay profile '{0}' referenced by APS '{1}'does not refer to exactly
one rotor type.
The assay point arrangement does not match the assay profile ‘{0}’. At
position ‘{1}’ the type ‘{2}’ was expected, but the type ‘{3}’ was found.
The QIAsymphony AS result file '{0}' cannot be imported: Reason: '{1}'
The created work list test samples contain replicated sample IDs, but the
referenced Assay Profile '{0}' does not allow this.
The QIAsymphony AS result file at ‘{0}’ contains an invalid checksum.
The file cannot be imported.
The unknown slot name '{0}' is not supported by Rotor-Gene
AssayManager.
The number of assay points is '{0}'. This number is not supported.
The unknown sample type '{0}' of assay point '{1}' at position '{2}' is
not supported by Rotor-Gene AssayManager. Select another sample
type.
The unknown assay point state '{0}' of assay point '{1}' at position '{2}'
is not supported by Rotor-Gene AssayManager.
The output position sequence of the assay points contains gaps,
positions multiple times or do not start at 1. This is not supported by
Rotor-Gene AssayManager.
The reaction volume of the APS '{0}' is not supported by the
corresponding assay profile '{1}'.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
The LIMS file at '{0}' does not match the interface specification. The
LIMS file cannot be imported.
The rotor type is not available in this system.
The required assay profile '{0}, {1}.{2}.{3}' is not available in this
system. Select another assay profile.
Enter a valid lot number for assay '{0}'.
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Error ID
190146
190148
190149
190150
190151
190152
190153
190154
190156
190157
190158
190160
190161
190165
190175
190176
190178
190180
190183
190184
190187
190191
190192
Error Text
The kit expiry date for assay {0} is expired or not specified. Use a non
expired kit.
The referenced assay profiles are not assay compatible. Reason: The
rotor types do not match.
The QIAlink/LIMS worklist at {0} contains an invalid checksum.
The unknown login mode "{0}" is not supported by Rotor-Gene
AssayManager.
The unknown sample type "{0}" is not supported by Rotor-Gene
AssayManager.
The unknown upstream status "{0}" is not supported by Rotor-Gene
AssayManager.
The export of the QIALink/LIMS result file failed. The samples were only
saved but not released.
The sample arrangement does not match the assay profile '{0}'.
The assay profile {0} does not allow replicates. Remove the replicates.
The file cannot be read. It will not be imported.
The referenced assay profiles are not cycling compatible. Reasons: .
No active Assay Profile matches the APS {0}.
The Rotor-Gene AssayManager work list from file {0} cannot be
imported. Reason: The assay {1} contains an invalid assay kit. Select a
work list with a valid assay kit.
The data cannot be used.
There are no test samples, positive or negative extraction controls
specified, but the referenced assay profile ‘{0}’ specifies a sample
eluate volume pair.
The specified sample input volume and the eluate volume pair do not
match the assay profile '{0}'. At position '{1}' the type '{2}' specifies
'{3} µl, {4} µl' but '{5} µl, {6} µl' was expected.
A work list with the name '{0}' already exists in the database. The file
'{1}' may already have been imported. Create a work list with a unique
name.
The file was created using Rotor-Gene AssayManager {0}, it cannot be
opened. Make sure the versions are the same.
The file cannot be read. The system supports interface version {0}, but
the file is designed for version {1}.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
Autogain is not defined for all channels which are used for acquisitions.
The QIALink/LIMS result file does not specify identical reaction volumes.
The referenced assay profiles are not assay compatible. Reason: The
reaction volumes do not match.
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Core Application User Manual - October 2012
Error ID
190193
270000
270001
270003
270004
310001
310002
310003
310005
310006
310007
310011
310015
350005
350010
350011
350013
350015
350016
350018
350019
350023
350034
390022
390028
390029
390030
390038
1-291
Error Text
The APS '{0}' do not specify identical reaction volumes.
The public token of the plug-in does not match with the public token
configured in the database. Plug-in: {0}.
The following plug-ins are missing in the plug-in manager: {0}.
Contact your system administrator to upgrade your installation. The
application will exit now.
RotorGene AssayManager is needed in version {0}, you have installed
version {1}. Please contact your system administrator to upgrade your
installation. The application will exit now
The following plug-in is not found on this system {0}. Please contact
your system administrator to upgrade your installation. The application
will exit now.
Could not load the plug-in assembly.
Could not find the IModule derived class to initialize the plug-in.
The public token of the assembly does not match with the public token
in the list.
Could not find experiment {0}
Plug-in not found for provided key.
Assembly name information does not match with the configuration of
the plug-in.
Error occurred during report generation. Retry report generation.
Failed to create file {0}.
Failed to generate report.
Failed to generate audit trail report.
File {0} not found.
Failed to create file {0}.
The import of the report profile failed. Reason: {0}
The export of the report profile failed. Reasons: {0}
The resource has an invalid document format. Contact QIAGEN
Technical Services.
Failed to delete the report profile.
The report profile version {0} does not match with the current RotorGene AssayManager version {1}. Update your report profile version.
Selected report profile is already deleted. Select another report profile.
Could not find a matching assay profile in the database for the given
experiment. Select another experiment.
The experiment {0} assay {1} is locked by user {2}.
The assay is locked by user {0}.
The lock for experiment {0} assay {1} was lost. Close the assay and
open it again.
Selected assay already released The assay {0} of experiment {1} has
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Error ID
390039
390040
390052
390054
430000
430001
430012
430020
430021
430023
430024
430030
430031
430032
430033
430035
430039
430041
430042
430043
430050
430051
430053
Error Text
already been released. The approval cannot be started. The assay data
can be found in the archive environment.
Report generation failed. Reason: {0}
Failed to create support package. Reason: {0}
Failed to create log file. Reason: {0}
Copy operation is cancelled. Selected cell(s) should be contiguous.
The channel {0} does neither have gain nor auto gain. The run cannot
be started.
The required channel {0} on the selected cycler could not be found. The
run cannot be started.
The run could not be started on the cycler with the serial number {0}.
Make sure the lid is closed.
Persisting the experiment failed. See error log for details.
Unknown error during run profile execution.
The merged contains a wrong acquisition type: {0}. Expected {1}. The
run cannot be started.
Within one cycle, the runProfileEntryIndex must not change. The run
cannot be started.
The run was stopped. For more information see experiment error log.
The application cannot be closed. Release all instruments before
closing the application.
The cycler with the serial number {0} cannot be modified in the current
state. The current cycler state is: {1}. Contact QIAGEN Technical
Services.
The optical configuration with the ID '{0}' is not supported by the
system. Select another optical configuration.
The optical configuration does not match with a previously connected
instrument with this serial number. Check the combination of serial
number and optical configuration of the cycler and remove potentially
wrong configured cycler from the cycler list.
The number of tubes configured in the samples exceeds the capacity of
the rotor. Reduce the number of tubes for that rotor.
The analysis of experiment {0} failed.
Enter a valid password.
This user is deactivated. Contact your local administrator.
This user was deactivated because the password was entered wrong too
many times. Contact your local administrator. The current session will
be closed.
An error occurred during the initialization of the device. Re-initialize the
cycler.
The run cannot be stopped. Switch off the cycler, switch it back on
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Core Application User Manual - October 2012
Error ID
470003
470018
470021
470086
470087
470095
470110
470111
470116
470118
470119
470121
470122
470123
470124
470128
470129
470131
470134
510000
510001
510003
1-293
Error Text
again, and restart the application.
An Experiment with this name already exists in the database.
The chosen experiment name has already been used in the meantime.
Select a different experiment name.
The work list has been removed by another user in the meantime. Check
availbale work lists.
The list of experiment names is not yet initialized. This could lead to a
database connection error. Check the database connection or contact
QIAGEN Technical Services.
Sample ID is not valid. Sample IDs for this assay must be unique.
The data from slot '{0}' in QIAsymphony AS result file '{1}' cannot be
imported to a work list.
Error occurred during report generation. Retry report generation.
Failed to create file {0}.
Copying of the selected cells failed. Only adjacent cells can be copied.
Copy and paste the selected cells individually.
Paste operation is cancelled. Selected cell(s) must be editable for
pasting.
Pasting failed. The selected target area is smaller than the clipboard
entry. Select a different target area or reduce data to be copied.
Paste operation is cancelled. Selected cell(s) must be contiguous.
Paste operation is cancelled. Selected cell(s) must be contiguous.
Paste operation is cancelled. Select some cell(s).
Selected work list locked The work list {0} has been locked for editing
by user {1} since the table has been updated. The work list cannot be
accessed.
There is not enough space for the information to be pasted.
The database is full. Approve and release experiments in the Approval
dialog to allow new runs.
The work list {0} has already been created in the meantime. Select a
different work list name.
The run cannot be started. The assay profile(s) contained in the work list
might have been deactivated or the work list settings have been
changed.
Fatal exception error occured during command execution: {0} Switch
off the cycler, switch it back on again, and restart application. If the
error persists, contact QIAGEN Technical Services.
Fatal exception error occured during command execution: {0} Switch
off the cycler, switch it back on again, and restart application. If the
error persists, contact QIAGEN Technical Services.
Cycler-device generated an error with error code {0}. Switch off the
cycler, switch it back on again, and restart application. If the error
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Error ID
510004
510005
510006
510007
510008
510010
510011
510012
510013
510014
510018
510019
510020
510021
510022
510023
510028
550016
550017
550018
Error Text
persists, contact QIAGEN Technical Services.
Device was disconnected. Reconnect the device and retry.
Fatal exception error occured during Optical Temperature Verification
(OTV) run: {0} Switch off the cycler, switch it back on again, and restart
application. If the error persists, contact QIAGEN Technical Services.
Fatal exception error occured during assay profile execution: {0} Switch
off the cycler, switch it back on again, and restart application. If the
error persists, contact QIAGEN Technical Services.
Reset cycler status failed. Switch off the cycler, switch it back on again,
and restart application. If the error persists, contact QIAGEN Technical
Services.
Fatal exception error occured during command execution. Switch off the
cycler, switch it back on again, and restart application. If the error
persists, contact QIAGEN Technical Services.
Update of OTV-calibration failed!
The air temperature has gone over 140° C. Check if the heater or the
thermistor are working properly. Contact QIAGEN Technical Services.
A communication error occurred. Contact QIAGEN Technical Services.
The machine's detector motor jammed. Contact QIAGEN Technical
Services.
The communication with the cycler was lost. Switch off the cycler, switch
it back on again. If error persists, contact QIAGEN Technical Services.
The rotor has stalled or stopped.
The machine's source motor jammed. Contact QIAGEN Technical
Services.
The cycler is taking too long to reach temperature. This can affect the
assay performance.
The temperature measurement thermistor has gone open circuit.
Contact QIAGEN Technical Services.
Undefined error. Switch off the cycler, switch it back on again, and
restart the application. If the error persists, contact QIAGEN Technical
Services.
An unexpected exception occurred during the run. Switch off the cycler,
switch it back on again, and restart the application. If the error persists,
contact QIAGEN Technical Services.
The requested rotor is not configured for this device. Check the rotor
configuration and retry.
Schema validation failed: {0}
Quantitation template could not be loaded. File reading failed. Check
Rotor-Gene .qut-file and retry.
Quantitation template could not be loaded. The file does not contain
all mandatory fields. Create a file where all fields including the
Core Application User Manual - October 2012 10/2012
Core Application User Manual - October 2012
Error ID
550033
550034
550036
550070
550073
550188
550199
550200
550212
550215
550216
550217
550218
550219
550229
550231
550233
550237
570016
570017
570018
570033
570034
570036
570070
570073
570202
1-295
Error Text
threshold are set.
The run template does not contain any cycling parameters.
The run profile must only contain "Cycling" and "Hold" steps. Check the
run profile and the assay profile for consistency.
The loaded rex-file contains a melt step. The assay profile does not
allow melt steps. Check the rex-file and the assay profile for consistency.
Failed to generate report. Reason: {0}
Failed to launch the application {0}. Reason:
Run profile must contain at least 7 cycles in the "Cycling" entries.
Enter a valid password.
This user is deactivated. Contact your local administrator.
Copying of the selected cells failed. Only adjacent cells can be copied.
Copy and paste the selected cells individually.
Paste operation is cancelled. Selected cell(s) must be contiguous.
Paste operation is cancelled. Selected cell(s) must be editable for
pasting.
Paste operation is cancelled. Select some cell(s).
Paste operation is cancelled. Selected cell(s) must be contiguous.
Pasting failed. The selected target area is smaller than the clipboard
entry. Select a different target area or reduce data to be copied.
There is not enough space for the information to be pasted.
This user was deactivated because the password was entered wrong too
many times. Contact your local administrator. The current session will
be closed.
The release was not performed.
The release was not performed but data was saved.
Schema validation failed: {0}
Quantitation template could not be loaded. File reading failed. Check
Rotor-Gene .qut-file and retry.
Quantitation template could not be loaded. The file does not contain
all mandatory fields. Create a file where all fields including the
threshold are set.
The run template does not contain any cycling parameters.
The run profile must only contain "Cycling" and "Hold" steps. Check the
run profile and the assay profile for consistency.
The loaded rex-file contains a melt step. The assay profile does not
allow melt steps. Check the rex-file and the assay profile for consistency.
Failed to generate report. Reason: {0}
Failed to launch the application {0}. Reason:
Enter a valid password.
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Error ID
570203
570220
570222
570223
570224
570225
570226
570229
570231
570233
570237
670016
670018
670020
1010000
1010001
1010002
1010003
1010004
1010005
1010010
1010012
1010013
1010016
1010018
1010027
1010028
1010029
Error Text
This user is deactivated. Contact your local administrator.
Copying of the selected cells failed. Only adjacent cells can be copied.
Copy and paste the selected cells individually.
Paste operation is cancelled. Selected cell(s) must be contiguous.
Paste operation is cancelled. Selected cell(s) must be contiguous.
Paste operation is cancelled. Selected cell(s) must be editable for
pasting.
Pasting failed. The selected target area is smaller than the clipboard
entry. Select a different target area or reduce data to be copied.
Paste operation is cancelled. Select some cell(s).
There is not enough space for the information to be pasted.
This user was deactivated because the password was entered wrong too
many times. Contact your local administrator. The current session will
be closed.
The release was not performed.
The release was not performed but data was saved.
The number of messages in the audit trail table to print exceeds {0}
messages. Adjust the filter settings.
File {0} not found.
An error occurred during report generation. Retry report generation.
The access to the selected file or folder is denied. Select a different file
or folder.
File not found. Check the file name and repeat the procedure.
The entered file name is invalid. Enter a valid file name without invalid
characters, i.e. / | ? * " < >.
File path must be less than 260 characters. Path too long: {0}.
Reserved Device Name {0} is a reserved device name and cannot be
used for a folder. Enter a different folder name.
The directory {0} does not exist. Select an existing directory.
Folder {0} could not be created. Either the permission was denied, or a
folder with this name already exists. Enter a different folder name.
{0} This file exists with Read Only attributes. Use a different file name.
Cannot create a new folder at the currently selected path. Directory path
must be less than 248 characters.
User name is unknown or password is incorrect. Enter user name and
password again.
Invalid user name or password. Enter user name and password again.
The new password has been used before. Use a different one.
Invalid password. The old password for the user is incorrect.
Invalid user name or password. Enter user name and password again.
Core Application User Manual - October 2012 10/2012
Core Application User Manual - October 2012
Error ID
1010031
1010032
1010033
1010035
1010037
1010039
1010040
1010041
1010042
1010043
1010044
1010046
1010047
1010050
1010054
1010055
1010057
1010058
1110000
1110007
1110008
1110009
1110010
1-297
Error Text
The entered name is reserved. It cannot be used as folder name. Enter a
different folder name.
The entered folder name is invalid. Enter a valid folder name.
This user is deactivated. Contact your local administrator.
The new password must be different from the previous {0} passwords.
Enter a unique password.
Enter a valid PIN.
QIAGEN service file could not be loaded. Unauthorized access to the
file system or a memory resource. Contact your local administrator.
QIAGEN service file could not be loaded. Signature is not valid.
Contact QIAGEN Technical Services.
QIAGEN service file could not be loaded. The resource provided has an
invalid document format. Contact QIAGEN Technical Services.
QIAGEN service file could not be loaded. The file was not found.
Contact QIAGEN Technical Services.
QIAGEN service file could not be loaded. Signature is not valid.
Contact QIAGEN Technical Services.
{0} is not accessible. Directory not found. Check the network connection
or create a new directory.
This user was deactivated because the old password has been entered
wrong too many times. Contact your local administrator. The current
session will be closed.
Could not log-in to the application. The database connection is lost.
Contact your local administrator.
This user was deactivated because the password has been entered
wrong too many times. Contact your local administrator.
Invalid name. Do not use special characters. Especially the following
characters are not acceptable: / > < " : * | ? \
A specified {0} name is a reserved name. Select a different name.
The password must not contain whitespaces.
The entered file name is invalid. File name must be less than 256
characters.
Login error. Unknown user name or invalid password. Repeat login
procedure.
Verification failed. No signature was found in the XML file. Retry with an
originally signed XML file.
Verification failed: More that one signature was found for the XML file.
Retry with an originally signed XML file.
File not found.
The folder you selected is not available or does not have memory
space left. The access is denied. Select a different folder.
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1-298
Core Application User Manual - October 2012
Error ID
1110011
1110012
1110014
1110015
1110016
1110017
1110018
1110019
1.9
Error Text
Signature could not be validated.
Signature not found.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
File not found.
Signature could not be validated.
The resource has an invalid document format. Contact QIAGEN
Technical Services.
Signature not found.
The folder you selected is not available or does not have memory
space left. The access is denied. Select a different folder.
Abbreviations
Note
Further information can be found in the
Glossary.
APS
Assay parameter set
AUDAS
Automatic data scan
CAL
Calibrator
CFR
Code of Federal Regulations
CLIA
Clinical Laboratory Improvement Amendments
COC
Cut-off control
CT
Cycle threshold
EC-
Negative extraction control
EC+
Positive extraction control
FDA
Food and Drug Administration
GMP
Good Manufacturing Practice
GUI
Graphical User Interface
IC
Internal control
LIMS
Laboratory Information Management System
LOQ
Limit of quantification
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Core Application User Manual - October 2012
1.10
NTC
No template control
OTV
Optical temperature verification
PCR
Polymerase chain reaction
PC
Positive control
R
Root extracted from R2
R2
Correlations coefficient
QS
Quantitation standard
S
Test sample
UDT Mode
User Defined Test Mode of operation
1-299
Glossary
A B C D E F G I K L M N O P Q R S T U V W
Click a letter to jump to the topics starting with the corresponding letter.
A
Acquisition
Acquisition is the collection of
fluorescent data during a PCR run. Each
acquisition step is related to a certain
channel and a certain cycling step.
Administrator
User role which has the permissions to
configure the software, add and delete
assay profiles, report profiles, and to
manage cyclers and users.
Amplification plot
Plot showing one or more amplification
curves.
Analysis
See "PCR analysis".
Analysis parameters
Parameters to define the different
analysis steps (e.g., fluorescence
thresholds, allowed ranges of CT values).
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Core Application User Manual - October 2012
Anomaly
Deviation from an ideal amplification
curve (e.g., peaks, baseline dips, or
rising/decreasing plateaus).
Application
Used here as a synonym for Rotor-Gene
AssayManager.
Approval (approve)
The process by which the approver
accepts or rejects sample results. After
approval of a sample result, it can be
released so that the related information
can be printed into a report or submitted
to a LIMS.
Approver
User role which gives the user the right to
approve and release sample results in
Closed Mode or in UDT Mode.
APS
See "Assay Parameter Set".
Archive (noun)
Part of the experiment repository that
contains experiments with completely
released sample results.
Assay
General molecular biology test (term
used here for real-time PCR assays).
In the context of the Rotor-Gene
AssayManager software the term "assay"
defines the collection of all samples
(including external controls) and their
corresponding sample results that are
related to one assay performed in one
run.
Assay and sample analysis
Analysis step that contains various rule
based checks to create the final results
for each sample by incorporating all
targets (including the internal control
and the external controls).
Assay developer
Role for a developer that gives the user
the right to develop assay profiles with
the assay profile editor. Users can only
develop assay profiles in UDT Mode.
Closed Mode assays are developed and
validated by QIAGEN.
Assay Parameter Set (APS)
File from QIAsymphony. The
combination of an Assay Definition with
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1-301
additional parameters defined (e.g.,
number of replicates and assay
standards). In Integrated run mode, it is
also connected to the Assay Control Set.
Assay profile
Consists of general information, e.g.,
about cycling compatibility, structural
information about targets and samples,
a run profile, and an analysis profile.
Assay profile editor
Environment in the UDT mode of RotorGene AssayManager to support the
assay developer to create an assay
profile.
Assay status
The assay status describes whether run
and analysis were successful or failed.
Reasons for failed can be “run failed”,
“run stopped”, or “assay
invalid” (according to failed analysis
rules).
AUDAS
See "Automatic Data Scan (AUDAS)".
Audit trail
A record of user actions.
Auto gain
Method to determine an appropriate
gain value for a PCR run. Thereby, the
gain is selected in a manner that the
background fluorescence is within a
defined interval (a typical interval is
fluorescence between 5 and 10 on the
measurement scale of the cycler) with the
intention to get a signal over the full
dynamic range but without driving into
saturation (>100).
Automatic Data Scan (AUDAS)
AUDAS is the name for the analysis step
of the real-time PCR analysis that tests
each curve for anomalies. Curves with
anomalies are flagged as invalid.
Unproblematic anomalies can be
flagged by a warning flag that does not
lead not to an invalid result.
Auto-lock (verb)
Locks the application after a predefined
time without any user interaction to
prevent misuse. Started runs are neither
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interrupted nor impacted if a user logs
out, another user starts a new session, or
if the application is locked
(automatically or manually).
Auto-lock timer
The auto-lock timer locks the application
after a predefined time without user
interaction.
B
Bar code
See "QIAGEN kit bar code".
C
CFR
Code of Federal Regulations.
See "FDA CFR Title 21 Part 11".
Channel
A channel consists of a light-emitting
diode (LED) with an excitation filter
paired with an emission filter. The LED
and excitation filter excite samples at a
given wavelength. Fluorescence emitted
by samples is passed through the
emission filter, before being detected by
a photomultiplier.
CLIA
Clinical Laboratory Improvement
Amendments.
CLIA compliant password rules
According to CLIA, a password must
contain at least:
8 characters
2 upper case characters
2 lower case characters
2 numeric characters
2 special characters
Closed mode
In Closed mode of operation only
validated QIAGEN assays can be
processed. The user does not have
permission to modify the assay profile.
Computer
In Rotor-Gene AssayManager the term
"computer" is used for a notebook or a
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PC, not a server.
Concentration factor
Factor to convert the calculated target
concentration within an eluate (i.e., the
quantitative result of the analysis) into
the concentration within the original
sample. The concentration factor is
optional for analysis but necessary if one
is interested in the target concentration
within the sample.
Conversion factor
Factor to convert the calculated target
concentration from the default unit to
another unit.
Core analysis
This term describes a part of the analysis
comprising the normalization, CT value
calculation, and (for quantitative assays)
the quantification. This analysis is
identical to the analysis used by the
Rotor-Gene Q software.
Core application
The Rotor-Gene AssayManager software
consists of different components working
together. The core application is
complemented by different plug-ins that
contain assay type-specific, analysisspecific options. The core application is
mandatory for working with Rotor-Gene
AssayManager. At least one plug-in must
be installed.
CT
See "Cycle threshold".
Curve
Unprocessed (raw data) or processed
data measured by an acquisition with
the cycler in a series of an assay-specific
number of cycles. Technically, the curve
is a discrete series of fluorescence
measurements. However, these
measurements are typically connected
and displayed as a curve. A curve
corresponds to one target of a specific
sample.
Cycle threshold (CT)
Fractional cycle at which a curve reaches
a predefined normalized fluorescence
threshold.
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Cycler
See "Rotor-Gene Q Cycler".
Cycler verification
General term for a maintenance method
to check whether the device works
properly.
Cycling compatible assays
Cycling compatible assays are assays
that can be used in different tubes during
the same PCR run in parallel. Assays are
cycling compatible if they are defined
and validated to be cycling compatible.
A cycling group can be set up, which
contains assays defined to be cycling
compatible. It is necessary that at least
the thermal profiles (part of the run
profile with number of cycles, steps, step
length, temperatures etc.) of cycling
compatible assays are identical. Other
run parameters (e.g., acquisitions) and
the analysis profiles can be, however,
individual for each assay.
D
Date picker
Calendar icon to help you selecting
the required date. Alternative to entering
the date manually.
Default name
Automatically generated name for a
newly created work list or an experiment.
The pattern for the generated name is
defined in the Configuration
environment.
E
EC-
Sample type (external controls):
Negative extraction control.
EC+
Sample type (external controls): Positive
extraction control.
Eluate
Purified nucleic acids from a sample.
Environment
The Rotor-Gene AssayManager software
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consists of several environments ("Setup",
"Approval", "Archive", "Service",
"Configuration", and "Cycler"). In these
environments, certain tasks can be
performed, such as setting up a run.
Error
See "System error".
Experiment
The process composed of a PCR run and
a PCR analysis yielding test results.
Experiment data
All data that are collected during an
experiment: work list, assay profiles, raw
data, processed data, logs, assay status,
approvals, release status, sample result,
and comments.
Experiment status
The 3 states of an experiment are
initialized, run performed, and run
failed.
Expiration date
Every kit has an expiration date. If a kit
has expired, QIAGEN will not guarantee
that the kit performs according to its
specification anymore.
Expiry date
Used here as a synonym for expiration
date.
Export
The process of transferring any kind of
data from Rotor-Gene AssayManager to
an external destination.
External controls
Collection of standards and controls
(such as the quantitation standard, the
negative control, or the positive control)
defined by an individual assay profile.
External controls are always located in
other tubes than the test samples of the
assay.
External control result
Assay-dependent final test outcome of
an external control summarizing all
corresponding target results.
External source/external destination
Location outside of the Rotor-Gene
AssayManager software.
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F
FDA
Food and Drug Administration is an
agency of the United States Department
of Health and Human Services
responsible for the safety regulation of
most types of foods, dietary
supplements, drugs, vaccines, biological
medical products, blood products,
medical devices, radiation-emitting
devices, veterinary products, and
cosmetics.
FDA CFR Title 21 Part 11
FDA CFR Title 21 Part 11 regulations
define the criteria for considering
electronic records and electronic
signatures to be trustworthy, reliable,
and equivalent to paper records. Part 11
requires drug makers, medical device
manufacturers, biotech companies,
biologics developers, and other FDAregulated industries (with some specific
exceptions), to implement controls,
including audits, system validations,
audit trails, electronic signatures, and
documentation for software and systems
involved in processing many forms of
data as part of business operations and
product development.
Flag
Annotation that may occur during the
run or the analysis. There are two types
of flags: Warning flags are just extra
information while invalid flags set the
corresponding target to invalid.
G
Gain
The Rotor-Gene Q uses a
photomultiplier to collect fluorescence
photons and convert them to electronic
signals. The gain is a setting that
determines the sensitivity of the
photomultiplier. If the gain is set too
high, the signal is oversaturated. If the
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gain is set too low, it is not possible to
differentiate signal from background
noise. A method to determine the gain is
the auto-gain function. See "Auto gain".
Gain Optimization
Gain Optimization is a process that
dynamically adjusts the gain setting,
allowing an appropriate setting to be
selected, which results in optimal signal
detection.
Global settings
Global settings are stored in the
database and affect all clients using this
database.These settings can be
configured in the "Configuration"
environment.
GUI
Graphical User Interface.
I
*.iap
File extension for a Rotor-Gene
AssayManager Assay Profile.
IC
See "Internal control".
Import
The process of transferring any kind of
data from an external source into RotorGene AssayManager.
Internal control (IC)
A standard reaction that is run
simultaneously with the sample within
the same tube and detected by a certain
acquisition. It is used to verify that the
PCR process was successfully performed
and has not been inhibited. Technically,
the IC is one of the targets of an assay
and is present in the test sample tubes as
well as in the external control tubes. In
some assays the internal control is
located in a different tube than the test,
for example, for SYBR® Green assays
where only one color channel can be
detected. In such cases the "internal"
control can be tested with the same
sample but in a separate tube.
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Invalid sample
Sample flagged as “invalid”. If a
sample is invalid, all its targets are
invalid.
*.irp
File extension for a Rotor-Gene
AssayManager report profile.
*.iwl
File extension for a Rotor-Gene
AssayManager work list.
K
Kit
A kit is a box with reagents sold by
QIAGEN to perform a biological
application. In the context of Rotor-Gene
AssayManager, a kit contains all
reagents to perform a PCR run with
eluates. PCR kits can contain master mix
components, positive and negative
controls, etc.
Kit bar code
See "QIAGEN kit bar code".
Kit information
A kit is labeled with, among others, the
following information: material number,
lot number, and expiration date.
L
LIMS
Laboratory Information Management
System. If configured, Rotor-Gene
AssayManager exports results in a file to
be read by a LIMS.
Local settings
Local settings are stored on the local
computer and affect no other clients
using the same database (in comparison
to the global settings). These settings can
be configured in the "Configuration"
environment.
Lock (verb)
Make the application inaccessible for
other users without logging out. Started
runs are neither interrupted nor
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impacted if a user logs out, another user
starts a new session, or if the application
is locked (automatically or manually).
Locking ring
Locking rings are metal rings that fit
onto the rotor to prevent tubes and caps
from coming loose during operation of
the Rotor-Gene Q. Loose caps and tubes
could cause damage to the instrument.
Log file
Log of the technical software behavior
that can be interpreted by the QIAGEN
Technical Services.
Lot number
Part of the kit information.
M
Material number
Part of the kit information.
Mode
See "Closed Mode of operation".
See "User Defined Test Mode of
operation".
Mode of operation
See "Closed Mode of operation".
See "User Defined Test Mode of
operation".
Multiplex assay
Multiplex assays are multi-target assays
that simultaneously test multiple targets
in single tubes by using different primers
and probes. The probes are labeled with
specific dyes, which anneal to the
different target sequences. The detection
is performed by different color channels.
However, internal controls, which are
technically targets as well, are typically
not regarded in this context.
Multi-target assay
General term for an assay that can
detect more than one target in parallel.
Thereby, internal controls, which are
technically targets as well, are typically
not regarded in this context. The multiple
targets can be independent or
interdependent or a combination of
both. Multi-target assays can be either
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multiplex assays, multi-tube assays, or a
combination of both.
Multi-tube assay
Multi-tube assays are multi-target assays
that simultaneously test multiple targets
in more than one tube. Before the PCR
process, the sample to be tested is split
and distributed over the different tubes.
N
Normalization
In this context, normalization is an
analysis step used for curve
preprocessing prior to CT value
calculation and the quantitation. It
includes typically a smoothing of the
curves and a removal of the background
noise by subtracting the baselines.
NTC
No template control.
O
Operator
User role with the rights to perform a
PCR run and to view the results (not
allowed to approve).
Optical configuration
The optical configuration of a RotorGene cycler is described by the
available excitation diodes that excite
the fluorescence and the emission filters
letting pass the emitted light. The optical
configuration differs between different
types of the Rotor-Gene. It can be read
out from the firmware.
OTV
Optical Temperature Verification.
OTV calibration run
The OTV calibration run is a special run
that measures the in-tube temperature in
the Rotor-Gene Q cycler and calibrates
the cycler according to the
measurements afterwards. A special
rotor is used for this run, which contains
3 thermochromatic liquid crystals that
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change their transparency according to
the temperature. OTV calibration can be
performed with the Rotor-Gene Q
software but not with Rotor-Gene
AssayManager.
P
PC
Sample type (external controls): Positive
control.
PCR
Polymerase chain reaction.
PCR analysis
Processing of the raw PCR data, for
example, by applying AUDAS,
normalization, CT value calculation,
quantification, and assay and sample
analysis algorithms to obtain a
quantitative or qualitative result.
PCR run
PCR process performed in a
thermocycler (e.g., the Rotor-Gene Q). In
this context PCR is always a real-time
PCR.
Plug-in
A plug-in allows Rotor-Gene
AssayManager to support a specific type
of assays. Plug-ins may not be available
in all countries.
Processed curve
Raw data that have been changed
during PCR analysis.
Processed data
Collection of processed curves.
Q
QIAGEN kit bar code
Identifies the QIAGEN kit. The bar code
consists of the material number (7
digits), the expiry date (6 digits), and the
lot number (4–10 digits).
QIAlink
Middleware at QIAGEN to support
specific LIMS systems. Contact QIAGEN
Technical Services for details.
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QIAsymphony
QIAGEN platform for automatic sample
preparation and assay setup.
QS
Sample type (external controls):
quantitation standard.
Qualitative result
Information whether a signal has been
detected for a target or not or whether
the target is invalid.
Quantification
Analysis step to determine the initial
concentration of a target.
Quantitative result
Information of the initial target
concentration of a result.
Quantitation standard
Reference sample with a given target
concentration used for quantification.
Note: In the Rotor-Gene Q software the
term “quantitation” may even be used
instead of the term “quantification”.
*.qut
File extension for Rotor-Gene
quantitation analysis template used by
the Rotor-Gene Q software. The file
contains all values to parameterize the
absolute quantification analysis.
Note: In the Rotor-Gene Q software the
term “quantitation” may be used
instead of the term “quantification”.
R
R
Root extracted from R2.
R2
Correlations coefficient:
The correlations coefficient is a statistical
parameter to measure the fit of the data
points to the regressed line. In general,
the standard curve should have an R2
value 0.990. The individual limit for
the R2 value can be defined in the assay
profile.
Raw curve
Unprocessed fluorescence data
measured in one tube on one channel
by the cycler in a series of an assay-
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specific number of cycles.
Raw data
Collection of unprocessed amplification
curves.
Reaction volume
Volume of liquid in the PCR tubes.
Real-time PCR
PCR with real-time monitoring of the
reaction products.
Regression line
In this context, a regression line is a
linear function derived from a regression
analysis between the CT values and
given concentrations of quantitation
standards. It is also known as the
standard curve. See "Standard curve".
Release
The process of publishing previously
approved sample results by generating
a report and optionally transferring the
data to a LIMS.
Release status
The release status is the status of an
assay that can be “not released”,
“partially released”, and “fully
released” where “fully released” means
that all sample results contained in the
assay have been released.
Renewal interval
Days until a password must be renewed.
Replicate
See "Sample replicate".
Report
Summary of selected sample results
(external control results are always
included) of one assay as a secure *.pdffile, which cannot be manipulated.
Report profile
Profile describing which information
shall be included in the report.
*.ret
File extension for a Rotor-Gene Q run
template file used by the Rotor-Gene Q
software. The file contains all values to
parameterize a PCR run.
*.rex
File extension for a Rotor-Gene Q
experiment file format used by the RotorGene Q software. It can be imported for
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testing an assay profile in the
"Development" environment of the UDT
mode.
Role
User rights are summarized in a certain
role: administrator, approver, operator,
assay developer, and super user are
available.
Rotor
The metal rotor holds tubes or RotorDiscs in the Rotor-Gene Q. It enables
samples to spin in the instrument
chamber and ensures that samples are
correctly aligned with the optical system.
The rotor is secured with a locking ring.
Rotor-Disc
Rotor-Discs are circular plates of
vertically oriented reaction wells. RotorDisc formats for 72 and 100 reactions
are available. Rotor-Discs are sealed
using Rotor-Disc® Heat Sealing Film and
the Rotor-Disc Heat Sealer.
Rotor-Gene Q Cycler
The real-time PCR cycler supported by
Rotor-Gene AssayManager.
Rotor-Gene Q Software
Open mode software to control the
Rotor-Gene Q cycler and to analyze the
acquired data.
Rotor type
See "Rotor".
Row selector
Specific table column to select complete
rows.
Run
See "PCR run".
Run parameters
Parameters specifying a PCR run (e.g.,
number of cycles, temperature,
acquisitions, rotor type, tube volume,
etc.).
Run profile
Set of all run parameters. It is part of the
assay profile.
S
S
Sample type: test sample
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Sample
Test sample or external control to be
analyzed.
Sample ID
Identifier of a sample. The sample ID
must not be empty and must consist of
1–40 characters.
Sample information
Annotations describing one sample. It
contains sample ID, reaction volume,
sample volume, sample type, flags set
by an upstream platform, and process
history.
Sample replicate
One sample split on several tubes to do
the same test in parallel in order to get
an estimate for the variance.
Sample result
General term for test result and external
control result.
Sample result status
The sample result status describes a
qualitative result by different assaydependent states corresponding to a test
result or an external control result.
Sample type
A sample can be of the following types:
test sample (S) or one of the following
external controls: quantitation standard
(QS), no template control (NTC), positive
control (PC), negative extraction control
(EC–), and positive extraction control
(EC+). Not all assays include all types of
external controls. This is assay
dependent.
Sample volume
Volume of the initial amount of material
for the sample preparation procedure.
Service user
User role that has all necessary
permissions to maintain the software at
customer site. The service user has no
permission to approve analysis results.
Session
Contains all user actions from login until
logout.
Standard curve
A standard curve is a linear function
derived from a regression analysis
between the CT values and given
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concentrations of quantitation
standards.
Super user
The super user has all available
permissions of all available roles as a
convenient way to grant all permissions
to one user.
Support package
Information wrapped up in a *.zip file to
be sent via an email program to
QIAGEN Technical Services to inform
QIAGEN what went wrong at the
customer's site and how to help the
customer. The support package can be
created in the "Approval" and in the
"Archive" environment.
System error
Technical errors (e.g., process errors,
software malfunctions, cycler errors) that
are not acceptable. User interaction is
required.
Note: Do not confuse with invalid
results.
T
Target
Specific DNA sequence (or RNA before
reverse transcription step) to be
amplified during the PCR.
Target result
The result of the analysis of one target
for one specific sample.
Test
Synonym of assay.
Test sample
Unknown sample to be tested with an
assay.
Test sample result
Assay-dependent final test outcome of
an assay for one test sample
summarizing all corresponding target
results.
Threshold
Predefined fluorescence value used to
calculate the cycle threshold (CT) of a
curve.
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Tube
1-317
Small container for liquids, in which the
PCR reaction takes place. A sample can
be split over multiple tubes.
U
UDT Mode
See "User Defined Test Mode of
operation (UDT Mode)".
Upstream process
From the PCR point of view, the
upstream process consists of the
sampling, the sample disruption, the
purification, and the assay setup.
Upstream status
Status which is set by QIAsymphony
system. It can be “valid”, “unclear”, or
“invalid”. If it is “invalid” or if RotorGene AssayManager is configured in a
way that “unclear” samples are
processed as if they are “invalid”, a
special invalid flag is set. Sample result
are not provided for samples with an
"invalid" upstream status.
User Defined Test Mode (UDT Mode)
This is the mode of operation for assays
that are created and validated by a user
of Rotor-Gene AssayManager software.
User role
See "Role".
V
Validation error
An error that occurs due to a missing or
invalid user input. User interaction is
required.
Verification
See "Cycler verification".
W
Warning
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A situation could be optimized by further
input. User interaction is possible, but
not mandatory.
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Work list
1.11
Appendices
The appendices contain a
terms.
1.11.1
Sample information for all samples to
be analyzed and a reference to an assay
profile for each sample. When using an
upstream platform, the work list contains
flags as well.
list of file endings, the
license
File Endings
Note
Further information can be found in the
1.11.2
liability clause, and
Glossary.
*.iap
Rotor-Gene AssayManager Assay Profile file.
*.irp
Rotor-Gene AssayManager report file.
*.iwl
Rotor-Gene AssayManager work list.
*.qut
Rotor-Gene quantitation analysis template used by the Rotor-Gene Q
software.
*.ret
Rotor-Gene Q run template file used by the Rotor-Gene Q software.
*.rex
Rotor-Gene Q experiment file format used by the Rotor-Gene Q software.
Liability Clause
QIAGEN shall be released from all obligations under its warranty in the event repairs
or modifications are made by persons other than its own personnel, except in cases
where the Company has given its written consent to perform such repairs or
modifications.
All materials replaced under this warranty will be warranted only for the duration of
the original warranty period and in no case beyond the original expiration date of
original warranty unless authorized in writing by an officer of the Company. Read-out
devices, interfacing devices, and associated software will be warranted only for the
period offered by the original manufacturer of these products. Representations and
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warranties made by any person, including representatives of QIAGEN, which are
inconsistent or in conflict with the conditions in this warranty shall not be binding upon
the Company unless produced in writing and approved by an officer of QIAGEN.
1.11.3
License Terms
The following section lists the license texts displayed during installation. These texts
are also available in the Rotor-Gene AssayManager software.
QIAGEN’s Rotor-Gene AssayManager™
Software License Agreement
TERMS AND CONDITIONS of an LEGAL AGREEMENT (the "Agreement") by and
between QIAGEN GmbH, QIAGEN Strasse 1, D-40724 Hilden, Germany, ("QIAGEN")
and you (either an individual or a legal entity), the licensee of the software (hereinafter
referred to as "SOFTWARE")
By opening the sealed software package(s) you are agreeing to be bound by the terms
of this Agreement. If you do not agree to the terms of this Agreement, promptly return
the unopened software package(s) and the accompanying items (including written
materials) to the place you obtained them for a full refund.
1. GRANT OF LICENSE
Scope. Subject to the terms and conditions of this agreement, QIAGEN grants you a
worldwide, perpetual, non-exclusive, and nontransferable license to use the
SOFTWARE solely for your internal business purposes.
You shall not:
- modify or alter the whole or any part of the SOFTWARE nor merge any part of it
with another software nor separate any components of the SOFTWARE from
the SOFTWARE nor, save to the extent and in the circumstances permitted by
law, create derivative works from, or, reverse engineer, decompile, disassemble
or otherwise derive source code from the SOFTWARE or attempt to do any of
these things
- copy the SOFTWARE (except as provided above)
- assign rent, transfer, sell, disclose, deal in, make available or grant any rights in
the Software Product in any form to any person without the prior written consent
of QIAGEN;
- remove alter, obscure, interfere with or add to any proprietary notices, labels,
trademarks, names or marks on, annexed to, or contained within the
SOFTWARE;
- use the SOFTWARE in any manner that infringes the intellectual property or
other rights of QIAGEN or any other party; or
- use the SOFTWARE to provide on-line or other database services to any other
person.
Single-Computer Use. In case you purchased a single-computer license of the
SOFTWARE this Agreement permits you to use only one copy of the SOFTWARE on a
single computer.
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Multi-Computer Use. In case you purchased a multi-computer license of the
SOFTWARE from QIAGEN, this Agreement permits you to use multiple copies of the
SOFTWARE on a maximum number of computers as specified in the purchase
Agreement between QIAGEN and you ("Purchase Agreement").
Trial versions. Trial versions of the SOFTWARE may expire after a period of 30 (thirty)
days without prior notice.
Open Software/Third Party Software. This Agreement does not apply to any other
software components identified as subject to an open source license in the relevant
notice, license and/or copyright files included with the programs (collectively the "Open
Software") Furthermore, this Agreement does not apply to any other software for which
QIAGEN is only granted a derived right to use ("Third Party Software"). Open
Software and Third Party Software may be supplied in the same electronic file
transmission as the SOFTWARE, but are separate and distinct programs. The
SOFTWARE is not subject to the GPL or any other open source license.
If and insofar QIAGEN provides Third Party Software, the license terms for such Third
Party Software shall additionally apply and prevail. If Open Software is provided, the
license terms for such Open Software shall additionally apply and prevail. QIAGEN shall
provide you with the corresponding source code of relevant Open Software, if the
respective license terms of the Open Software include such obligation. QIAGEN shall
inform if the SOFTWARE contains Third Party Software and/or Open Software and
make available the corresponding license terms on request.
2. UPGRADES
If the SOFTWARE is an upgrade from a previous version, you are granted a single
license to both copies, and you may not separately transfer the prior version(s) except
as a one-time permanent transfer to another user of the latest upgrade and all prior
versions as allowed in Section 4 below.
3. COPYRIGHT
The SOFTWARE, including any images, and text incorporated in the SOFTWARE, is
copyrighted and is protected by German copyright laws and international treaty
provisions. You may not copy any of the printed materials accompanying the
SOFTWARE.
4. OTHER RESTRICTIONS
You may not rent or lease the SOFTWARE, but you may transfer the SOFTWARE and
accompanying written materials on a permanent basis to another end user provided
you delete the setup files from your computer, and the recipient agrees to the terms of
this Agreement. You may not reverse engineer, decompile, or disassemble the
SOFTWARE. Any transfer of the SOFTWARE must include the most recent upgrade
and all prior versions.
5. NO WARRANTY
The SOFTWARE is provided "as is" without warranty of any kind, express or implied,
including without limitation any implied warranties of merchantability, fitness for a
particular purpose or non-infringement with respect to the SOFTWARE and the
accompanying written materials.
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6. CUSTOMER REMEDIES
QIAGEN entire liability and your exclusive remedy shall be, at QIAGEN's option, either
(a) return of the price paid or (b) repair or replacement of the SOFTWARE that does not
meet QIAGEN's Limited Warranty and that is returned to QIAGEN with a copy of your
receipt. This Limited Warranty is void if failure of SOFTWARE has resulted from
accident, abuse or misapplication. Any replacement of SOFTWARE will be warranted
for the remainder of the original warranty period or thirty (30) days, whichever is longer.
7. LIMITED LIABILITY
In no event shall QIAGEN or its suppliers be liable for any damages whatsoever
(including, without limitation, damages for loss of business profits, business
interruption, loss of business information, or other pecuniary loss, unforeseeable
damage, lack of commercial success, indirect damage or consequential damage - in
particular financial damage – or for damage resulting from third party claims) arising out
of the use or inability to use the SOFTWARE, even if QIAGEN has been advised of the
possibility of such damages.
The above restrictions of liability shall not apply in cases of personal injury or any
damage resulting from willful acts or gross negligence or for any liability based on the
Product Liability Act (Produkthaftungsgesetz), guarantees or other mandatory
provisions of law.
The above limitation shall apply accordingly in case of:
- delay,
- compensation due to defect,
- compensation for wasted expenses.
8. NO SUPPORT
Nothing in this agreement shall obligate QIAGEN to provide any support for the
SOFTWARE. QIAGEN may, but shall be under no obligation to, correct any defects in
the SOFTWARE and/or provide updates to licensees of the SOFTWARE. You shall
make reasonable efforts to promptly report to SOFTWARE any defects you find in the
SOFTWARE, as an aid to creating improved revisions of the SOFTWARE.
Any provision of support by QIAGEN for the SOFTWARE (including network installation
support), if any, shall solely be governed by the Purchase Agreement or an according
Support Agreement.
9. TERMINATION
If you fail to comply with the terms and conditions of this Agreement, QIAGEN may
terminate this Agreement and your right and license to use the SOFTWARE. You may
terminate this Agreement at any time by notifying QIAGEN. Upon the termination of this
Agreement, you must delete the SOFTWARE from your computer(s) and archives.
YOU AGREE THAT UPON TERMINATION OF THIS AGREEMENT FOR ANY
REASON, QIAGEN MAY TAKE ACTIONS SO THAT THE SOFTWARE NO LONGER
OPERATES.
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10. GOVERNING LAW, VENUE
This Agreement shall be construed and interpreted in accordance with the laws of
Germany, without giving effect to conflict of laws provisions. The application of the
provisions of the UN Sales Convention is excluded. Notwithstanding any other provision
under this Agreement, the parties to this Agreement submit to the exclusive jurisdiction
of the Düsseldorf courts.
Rotor-Gene AssayManager™ is a trademark of QIAGEN.
1.11.3.1
Microsoft Software License Terms
Microsoft SQL Server 2008 R2 Express
These license terms are an agreement between Microsoft Corporation (or based on
where you live, one of its affiliates) and you. Please read them. They apply to the
software named above, which includes the media on which you received it, if any. The
terms also apply to any Microsoft
updates,
supplements,
Internet-based services, and
support services
for this software, unless other terms accompany those items. If so, those terms apply.
By using the software, you accept these terms. If you do not accept them, do
not use the software.
If you comply with these license terms, you have the rights below.
1. Installation and use rights: You may install and use any number of copies of the
software on your devices.
2. Scope of license. The software is licensed, not sold. This agreement only gives you
some rights to use the software. Microsoft reserves all other rights. Unless
applicable law gives you more rights despite this limitation, you may use the
software only as expressly permitted in this agreement. In doing so, you must
comply with any technical limitations in the software that only allow you to use it in
certain ways. You may not
disclose the results of any benchmark tests of the software to any third party
without Microsoft’s prior written approval;
work around any technical limitations in the software;
reverse engineer, decompile or disassemble the software, except and only to the
extent that applicable law expressly permits, despite this limitation;
make more copies of the software than specified in this agreement or allowed
by applicable law, despite this limitation; or
publish the software for others to copy.
3. Backup copy. You may make one backup copy of the software. You may use it
only to reinstall the software.
4. Documentation. Any person that has valid access to your computer or internal
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network may copy and use the documentation for your internal, reference purposes.
5. Transfer to a third party. The first user of the software may transfer it and this
agreement directly to a third party. Before the transfer, that party must agree that
this agreement applies to the transfer and use of the software. The first user must
uninstall the software before transferring it separately from the device. The first user
may not retain any copies.
6. Export restrictions. The software is subject to United States export laws and
regulations. You must comply with all domestic and international export laws and
regulations that apply to the software. These laws include restrictions on
destinations, end users and end use. For additional information, see www.
microsoft.com/exporting.
7. Support services. Because this software is “as is,” we may not provide support
services for it.
8. Entire agreement. This agreement, and the terms for supplements, updates,
Internet-based services and support services that you use, are the entire agreement
for the software and support services.
9. Applicable law.
a. United States. If you acquired the software in the United States, Washington state
law governs the interpretation of this agreement and applies to claims for breach
of it, regardless of conflict of laws principles. The laws of the state where you live
govern all other claims, including claims under state consumer protection laws,
unfair competition laws, and in tort.
b. Outside the United States. If you acquired the software in any other country, the
laws of that country apply.
10.Legal effect. This agreement describes certain legal rights. You may have other
rights under the laws of your country. You may also have rights with respect to the
party from whom you acquired the software. This agreement does not change your
rights under the laws of your country if the laws of your country do not permit it to
do so.
11.Disclaimer of warranty. The software is licensed "as-is". You bear the risk of
using it. Microsoft gives no express warranties, guarantees or conditions. You may
have additional consumer rights under your local laws which this agreement cannot
change. To the extent permitted under your local laws, Microsoft excludes the
implied warranties of merchantability, fitness for a particular purpose and noninfringement.
12.Limitation on and exclusion of remedies and damages. You can recover from
Microsoft and its suppliers only direct damages up to U.S. $5.00. You cannot
recover any other damages, including consequential, lost profits, special, indirect
or incidental damages.
This limitation applies to
anything related to the software, services, content (including code) on third party
Internet sites, or third party programs; and
claims for breach of contract, breach of warranty, guarantee or condition, strict
liability, negligence, or other tort to the extent permitted by applicable law.
It also applies even if Microsoft knew or should have known about the possibility of
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the damages. The above limitation or exclusion may not apply to you because your
country may not allow the exclusion or limitation of incidental, consequential or other
damages.
1.11.3.2
Microsoft .NET Framework 4
Microsoft software supplemental license terms
Microsoft .NET framework 4 for Microsoft Windows operating system
Microsoft .NET framework 4 client profile for Microsoft Windows operating
system and associated language packs
Microsoft Corporation (or based on where you live, one of its affiliates) licenses this
supplement to you. If you are licensed to use Microsoft Windows operating system
software (for which this supplement is applicable) (the “software”), you may use this
supplement. You may not use it if you do not have a license for the software. You may
use a copy of this supplement with each validly licensed copy of the software.The
following license terms describe additional use terms for this supplement. These terms
and the license terms for the software apply to your use of the supplement. If there is a
conflict, these supplemental license terms apply.
By using this supplement, you accept these terms. If you do not accept
them, do not use this supplement.
If you comply with these license terms, you have the rights below.
1. Support services for supplement. Microsoft provides support services for this
software as described at www.support.microsoft.com/common/international.aspx.
2. Microsoft .NET framework benchmark testing. The software includes one or
more components of the .NET Framework (.NET Components). You may conduct
internal benchmark testing of those components. You may disclose the results of
any benchmark test of those components, provided that you comply with the
conditions set forth at http://go.microsoft.com/fwlink/?LinkID=66406.
Notwithstanding any other agreement you may have with Microsoft, if you disclose
such benchmark test results, Microsoft shall have the right to disclose the results of
benchmark tests it conducts of your products that compete with the applicable .NET
Component, provided it complies with the same conditions set forth at http://go.
microsoft.com/fwlink/?LinkID=66406.
1.11.3.3
Microsoft Reportviewer 2010
Microsoft Software License Terms
Microsoft Reportviewer 2010
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These license terms are an agreement between Microsoft Corporation (or based on
where you live, one of its affiliates) and you. Please read them. They apply to the
software named above, which includes the media on which you received it, if any. The
terms also apply to any Microsoft
updates,
supplements,
Internet-based services, and
support services
for this software, unless other terms accompany those items. If so, those terms apply.
By using the software, you accept these terms. If you do not accept them, do
not use the software.
If you comply with these license terms, you have the rights below.
1. Installation and use rights. You may install and use any number of copies of the
software on your devices.
2. Additional licensing requirements and/or use rights.
a. Distributable code. You are permitted to distribute the software in programs
you develop if you comply with the terms below.
i.
Right to use and distribute. The software is “Distributable Code.”
Distributable Code. You may copy and distribute the object code
form of the software.
Third party distribution. You may permit distributors of your
programs to copy and distribute the Distributable Code as part of
those programs.
ii.
Distribution requirements. For any Distributable Code you distribute,
you must
add significant primary functionality to it in your programs;
require distributors and external end users to agree to terms that
protect it at least as much as this agreement;
display your valid copyright notice on your programs; and
indemnify, defend, and hold harmless Microsoft from any claims,
including attorneys’ fees, related to the distribution or use of your
programs.
iii.
Distribution restrictions. You may not
alter any copyright, trademark or patent notice in the Distributable
Code;
use Microsoft’s trademarks in your programs’ names or in a way
that suggests your programs come from or are endorsed by
Microsoft;
distribute Distributable Code to run on a platform other than the
Windows platform;
include Distributable Code in malicious, deceptive or unlawful
programs; or
modify or distribute the source code of any Distributable Code so
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that any part of it becomes subject to an Excluded License. An
Excluded License is one that requires, as a condition of use,
modification or distribution, that
the code be disclosed or distributed in source code form; or
others have the right to modify it.
3. Scope of license. The software is licensed, not sold. This agreement only gives you
some rights to use the software. Microsoft reserves all other rights. Unless
applicable law gives you more rights despite this limitation, you may use the
software only as expressly permitted in this agreement. In doing so, you must
comply with any technical limitations in the software that only allow you to use it in
certain ways. You may not
work around any technical limitations in the software;
reverse engineer, decompile or disassemble the software, except and only to
the extent that applicable law expressly permits, despite this limitation;
make more copies of the software than specified in this agreement or allowed
by applicable law, despite this limitation;
publish the software for others to copy;
rent, lease or lend the software; or
use the software for commercial software hosting services.
4. Backup copy. You may make one backup copy of the software. You may use it
only to reinstall the software.
5. Documentation. Any person that has valid access to your computer or internal
network may copy and use the documentation for your internal, reference purposes.
6. Transfer to a third party. The first user of the software may transfer it and this
agreement directly to a third party. Before the transfer, that party must agree that
this agreement applies to the transfer and use of the software. The first user must
uninstall the software before transferring it separately from the device. The first user
may not retain any copies.
7. Export restrictions. The software is subject to United States export laws and
regulations. You must comply with all domestic and international export laws and
regulations that apply to the software. These laws include restrictions on
destinations, end users and end use. For additional information, see www.
microsoft.com/exporting.
8. Support services. Because this software is “as is,” we may not provide support
services for it.
9. Entire agreement. This agreement, and the terms for supplements, updates,
Internet-based services and support services that you use, are the entire agreement
for the software and support services.
10.Applicable law.
a. United States. If you acquired the software in the United States, Washington
state law governs the interpretation of this agreement and applies to claims for
breach of it, regardless of conflict of laws principles. The laws of the state
where you live govern all other claims, including claims under state consumer
protection laws, unfair competition laws, and in tort.
b. Outside the United States. If you acquired the software in any other country,
the laws of that country apply.
11.Legal effect. This agreement describes certain legal rights. You may have other
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rights under the laws of your country. You may also have rights with respect to the
party from whom you acquired the software. This agreement does not change your
rights under the laws of your country if the laws of your country do not permit it to
do so.
12.Disclaimer of warranty. The software is licensed "as-is". You bear the risk of
using it. Microsoft gives no express warranties, guarantees or conditions. You may
have additional consumer rights under your local laws which this agreement cannot
change. To the extent permitted under your local laws, Microsoft excludes the
implied warranties of merchantability, fitness for a particular purpose and noninfringement.
13.Limitation on and exclusion of remedies and damages. You can recover from
Microsoft and its suppliers only direct damages up to U.S. $5.00. You cannot
recover any other damages, including consequential, lost profits, special, indirect
or incidental damages. This limitation applies to
a. anything related to the software, services, content (including code) on third
party Internet sites, or third party programs; and
b. claims for breach of contract, breach of warranty, guarantee or condition, strict
liability, negligence, or other tort to the extent permitted by applicable law.
It also applies even if Microsoft knew or should have known about the possibility
of the damages. The above limitation or exclusion may not apply to you because
your country may not allow the exclusion or limitation of incidental,
consequential or other damages.
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