Thermo Fisher Scientific GeneMapper Software 5 User Guide

USER GUIDE
GeneMapper® Software 5
Installation and Administration
Publication Part Number 4476603 Rev. A
Revision Date March 2012
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.
Information in this document is subject to change without notice.
LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT,
EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE, OR NON-INFRINGEMENT. TO THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS
AFFILIATE(S) BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR
SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM
THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.
LIMITED PRODUCT WARRANTY
Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and
Conditions of Sale found on Life Technologies' website at www.lifetechnologies.com/termsandconditions. If you have any questions,
please contact Life Technologies at www.lifetechnologies.com/support.
NOTICE TO PURCHASER: DISCLAIMER OF LICENSE
Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system,
composition, reagent or kit rights under patent claims owned or otherwise controlled by Life Technologies, either expressly, or
by estoppel.
GeneMapper® Software has not undergone specific developmental validation for human identification applications. Human
identification laboratories analyzing single-source or parentage samples which choose to use GeneMapper® Software for data
analysis should perform their own developmental validation studies.
The AFLP process is covered by patents owned by Keygene N.V.
TRADEMARKS
The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.
Oracle is a registered trademark of Oracle International Corporation. AFLP is a registered trademark of Keygene N.V. Adobe, Reader
and Acrobat are registered trademarks of Adobe Systems, Inc. Dell and OptiPlex are registered trademarks of Dell, Inc. Intel and
Pentium are registered trademarks of Intel Corporation. Core is a trademark of Intel Corporation. Microsoft and Windows are
registered trademarks of Microsoft Corporation.
© 2012 Life Technologies Corporation. All rights reserved.
Contents
Preface
7
How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . 9
How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Safety Information
11
Safety Conventions Used in This Document . . . . . . . . . . . . . . . . 12
General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Chapter 1
Getting Started
15
Start Here: Getting the Most Out of This Guide . . . . . . . . . . . . . . . 16
For Applied Biosystems 3500 Series Genetic Analyzers . . . . . . . . 17
Oracle® Database License Agreement . . . . . . . . . . . . . . . . . . . . . . 18
GeneMapper® Software Workflow . . . . . . . . . . . . . . . . . . . . . . . . . 19
Chapter 2
Installation Requirements
and Software Compatibility
21
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Computer Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Instrument, Software, and Data Compatibility . . . . . . . . . . . . . . . . 26
User Account Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
GeneMapper® Software Installation DVDs . . . . . . . . . . . . . . . . . . . 28
GeneMapper® Software 5 Installation and Administration Guide
3
Contents
Chapter 3
Performing a New Installation
of the GeneMapper® Software
29
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Exporting GeneMapper® Software from a Windows XP Computer 30
Importing GeneMapper® Software to a Windows 7 Computer . . . 30
Determining Your Installation Options . . . . . . . . . . . . . . . . . . . . . . 32
Section 3.1: Full Installation Procedures . . . . . . . . . . . . . . . . . . . 35
Instrument Configuration Procedures . . . . . . . . . . . . . . . . . . . . . . 36
Stand-alone Configuration Procedures . . . . . . . . . . . . . . . . . . . . . 43
Section 3.2: Client Installation Procedures . . . . . . . . . . . . . . . . . 48
Client Configuration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Section 3.3: Software Login Procedures . . . . . . . . . . . . . . . . . . . 53
Registering the Software After a New Installation . . . . . . . . . . . . . 54
Logging In to the Software for the First Time After a
New Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Logging In to the Database Dashboard for the First Time . . . . . . 57
What Next? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Logging In to and Out of the Software . . . . . . . . . . . . . . . . . . . . . 59
Chapter 4
Managing Database Security
and User Access
63
About GeneMapper® Software Security . . . . . . . . . . . . . . . . . . . . 64
Configuring the Password Policies . . . . . . . . . . . . . . . . . . . . . . . . 66
Managing User and Security Groups . . . . . . . . . . . . . . . . . . . . . . 70
Setting Up User and Security Groups . . . . . . . . . . . . . . . . . . 75
Managing Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Managing Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Managing User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Exporting and Importing the Security Settings . . . . . . . . . . . . . . . 96
4
GeneMapper® Software 5 Installation and Administration Guide
Contents
Chapter 5
Managing the Auditing and
Electronic Signature Systems
97
About the Data Tracking Systems . . . . . . . . . . . . . . . . . . . . . . . . . 98
Section 5.1: Setting Up the Auditing System . . . . . . . . . . . . . . . . 99
About the Auditing System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Audit Maps, Objects, and Attributes . . . . . . . . . . . . . . . . . . . . . . 102
Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Managing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Viewing the Audit History . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Backing Up, Removing, and Restoring Audit Data . . . . . . . . 118
Section 5.2: Setting Up the Electronic Signature System . . . . . 121
About the Electronic Signature System . . . . . . . . . . . . . . . . . . . . 122
About Electronic Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Configuring the Electronic Signature Settings . . . . . . . . . . . . . . . 125
Configuring the GeneMapper® Software Action Map . . . . . . . . . 126
Viewing the Electronic Signature History . . . . . . . . . . . . . . . . . . . 128
Chapter 6
Maintaining the Software
and Database Application
131
Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Section 6.1: Managing Study, Project, and Sample Data . . . . . 133
Exporting Data Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Exporting GeneMapper Data Objects . . . . . . . . . . . . . . . . . . . . . 137
Exporting and Importing Projects . . . . . . . . . . . . . . . . . . . . . 137
Exporting and Importing Studies . . . . . . . . . . . . . . . . . . . . . . 140
Exporting and Importing Reference Data . . . . . . . . . . . . . . . . . . . 142
Exporting Kits, Panels, and Bin Sets . . . . . . . . . . . . . . . . . . . 143
Exporting All Other Reference Data . . . . . . . . . . . . . . . . . . . . 144
Section 6.2: Managing the Database . . . . . . . . . . . . . . . . . . . . . 145
Using the Oracle® Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
About the Dashboard Software . . . . . . . . . . . . . . . . . . . . . . . . . . 149
GeneMapper® Software 5 Installation and Administration Guide
5
Contents
Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . . . . . . 151
Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Viewing Project Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
Generating a Database Report . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Appendix A
Troubleshooting the Installation
161
Troubleshooting Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Uninstalling the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Troubleshooting Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
Appendix B
Operating the Software
from a Command Line
173
Operating the Software from a Command Line . . . . . . . . . . . . . 174
Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Example #1: Basic Sample File Analysis . . . . . . . . . . . . . . . 179
Example #2: SNPlex® System Analysis . . . . . . . . . . . . . . . . 180
Example #3: Sample File Analysis with Named Ladders . . . 181
Example #4: Export of Project Data . . . . . . . . . . . . . . . . . . . 182
Command Line Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Appendix C
Appendix D
6
Migrating Data Using the GeneMapper®
Database Utility Wizard
189
Migrating Data Manually
193
Glossary
197
Index
207
GeneMapper® Software 5 Installation and Administration Guide
Preface
How to Use This Guide
Purpose of
This Guide
This guide describes the procedures for installing, securing, and
maintaining the GeneMapper® Software 5.
Note: For instructions on analyzing sample data using the
GeneMapper® Software, see the appropriate applications getting
started guide for your fragment analysis chemistry as explained on
page 9.
Audience
Assumptions
Text Conventions
This guide is written for laboratory personnel responsible for installing
and maintaining the GeneMapper® Software.
This guide assumes that you have a working knowledge of the
Microsoft® Windows® operating system.
This guide uses the following conventions:
• Bold indicates user action. For example:
Type 0, then press Enter for each of the remaining fields.
• Italic text indicates new or important words and is also used for
emphasis. For example:
Before analyzing, always prepare fresh matrix.
• A right arrow bracket () separates successive commands you
select from a drop-down or shortcut menu. For example:
Select FileOpenSpot Set.
Right-click the sample row, then select View Filter
View All Runs.
GeneMapper® Software 5 Installation and Administration Guide
7
User Attention
Words
Two user attention words appear in Life Technologies user
documentation. Each word implies a particular level of observation
or action as described below:
Note: Provides information that may be of interest or help but is not
critical to the use of the product.
IMPORTANT! Provides information that is necessary for proper
instrument operation, accurate chemistry kit use, or safe use of a
chemical.
Examples of the user attention words appear below:
Note: The size of the column affects the run time.
Note: The Calibrate function is also available in the Control
Console.
IMPORTANT! To verify your client connection to the database, you
need a valid Oracle® user ID and password.
IMPORTANT! You must create a separate Sample Entry Spreadsheet
for each 96-well plate.
8
GeneMapper® Software 5 Installation and Administration Guide
How to Obtain More Information
Related
Documentation
Portable document format (PDF) versions of this guide and the
documents listed below are available on the GeneMapper® Software
Documentation CD.
• GeneMapper® Software Getting Started Guides for
microsatellite analysis (PN 4403672), loss of hetereozygosity
(LOH) analysis (PN 4403621), AFLP® system analysis
(PN 4403620), SNaPshot® kit analysis (PN 4403618), and
SNPlex® system analysis (PN 4403617) – Five guides that
explain how to analyze the application-specific example data
provided with the GeneMapper Software. The guides provide
brief, step-by-step procedures for the analysis of microsatellite,
LOH, AFLP® system, SNaPshot® kit, and SNPlex® system data
generated by compatible Life Technologies electrophoresis
instruments and Data Collection Software. The guides are
designed to help you quickly learn to use basic functions of the
GeneMapper Software.
• GeneMapper® Software Quick Reference Guide (PN 4403615)
– Provides workflows for specific analysis types and lists
instruments, software, and analysis applications compatible with
the GeneMapper Software.
• GeneMapper® Software Reference and Troubleshooting
Guide (PN 4403673) – Provides reference information such as
theory of operation and includes troubleshooting information.
Note: For additional documentation, see “How to Obtain Support”
on page 10.
GeneMapper® Software 5 Installation and Administration Guide
9
Obtaining
Information from
the Online Help
The GeneMapper® Software online help system describes the
GeneMapper Software and provides procedures for common tasks.
Access online help by clicking
in the toolbar of the GeneMapper
window, selecting HelpContents and Index, or pressing F1.
How to Obtain Support
For the latest services and support information for all locations, go to
www.lifetechnologies.com/support.
At the Support page, you can:
• Access to worldwide telephone and fax numbers to contact
Life Technologies Technical Support and Sales facilities
• Search through frequently asked questions (FAQs)
• Submit a question directly to Technical Support
• Order Life Technologies user documents, SDSs, certificates of
analysis, and other related documents
• Download PDF documents
• Obtain information about customer training
• Download software updates and patches
10
GeneMapper® Software 5 Installation and Administration Guide
Safety Information
This section covers:
■ Safety Conventions Used in This Document . . . . . . . . . . . .
12
■ General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . .
13
■ Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
14
GeneMapper® Software 5 Installation and Administration Guide
11
Safety Conventions Used in This Document
Safety Alert
Words
Four safety alert words appear in Life Technologies user
documentation at points in the document where you need to be aware
of relevant hazards. Each alert word–IMPORTANT, CAUTION,
WARNING, DANGER–implies a particular level of observation or
action, as defined below:
Definitions
– Indicates a potentially hazardous situation that,
if not avoided, may result in minor or moderate injury. It may also be
used to alert against unsafe practices.
– Indicates a potentially hazardous situation that,
if not avoided, could result in death or serious injury.
– Indicates an imminently hazardous situation
that, if not avoided, will result in death or serious injury. This signal
word is to be limited to the most extreme situations.
Examples
The following examples show the use of safety alert words:
MUSCULOSKELETAL AND REPETITIVE
MOTION HAZARD. These hazards are caused by potential risk
factors that include but are not limited to repetitive motion, awkward
posture, forceful exertion, holding static unhealthy positions, contact
pressure, and other workstation environmental factors.
Do not attempt to lift or move the computer or
the monitor without the assistance of others. Depending on the
weight of the computer and/or the monitor, moving them may require
two or more people.
12
GeneMapper® Software 5 Installation and Administration Guide
General Instrument Safety
PHYSICAL INJURY HAZARD. Use this
product only as specified in this document. Using this instrument in a
manner not specified by Life Technologies may result in personal
injury or damage to the instrument.
Moving and
Lifting
Stand-Alone
Computers and
Monitors
Do not attempt to lift or move the computer or
the monitor without the assistance of others. Depending on the
weight of the computer and/or the monitor, moving them may require
two or more people.
Things to consider before lifting the computer and/or the monitor:
• Make sure that you have a secure, comfortable grip on the
computer or the monitor when lifting.
• Make sure that the path from where the object is to where it is
being moved is clear of obstructions.
• Do not lift an object and twist your torso at the same time.
• Keep your spine in a good neutral position while lifting with
your legs.
• Participants should coordinate lift and move intentions with
each other before lifting and carrying.
• Instead of lifting the object from the packing box, carefully tilt
the box on its side and hold it stationary while someone slides
the contents out of the box.
GeneMapper® Software 5 Installation and Administration Guide
13
Workstation Safety
Correct ergonomic configuration of your workstation can reduce or
prevent effects such as fatigue, pain, and strain. Minimize or
eliminate these effects by configuring your workstation to promote
neutral or relaxed working positions.
MUSCULOSKELETAL AND REPETITIVE
MOTION HAZARD. These hazards are caused by potential risk
factors that include but are not limited to repetitive motion, awkward
posture, forceful exertion, holding static unhealthy positions, contact
pressure, and other workstation environmental factors.
To minimize musculoskeletal and repetitive motion risks:
• Use equipment that comfortably supports you in neutral
working positions and allows adequate accessibility to the
keyboard, monitor, and mouse.
• Position the keyboard, mouse, and monitor to promote relaxed
body and head postures.
14
GeneMapper® Software 5 Installation and Administration Guide
Chapter 1
Getting Started
This chapter covers:
■ Start Here: Getting the Most Out of This Guide . . . . . . . . .
16
■ For Applied Biosystems 3500 Series Genetic Analyzers. . .
17
■ Oracle® Database License Agreement . . . . . . . . . . . . . . . . .
18
■
GeneMapper®
Software Workflow . . . . . . . . . . . . . . . . . . . 19
GeneMapper® Software 5 Installation and Administration Guide
15
Chapter 1
Start Here: Getting the Most Out of This Guide
The GeneMapper® Software 5 Installation and Administration Guide
describes how to install the GeneMapper® Software 5 and manage
the software, database, and auditing functions.
Note: GeneMapper® Software 5 does not support autoanalysis on
any instrument platform.
Installation
To get the most out of this guide:
1. Read through this chapter to familiarize yourself with the
Oracle® database licensing agreement.
2. Review the general installation requirements in Chapter 2:
•
•
•
•
Installation overview workflow
Computer requirements and compatible operating systems
Supported instruments and software applications
User account requirements
3. Install the GeneMapper® Software as described in Chapter 3.
4. Log in to and configure the GeneMapper® Software as described
in Chapter 3.
Administration
Maintenance
16
Review the procedures for setting up and maintaining the:
• GeneMapper® Software security settings
• Password policies
• Profiles and user accounts
• Data tracking system
• Audit map and audit history
• Electronic Signature settings
Review the procedures for using the Database Dashboard to:
• Review database statistics
• Export and import projects and supporting data
• Maintain the GeneMapper® Software by backing up data and
allocating disk space
GeneMapper® Software 5 Installation and Administration Guide
Chapter 1
Troubleshooting
If you have trouble with the installation, see Appendix A. Be sure to
perform the troubleshooting procedures in the order given:
1. Read through the troubleshooting procedures starting on
page 162.
2. If you continue to have problems, complete the Troubleshooting
Checklist on page 170, then contact Technical Support
(page 10).
For Applied Biosystems 3500 Series Genetic
Analyzers
If you are installing the GeneMapper® Software on an Applied
Biosystems 3500 series genetic analyzer, refer to the user guide for
instructions for:
• Starting the Data Collection services on the local computer
• Installing the GeneMapper® Software on the same computer as
the Data Collection Software
Document
Part number
Applied Biosystems 3500/3500xL Genetic Analyzer User
Guide
4401661
Applied Biosystems 3500 Dx/3500xL Dx Genetic
Analyzer User Guide
4401688
GeneMapper® Software 5 Installation and Administration Guide
17
Chapter 1
Oracle® Database License Agreement
About the
Database
Database Access
User Access
18
The GeneMapper® Software uses an Oracle® database to store all
project-related data. In addition to serving as a common data
repository, the database provides user authentication, robust and
scalable data management, and flexible archive capabilities through
the utilities provided with the GeneMapper® Software.
Life Technologies does not support access to the Oracle® database
through any means other than the GeneMapper® Software.
The version of the Oracle® database included with the GeneMapper®
Software is an embedded-license database. This license allows access
to the database for up to five named users at any one time. If you
want to accommodate more than five named users, you can purchase
either additional GeneMapper® Software licenses or additional
Oracle®-named user privileges and thereby honor Life Technologies
agreement with the Oracle® Corporation.
GeneMapper® Software 5 Installation and Administration Guide
GeneMapper® Software 5 Installation and Administration Guide
GeneMapper® Software Workflow
Compatible Applied Biosystems
electrophoresis instrument
Access Control
Sample files
.fsa
app
GeneM
Set Up
Fragment Analysis
Gene Ma
er ®
Software
pper Soft ware Database
Examine
Results
Panel Manager
Size standards
Kits,
panels,
bin sets
Create,
import, or edit
Import/export
Kits,
panels,
markers,
bins
Projects
Analyze
Projects
Apply
panels
Raw data
Apply
Projects
Analysis methods
Size standards
SNP sets
Import/
export
Samples table
Genotypes table
Analysis methods
Size standards
SNP sets
GeneMapper Manager
Create,
import,
or edit
Apply
Cluster plot
Table settings
Plot settings
Import/
export
Samples plot
Genotypes plot
Table settings
Plot settings
Archive
CD
Secondary
database
Chapter 1
Log
Delete
Auditing
19
Export to
*.ser, *.txt
Print
Chapter 1
20
GeneMapper® Software 5 Installation and Administration Guide
Chapter 2
Installation Requirements
and Software Compatibility
This chapter covers:
■ Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
22
■ Computer Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . .
23
■ Instrument, Software, and Data Compatibility. . . . . . . . . . .
26
■ User Account Requirements. . . . . . . . . . . . . . . . . . . . . . . . .
27
■ GeneMapper® Software Installation DVDs . . . . . . . . . . . . .
28
GeneMapper® Software 5 Installation and Administration Guide
21
Chapter 2
Overview
This chapter specifies the requirements for installing the
GeneMapper® Software 5.
Step
See page
Verify that the computer meets requirements
23
Verify that you have Administrator privileges on the computer
27
Is a current version
of GeneMapper®
Software installed?
No
Export data from the current
database
Yes
Perform a full installation
or
Perform a client installation
Import data into the new database
Register and log in to the GeneMapper® Software
22
30
35
or
48
30
54 and 55
GeneMapper® Software 5 Installation and Administration Guide
Chapter 2
Computer Requirements
Computer
Configuration
Table 2-1 shows the computer specifications that Life Technologies
recommends for use with the GeneMapper® Software 5.
Even though you can install the GeneMapper® Software on a
computer containing the minimum supported RAM,
Life Technologies highly recommends using 4 GB of RAM (or
higher) for better performance.
Note: The following specifications are for the 3130 and 3730 series
instrument computer. The 310 instrument computer has less RAM
and HD capacity than the 3130 and 3730 series computer, so
performance may vary.
Table 2-1
GeneMapper® Software computer requirements
Computer
•
Dell®
OptiPlex® CE, Intel®
Core™2
Duo Processor,
E8400/3.0 GHz
• 4 MB of RAM, Non-ECC,
667 MHz DDR2 2 × 1 GB
• 320 GB SATA hard drive,
3.0 Gb/s and 8 MB Data
Burst Cache
• 16✕ DVD +/- RW IDE
Combo Drive
• Free disk space: 500MB
on the boot drive, 7 GB on
the drive on which the
GeneMapper® Software is
installed
Monitor
Minimum Configuration ‡
Recommended
Configuration
Component
Full Installation
•
Intel®
Core™2
Duo
Processor,
E8400/3.0 GHz
• 4 GB of RAM
• 10/100 NIC network
card with RWU
(internal)
Client Installation
• Intel® Pentium® 4
Processor, 2 GHz
• 2 GB of RAM
• 10/100 NIC network
card with RWU
(internal)
• Free disk space: 1 GB
• Free disk space:
500MB on the boot
drive, 7 GB on the
drive on which the
GeneMapper®
Software is installed
• 1280 × 1024 or higher pixel resolution
• 17-inch color monitor
Operating
System
‡
• Microsoft® Windows® 7 Professional operating system, Service Pack 1
The memory and hard disk space requirements need to be considerably higher than the minimum configuration if
the product is deployed in a multi-user environment.
GeneMapper® Software 5 Installation and Administration Guide
23
Chapter 2
Verifying that
Your Computer
Meets the
Minimum
Requirements
24
1. In the desktop, right-click Computer, then select Properties.
2. Verify that your computer meets the minimum requirements for
the operating system, processor, and memory as shown in
“Computer Requirements” on page 23.
GeneMapper® Software 5 Installation and Administration Guide
Chapter 2
Operating System
(OS)
Latest Service Pack
installed
Computer model
Microprocessor
type and speed
Installed memory
GeneMapper® Software 5 Installation and Administration Guide
25
Chapter 2
Instrument, Software, and Data Compatibility
Compatibility
Matrix
Table 2-2 shows the version(s) of the Data Collection Software,
Windows operating system, and sample data files that are supported
by the GeneMapper® Software for specified instruments.
Note: The columns in Table 2-2 are described on page 27.
Table 2-2
Compatibility matrix
Genetic Analysis
Instrument
Applied Biosystems
3500/3500xL
Genetic Analyzer
Applied Biosystems
3730/3730xl
DNA Analyzer
Compatible Data Collection Software
and Operating System
Sample Data
Compatibility
• Data Collection v2.0
• Windows 7 Professional, 32-bit, SP1
• Sample files
• Co-installation
• Data Collection v4.0
• Windows 7 Professional, 32-bit, SP1
• Sample files
• Co-installation
Applied Biosystems
3130/3130xl
Genetic Analyzer
Applied Biosystems
3100 Genetic
Analyzer
Applied Biosystems
310 Genetic
Analyzer
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 2
Compatible Data Collection Software and Operating System Column
This column displays the version(s) of the Data Collection Software,
Windows operating system, and any associated service pack(s)
supported by the GeneMapper® Software for the specified
instrument.
Sample Data Compatibility Column
This column indicates the methods by which the GeneMapper®
Software can process sample data produced by the associated
combination of instrument, Data Collection Software, and Windows
operating system.
• Sample Files – The software can import sample files created by
the specified combination of the Data Collection Software and
Windows operating system.
• Co-installation – The software can be installed on the same
computer that contains the specified combination of the Data
Collection Software and Windows operating system.
PDF File Reader
To open the user documentation included on the GeneMapper®
Software Documentation CD, use the Adobe® Acrobat® Reader®
software available from www.adobe.com.
User Account Requirements
Log On
Requirements
To install the GeneMapper® Software, you must:
• Have administrator privileges (complete and unrestricted
access) on the local computer.
Note: This level of access is required only to install the
GeneMapper® Software. After it is installed, you can run
the GeneMapper® Software without administrator privileges.
Verifying that
Your User
Account Meets
the Requirements
1. In the desktop, select StartControl Panel.
2. In the Control Panel window, double-click User Accounts.
GeneMapper® Software 5 Installation and Administration Guide
27
Chapter 2
3. In the Users tab of the User Accounts dialog box, verify that the
user account you are using belongs to the Administrators group.
If you are performing a full installation, verify that the domain is
the same name as the computer name.
Example:
Belongs to the
Administrators
Domain is the same
as the computer
name
4. Click OK.
GeneMapper® Software Installation DVDs
Before installing/upgrading the GeneMapper® Software, verify that
you have the appropriate installation DVD(s).
Table 2-3
GeneMapper® Software installation DVDs
If you are
performing a …
28
Use the DVD …
A full installation
GeneMapper® Software Full Installation
A client installation
GeneMapper® Software Installer for Client
GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Performing a New Installation
of the GeneMapper® Software
This chapter covers:
■ Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
■ Exporting
30
GeneMapper®
Software from a Windows XP
Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
■ Importing GeneMapper® Software to a
Windows 7 Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
■ Determining Your Installation Options . . . . . . . . . . . . . . . .
32
Section 3.1: Full Installation Procedures . . . . . . . . . . . . . . . . 35
■ Instrument Configuration Procedures . . . . . . . . . . . . . . . . .
36
■ Stand-alone Configuration Procedures. . . . . . . . . . . . . . . . .
43
Section 3.2: Client Installation Procedures . . . . . . . . . . . . . . 48
■ Client Configuration Procedures . . . . . . . . . . . . . . . . . . . . .
48
Section 3.3: Software Login Procedures. . . . . . . . . . . . . . . . . 53
■ Registering the Software After a New Installation . . . . . . .
54
■ Logging In to the Software for the First Time After a New
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
■ Logging In to the Database Dashboard for the First Time. .
57
■ What Next?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
58
■ Logging In to and Out of the Software . . . . . . . . . . . . . . . .
59
GeneMapper® Software 5 Installation and Administration Guide
29
Chapter 3
Overview
This chapter describes how to perform a new installation of the
GeneMapper® Software on a Windows 7 computer. To perform a
new installation, you cannot have a previous version of the
GeneMapper® Software on your computer.
Exporting GeneMapper® Software from a
Windows XP Computer
To export GeneMapper® Software data from a Windows XP
computer:
If the GeneMapper® Software
Configuration is
• Stand-alone (not co-installed
with Data Collection software)
• Co-installed on a 3500 Series
computer
• Co-installed on a 3730 Series,
3130 Series, 3100, or 310
computer
Follow the procedure in
Appendix C, Migrating Data Using
the GeneMapper® Database
Utility Wizard
Appendix D, Migrating Data
Manually
Importing GeneMapper® Software to a Windows 7
Computer
To import GeneMapper® Software data to a Windows 7 computer:
If the GeneMapper® Software
Configuration is
• Stand-alone (not co-installed
with Data Collection software)
• Co-installed on a 3500 Series
computer
30
Follow the procedure in
Appendix C, Migrating Data Using
the GeneMapper® Database
Utility Wizard
GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
If the GeneMapper® Software
Configuration is
• Co-installed on a 3730 Series,
3130 Series, 3100, or 310
computer
GeneMapper® Software 5 Installation and Administration Guide
Follow the procedure in
Appendix D, Migrating Data
Manually
31
Chapter 3
Determining Your Installation Options
Your installation options depend on the type of computer on which
you are installing the software:
• Instrument computer (connected to the instrument)
• Stand-alone computer (not connected to the instrument)
Table 3-1
GeneMapper® Software installation options
Computer
Description
See page
Instrument:
Full Installation
only (software
and database)
36
Local computer
GeneMapper® software
+
GeneMapper® database
Instrument
Data
collection
software
The Data Collection Software and the GeneMapper® Software are
installed on the same computer.
In this configuration, you can use the GeneMapper® Software to:
• Add sample files and studies to a project from a local Data
Collection Software database.
• Perform manual analysis of the project or study.
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Chapter 3
Table 3-1
GeneMapper® Software installation options
Computer
Description
See page
43
Stand-alone:
Client
Installation
(software only)
Local computer
GeneMapper® software
Data
transfer
Remote computer
GeneMapper® software
+
GeneMapper® database
Data
transfer
Remote
computer
Data
collection
software
HOST
Instrument
The Data Collection Software and the GeneMapper® Software are
installed on separate computers.
In a stand-alone configuration, you can use the GeneMapper®
Software to:
• Add sample files and studies to a project from a remote Data
Collection Software database.
• Perform manual analysis of the project or study.
Stand-alone:
Full Installation
(software and
database)
Local computer
®
GeneMapper software
+
GeneMapper® database
HOST
Data
transfer
48
Remote
computer
Data
collection
software
Instrument
The Client GeneMapper® Software can be installed on multiple client
computers. The Full GeneMapper® Software is installed on one
computer separate from the client computers. The Data Collection
Software is installed on a computer separate from the client
computers.
In a client configuration, you can set up the Client GeneMapper®
Software to:
• Obtain sample files from the remote Data Collection Software
database.
• Store sample files, panel and bin definitions, analysis methods, size
standards, table and plot settings, and projects on the
GeneMapper® Software instrument computer.
GeneMapper® Software 5 Installation and Administration Guide
33
Chapter 3
34
GeneMapper® Software 5 Installation and Administration Guide
Section
Section 3.1 Full Installation Procedures
This section covers:
■ Instrument Configuration Procedures . . . . . . . . . . . . . . . . .
36
■ Stand-alone Configuration Procedures. . . . . . . . . . . . . . . . .
43
Note: To perform a client installation, go to Section 3.2, “Client
Installation Procedures,” on page 48.
IMPORTANT! Be sure you use the GeneMapper® Software Full
Installation DVD when performing the installation procedures
described in this section.
GeneMapper® Software 5 Installation and Administration Guide
35
Chapter 3
Instrument Configuration Procedures
Install the instrument configuration if the Data Collection Software is
installed on the local computer.
Local computer
GeneMapper® software
+
GeneMapper® database
Instrument
Data
collection
software
Figure 3-1
Example of an instrument configuration
If you do not have the Data Collection Software on the computer, do
one of the following:
• Install the Data Collection Software before proceeding
• Install the stand-alone configuration (see page 43)
Installation Tasks
for an Instrument
Configuration
Installing the GeneMapper® Software in an instrument configuration
requires that you:
Task
See page
1. Export from the database on the Windows XP computer:
– 3500 Series computer
189
– 3730 Series, 3130 Series, 3100, or 310 computer
193
2. Start the Data Collection services on the computer.
3. Install the
36
GeneMapper®
Software on the computer.
37
39
GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Starting the
Data Collection
Services on the
Local Computer
Before you install the GeneMapper® Software, start the
Data Collection services on the local computer.
Note: For information on starting the Data Collection services for
the 3500 series genetic analyzers, refer to the instrument user guide.
1. Select StartAll ProgramsApplied Biosystems
Data CollectionRun <Data Collection version>, where
<Data Collection version> is one of the following:
• 3730/3730xl Data Collection v3.1
• 3130/3130xl Data Collection v3.1
After the Service Console opens, wait until all four symbols
change to green squares.
Note: If the services do not start automatically, click Start All.
2. If the Data Collection Software requires a password, a login
dialog box opens. Type the Login Name and Password, then
click OK.
Note: If you do not know the Login Name or Password, contact
the administrator.
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37
Chapter 3
3. Verify that Data Service started without errors:
a. In the Service Console, right-click the square next to Data
Service and select Show Console to display the Data
Service output window.
Right-click here
b. Verify that no errors are displayed in the lower pane of the
window, then close the Data Service output window.
No errors
displayed
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Installing the
Instrument
Configuration
of the
GeneMapper®
Software
To install the GeneMapper® Software on the same computer as
the Data Collection Software:
1. Insert the GeneMapper® Software Full Installation DVD into
the DVD drive to start the installer.
If the installer does not start automatically:
a. Right-click Computer and select Explore.
b. Expand the DVD drive, then select the GeneMapper 5
folder to display the contents.
c. Double-click
GeneMapper5 to start the installer.
2. Be sure that the Data Collection services are running
(see page 37). Close all other applications and windows, then
click OK to close the following message:
3. In the Welcome window, click Next.
4. Review the installation requirements status, then click Next.
5. Read the release notes, then click Next.
GeneMapper® Software 5 Installation and Administration Guide
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Chapter 3
6. If you want to install the GeneMapper® Software to a drive
different from the default drive, select the destination folder:
Note: We recommend installing the GeneMapper® Software on
the E drive when co-installing the GeneMapper® Software on
the same computer as the Data Collection Software.
a. Confirm that the boot drive has at least 200 MB of
available free space.
b. Select a destination folder with at least 7 GB of free space,
then click Next.
Note: On 3500 Series computers, the installation prompts you
to import the database that you exported from the Windows XP
computer. On 3730 Series, 3130 Series, 3100, or 310 computers,
the installation does not prompt you to import; you must
manually import the database contents from the Windows XP
computer (see 193).
7. On 3500 Series computers only: To import data you exported
from the GeneMapper Windows XP computer:
a. Click Yes in the Import Data dialog box.
40
GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
b. Select the version you are importing in the Setup Type
window, then click Next.
8. View the amount of disk space that is preallocated for the
GeneMapper® Software database, then click Next.
Note: The amount of disk space that is preallocated varies
according to your computer configuration.
9. Review the settings, then click Next to start the installation.
IMPORTANT! During installation, DOS commands are executed
and the DOS window may open. Do not delete, close, or click
the DOS window. If you do click it, press the Esc key.
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41
Chapter 3
10. After the installer completes the installation, it displays an
InstallShield Wizard Complete window. Be sure to stop the Data
Collection services before restarting your computer:
a. In the Service Console, click Stop All.
b. Remove the installation DVD from the drive.
c. In the InstallShield Wizard Complete window, select Yes, I
want to restart my computer now, then click Finish.
11. Go to Section 3.3, “Software Login Procedures,” on page 53.
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Stand-alone Configuration Procedures
Install the stand-alone configuration on a computer that does not
contain the Data Collection Software.
Local computer
GeneMapper® software
+
GeneMapper® database
Data
transfer
Data
collection
software
HOST
Figure 3-2
Installation Tasks
for a Stand-alone
Configuration
Remote
computer
Instrument
Example of a stand-alone configuration
Installing the GeneMapper® Software as a stand-alone configuration
requires that you:
Task
Installing the
Stand-alone
Configuration
of the
GeneMapper®
Software
See page
Export the database using the GeneMapper® Database
Utility Wizard
189
Install the GeneMapper® Software on the local computer.
43
To install the GeneMapper® Software on a computer separate
from the Data Collection computer:
1. Insert the GeneMapper® Software Full Installation DVD into
the DVD drive to start the installer.
If the installer does not start automatically:
a. Right-click Computer and select Explore.
b. Expand the DVD drive, then select the GeneMapper5
folder to display the contents.
c. Double-click
GeneMapper5 to start the installer.
GeneMapper® Software 5 Installation and Administration Guide
43
Chapter 3
2. Close all other applications and windows, then click OK to
close the following message.
3. Review the installation requirements status, then click Next.
4. Select Stand-alone for type of installation, then click Next.
5. Read the release notes, then click Next.
6. If you want to install the GeneMapper® Software to a drive
different from the default drive, select the destination folder:
a. Confirm that the boot drive has at least 200 MB of
available free space.
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
b. Select a destination folder with at least 7 GB of free space,
then click Next.
7. To import data you exported from the GeneMapper Windows 7
computer:
a. Click Yes in the Import Data dialog box.
b. Select the version you are importing in the Setup Type
window, then click Next.
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45
Chapter 3
8. (Optional) Allocate space for the GeneMapper® Software
database, then click Next.
IMPORTANT! The minimum allocation for the install drive is
3 GB. If you want to increase the drive space allocation,
increase it in increments of 5 GB.
Note: You can allocate more drive space later using the
Database Dashboard. See “Allocating Additional Disk Space”
on page 155.
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GeneMapper® Software 5 Installation and Administration Guide
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9. Read the current settings, then click Next to start the
installation.
IMPORTANT! During installation, DOS commands are executed
and the DOS window may open. Do not delete, close, or click
the DOS window. If you do click it, press the Esc key.
10. In the InstallShield Wizard Complete window, select Yes, I
want to restart my computer now, remove the installation
DVD from the drive, then click Finish.
11. Go to Section 3.3, “Software Login Procedures,” on page 53
GeneMapper® Software 5 Installation and Administration Guide
47
Chapter 3
Section 3.2 Client Installation Procedures
Client Configuration Procedures
Install the client configuration on computers that share one central
GeneMapper® Software database. You can install the GeneMapper®
Software clients as a stand-alone configuration.
Stand-alone
Client
Configuration
In stand-alone configuration, the GeneMapper® Software client
does not interact with the Data Collection Software.
You can use the stand-alone client to:
• Add sample files from a remote Data Collection Software
database to a project, then perform manual analysis of the
project.
• Add sample files from the GeneMapper® Software to a project,
then perform manual analysis of the project.
Local computer
GeneMapper® software
Data
transfer
Remote computer
GeneMapper® software
+
GeneMapper® database
Data
transfer
Data
collection
software
HOST
Figure 3-3
Installation Tasks
for a Stand-alone
Client
Configuration
48
Remote
computer
Instrument
Example of stand-alone client configuration
To install the GeneMapper® Software as a stand-alone client
configuration, perform the following tasks:
Task
See
page
1. Obtain the name of the GeneMapper® Software instrument
computer.
49
2. Install the GeneMapper® Software client on the local computer.
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Obtaining the
GeneMapper®
Software
Instrument
Computer Name
When installing the GeneMapper® Software clients, you need the
name of the GeneMapper® Software instrument computer.
1. Right-click Computer in the desktop and select Properties.
2. Locate the full computer name. You will need to enter the name
when you install the GeneMapper® Software.
Note: The full computer name is the host name.
3. Close the dialog box.
GeneMapper® Software 5 Installation and Administration Guide
49
Chapter 3
Installing
the Client
Configuration
of the
GeneMapper®
Software
1. Insert the GeneMapper® Software 5 Installer for Client DVD
into the DVD drive to start the installer.
If the installer does not start automatically, then:
a. Right-click Computer and select Explore.
b. Expand the DVD drive.
c. Select the GeneMapper 5 folder to display the contents.
d. Double-click
GeneMapper5 to start the installer.
2. In the Welcome window, click Next.
3. Review the installation requirements status, then click Next.
4. Type the instrument computer name (host name or full computer
name) for the GeneMapper® Software database computer (see
page 49), then click Next.
5. After the installer establishes a connection with the
GeneMapper® Software instrument computer, click OK to
continue.
6. Select Stand-alone for the type of installation:
7. Read the release notes, then click Next.
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
8. If you want to install the GeneMapper® Software to a drive
different from the default drive, select the destination folder:
a. Confirm that the boot drive has at least 200 MB of
available free space.
b. Select a destination folder with at least 7 GB of free space,
then click Next.
[
9. Read the current settings, then click Next to start the
installation.
IMPORTANT! During installation, DOS commands are executed
and the DOS window may open. Do not delete, close, or click
the DOS window. If you do click it, press the Esc key.
10. In the InstallShield Wizard Complete window, click Finish.
11. Go to Section 3.3, “Software Login Procedures,” on page 53.
Note: To import data from a previous version of the software after
you log in, see Appendix D, Migrating Data Manually,
GeneMapper® Software 5 Installation and Administration Guide
51
Chapter 3
52
GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Section 3.3 Software Login Procedures
This section covers:
■ Registering the Software After a New Installation . . . . . . .
54
■ Logging In to the Software for the First Time After a New
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
■ Logging In to the Database Dashboard for the First Time. .
57
■ What Next?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
58
■ Logging In to and Out of the Software . . . . . . . . . . . . . . . .
59
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53
Chapter 3
Registering the Software After a New Installation
Register the software the first time that you start the software.
Note: If you cannot to register the software as described, see
Appendix A on page 161.
1. In the desktop, double-click
GeneMapper5 or
select StartAll ProgramsLife Technologies
GeneMapper GeneMapper5.
2. Complete the Registration dialog box:
Note: The registration code is on the registration card packaged
with the software. Keep your registration code where you can
retrieve it easily. If you need to reinstall the software, you will
be prompted for the registration code.
3. Click OK.
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GeneMapper® Software 5 Installation and Administration Guide
Section
Logging In to the Software for the First Time
After a New Installation
1. Complete the Login to GeneMapper dialog box:
a. Use the default user name gm.
b. Type the password password.
c. Click OK.
2. Click OK when the software prompts you to change the
password.
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55
Chapter 3
3. Change the password:
a. Type a new password.
b. Retype the new password to confirm.
c. Click OK.
Note: Type a password that is 6 to 10 alphanumeric characters.
IMPORTANT! Keep the new password for the default user gm
where you can retrieve it easily. If you forget or lose your
password for the default user gm, it is not possible for
Life Technologies to retrieve it.
4. Read the license agreement, then click Yes if you agree with the
terms.
5. Review the license agreement and product warranty. You can:
• Click Decline to quit the application.
• Click Service to bypass the agreement and proceed to the
Project window.
IMPORTANT! You can click Service (and bypass the
agreement) up to three times before you are locked out of
the software. After you make this selection one or two
times, the license agreement and product warranty are
displayed the next time that you log in to the software.
• Click Print to print the agreement.
• Click Accept to accept the terms of the agreement and open
a new, untitled Project window.
6. If necessary, see the “Creating a User Account” on page 89 for
instructions on adding users.
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Logging In to the Database Dashboard for the
First Time
Use the following procedure to log in to the Database Dashboard for
the first time after performing a new full installation of the
GeneMapper® Software.
To log in to the Database Dashboard for the first time:
1. Select StartAll ProgramsLife Technologies Database
DashboardDashboard.
2. Complete the Login to Dashboard dialog box:
a. Type the password password.
b. Click OK.
3. Click OK when the software prompts you to change the
password.
4. Change the password:
a. Type a new password.
b. Retype the new password to confirm.
c. Click OK.
Note: Type a password that is 6 to 10 alphanumeric characters.
IMPORTANT! Keep the new password for the Database
Dashboard where you can retrieve it easily. If you forget or lose
your password for the Database Dashboard, it is not possible for
Life Technologies to retrieve it.
5. See “About the Dashboard Software” on page 149 and the
GeneMapper® Software Online Help for more information
about using the Database Dashboard to maintain the
GeneMapper® Software database.
GeneMapper® Software 5 Installation and Administration Guide
57
Chapter 3
What Next?
For user instructions, refer to the:
• GeneMapper® Software Getting Started Guides
• GeneMapper® Software Online Help
To access the online help from the GeneMapper® Software, do
one of the following:
– Click
in the toolbar
– Select HelpContents and Index
– Press F1
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 3
Logging In to and Out of the Software
Logging In
1. In the desktop, double-click
GeneMapper5 or select
StartAll ProgramsLife Technologies
GeneMapperGeneMapper5.
2. Select your user name from the User Name drop-down list. If
your name is not listed, type it in.
If you do not have a user name, request a user name and/or
password from the administrator. If you are the administrator,
use:
• User Name: Administrator
• Password: Administrator
If your password is pre-expired, the software prompts you to
create a password after you click OK.
3. Type your password.
IMPORTANT! Life Technologies recommends changing the
password for the Administrator user account after installing the
software.
GeneMapper® Software 5 Installation and Administration Guide
59
Chapter 3
4. Click OK.
Note: If you unsuccessfully attempt to log in to the software
more times than allowed by your password policy, your account
becomes suspended. To activate a suspended user account,
either wait the time specified by the policy associated with the
account, or ask your administrator to reactivate the account (see
“Activating, Deactivating, and Suspending User Accounts” on
page 93 for more information).
Connecting to a
New Host
1. Click New Host on the Login to GeneMapper dialog box.
2. Complete the fields in the New Host dialog box to connect to a
GeneMapper® Software database on another computer:
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GeneMapper® Software 5 Installation and Administration Guide
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a. In the Host Name field, type the instrument computer name
or IP address of the database host.
The window displays the new database host and its user
names list. If the GeneMapper® Software cannot connect to
the database host you entered, the error message “You have
entered an invalid host” is displayed. Click OK to exit, then
retype the database host information.
b. Select the appropriate machine type.
c. Click OK.
IMPORTANT! If, at any time, the network connection is
interrupted or lost, the GeneMapper® Software becomes
unusable. To restore the connection, exit the software, then
restart it using a user account that belongs to the Administrator
user group.
Logging Out
You can close the GeneMapper® Software in one of three ways:
• Select FileLogout
• Select FileExit
• Click (the Close button).
When you log out of the GeneMapper® Software with a GeneMapper
project that has unsaved changes, the software prompts you to save or
discard the changes you made since the last time you updated the
project.
If you close the GeneMapper® Software using the FileLogout
command, the login window reopens after you select either “Yes” or
“No.” GeneMapper® Software closes completely if you use either the
FileExit command or the Close button.
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 4
.
Managing Database Security
and User Access
This chapter covers:
■ About GeneMapper® Software Security . . . . . . . . . . . . . . .
64
■ Configuring the Password Policies . . . . . . . . . . . . . . . . . . .
66
■ Managing User and Security Groups . . . . . . . . . . . . . . . . . .
70
■ Managing Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . .
78
■ Managing Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
78
■ Managing User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . .
88
■ Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . . .
94
■ Exporting and Importing the Security Settings . . . . . . . . . .
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63
Chapter 4
About GeneMapper® Software Security
Security System
Components
The GeneMapper® Software uses two applications to secure and
monitor the data it stores:
• Security Manager
• Audit Map Configuration Software
This chapter describes how to use the Security Manager utility to
control user access to the GeneMapper® Software. For more
information on monitoring use and modification of data stored by the
GeneMapper® Software, see Chapter 5, “Managing the Auditing and
Electronic Signature Systems.”
About the
Access Control
Administration
Software
The Access Control Administration Software restricts user access to
the functions of the GeneMapper® Software and to the data it stores.
Using the Security Manager, you can create or remove user accounts,
control user access to functions of the GeneMapper® Software, and
define general policies for password use.
IMPORTANT! Use of the Access Control Administration Software is
not optional.
Note: The Access Control Administration Software is an integral part
of the GeneMapper® Software that cannot be deactivated or
uninstalled.
Starting the
Access Control
Administration
Software
IMPORTANT! Only users that belong to the Administrator user group
(see page 83) can use the Access Control Administration Software.
IMPORTANT! After the installation of the software, the first person
to log in must do so using the default user account (user name: gm;
password: password), then configure user names for his or her
department.
1. Start and log in to the GeneMapper® Software (see “Logging In
to and Out of the Software” on page 59).
2. In the GeneMapper window, select ToolsSecurity Manager.
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3. In the AdminToolAcc dialog box, type a user name and
password for a user account with administrative privileges, then
click OK.
Setting Up the
Security System
The following tasks must be performed to set up the Security System
Software for the GeneMapper® Software.
Start the Access Control Administration Software (see page 64).
Configure the password policies (see page 66).
Can you use the default profiles provided with the
installation? (see page 84).
No
Yes
Create custom security profiles for your users (see page 81).
Create user accounts for all users of the GeneMapper® Software
(see page 89).
If you just installed the GeneMapper® Software, change the
passwords for the default Administrator and gm user accounts
(see page 92).
Exit the Access Control Administration Software (see page 64).
Maintaining the
Security System
Perform the tasks in the following table to maintain the security
system for the GeneMapper® Software.
Frequency
As needed
Tasks
• Create, modify, or retire user accounts as needed
(see page 89).
• Create, modify, or retire security profiles as needed
(see page 81).
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Chapter 4
Configuring the Password Policies
About Password
Policies
The password policies system of the Access Control Administration
Software is a set of rules that control various aspects of password use
and how the software responds to failed login attempts. The Access
Control Administration Software applies the password policies
settings uniformly to all user accounts, including those with
administrative privileges. Configuring the password policies system
is not optional. We recommend that you configure the password
policies immediately after you install the GeneMapper® Software,
and review the policies every six months as part of routine
maintenance.
Setting the
Password
Policies
1. Start the Access Control Administration Software (see page 64).
2. Select SettingsPassword Policies.
3. In the Password Policies dialog box, configure the Attempts
settings to determine how the software handles failed login
attempts (when a user attempts to log in using the wrong
password):
Max Login
Attempts field
Send log
message check
box
Remain Active
radio button
Suspended for
_ hour(s) radio
button/field
• Max Login Attempts – Type the number of failed login
attempts that the software should allow before suspending
the user account.
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• Send log message – Select this if you want the software to
record the failed login attempts to the security log.
Note: The security log for the GeneMapper® Software is
an ASCII text file located in <drive>:\
AppliedBiosystems\ GeneMapper\
GeneMapper_Log.txt. For more information on
interpreting the notations in the security log, see “Viewing
the Security Report” on page 94.
• Set User State – Select an option to determine the way that
the software responds to users who exceed the number of
failed login attempts (defined by the Max Login Attempts
field):
– Remain Active – If selected, the user account remains
active when a user exceeds the maximum login attempts.
– Suspended for _ hour(s) – If selected, the software
suspends the user account for the specified number of
hours when a user exceeds the maximum login attempts.
Note: If a user exceeds the maximum number of login
attempts, you can reactivate the user account before the
specified time period elapses as explained in “Activating,
Deactivating, and Suspending User Accounts” on page 93.
Otherwise, the user must wait for the specified number of
hours to elapse before he or she can attempt another login.
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Chapter 4
4. Configure the Password settings to determine the length of time
that passwords are valid on the system:
Password
Lifetime check
box/field
Password
Grace Logins
field
• Password Lifetime – Select this if you want the software
to retire the password of each user account after the
specified number of days elapses.
Note: When the software retires a password, it
automatically prompts the user to create a new password
the next time he or she uses the GeneMapper® Software.
• Password Grace Logins – Type the number of times that a
user can delay changing his or her password after the
software prompts the user to change it. Once the user
exceeds the number of specified logins, the software
requires the user to change his or her password.
5. Configure the Password Reusability settings to determine how
long users can use the same password:
Password
Reuse Period
check box/field
Password kept
per usage field
• Password Reuse Period – Select this if you want the
software to allow a user to reuse a former password after
the specified number of days has elapsed since its last use.
• Password kept per usage – Type the number of former
passwords per user that the Access Control Administration
Software should store.
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6. In the Minimum Password Width field of the Password Format
settings, type the number of characters that the software should
enforce as the lower limit for all user passwords.
Minimum
Password
Width field
For example, if you type “6” in the Minimum Password Width
field (as shown in the figure above), all users must choose
passwords at least 6 characters in length.
Note: By default, all passwords must be at least 6 characters.
7. Click Save Changes.
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Chapter 4
Managing User and Security Groups
Overview
The GeneMapper® Software employs a system of user and security
groups to manage data access privileges in a multi-user environment.
By combining the groups you can create multiple public and private
data pools for the users of the GeneMapper® Software. In addition to
the control provided by the user and security groups, the
GeneMapper application provides a locking mechanism to prevent
users from unknowingly overwriting each other’s changes.
IMPORTANT! Use of the user and security groups is applicable only
to multi-user environments (such as the client installation and situations
in which multiple users operate the GeneMapper® Software on a single
computer). Individual users who do not plan to share the application, do
not need to alter the user and security group settings.
About User
Groups
As the name implies, user groups associate user accounts for the sole
purpose of bestowing them with data access privileges. Each user
group can be individually configured to provide users with Read or
Update access to the data object controlled by the associated security
groups. When rights conflict, the most permissive right prevails. A
user account can belong to multiple user groups, and a user group can
be associated with multiple security groups.
Note: If a user belongs to multiple user groups, the user's access
privileges are a combination of all the rights granted by the
associated groups.
The GeneMapper® Software installs two default user groups:
• Administrators – The default user group created for users
responsible for maintaining and administrating the software.
The Administrator user group has Read/Update privileges
(uneditable) to all data objects.
• All Users – All users are automatically members of the All
Users group. By default, the All Users user group has
Read/Update privileges to all data objects belonging to the
default GeneMapper security group.
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About Security
Groups
Top-level GeneMapper® Software data (such as individual analysis
methods, projects, and panels) are assigned to a single security group.
When a security group is associated with a user group, the
GeneMapper® Software defines the access rights of that user group to
the data of the security group. Security groups provide the basis for
ownership of the objects used by the GeneMapper® Software. For
example, if a user creates a new project and associates it with a
particular security group, only users who belong to a user group that
has Read or Update permissions for the same security group can view
the project. Security groups restrict access to: projects, table settings,
plot settings, cluster plot settings, report settings, reference data,
chemistry kits, and panels.
IMPORTANT! Security groups do not restrict access to sample data.
After samples are added to a project, the GeneMapper® Software
stores the pertinent data from the sample files to the database, where
any user can access it for use in additional projects.
The GeneMapper® Software installs two default security groups:
• Admin Security Group – Contains all data objects for the:
– Access Control Administration Software (user accounts, user
profiles, user and security groups, and applications)
– Electronic Signature Software (electronic signature settings
and records)
– Audit Manager Software (audit map settings and records)
• GeneMapper – By default, the GeneMapper security group
contains all data objects used by the GeneMapper® Software
(until the addition of other security groups).
User and Security
Groups From the
User’s
Perspective
After you configure the GeneMapper® Software with user and
security groups and associate user accounts to the user and security
groups, the software modifies the content of specific dialog boxes
and windows accordingly. When a user creates, opens, or attempts to
modify a controlled data object, the software includes in the
appropriate element of the user interface, a drop-down list that
prompts the user to assign a Security Group to the data object.
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Chapter 4
Examples
This section illustrates the function of user and security groups
through a series of example scenarios. Figure 4-1 on page 74 displays
a diagram of the user and security group configuration for each
example.
Example 1: Simple Public and Private Data Configuration
This configuration supports two users who do not co-author projects,
but share data resources, such as analysis methods, size standard
definitions, panels and bin sets, or SNP sets.
In Example 1:
• Both users can read and update data belonging to the Public
security group (shared data such as analysis methods, size
standard definitions, panels and bin sets).
• Each user can read and update data belonging to his or her
personal security group (projects)
• The users cannot read each other’s private data.
Example 2: Public and Private Data Configuration with Viewer
This configuration provides the same support explained in
Example 1, except that it features the Private Viewer user group that
allows Users 1 and 2 to view each other’s private data.
In Example 2:
• Both users can read and update public data belonging to the
Public security group (multi-author projects and other shared
data such as analysis methods, size standard definitions, panels
and bin sets).
• Each user can read and update private data belonging to his or
her personal security group (single-author projects).
• Because both users belong to the Private Viewer user group,
they can read each other’s private data.
Note: The Private Viewer user group prevents the users from
updating each other’s projects, but it allows them to use and
create copies of the viewable projects.
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Example 3: Workgroup Configuration
This configuration contains two duplicate workgroups in the
configuration shown in Example 2. Also included in Example 3 are
user and security groups for a principal investigator (PI) who is
responsible for managing and reviewing the data generated by the
work groups.
In Example 3:
• The users of the workgroups can read and update public data
belonging to the Workgroup security group for their workgroup.
For example, Users 1 and 2 can read and update data objects
belonging to the Workgroup 1 security group (multi-author
projects and other shared data, such as analysis methods, size
standard definitions, panels and bin sets).
• All users can read and update the private data belonging to their
personal security group (single-author projects).
• Because the members of each workgroup belong to a
Workgroup user group, they can view each other’s private data.
Note: The Workgroup user group prevents the users from
altering each other’s private data, but the users can use and
create copies of the viewable data objects.
• The user assigned to the principal investigator user group can
read and update the private data of all other users.
Note: One possible application of the Example 3 configuration is
version control of reference data (such as analysis methods, panels,
and bin sets). The principal investigator could assume the
responsibility of maintaining the reference data used by the members
of the workgroups. By storing all reference data in the security group
for the principal investigator, the other members could use the
reference data to analyze their respective projects, but control of the
data objects would belong only to the principal investigator.
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Chapter 4
Key
Example 1: Public and Private Data Setup
Create/View
View Only
User Account
User 1
User 2
Private: User 1
Public
Public
User 1
Private: User 2
User 1
User Group
Security Group
User 1
User 1
Data
Example 2: Public and Private Data Configuration with Viewer
User 1
User 1
Private: User 1
Private Viewer
Public
Public
User 1
User 1
Private: User 2
User 1
User 1
Private: User 1
Workgroup 1
Public: Wrkgrp
Public: Wrkgrp
User 2
User 2
Private: User 2
PI
PI
Private: PI
User 4
User 4
Private: User 4
Workgroup 2
Public: Wrkgrp
Public: Wrkgrp
User 5
User 4
Private: User 5
User 1
User 2
Example 3: Workgroup Configuration
User 1
User 2
User 3 (PI)
User 4
User 5
Figure 4-1
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Examples of user and security group configurations
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Chapter 4
Setting Up User and Security Groups
Overview
Setting up user and security groups for the GeneMapper® Software
requires that you:
• Carefully read “Managing User and Security Groups” on page 70
and determine the appropriate user and security group structure
for your users.
• Create security groups as explained below.
• Create user groups as explained in “Creating a User Group” on
page 77 (associate the security groups and user accounts during
or after the creation of each).
• If necessary, create security profiles as explained in “Creating a
Profile” on page 81.
• Create user accounts for your users as explained in “Creating a
User Account” on page 89.
• Test the access control system you created by creating,
modifying, deleting, and viewing data objects using the
appropriate user accounts.
• Modify the system as necessary.
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Chapter 4
Creating Security
Groups
1. Start the Access Control Administration Software (see page 64).
2. In the Access Control Administration window, click
(File
New Security Group).
3. In the Create Security Group dialog box, click Next.
4. In the Create Security Group screen, type a name and
description for the new group, then click Next.
Note: The name cannot begin with a number (1, 2, 3, …) or
contain symbols (&, $, #, …).
IMPORTANT! Do not modify the Control Security Group
setting. The Control Security Group drop-down list assigns the
security group data object you are editing to an existing security
group. If you assign it to an unassociated security group, the
group you are editing becomes unavailable.
5. In the Associate User Groups settings:
a. Select Associate for each user group that you want to
associate with the new security group.
b. For each associated user group, select Read or Update to
determine the data access privileges to provide users of the
group.
c. When finished, click Next.
6. Click Finish to complete the setup.
7. Click
(FileSave).
To edit an existing Security Group:
1. Expand
Security Groups in the Navigation Pane of the
Access Control Administration window, then select a security
group.
2. Modify the settings for the selected security group displayed in
the Security Group Properties pane.
3. When you finish, click
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Creating a
User Group
1. In the Access Control Administration window, click
(File
New User Group).
2. In the Create User Group dialog box, click Next.
3. In the Configure the New User Group screen, type a name and
description for the new group. The name cannot begin with a
number (1, 2, 3, …) or contain symbols (&, $, #, …).
4. Select the default rights for the software to apply when
associated with a security group:
• Read – Select to allow the user to read the data objects of
the security groups that you will associate with the user
group.
• Update – Select to allow the user to modify the data
objects of the security groups that you will associate with
the user group.
IMPORTANT! Do not modify the Control Security Group
setting. The Control Security Group drop-down list assigns the
security group data object you are editing to an existing security
group. If you assign it to an unassociated security group, the
group you are editing becomes unavailable.
5. Click Next.
6. Select Associate for each user account that you want to associate
with the new user group, then click Next.
7. In the Associate Security Groups settings:
a. Select Associate for each security group that you want to
associate with the new user group.
b. For each associated security group, select Read or Update
to determine the data access rights to provide users of the
new users group for the associated security group data
objects.
c. When finished, click Next.
8. Click Finish to complete the profile setup.
9. Click
(FileSave).
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Chapter 4
Editing an
Existing User
Group
1. In the Navigation Pane of the Access Control Administration
window, expand User Groups, then select a user group.
2. Modify the settings for the selected user group displayed in the
User Group Properties pane.
3. When you finish, click
(FileSave).
Managing Applications
About
Applications
The applications settings are for use by Life Technologies support
personnel and should not be modified.
Managing Profiles
About Profiles
A profile is a set of rules that limit user access to:
• Aspects of the GeneMapper® Software
• Data contained by the GeneMapper® Software
• Security and audit management software of the GeneMapper®
Software
You can limit the access of individual users by assigning each user
account a profile that provides the user with access to appropriate
functions. By default, the Access Control Administration Software
installs three generic security profiles (Technician, Scientist, and
Administrator) that correspond to the typical professional roles in a
laboratory environment. We recommend that you use the default
profiles until you are familiar with the software, then you can either
create custom profiles for your workplace or modify the settings of
the default profiles as necessary.
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Profile Elements
and Inheritance
Each profile consists of a set of switches called Installed Elements
that grant a user permission to perform an action on a specific aspect
of the GeneMapper® Software or one of the software utilities that
install with the software. Each Installed Element has two settings that
exist in the on ( ), off ( ), or inherited ( / ) states:
• Execute – If selected, the software allows users of the
associated profile to perform the action defined by the Installed
Element.
• OIR (Override Inherited Rights) – If selected, the Installed
Element overrides the setting it inherits from its aggregate
element.
The Installed Elements exist in a relational hierarchy where the
settings of the aggregate elements (denoted by the
and icons)
determine the default settings of the elements in the group they
define. In this way, the subordinate Installed Elements are said to
inherit the setting of the element to which they belong. Note that you
can override the inherited setting of any Installed Element by
selecting OIR ( ), then selecting or deselecting the Execute check
box. Figure 4-2 on page 80 illustrates the concept of the inheritance
hierarchy using the Installed Elements of the GeneMapper
applications group.
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Chapter 4
Example of Installed Element Inheritance
Figure 4-2 illustrates an example of inherited rights in the installed
elements for the GeneMapper® Software.
Default Rights element
GeneMapper application
element
Analysis Method action
group
READ_ANALYSIS_METHOD
installed element
Figure 4-2
Hierarchy of Installed Elements
• Default Rights element – Because Execute is not selected ( ),
the software assigns the value as the default ( ) for all Installed
Elements of the profile.
• GeneMapper application element – Because OIR is selected
( ), the Execute value ( ) overrides the inherited value ( ).
Also, the software assigns the override Execute value ( ) to all
Installed Elements that belong to the GeneMapper application
element.
• Analysis Method action group – Because OIR is selected ( ),
the Execute value ( ) overrides the inherited value ( ). Also,
because Execute is not selected ( ), the software assigns the
override Execute value ( ) to all Installed Elements of the
action group.
• READ_ANALYSIS_METHOD installed element – Because
OIR is selected ( ), the software overrides the inherited Execute
value ( ) and applies the selected Execute value ( ) for the
individual Installed Element.
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Creating a Profile
1. Start the Access Control Administration Software (see page 64).
2. Click
(FileNew Profile).
3. In the Create Profile dialog box, click Next.
4. In the Configure the New Profile screen, enter:
• A name for the new profile (≤30 characters).
• A brief description of the new profile (≤1024 characters).
5. Select Control Security Group<security group>.
IMPORTANT! Do not modify the Control Security Group
setting. The Control Security Group drop-down list assigns the
security group data object you are editing to an existing security
group. If you assign it to an unassociated security group, the
group you are editing becomes unavailable.
6. Configure the Installed Elements as desired to provide users of
the profile with the appropriate level of access to the
GeneMapper® Software and other applications.
Note: See Table 4-1 on page 84 for a description of the
functions displayed in the Installed Elements table.
a. Select ( ) or deselect ( )
Default Rights to determine
the default value for all Installed Elements in the profile.
b. For each Installed Element, select ( ) or deselect ( )
OIR and/or Execute.
c. When you finish assigning rights to the profile, click Next.
7. Click Finish to complete the profile setup.
8. Click
(FileSave).
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Chapter 4
Editing a Profile
IMPORTANT! We strongly recommend against modifying the
Admin(istrator) Profile.
1. Start the Access Control Administration Software (see page 64).
2. In the Navigation Pane of the Access Control Administration
window, expand Profiles, then select the desired profile.
3. In the Profile Properties pane, modify the Installed Elements
settings for the selected profile.
Edit the
properties of
the Installed
Elements
Select the
desired profile
4. When you finish, click
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GeneMapper® Software 5 Installation and Administration Guide
Chapter 4
About Default
Profiles and
Privileges
By default, the Access Control Administration Software installs the
following security profiles:
• Administrator – Designed for laboratory personnel responsible
for installing and maintaining the GeneMapper® Software, and
for managing user profiles and user accounts.
• Scientist – Designed for laboratory personnel responsible for
analyzing sample data using the GeneMapper® Software.
• Technician – Designed for laboratory personnel responsible for
operating the genetic analysis instrument, and for uploading
sample data to the GeneMapper® Software database.
Note: If the GeneMapper® Software is installed on a computer that
contains other Life Technologies products, the Installed Elements
table may contain elements other than those listed in Table 4-1. Most
Life Technologies products employ the Access Control
Administration Software and install their elements to the same
location.
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84
Admin Profile
Service
Action)
Scientist
Installed Elements
Application/ Action Group/
✓
✓
✓
✓
Grants the user permission(s) to…
All or none of the installed elements (determines the
default value for all installed elements)
✓
✓
All aspects of the Access Control Administration Software
✓
✓
May Run Application
✓
✓
Use the general functions of the Access Control
Administration Software, which include:
Add User to User Group
✓
✓
• Starting the Access Control Administration Software
(see page 64)
Associate User Groups with Security
Groups
✓
✓
• Editing user accounts (see page 91)
Associate User Groups with Users
✓
✓
• Changing the password policies (see page 66)
Change Password Policies
✓
✓
• Exporting/importing security settings (see page 94)
Import Security Data
✓
✓
Export Security Data
✓
✓
User Groups
✓
✓
Create
✓
✓
Modify
✓
✓
Change Control Security Group
✓
✓
Delete
✓
✓
Default Rights
Admin Tool Acc(ess)
General
GeneMapper® Software 5 Installation and Administration Guide
• Editing user groups
Create, delete, or modify user groups (
).
Chapter 4
(
User groups and privileges
Technician
Table 4-1
Admin Profile
Service
✓
✓
Create
✓
✓
Modify
✓
✓
Change Control Security Group
✓
✓
Delete
✓
✓
Applications
✓
✓
Create
✓
✓
Modify
✓
✓
Delete
✓
✓
✓
✓
Create
✓
✓
Modify
✓
✓
Change Control Security Group
✓
✓
Delete
✓
✓
Installed Elements
Application/ Action Group/
Action)
Scientist
(
User groups and privileges (Continued)
Technician
GeneMapper® Software 5 Installation and Administration Guide
Table 4-1
Profiles
Users
—
✓
✓
Create
—
—
✓
✓
Modify
—
—
✓
✓
Change Control Security Group
—
— ✓
✓
Create, delete, or modify user profiles ( ).
User profile
Note: See page 78 for more information on user profiles.
Create, delete, or modify applications (
).
Application
Note: See page 70 for more information on applications.
Create, delete, or modify user accounts (
).
User account
Note: See page 88 for more information on user
accounts.
Create, delete, or modify security groups (
).
Chapter 4
—
Security Groups
Grants the user permission(s) to…
85
Admin Profile
Service
✓
✓
All aspects of the Audit Map Configuration Software and
the Audit History Viewer Software.
✓
✓
Use the Audit History Viewer Software.
✓
✓
✓
✓
Enable and Disable Maps
✓
✓
May Run Application
✓
✓
Change Auditing State
✓
✓
✓
✓
All aspects of the Data Collection Software
✓
✓
All aspects of the GeneMapper® Software
✓
✓
Use the functions of the Database Manager including:
READ_DATABASE_INFO(rmation)
✓
✓
• Viewing (reading) database statistics (see page 151)
and project information (see page 156)
UPDATE_DATABASE_CONGIF(uration)
✓
✓
• Modifying (updating) the disk space allocated for the
GeneMapper® Software database (see page 154)
Action)
Scientist
Grants the user permission(s) to…
Installed Elements
Application/ Action Group/
Audit GUI
Audit History Viewer
May Run Application
GeneMapper® Software 5 Installation and Administration Guide
Map Configuration Tool
Foundation Data Collection
GeneMapper
Database Manager
✓
Note: See page 114 for more information on the Audit
History Viewer Software and the audit history.
Use the Audit Map Configuration Software including
enabling, disabling, and modifying audit maps.
Note: See page 107 for more information on the Audit
Map Configuration Software and the auditing system for
the GeneMapper® Software.
Chapter 4
(
User groups and privileges (Continued)
Technician
86
Table 4-1
READ_PANEL
UPDATE_PANEL
Service
Panel Manager
Action)
Admin Profile
Installed Elements
Application/ Action Group/
Scientist
(
User groups and privileges (Continued)
Technician
GeneMapper® Software 5 Installation and Administration Guide
Table 4-1
✓
✓
✓
✓
✓
✓
Grants the user permission(s) to…
Use the functions of the Panel Manager including:
• Viewing (reading) panels, bin sets, and bin definitions
• Creating/modifying (updating) panels, bin sets, and
bins
Note: For more information on panels, bin sets, bins, or
the GeneMapper Manager, see the Online Help. ‡
Size Standard
READ_SIZE_STANDARD
UPDATE_SIZE_STANDARD
✓
✓
✓
✓
Use the GeneMapper Manager to view (read) and create
or modify (update) the size standard definitions stored by
the GeneMapper® Software.
Note: For more information on size standard definitions
✓
✓
or the GeneMapper Manager, see the online help. ‡
✓
✓
READ_ANALYSIS_METHOD
✓
✓
Use the GeneMapper Manager to view (read) and create
or modify (update) the analysis methods stored by the
GeneMapper® Software.
UPDATE_ANALYSIS_METHOD
✓
✓
GeneMapper Manager, see the online help. ‡
✓
✓
READ_STUDY
✓
✓
Use the GeneMapper Manager to view (read) and create
or modify (update) the studies stored by the
GeneMapper® Software.
UPDATE_STUDY
✓
✓
Analysis Method
Study
Note: For more information on analysis methods or the
GeneMapper Manager, see the online help. ‡
87
‡ You can access the Online Help at any time by clicking
in the toolbar of the GeneMapper window, selecting Help Contents and Index, or
pressing F1. See “Related Documentation” on page 9 for more information.
Chapter 4
Note: For more information on analysis methods or the
Chapter 4
Managing User Accounts
About User
Accounts
The GeneMapper® Software user account system is similar to that
used by the Windows operating system, in which each user is assigned
a user account with a personalized password. The account provides
the user with specific privileges to operate the GeneMapper®
Software and its utilities based on the profile assigned to it. See
“Managing Profiles” on page 78 for more information on user
profiles.
User accounts not only provide direct control of user access to the
GeneMapper® Software, they also serve as the basis for auditing user
activity. When a user performs an audited activity, the auditing software
creates an audit record that includes the name of the user account
used to perform the action. In this way, the auditing software uses
user accounts to identify the users responsible for performing audited
activities. For more information about auditing or audit records, see
Chapter 5, “Managing the Auditing and Electronic Signature Systems.”
Default User
Names and
Passwords
Table 4-2 lists the default user accounts that install automatically
with the GeneMapper® Software. Both default accounts belong to the
Administrator profile and should be used to install and configure the
GeneMapper® Software, not to analyze sample data.
IMPORTANT! To ensure the security of your data, we strongly
recommend that you reassign the passwords for both default user
accounts after installing the GeneMapper® Software.
IMPORTANT! Do not misplace the password for the Administrator
account. If the administrator password is lost, the access control
system must be reset, resulting in the loss of all users and profiles
Table 4-2
Default user accounts and passwords
User Name
Password
Description
Administrator
Administrator
A user account for the person responsible for configuring and managing
the security and auditing systems of the GeneMapper® Software §
gm
password ‡
A user account for logging into the GeneMapper® Software for the first
time after installation.
‡ The password for the “gm” user account is changed during the installation of the GeneMapper® Software.
§ The “Administrator” user account cannot be deleted.
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Creating a
User Account
1. Start the Access Control Administration Software (see page 64).
2. Click
(FileNew User).
3. In the Create User dialog box, click Next.
4. In the Configure the New User screen, type a name and
description for the new user.
IMPORTANT! The user name cannot begin with a number
(1, 2, 3, …) or contain symbols (&, $, #, …).
IMPORTANT! You cannot create a user account with the same
name as a user account that has been deleted.
5. Configure the user details for the new user:
• Full Name – Type the first and last name of the new user
separated by a space character.
• Show EULA – (Optional) If selected, the software displays
the End User License Agreement (EULA) when the user
logs in.
• Status – Select the appropriate status for the user account.
Status
Definition
Active
The user can log in to and use the software.
Inactive
The user cannot log in to the software.
Suspended
The user cannot log in to the software.
Note: Depending on the Password Policy
settings (see page 78), the software assigns
the Suspended status to user accounts that
have been subject to multiple unsuccessful
login attempts.
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6. Select the control properties for the new user:
• Profile – Select the appropriate profile from the drop-down
list.
• Default Security Group – Select the appropriate security
group from the drop-down list.
• Control Security Group – Select the appropriate security
group from the drop-down list.
Do not modify the Control Security
Group setting. The Control Security Group drop-down list
assigns the security group data object you are editing to an
existing security group. If you assign it to an unassociated
security group, the group you are editing will be
unavailable.
7. Set the password for the new user:
a. Click Set Password.
b. In the Change Password dialog box, type a temporary
password in the Type and Retype fields.
c. Click OK.
Note: Because the password is configured to Pre-Expire by
default, the password set in this step is temporary. When the user
logs in for the first time, the software prompts for a new
password.
8. When finished assigning rights to the user, click Next.
9. Select the appropriate check boxes in the Associate column to
associate the user account with the appropriate user groups, then
click Next.
10. Click Finish to complete the user setup.
11. Select File Save (or click
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Editing a
User Account
1. Start the Access Control Administration Software (see page 64).
2. In the Navigation Pane of the Access Control Administration
window, expand Users, then select a user account.
3. Modify the settings for the selected user account displayed in
the User Properties pane.
4. When you finish, click
Deleting a User
Account
(FileSave).
The Access Control Administration Software allows you to delete
any user account except for the default Administrator account
(see page 88). After you delete a user account, you cannot retrieve or
restore it, nor can you create another user account of the same name.
We recommend using the delete function sparingly, and only when
you are certain to have no further need of a user account.
Note: Instead of deleting a user account, consider deactivating or
suspending the user account as explained in “Activating,
Deactivating, and Suspending User Accounts” on page 93.
To delete a user account:
1. Start the Access Control Administration Software (see page 64).
2. In the Navigation Pane of the Access Control Administration
window, expand Users, then select the user account to delete.
3. Click
(EditDelete).
4. In the Delete Identifiers dialog box, click Yes to confirm the
action.
5. Click
(FileSave).
IMPORTANT! After the user account has been deleted, you
cannot create another user account of the same name.
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Changing the
Password of an
Existing User
Account
In the event that a user forgets his or her password or you identify a
security risk, you can log in to the Access Control Administration
Software using an administrative user account to change the
password for a user account.
IMPORTANT! To ensure the security of your data, We strongly
recommend that you reassign the passwords for both default user
accounts (gm and Administrator) after installing the GeneMapper®
Software.
To change the password of an existing user account:
1. Start the Access Control Administration Software (see page 64).
2. In the Navigation Pane of the Access Control Administration
window, expand Users, then select the user account ( ) of
interest.
3. In the User Properties pane, set the new password for the user:
a. Click Set Password.
b. In the Change Password dialog box, type a password in the
Type and Retype fields.
c. Click OK.
4. Select ( ) or deselect ( ) Pre-Expire.
– When the user logs in for the first time, the software
prompts the user to enter a password of their choice.
– The user must use the password assigned in step 3.
Click
Select the desired
user account
Select or deselect
5. When finished, select File Save (or click
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Activating,
Deactivating, and
Suspending
User Accounts
The Access Control Administration Software allows you to change
the status (Active, Suspended, or Inactive) of individual user
accounts. This function is useful when:
• You want to deactivate a user account without deleting it
• A user exceeds the maximum number of failed login attempts
and you want to activate the user account manually
Note: The software can suspend a user account if the user repeatedly
enters an incorrect password (see page 66).
To reactivate, deactivate, or suspend the user account:
1. Start the Access Control Administration Software (see page 64).
2. In the Navigation Pane of the Access Control Administration
window, expand Users, then select the user account ( ).
3. In the Status menu of the User Properties pane, select the
appropriate account status for the user account.
Status
Definition
Active
The user can log in to and use the software.
Inactive
The user cannot log in to the software.
Suspended
The user cannot log in to the software.
Note: Depending on the Password Policy
settings (see page 78), the software assigns the
Suspended status to user accounts that have
been subject to multiple unsuccessful login
attempts.
Select the desired
status
Select the desired
user account
4. When finished, select File Save (or click
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in the toolbar).
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Chapter 4
Viewing the Security Report
About the
Security Report
The Access Control Administration Software can print a summary of
one or more components of the security system (user accounts,
applications, and profiles).
Note: The security report does not summarize login attempts or other
user activity. To monitor and record user activity, you must configure
the software for auditing (see Chapter 5, “Managing the Auditing and
Electronic Signature Systems,” for more information).
Example record for
a user account
Example record for
an Application
Example record for
a profile
Figure 4-3
Printing the
Security Log
Security report example records
Note: The security log is regenerated daily.
1. Start the Access Control Administration Software (see page 64).
2. If you want to print a report for a specific user account or
profile, select a user account or profile in the Navigation Pane of
the Access Control Administration window.
3. Click
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(FileReport).
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4. In the Print Access Control Identifiers dialog box, select an
option to determine the content of the report:
• Entire Access Control – Select to print a summary of all
user accounts, applications, and profiles.
• Selection only – Select to print a report of the selected user
account, application, or profile selected in the left pane of
the Access Control Administration Software window.
• Print checked objects below – Select to print a report of
all elements of a specific type (user accounts, applications,
or profiles), then select one or more of the following:
– Users – Select to print a report of all user accounts.
– Applications – Select to print a report of all
applications.
– Profiles – Select to print a report of all profiles.
5. Click Preview to view a preview of the report.
6. Review the report preview. If the preview contains all of the
information of interest, click Print. Otherwise, click Close and
go to step 4 to modify the report settings as desired.
7. Click Close to close the report preview.
8. Click Cancel to close the Print Access Control Identifiers dialog
box.
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Exporting and Importing the Security Settings
Transferring
Security Settings
Between
Computers
The Access Control Administration Software allows you to export a
summary of all security settings for backup or transfer to another
computer. The exported Access Control file is small (≤100KB) and
contains the password policies for the software and all user accounts,
applications, and profiles.
Note: The security settings for the Access Control Administration
Software are not stored as part of the GeneMapper® Software project
data and must be backed up separately as an exported file.
Exporting the
Security Settings
1. Start the Access Control Administration Software (see page 64).
2. In the Access Control Administration window, select
FileExport Database.
3. In the Save dialog box, type a file name for the exported file,
select Access Control files (.acc), then click Save to export the
security settings as an .acc file.
4. In the Export Users dialog box, click OK.
Importing the
Security Settings
IMPORTANT! Importing security settings from an .acc file
automatically replaces all existing settings.
1. Start the Access Control Administration Software (see page 64).
2. In the Access Control Administration window, select
FileImport Database.
3. In the Save dialog box, navigate to the appropriate location,
select the desired .acc file, then click Open.
4. In the Import Users dialog box, click OK.
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Chapter 5
Managing the Auditing and
Electronic Signature Systems
This chapter covers:
■ About the Data Tracking Systems . . . . . . . . . . . . . . . . . . . .
98
Section 5.1: Setting Up the Auditing System . . . . . . . . . . . . . 99
■ About the Auditing System . . . . . . . . . . . . . . . . . . . . . . . .
100
■ Audit Maps, Objects, and Attributes . . . . . . . . . . . . . . . . .
102
■ Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . .
107
■ Managing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Section 5.2: Setting Up the Electronic Signature System . . 121
■ About the Electronic Signature System . . . . . . . . . . . . . . .
122
■ About Electronic Signatures. . . . . . . . . . . . . . . . . . . . . . . .
124
■ Configuring the Electronic Signature Settings. . . . . . . . . .
125
■ Configuring the GeneMapper® Software Action Map. . . .
126
■ Viewing the Electronic Signature History . . . . . . . . . . . . .
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Chapter 5
About the Data Tracking Systems
About the Data
Tracking Systems
The GeneMapper® Software installs two software utilities that you
can use to monitor user activity and modify data stored by the
software:
• Audit Mapping Software
• Electronic Signature Software
Use of the data tracking system does not interfere with the operation
of the software and is optional. By default, both utilities install
automatically with the client installation of the GeneMapper®
Software and must be activated as described in this chapter before
they monitor data activity.
Table 5-1 summarizes the functions of the utilities.
Table 5-1
Elements of the data tracking systems
Utility
Description/Function
See Page
Audit Mapping
Software
Creates an audit trail for data objects (such as projects and
analysis methods) used by the GeneMapper® Software that
have been configured for auditing. Each audit trail lists the
changes (creation, modification, and deletion) made to the
associated data object. Depending on the configuration of the
utility, the software can track changes with or without (silent
auditing) the users knowledge.
99
Electronic Signature
Software
Restricts the creation, deletion, and modification of data stored
by the GeneMapper® Software. Similar to the auditing system,
the Electronic Signature (e-Signature) System creates a history
of user activity based on actions performed on the data objects
stored by the GeneMapper® Software. However, unlike the
auditing system, the e-Signature system requires the user to
authenticate or “sign” for actions by entering a user name
(optional) and password.
121
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Section
Section 5.1 Setting Up the Auditing System
This section covers:
■ About the Auditing System . . . . . . . . . . . . . . . . . . . . . . . .
100
■ Audit Maps, Objects, and Attributes . . . . . . . . . . . . . . . . .
102
■ Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . .
107
■ Managing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
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Chapter 5
About the Auditing System
Components of
the Auditing
System
The GeneMapper® Software uses two applications, the Security
Manager Software and the Audit Map Configuration Software, to
secure and monitor the data it contains. This chapter describes how to
use the Audit Map Configuration Software to control and monitor
use and modification of the data stored by the GeneMapper®
Software. For information about securing the GeneMapper®
Software, see Chapter 4, “Managing Database Security and User
Access.”
About the
Audit Map
Configuration
Software
The Audit Map Configuration Software monitors and records the
modification of data stored by the GeneMapper® Software. Using the
Audit Map Configuration Software, you can determine what data
elements the software monitors and how it monitors them. Use of the
Audit Map Configuration Software is optional and is inactive by
default.
Setting Up the
Auditing System
The following tasks must be performed to set up the auditing system
for the GeneMapper® Software.
Start the software (see page 101).
Can you use the default settings for the software?
(see page 102)
No
Yes
Configure the audit map settings as needed (see page 107).
Close the software.
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Maintaining the
Auditing System
Perform the tasks in the following table to maintain the auditing
system for the GeneMapper® Software.
Frequency
As needed
Tasks
• Review the audit report for the GeneMapper®
Software (see page 114).
• Backup/restore audit records (page 118).
Semi-annually
Starting the
Audit Map
Configuration
Software
Review the audit map for the GeneMapper® Software
and modify it as necessary to meet the regulation
requirements of your laboratory (see page 107).
1. Start and log in to the GeneMapper® Software (see “Logging In
to and Out of the Software” on page 59).
2. In the GeneMapper window, select ToolsAudit Manager
Setting.
3. In the AuditMapConfiguration dialog box, type a user name and
password for a user account with administrative privileges, then
click OK.
IMPORTANT! Only users that belong to the Administrator user
group (see page 83) can use the Audit Map Configuration
Software.
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Chapter 5
Audit Maps, Objects, and Attributes
About the
GeneMapper®
Software
Audit Maps
102
The Audit Map Configuration Software monitors GeneMapper®
Software activity based on the configuration of the “audit map” for
the application. An audit map is a collection of rules that define
which data elements of an application the Audit Map Configuration
Software monitors, and how it monitors them. The audit map consists
of two elements: audit map objects and object attributes. In terms of
the GeneMapper® Software, audit map objects represent the types of
data used by the software (such as bins, projects, and samples), and
object attributes describe the ways that users can modify them. For
example, the audit map object “Analysis Method” shown in
Figure 5-1 has the attributes “created, deleted, and modified” because
users can create, delete, or modify analysis methods using the
GeneMapper® Software.
GeneMapper® Software 5 Installation and Administration Guide
Chapter 5
Audit Map Objects
(AnalysisMethod selected)
Figure 5-1
Attributes for the
“AnalysisMethod” audit map object
Audit map objects and attributes
Note: Because most Life Technologies products use the Audit Map
Configuration Software to monitor data activity, the auditing
software may display additional audit map objects if the
GeneMapper® Software is installed on a computer that contains other
software.
About Audit State
Inheritance
The audit map, each audit map object, and each object attribute have
an audit state that determines which elements of the GeneMapper®
Software the Audit Map Configuration Software monitors, and how
it monitors them. By configuring the audit states of the components
of the audit map, you can customize the system to meet the
regulatory requirements of your laboratory workplace. Figure 5-2
displays the locations of the audit state controls in the software.
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Audit map setting
Selected audit
map object
(enabled)
Current attribute
state
Possible states
for the selected
attribute
Figure 5-2
States of the audit map, audit objects, and attributes
The audit states of the audit map, the audit map objects, and the
object attributes are linked in a hierarchical relationship, where the
states of the audit map and objects override those of the object
attributes. Understanding this relationship is crucial to successfully
configuring the audit map. Table 5-2 shows the result of all possible
combinations of the audit states for the audit map objects and object
attributes.
Table 5-2
Audit state inheritance matrix
State of the
Audit Object
(Enabled)
Auditing from
the Users
Perspective
Audit State of the Attribute
ON
Silent
OFF
(Yes)
ON
Silent
OFF
(No)
OFF
OFF
OFF
When a user changes an audited object attribute, the software
displays the Reason(s) For Change dialog box (see Figure 5-3). To
proceed with the action, the user must type a description of the reason
for the change and click OK. If the user clicks OK, the software
changes to the attribute and saves the information as an audit record.
The user cannot cancel the audited action.
Note: If the audit map is configured for silent auditing (
Silent),
the software does not display the Reasons for Change dialog box and
just records the action to the audit history.
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Name of the affected
audit object attribute
Former (Old) and current
(New) values of the audit
object (if applicable)
User-provided
justification for the
change
Figure 5-3
Reason(s) For Change dialog box
Note: Figure 5-3 shows the Reason(s) for Change dialog box that the
software displayed when a user changed the Orange Peak Amplitude
Threshold setting of the “Temp” analysis method from 50 to 30 RFU.
Example
Figure 5-4 displays the settings for the Allele audit object of the
GeneMapper® Software. In the example configuration, the Audit
Map Configuration Software:
• Displays the Reason(s) for Change dialog box when a user
deletes an allele call
• Passively creates a record when a user changes an allele call
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Figure 5-4
Auditing Settings for the Allele audit object
Note: If you have installed the GeneMapper® Software on a
computer that contains other Applied Biosystems software, the audit
map may display additional auditable objects and attributes. Because
most Applied Biosystems products use the Audit Map Configuration
Software for auditing purposes, the audit map may display more
objects and attributes than displayed in Figure 5-4.
IMPORTANT! When a user makes a change to an audited object, the
auditing software writes the name of the user account that was used
to make the change to the audit record. The software does not require
the user to authenticate himself or herself to make the change.
IMPORTANT! The audit information is saved when the user saves
modified documents back to the database (for example, FileSave).
If the user closes a document or object without saving it, the software
discards the audit information.
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Configuring the Audit Map
Guidelines for
Configuring the
Audit Map
Configuring the
Audit Map
Observe the following guidelines when modifying the audit map:
• All changes made to the audit map are applied immediately. The
software does not have a “save” function.
• When the audit map is changed, the software must be closed
before the changes take effect.
1. Start the Audit Map Configuration Software (see page 101).
2. In the Audit Map Configuration window, select Auditing
<audit state>.
The Auditing setting of the Audit Map Configuration Software
determines how the software audits changes to the audit map.
The Auditing setting exists in two states:
•
On – Configures the software to display the Reason(s)
for Change dialog box whenever a user modifies the audit
map.
•
Silent – Configures the software to audit all changes the
audit map passively (the software records each change but
does not prompt the user to enter a reason for the change).
3. For each audit map object displayed in the Audit Map Objects
(left) pane:
a. Decide whether to track modifications to the audit map
object (see Table 5-3 on page 110 for descriptions of all
objects).
b. Select ( ) or deselect ( ) the Enabled check box.
The state of an audit map object determines whether the
software creates audit records for the data type that the
object represents. Audit map objects can exist in two states:
•
(enabled) – Configures the software to audit all
object attributes according to their individual audit
states.
•
(disabled) – Configures the software to ignore
changes made to the audit map object.
c. Repeat steps 3a and 3b for the remaining audit map objects.
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4. For each audit map object that you enabled, perform the
following actions for each attribute in the right pane:
a. Select the audit map object.
b. Decide how you want the software to audit the associated
data type.
c. Click the cell in the State column for each attribute, then
select a state for the attribute.
The state of an audit map object determines whether the
software creates audit records for the data type that the
object represents. Audit map object attributes can exist in
three states:
•
On – The software actively creates an audit trail
for the attribute. When an attribute is set to “On” and a
user performs the action associated with the attribute,
the software displays the Reasons For Change dialog
box (see page 105). When the user clicks OK, the
software creates an audit record for the change that
includes the description of the reason for the change
entered by the user.
•
Silent – The software passively creates an audit
trail for the attribute. When an attribute is set to
“Silent” and a user performs the action associated with
the attribute, the software automatically creates an
audit record, but does not prompt the user to enter an
explanation for the change.
•
Off – The software ignores changes made to the
attribute. When an attribute is set to “Off” and a user
performs the action associated with the attribute, the
software does not create an audit record.
d. Repeat steps a and b for each audit map object you enabled
in step 3 on page 115.
5. When you finish configuring the audit map, select FileExit to
close the software.
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About the Audit
Map, Audited
Objects, and
Attributes
Table 5-3 shows the components of the audit map for the GeneMapper® Software that installs
with the Audit Map Configuration Software.
Note: If the GeneMapper® Software is installed to a computer that contains other
Applied Biosystems products, the Audit Map Objects table may contain elements other than
those listed in Table 5-3. Most Applied Biosystems products employ the Audit Map
Configuration Software and install their audit map objects to the same location.
Chapter 5
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110
Table 5-3
Elements of the audit map for the GeneMapper® Software
Allele
Analysis Method
GeneMapper® Software 5 Installation and Administration Guide
Bin
BinSet
Kit
Attribute(s)
Default
State
Definition
created
Off
Represents allele calls made by the software.
deleted
Off
modified
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the Cluster Plot Manager, the
Samples Plot, or the Genotypes Plot.
created
Off
Represents the analysis methods used to analyze project data.
deleted
Off
modified
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the Analysis Method Editor.
created
Off
deleted
Off
modified
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the Panel Manager or the
Samples or Genotypes Plots.
created
Off
Represents the bin sets used to analyze project data.
deleted
Off
When configured for auditing, the software creates a record of the
creation and/or deletion of bin sets using the Panel Manager.
BINSET
On
Represents the kits used to analyze project data.
created
Off
deleted
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the Panel Manager.
modified
Off
PANEL
On
Represents the individual bins of the bin sets used to analyze project
data.
Note: When the BINSET or PANEL attributes are activated, the
software creates audit records for edits made to bin sets or panels
that are associated with kits.
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Object
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Table 5-3
Elements of the audit map for the GeneMapper® Software (Continued)
Object
Marker
Attribute(s)
Default
State
Definition
BIN
On
Represents the markers of the bin sets used to analyze project data.
created
Off
deleted
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the Panel Manager or the
Samples or Genotypes Plots.
modified
Off
Note: When the BIN attribute is activated, the software creates
audit records for edits made to bins that are associated with markers.
Matrix
Panel
created
Off
Represents the matrices used to analyze project data.
deleted
Off
modified
Off
When configured for auditing, the software creates a record of the
associated modification(s) made using the GeneMapper Manager.
created
Off
Represents the panels used to analyze project data.
deleted
Off
MARKER
On
When configured for auditing, the software creates a record of the
associated modification(s) made from the Panel Manager or the
Samples or Genotypes Plots.
modified
Off
Note: When the MARKER attribute is activated, the software
creates audit records for edits made to markers that are associated
with panels.
Project
Off
Represents the project data object that associates analysis
parameters, settings, and sample data for projects.
created
Off
deleted
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the GeneMapper window.
modified
Off
Note: When the RUN attribute is activated, the software creates
RUN
On
audit records for edits made to the run folders within projects.
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analyzed
111
112
Table 5-3
Elements of the audit map for the GeneMapper® Software (Continued)
Object
Default
State
created
Off
deleted
Off
SAMPLE
On
Definition
Represents the run folders of the project data object that contain
samples for an analysis.
When configured for auditing, the software creates a record of the
associated modification(s) made from the GeneMapper window.
Note: When the SAMPLE attribute is activated, the software creates
audit records for edits made to the samples within run folders.
Sample
GeneMapper® Software 5 Installation and Administration Guide
ALLELE
On
Represents the sample data added to projects.
created
Off
deleted
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the Samples or Genotypes
tabs of the GeneMapper window.
modified
Off
Note: When the ALLELE attribute is activated, the software creates
OverrideGQ
Off
audit records for edits made to the alleles of individual samples.
OverrideSQ
Off
Note: When the OverrideGQ attribute is activated, the software
creates an audit record when users override the GQ PQV made by
the software.
Note: When the OverrideSQ attribute is activated, the software
creates an audit record when users override the SQ PQV made by
the software.
Size Standard
created
Off
deleted
Off
modified
Off
Represents the size standard definitions used to analyze project
data.
When configured for auditing, the software creates a record of the
associated modification(s) that are made using the GeneMapper
Manager.
Chapter 5
Run
Attribute(s)
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Table 5-3
Elements of the audit map for the GeneMapper® Software (Continued)
Object
Study
Attribute(s)
Default
State
Definition
analyzed
Off
Represents the study data object that associates projects for the
analysis of SNPlex® System data.
created
Off
deleted
Off
When configured for auditing, the software creates a record of the
associated modification(s) made from the Study Manager.
OverrideStatus
Off
Note: When the PROJECT attribute is activated, the software
PROJECT
On
creates audit records for edits made to the projects that are attached
to studies.
ProjectAdded
Off
ProjectRemoved
Off
RunAnalyzed
Off
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Chapter 5
Managing Audit Records
Overview
You can view, back up, remove, and restore the audit history records
generated by the GeneMapper® Software.
■ Viewing the Audit History. . . . . . . . . . . . . . . . . . . . (see below)
■ Backing Up, Removing, and Restoring Audit Data. . . . . . . . 118
Viewing the Audit History
About the
Audit Map Viewer
Software
The Audit Map Viewer Software is the GeneMapper® Software
utility that allows users belonging to the Administrator user group to
view historic audit data. The software provides read-only access to
audit records and data filters so that audit records can be viewed in
different formats.
Note: Only users of the Administrator user group (see page 83) can
use the Audit Map Viewer software.
Audit Details (show)
Filter tool (show)
Audit object
Attribute (selected)
Filter tool
Audit records for the
selected audit object
attribute
Details of the selected
audit record
Figure 5-5
114
Components of the Audit History Viewer window
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Starting the
Audit History
Viewer
IMPORTANT! Only users that belong to the Administrator user group
(see page 83) can use the Audit History Viewer Software.
1. Start and log in to the GeneMapper® Software (see “Logging In
to and Out of the Software” on page 59).
2. In the GeneMapper window, select ToolsAudit Manager
Report.
3. In the AuditHistoryViewer dialog box, type a user name and
password for a user account with administrative privileges, then
click OK.
Viewing Audit
History Records
1. Start the Audit History Viewer Software (see above).
2. In the Audit Objects pane, select the audit object of interest, or
click + to the left of an object to display its attributes.
3. Select the audit object attribute for which you want to display
audit records.
Audit object category
(Analysis Methods)
Audited object
(analysis method named “Temp”)
Audited object
(analysis method named “Temp”)
The following options are available:
• View the audit record details
• Filter or Sort the audit records
• Print the audit records (by selecting FilePrint Preview).
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Viewing Audit
Record Details
If you configured an audit object attribute for active auditing
(see step 4c on page 108), then you can view the details of the
associated audit records.
To view the details of the audit history records:
1. Click
(ViewDetails Panel) to show the Audit Record
Details panel.
2. Select individual records from the Audit Records list.
Sorting the
Record Data by
Column
You can sort the audit history records in the Audit Records list by
clicking one of the column headers. When the software sorts data by
a column, a triangle (▲) appears inside the header to indicate the
direction of the sort.
Selected audit history record
Sort triangle ▲
Details Panel
(show)
Audit object category
(AuditMapAUD)
Audit records for the
Temp audit object
Details of the selected
audit history record
Figure 5-6 Details of the Audit Record created for the change
shown in Figure 5-3 on page 105
Filtering the
Record Data
116
The Audit History Viewer software includes a Filter tool to help you
organize the large sets of audit history records generated through
routine use of the GeneMapper® Software. The tool allows the
software to display a subset of the total number of records based on a
set of predefined criteria.
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To filter the audit history records:
1. Make sure that the Audit Records list contains the record data
that you want to filter.
2. Click
(ViewFilter Records) to display the Filter Audit
Records pane.
3. Type search criteria in the applicable fields:
To display records containing a specific word or phrase:
a. In the Find What field, type the word or phrase.
b. Select the Name or User option button to specify the
column in which you expect the word or phrase to occur.
c. Select the appropriate options for the text search:
• Match Whole Word – The software retrieves only
records that contain words that match the specified
text exactly.
• Match Case – The software retrieves only records
that match the case (upper or lower) of the specified
text.
To display records created within a specific period of time:
a. To display records that were created before a specific date,
select Before, then click the adjacent field and select a date.
b. To display records that were created after a specific date,
select After, then click the adjacent field and select a date.
4. Click Query.
Filter records
(show)
Sort criteria
Sorted audit
history records
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Backing Up, Removing, and Restoring Audit Data
Overview
The GeneMapper® Software allows you to backup, remove, and
restore audit records from the GeneMapper database application.
Depending on the configuration of the electronic signature system
and the frequency of software use, the system can generate a
significant number of audit records in a very short period. Over time,
the amount audit data may begin to hinder the database and will need
to be removed to optimize performance.
Scheduling Backups and Data Removal
Depending on your circumstances you may need to devise a schedule
for backing up and removing audit data. As part of regular
maintenance of the GeneMapper® Software, routinely review the
amount of space occupied by audit records using the Database
Dashboard utility (see “Reviewing the Database Statistics” on
page 151). As the Audit Data tablespace approaches the maximum
limit defined in the software, you must either:
• Increase the size of the Audit Data tablespace as explained in
“Allocating Disk Space” on page 154, or
• Back up and remove the audit records as explained below.
Backing Up and
Removing
Audit Records
IMPORTANT! The GeneMapper® Software automatically backs up
the audit data with the main database application (see “Backing Up
the Database” on page 158). Therefore, the primary use of the
Backup Audit Records function described here is for transferring
audit data to a flat file for archival.
1. Start and log in to the GeneMapper® Software (see “Logging In
to and Out of the Software” on page 59).
2. In the GeneMapper window, select ToolsAudit Manager
Backup Audit Records.
3. In the Backup Audit Records dialog box:
a. Navigate to the desired location.
b. Type a name for the exported file.
c. Click Backup.
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4. In the GeneMapper window, select ToolsAudit Manager
Delete All Audit Records.
5. In the Delete All Audit Records dialog box, click Yes.
The exported GeneMapper audit file (*.aud) can now be
compressed and transferred to a storage medium for archival. If
you ever need to view the archived records, restore the records
as explained below and view them using the Audit History
Viewer Software (see “Viewing the Audit History” on page 114).
Restoring Audit
Records
1. Start and log in to the GeneMapper® Software (see “Logging In
to and Out of the Software” on page 59 for more information).
2. In the GeneMapper window, select ToolsAudit Manager
Backup Audit Records.
3. In the Backup Audit Records dialog box, navigate to and select
the desired GeneMapper audit file (*.aud).
4. Click Restore.
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Chapter 5
Section 5.2 Setting Up the Electronic
Signature System
This section covers:
■ About the Electronic Signature System . . . . . . . . . . . . . . .
122
■ About Electronic Signatures. . . . . . . . . . . . . . . . . . . . . . . .
124
■ Configuring the Electronic Signature Settings. . . . . . . . . .
125
■ Configuring the GeneMapper® Software Action Map. . . .
126
■ Viewing the Electronic Signature History . . . . . . . . . . . . .
128
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Chapter 5
About the Electronic Signature System
About the
Electronic
Signature
Software
The Electronic Signature (eSig) Software is the GeneMapper®
Software utility that allows users belonging to the Administrator
group to setup, monitor, and maintain the electronic signature system.
Guidelines for Using the Electronic Signature Software
• Only users of the Administrator user group (see page 83) can
use the software.
• Unlike the audit trail utilities, you must save changes made to
the electronic signature system before the database can
implement them.
Setting Up the
Electronic
Signature System
The following tasks must be performed to set up the electronic
signature system for the GeneMapper® Software.
Start the software (see page 123).
Can you use the default settings for the software?
(see page 126)
No
Yes
Configure the eSig settings as needed (see page 126).
Close the software.
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Maintaining the
Electronic
Signature System
Perform the tasks in the following table to maintain the electronic
signature system for the GeneMapper® Software.
Frequency
Starting the
Electronic
Signature
Administration
Software
Tasks
As needed
Review the electronic signature history for the
GeneMapper® Software (see page 128).
Semi-annually
Review the electronic signature system settings and
modify them as necessary to meet the regulation
requirements of your laboratory (see page 125).
1. Start and log in to the GeneMapper® Software (see “Logging In
to and Out of the Software” on page 59).
2. In the GeneMapper window, select Tools
Esig Administrator.
3. In the ESigAdministration dialog box, type a user name and
password for a user account with administrative privileges, then
click OK.
IMPORTANT! Only users that belong to the Administrator
user group (see page 83) can use the Electronic Signature
Administration Software.
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About Electronic Signatures
Electronic
Signatures from
the User’s
Perspective
The GeneMapper® Software has an Electronic Signature (eSig)
system that can be used to regulate the creation, deletion, and
modification of data stored by the database. When a user performs an
action (such as the detection of data) that has been configured for an
electronic signature, the GeneMapper® Software displays the
Electronic Signature Verification dialog box (see Figure 5-7). The
user must then authenticate or “sign” for the action by typing the user
name (optional) and password of his or her account.
A default warning to the
user that explains the
validation request
An additional custom
message to the user
User types his or her
user name
User types his or her
password
Figure 5-7
Electronic Signature Verification dialog box
If a user enters the correct password, the GeneMapper® Software
performs the requested action and records the electronic signature
transaction. If the password fails, the software either locks out the
user or returns the user to the screen from which the user attempted
the action, depending on the password policies.
Note: The Electronic Signature Software tracks the number of failed
login attempts.
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Configuring the Electronic Signature Settings
About the
Configuration Tab
Settings
Enabling
Electronic
Signatures
The Electronic Signature Software allows you to activate (and
deactivate) the electronic signature system using the Configuration
tab of the software. The setting is system-wide and can be customized.
1. Start the Electronic Signature Software (see page 123).
2. In the Electronic Signature window, select the Configuration
tab.
3. In the Configuration tab, select Yes to activate the Electronic
Signature System.
4. Select MethodUsernamePassword.
5. (Optional) If you want the software to require the user to enter
his or her user name as part of the electronic signature
verification, select Require UserID?
IMPORTANT! Users belonging to the Administrator user group
can reconfigure the requirement for entering a user name in the
Electronic Signature Verification dialog box.
6. (Optional) In the Description field, type a brief description of
the electronic signature settings.
Note: The software does not use the Checksum settings.
Require UserID check box
Electronic signature activation
(system-wide)
Description of the electronic
signature settings
7. Click
(FileSave) to save the settings.
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Configuring the GeneMapper® Software
Action Map
About the Action
Administration
Tab Settings
The Action Administration tab of the Electronic Signature Software
allows you to configure the electronic signature requirements for the
controlled actions (creating, deleting, and editing) of the
GeneMapper® Software applications.
About the
GeneMapper®
Software
Action Maps
Electronic signatures for the GeneMapper® Software are configured
through a set of GM_ action maps that represent the data objects of
the GeneMapper® Software. For each action map, you can enable or
disable the electronic signature requirement for the corresponding
data object and customize the challenge text that appears in the
Electronic Signature Verification dialog box (see Figure 5-7 on
page 124).
Configuring the
Action Maps
IMPORTANT! You must enable the electronic signature system as
explained on page 125 and save it before changes to the ESig Action
map can take effect.
1. If necessary, start the Electronic Signature Software (see
page 125).
2. In the ESig Administration window, select the Action
Administration tab.
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Enable Esig check box (enabled)
Selected action group
Challenge text displayed in the
Electronic Signature Verification dialog
box
Actions for the selected actions group
Definition text displayed in the
Electronic Signature Verification dialog
3. For each GM_ action group in the left pane of the Action
Administration tab:
a. Select a GM_ action group.
b. Carefully review the information displayed in the Action
Groups - Approve group box for the associated action map.
c. If you want to require electronic signatures for the actions
displayed in the Actions List, select the Enable ESig check
box.
d. In the Electronic Signature Challenge Text field, type a
short message to your users. The software displays the text
you enter here when the software prompts the user for an
electronic signature
e. Repeat steps 3a through 3d for each action map in the ESig
Action Maps pane.
4. Click
(FileSave) to save the electronic signature settings.
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Chapter 5
Viewing the Electronic Signature History
About the History
Viewer Tab
Settings
The History Viewer tab of the Electronic Signature Software allows
you to query, retrieve, and view the event history for the controlled
actions (creating, deleting, and editing) of the GeneMapper®
Software.
Note: The Electronic Signature Software does not record printing or
exporting in the event history.
Viewing Histories
1. If necessary, start the Electronic Signature Software
(see page 125).
2. In the Electronic Signature window, select the History Viewer
tab.
GM_ANALYSIS_METHOD
Action Group
DELETE_ANALYSIS_METHOD
Action
Deleted analysis method
electronic signature event
Details of the electronic
signature event
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3. In the Query Electronic Signature Events group box, enter
parameters to refine the query of electronic signature records:
Note: Enter parameters only in those fields that are relevant to
your search. The software can perform a query regardless of
whether the remaining fields and menus contain values.
• Object Name – Enter the name of an object. For example,
entering “Study 123” in the Object Name field retrieves all
events for study “Study 123.”
• Object Type – Enter the type of object (study, project, or
analysis method). For example, entering “study” in the
Object Type field retrieves events for all studies.
• User ID – Enter the name of a user account to query the
electronic signature events created by a specific user.
• Full Name – Enter the full name of a user to query the
electronic signature events created by a specific user.
• Action Group – Select an action group to view all events
for the group. For example, selecting Action Group
GM_ANALYSIS_METHOD retrieves all events created
when a user created, deleted, or modified an analysis
method.
• Action – After selecting an action group, select an action to
further refine the search by isolating it to a specific action
of the group. For example, after selecting Action Group
GM_ANALYSIS_METHOD, selecting Action
DELETE_ANALYSIS_METHOD retrieves all events
created when a user deletes an analysis method.
• Event Date/Time – Enter a date or dates to display records
created in a specific time period.
From – Restricts the search to events created after the date.
To – Restricts the search to events created before the date.
4. Click Find.
5. (Optional) In the Events list, select an event to view the details
for the electronic signature.
6. If you want to run another query, click Clear, then repeat
steps 3 through 5.
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Chapter 6
Maintaining the Software
and Database Application
This chapter covers:
■ Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . .
132
Section 6.1: Managing Study, Project, and Sample Data . . 133
■ Exporting Data Objects . . . . . . . . . . . . . . . . . . . . . . . . . . .
135
■ Exporting GeneMapper Data Objects . . . . . . . . . . . . . . . .
137
■ Exporting and Importing Reference Data . . . . . . . . . . . . .
142
Section 6.2: Managing the Database. . . . . . . . . . . . . . . . . . . 145
■ Using the Oracle® Database . . . . . . . . . . . . . . . . . . . . . . . .
146
■ About the Dashboard Software . . . . . . . . . . . . . . . . . . . . .
149
■ Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . .
151
■ Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . .
154
■ Viewing Project Information . . . . . . . . . . . . . . . . . . . . . . .
156
■ Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . .
158
■ Generating a Database Report . . . . . . . . . . . . . . . . . . . . . .
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Chapter 6
Maintenance Overview
Overview
The GeneMapper® Software requires regular maintenance to ensure:
• Optimal performance of the software and database application
• Protection against data loss (due to hardware or software failure)
• Security of the stored data (projects, analysis methods, etc.)
• Compliance with changes in regulatory requirements
This chapter explains how to maintain the GeneMapper® Software
and the associated database application. The procedures for
maintaining the security, auditing, and electronic signature systems
are referred to in Table 6-1, but are explained in Chapters 4 and 5
respectively.
Recommended
Maintenance
Schedule
Table 6-1
IMPORTANT! The maintenance schedule shown in Table 6-1
contains general recommendations and may require adjustment based
on system throughput.
Database maintenance activities
Frequency
Weekly
Tasks
• Exit the GeneMapper® Software and cycle the computer power (see page 61).
• (Optional) Back up the GeneMapper database application (see page 158).
• Review the statistics for the database (see page 151), and if necessary:
– Export unused projects and data (see page 138).
– Allocate additional disk space (see page 154).
Monthly
• Defragment the computer hard drive.
• If using the auditing system, review the audit report (see page 114).
• If using the electronic signature system, review the history (see page 128).
Semi-annually
(6 months)
• If using the auditing system, review the audit map and modify the settings as
necessary (see page 107).
• If using the electronic signature system, review the electronic signature settings
and modify them as necessary (see page 125).
As Needed
132
Export projects (see page 138), studies (see page 140), and audit records (see
page 118).
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Section 6.1 Managing Study, Project, and
Sample Data
This section covers:
■ Exporting Data Objects . . . . . . . . . . . . . . . . . . . . . . . . . . .
135
■ Exporting GeneMapper Data Objects . . . . . . . . . . . . . . . .
137
■ Exporting and Importing Reference Data . . . . . . . . . . . . .
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Chapter 6
Exports Not
Covered in this
Section
This section does not explain how to export elements of the
GeneMapper® Software user interface. The software can export most
of the tables and plots displayed during an analysis of a project or
study for:
• Transfer to a third-party application for secondary analysis
(such as a spreadsheet or a database), or
• Inclusion in a report, paper, or slide show presentation
Table 6-2 lists the elements of the user interface that can be exported
by the GeneMapper® Software. See the GeneMapper® Software Online
Help or the individual GeneMapper® Software Getting Started Guides
for information on exporting the individual tables and plots.
Table 6-2
Exportable elements of the GeneMapper® Software user interface
Interface Element
Can be exported as…
Cluster Plot
A *.jpg graphic generated from the plot(s) of the Cluster Plot Manager
Genotypes Plot
A screen capture of the Genotypes Plot dialog box
Genotypes table of
the Cluster Plot
A tab/comma-delimited text file (*.txt) containing all columns of the
Genotypes table in the Cluster Plot Manager.
Genotypes table of
the Samples Plot
A tab/comma-delimited text file (*.txt) containing all columns of the
Genotypes table in the Samples Plot
Project
A tab/comma-delimited text file (*.txt) containing columns of the
Samples/Genotypes tables for an individual project
Samples Plot
A screen capture of the Samples Plot dialog box
Sizing table of the
Samples Plot
A tab/comma-delimited text file (*.txt) containing all columns of the Sizing
table in the Samples Plot
SNP table of the
Cluster Plot
A tab/comma-delimited text file (*.txt) containing all columns of the
Genotypes table in the Cluster Plot Manager.
Study (table and
genotypes data)
A tab/comma-delimited text file (*.txt) containing specific columns of the
Samples/Genotypes tables of the projects that belong to the study
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Exporting Data Objects
Overview
The GeneMapper® Software can export most of the data objects
stored by the GeneMapper database application. Exported data
objects can be used to:
• Transfer the data object(s) to other computers running additional
copies of the GeneMapper® Software
• Store or archive the associated data object(s)
Table 6-2 lists the exportable data objects of the GeneMapper®
Software.
Table 6-3
Exportable data objects of the GeneMapper® Software
Data Object(s)
Export Format/Description
See Page
An *.xml file containing the metadata equivalents of the
settings displayed in the associated editor dialog box
when accessed from the GeneMapper Manager. For
example, an exported analysis method file contains the
metadata equivalent of all settings found in the Analysis
Method Editor dialog box.
144
Audit Records
An *.aud file containing the metadata equivalents of the
audit records generated by the GeneMapper® Software
118
Bin Set
An *.xml file containing the metadata equivalents of the
base pair ranges of all bins in the bin set
143
Panel
An *.xml file containing the metadata equivalents of the kit,
panel, and marker definitions
143
Projects
A *.ser file containing all of the analyzed data for a
project ‡
137
Security Settings
An *.acc file containing the metadata equivalents of the
security settings of the Access Control Administration
Software (user accounts, profiles, user and security
groups).
96
Study
A *.ser file containing all of the analyzed data for a study
and associated projects ‡
140
• Analysis Method
• Cluster Plot Setting
• Plot Setting
• Size Standard Definition
• SNP Set
• Report Setting
• Table Setting
‡ Exported projects and studies contain the associated supporting data used to perform the analysis (such as the
analysis method, size standard definition, and SNP set). Therefore, you do not need to export the supporting files
separately and imported again to reanalyze the project or study.
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Export Formats
136
The GeneMapper® Software supports the following export formats:
• Access Control File (*.acc) – An encoded flat file that contains
the security settings of the Access Control Administration
Software.
• Audit File (*.aud) – An encoded flat file that contains exported
audit records created by the GeneMapper® Software Audit
Management System.
• Extensible Markup Language File (*.xml) – An ASCII text
file that contains the essence of a data object used by the
GeneMapper® Software (such as analysis methods, panels and
bin sets, or size standard definition). The data stored by the file is
encoded in an extensible markup language (XML) standard used
by the GeneMapper® Software.
• Java Serialized File (*.ser) – An encoded flat file that contains
the essence of a data object used by the GeneMapper® Software.
Only projects and studies can be saved as Java serialized files
usually for the purpose of storage, backup, or transfer of the
associated data.
• Joint Photographic Experts Group File (*.jpg or *.jpeg) – A
compressed color image format recognized as an internet and
multimedia standard. Jpeg graphics can be imported by most
major word processing applications or referenced by an HTML
document for web publishing.
• Tab/Comma-Delimited Text Files (*.txt) – An ASCII text file
that contains tabular data in which each row is exported as a
single line of text and the cells are separated by the tab
(ASCII#009) or the comma (ASCII#044) characters.
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Exporting GeneMapper Data Objects
Overview
The GeneMapper® Software can export most types of data objects
(such as projects, studies, and analysis methods) stored by the
GeneMapper database application.
The exported files can be used to:
• Back up the related data objects by transferring the files to an
offline storage device (such as an external hard drive,
DVD ROM, or other storage media)
• Transfer studies or projects to other computers running
additional copies of the GeneMapper® Software
• Update the reference data (such as analysis methods, bin sets,
and panels) on other computers running additional copies of the
GeneMapper® Software
Exporting and Importing Projects
Overview
The GeneMapper® Software allows you to export projects from the
GeneMapper database application as *.ser files. The exported files
contain the analyzed sample data and analysis parameters of each
project. Depending on the configuration of the export settings, the
files can also contain the reference data (analysis methods, size
standard definitions, etc.) used to perform the analysis.
Note: Exported projects do not contain the raw data of the sample
files associated with the project. If the sample files for a project are
lost, the project cannot be used to regenerate them.
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Exporting
Projects
1. In the GeneMapper window, click
(Tools
GeneMapper Manager).
2. In the GeneMapper Manager, select the Projects tab.
3. Using the Shift and Ctrl keys, select the project(s) that you want
to export, then click Export.
4. In the Export Project dialog box:
a. Navigate to the location where you want to save the
exported project(s).
b. Configure the options for the export:
• Autoname – Configures the software to name the
exported file(s) automatically using the project(s)
name.
• Overwrite existing files – Configures the software to
overwrite existing files of the same name.
• Export reference data – Configures the software to
include the supporting data objects (such as panels,
bin sets, size standards, and SNP sets) in the exported
file.
c. If you did not select Autoname, type a name for the
exported project file in the File name field.
5. Click Save.
Note: If you did not select Autoname, the software prompts you to
name each project as it is exported. Note that at any time, you can
select Autoname to have the software automatically name the files.
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Importing
Projects
Before importing projects, make sure that the projects were exported
with the associated reference data. If not, before importing the
projects, import the associated reference data including:
• Panels and bin sets (see page 143)
• Supporting data such as analysis methods, table settings, plot
settings, cluster plot settings, matrices, size standard definitions,
SNP sets, or report settings (see page 144)
To import one or more projects:
1. In the GeneMapper window, click
(Tools
GeneMapper Manager).
2. In the GeneMapper Manager, select the Projects tab.
3. In the Import Project dialog box:
a. Navigate to the location containing the exported project(s).
b. While pressing Ctrl, select the project(s) that you want to
import.
c. Configure the Reference Data options to determine what
the software does when it attempts to import reference data
(analysis methods, size standard definitions, etc.) with the
same name as an existing data object:
• Skip – Configures the software to proceed without
importing the reference data.
• Overwrite – Configures the software to overwrite
existing reference data.
4. Click Import.
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Chapter 6
Exporting and Importing Studies
Overview
The GeneMapper® Software allows you to export studies from the
GeneMapper database application for transfer to offline storage, such
as a hard drive, a CD ROM, or other storage media.
Note: Sample files used by the projects are not exported with the
study.
Exporting a Study
1. In the GeneMapper window, select ToolsStudy Manager.
2. In the Study Manager, open the study you want to export:
a. Click
(FileOpen).
b. In the Open Study dialog box, select a study, then
click OK.
3. In the Study Manager, select FileExport.
4. In the Export Study dialog box, navigate to the location where
you want to save the exported study.
5. If necessary, select Export reference data to include the
supporting data objects (such as panels, bin sets, size standards,
and SNP sets) for the associated projects in the exported file.
6. Type a name for the exported study file.
7. Click Export.
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Chapter 6
Importing a Study
Before importing a study, make sure that the study was exported with
the reference data for the associated projects. If not, before importing
the study, import the associated reference data including:
• Panels and bin sets (see page 143)
• Supporting data such as analysis methods, table settings, plot
settings, cluster plot settings, matrices, size standard definitions,
SNP sets, or report settings (see page 144)
To import one or more studies:
1. In the GeneMapper window, select ToolsStudy Manager.
2. In the Study Manager, select FileImport.
3. In the Import Study dialog box, navigate to the location
containing the exported study.
4. Configure the Reference Data options to determine what the
software should do when it attempts to import reference data
(analysis methods, size standard definitions, etc.) with the same
name as an existing data object:
• Skip – Configures the software to proceed without
importing the reference data.
• Overwrite – Configures the software to overwrite existing
reference data.
5. Click Import.
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Chapter 6
Exporting and Importing Reference Data
Overview
The GeneMapper® Software allows you to export and import
reference data independently of studies and projects. Reference data
refers to the data objects that are used to analyze projects, but are not
altered by the process (such as analysis methods, size standard
definitions, and panels).
Table 6-4
Exportable reference data
Reference Data
• Kits
• Panels
Exported
from the…
See
Page
Panel
Manager
143
GeneMapper
Manager
144
• Bin sets
142
• Analysis methods
• Report settings
• Cluster plot
settings
• Size standard
definitions
• Matrices
• SNP sets
• Plot settings
• Table settings
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Chapter 6
Exporting Kits, Panels, and Bin Sets
Export All Kits
From the Panel Manager, you can export the panels and bin sets for
all of the kits in your current GeneMapper® Software database.
Note: This procedure allows you to export all panels and bin sets at
once. If you want to export only specific panels and bin sets, see
“Exporting Panels” on page 143 and “Exporting Bin Sets” on
page 144.
To export all kits (all panels and bin sets at once):
1. In the GeneMapper window, select ToolsPanel Manager.
2. In the Panel Manager, select FileExport All Kits to open the
Export All Kits dialog box.
3. Select a folder where you want to save the exported kits (panels
and bin sets), then click Export All Kits.
The software exports the panel and bin set *.txt files for all of
the kits to the selected folder.
Note: The names of the exported panels and bin sets correspond to
the names used in the GeneMapper® Software.
Exporting Panels
From the Panel Manager, you can export specific panels from the
GeneMapper® Software database as tab-delimited *.txt files.
Note: This procedure allows you to export specific panels. If you
want to export all panels at once, see “Export All Kits” on page 143.
To export specific panels:
1. In the GeneMapper window, select ToolsPanel Manager.
2. In the navigation pane of the Panel Manager, select a kit folder.
3. Select FileExport Panels to open the Export Panels dialog
box.
4. Select the folder where you want to save the exported panel(s),
type a file name, then click Export.
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Chapter 6
Exporting Bin
Sets
From the Panel Manager, you can export specific bin sets from the
GeneMapper® Software database as tab-delimited *.txt files.
Note: This procedure allows you to export specific bin sets. If you
want to export all bin sets at once, see “Export All Kits” on page 143.
To export specific bin sets:
1. In the GeneMapper window, select ToolsPanel Manager.
2. In the navigation pane of the Panel Manager, select a kit folder.
3. Select FileExport Bin Sets to open the Export Bin Set dialog
box.
4. Select the folder where you want to save the exported bin set(s),
type a file name, and click Export.
Exporting All Other Reference Data
Exporting
Reference Data
Using the
GeneMapper
Manager
1. In the GeneMapper window, select Tools
GeneMapper Manager.
2. In the GeneMapper Manager, select the appropriate tab
(Analysis Methods, Table Settings, Plot Settings, Cluster Plot
Settings, Matrices, Size Standards, SNP Sets, or Report
Settings).
3. Using the Shift or Ctrl keys, select one or more analysis
methods to export, then click Export.
4. In the Export Analysis Method dialog box, navigate to the
location where you want to save the exported data object
5. Type a file name for the exported file.
6. Click Export.
Note: The only file type available for exported analysis
methods files is *.xml.
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Section
Section 6.2 Managing the Database
This section covers:
■ Using the Oracle® Database . . . . . . . . . . . . . . . . . . . . . . . .
146
■ About the Dashboard Software . . . . . . . . . . . . . . . . . . . . .
149
■ Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . .
151
■ Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . .
154
■ Viewing Project Information . . . . . . . . . . . . . . . . . . . . . . .
156
■ Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . .
158
■ Generating a Database Report . . . . . . . . . . . . . . . . . . . . . .
160
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145
Chapter 6
Using the Oracle® Database
About the
Oracle® 11g
Database
The GeneMapper® Software employs a relational Oracle® 11g
Database for all of its data management needs. The database serves
as a common repository for the analyzed fragment analysis data
(projects and studies), and the supporting data objects (such as
analysis methods, size standard definitions, and SNP sets).
IMPORTANT! Do not install third-party database applications to the
computer running the GeneMapper® Software. If co-installed with
the GeneMapper® Software, third-party database applications can
produce unexpected results including loss of data and corruption of
the GeneMapper database application. Consult a certified Oracle®
database administrator before making any changes to the configuration
of the Oracle® 11g database or before using any of the Oracle®
utilities.
Database
Access
Life Technologies does not support access to the Oracle® database
through any means other than the GeneMapper® Software and
associated tools (such as the Database Dashboard, the Security
Manager Software, and Audit Map Configuration Software).
SQL Support
Life Technologies does not support the use of SQL (using SQLMGR
or SQL*Plus) to query or modify the tables of the GeneMapper
database application.
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Chapter 6
API Support
The GeneMapper® Software does not feature an application
programming interface (API) for linking the GeneMapper database
application with a LIMS. However, the software can export data from
the database application in a variety of formats, many of which can be
imported by major third-party data storage and analysis applications.
Note: The GeneMapper® Software features a command line
interface that can be useful when integrating the software into an
existing LIMS. The interface allows you to automate most of the
software operations via a scripting language or batch file so that most
maintenance and data-entry tasks can be minimized or eliminated
altogether. See Appendix B, “Operating the Software
from a Command Line,” for more information.
Database License
Use of the Oracle® 11g Database bundled with the GeneMapper®
Software is limited by the terms of an embedded license agreement
that prohibits the installation and use of additional third-party
database applications. The license included with the purchase of the
GeneMapper® Software allows access to the database for up to five
named users at any given time. If you want to accommodate more
than five named users, you can purchase either additional
GeneMapper® Software licenses, or additional Oracle®-named user
privileges and thereby, honor Life Technologies’ agreement with the
Oracle® Corporation.
IMPORTANT! Life Technologies strongly advises against using the
database for any purpose other than as a data repository for the
GeneMapper® Software.
Oracle® 11g
Database Tools
IMPORTANT! The operation and maintenance of the GeneMapper®
Software does not require the use of the Oracle® tools.
The Oracle® Corporation provides utilities for accessing and
maintaining their database products. Life Technologies does not
support the use of the Oracle® utilities and recommends against their
use by anyone other than a certified Oracle® database administrator.
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Chapter 6
Oracle®
Documentation
Additional documentation for the Oracle® 11g Database is available
from the Oracle® web site:
www.oracle.com
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Chapter 6
About the Dashboard Software
Overview
The Database Dashboard utility that installs with the full version of
the GeneMapper® Software provides tools for maintaining the
Oracle® 11g Database and for evaluating the performance of the
GeneMapper database application. This section explains how to use
the Database Dashboard to maintain the GeneMapper database
application that resides in the Oracle® 11g Database.
About the Utility
The Database Dashboard provides multiple views for evaluating the
characteristics and performance of the Oracle® 11g Database, and
several features for maintaining and optimizing the system.
The interface includes the following tabs:
• Dashboard Tab – Provides real-time information about
database performance, space utilization, and operating systems
space usage. The traffic light displays the current state of the
database.
• Report Tab – Provides a comprehensive view for
troubleshooting the Oracle® 11g Database or the GeneMapper
database application. The top of the report provides a list of
potential problems that the software has identified.
• Administration Tab–Provides a limited set of database
administration functions.
• GeneMapper Tab –Provides statistical summaries and tools for
the GeneMapper database application.
Note: If the GeneMapper® Software is installed to a computer
containing additional Life Technologies software products, the
Database Dashboard utility may contain additional tabs for the
administration of the related applications.
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Chapter 6
Features Not
Covered in This
Manual
The Database Dashboard provides several advanced features not
discussed in this manual that can be used by a certified Oracle®
Database Administrator to optimize the performance of the Oracle®
11g Database. Life Technologies strongly recommends against using
the features of the Dashboard, Report, and Administration tabs unless
you have been trained to administer Oracle® databases. Many of the
features require advanced knowledge of Oracle® systems to ensure
the integrity of the database.
Advanced features
About the
Administrator
Role
When operating the GeneMapper® Software in a multi-user
environment, Life Technologies recommends designating a single
user as an administrator for the workgroup. The administrator need
not have prior knowledge of the Oracle® 11g and should be
responsible for performing the basic database administration tasks
described in this section. By designating an administrator in a multiuser environment, you can avoid most problems caused by usage
conflicts.
Note: Ideally, Life Technologies recommends that the maintenance
of the Oracle® 11g Database be performed by a certified Oracle®
Database Administrator, preferably one with prior knowledge of the
application.
Starting the
Software
IMPORTANT! Only users that belong to the Administrator user group
(see page 83) can use the software.
1. In the desktop, select StartAll Programs
Life TechnologiesDatabase DashboardDashboard.
2. In the Enter Database Details dialog box:
a. In the DB Name field, type IFA.
b. In the Machine Name field, type the name of the computer
that contains the instance of the Oracle® database.
c. In the Port Number field, type 1521.
d. In the SYSTEM Password field, type manager.
e. Click OK.
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Chapter 6
Reviewing the Database Statistics
Overview
As part of regular maintenance, you should compute the statistics of
the GeneMapper database application regularly to ensure optimal
performance of the GeneMapper® Software. The statistics can warn
you of potential problems and help you troubleshoot existing ones.
About the
Database
Statistics
The Database Dashboard displays the statistics for the GeneMapper
database application in the Database Statistics table of the
GeneMapper Statistics tab. The values displayed in the table are
calculated from the space that is allocated for the Oracle® database
itself and the and that which is used by the GeneMapper database,
including tables, indexes, and other information.
Figure 6-1
Database Statistics table of the Dashboard Software
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Chapter 6
Columns of the Database Statistics Tab
Note: Values displayed by the Database Statistics tab are
approximate.
• Category – Lists the names of the tables used by the
GeneMapper database application to store data.
Table
Audit Data
Stores
If auditing is turned on, audit records generated
from changes made to the software
Project Data
Studies and projects, including samples and
result data
Reference
Data
Supporting data such as analysis methods,
bin sets, kits, markers, matrices, panels, size
standard definitions, SNP sets, and all other
settings
• Allocated MB – Displays the amount of disk space allocated for
the table space.
• Used (MB) – Displays the amount of disk spaced used by the
table space.
• Free (MB) – Displays the amount of disk space available to be
allocated to the total table space.
• Used (%) – Displays the used value divided by the Allocated
Size value.
• Auto Extend – Indicates whether the Oracle® database can
automatically increase the Allocated Size of the associated table.
Auto Extend
Value
152
Effect
YES
The Oracle® database can automatically increase
the allocated size of the associated table when the
Used (MB) approaches Allocated Size limit.
NO
the allocated size is not increased automatically.
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Chapter 6
Determining
Whether
Database
Maintenance is
Necessary
When reviewing the database statistics, use the following procedure
to determine if maintenance is required to optimize performance of
the GeneMapper® Software.
To determine whether the database requires maintenance:
1. Start the Database Dashboard (see page 150).
2. In the Database Dashboard window, select the GeneMapper
tab.
3. In the GeneMapper Statistics tab, select the Database Statistics
tab.
4. Review the content of the statistics table and determine whether
database maintenance is required using the following table.
Used (%)
Value
Auto
Extend
Value
> 80%
YES
Required Action
Allocate more space for data as
explained in “Allocating Disk Space”
on page 154, if:
• The Used (MB) is approaching
Maximum Allocated (MB), or
• The available Disk Space on
allocated drives is low
NO
Allocate more space for data as
explained in “Allocating Disk Space”
on page 154.
If Available Space on the computer is
insufficient for disk allocation, export
data and delete it from the
GeneMapper database application.
< 80%
n/a
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No maintenance required
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Chapter 6
Allocating Disk Space
Overview
The GeneMapper® Software allows you to allocate additional space
on the computer hard drive for use by the GeneMapper database
application. When the Used (%) value of any database table
approaches 80%, you must allocate additional disk space for the
GeneMapper database application.
Alternative to Allocating Additional Disk Space
Instead of increasing the disk space occupied by the Oracle®
database, you can export and remove existing data objects to provide
more room for new analyses. The type of data objects that you export
and remove depends on which table space is approaching its limit.
Table 6-5 lists the data objects that you can export and remove to
reduce the size of the corresponding tables of the GeneMapper
database application.
Note: See “Reviewing the Database Statistics” on page 151 to view
the table size statistics.
Table 6-5
Table spaces and related exportable data objects
Table
Approaching
Limit
Audit Data
154
Export and Remove
Audit records
See Page
118
Project Data
Projects and studies
137 / 140
Reference
Data
• Analysis methods
• Panels
• Bin sets
• Plot settings
• Cluster plot
settings
• Size standard
definitions
• Kits
• SNP sets
• Markers
• Report settings
• Matrices
• Table settings
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Chapter 6
Allocating
Additional Disk
Space
Note: The Project Data tablespace consists of three subdivisions that
can be allocated separately to maximize application performance. For
more information on refining the Project Data tablespace allocation,
see the Database Dashboard Online Help.
1. Start the Database Dashboard (see “Starting the Software” on
page 150 for more information).
2. In the Database Dashboard window, select the GeneMapper tab.
3. In the GeneMapper Statistics tab, select the Database Statistics
tab.
4. In the bottom portion of the Database Dashboard, select the
Default Allocation tab.
5. In the Default Allocation tab, select Available Drives
<select a drive>.
6. Select Table Space<select a database table>.
Note: See “Columns of the Database Statistics Tab” on
page 152 for more information on the tables used by the
GeneMapper database application.
7. In the Add disk space (MB) field, increase the additional disk
space in MB to allocate for the selected table.
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8. Click Allocate.
9. In the Alert dialog box, click Yes.
IMPORTANT! Allocating disk space cannot be undone.
10. Wait until the progress bar indicates that the allocation is
complete, then select DatabaseRefresh (or press Alt-R) to
refresh the screen and verify that the software has increased the
Allocated Size and Maximum Allocation values in the data
table.
Viewing Project Information
Viewing the
Statistics
The GeneMapper® Software can summarize the statistics for the
projects that are stored by the GeneMapper database application. The
Database Dashboard that performs the computations automatically.
To view project information:
1. Start the Database Dashboard (see page 150).
2. In the Database Dashboard window, select the GeneMapper
tab.
3. In the GeneMapper Statistics tab, select the Project Statistics
tab to display table space values and table values for each data
type.
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Chapter 6
Backing Up the Database
Note: This section presents general recommendations only. The
backup and restore strategy appropriate for your site depends on your
circumstances and your organization’s data-protection policies. An
experienced Oracle® database administrator knows the appropriate
commands to enter to back up or restore the Oracle® database.
When to Back Up
the Oracle® 11g
Database
We recommend that you back up the Oracle® 11g Database bundled
with the GeneMapper® Software onto an external storage medium
(such as 4-mm tape) at least once weekly, or more frequently
depending on software use.
Note: The security settings for the Security Manager Software are
not stored as part of the GeneMapper® Software project data and
must be backed up separately as an exported file. See “Exporting and
Importing the Security Settings” on page 96 for more information.
Performing a
Logical Backup
IMPORTANT! The GeneMapper database application can become
very large, and the amount of disk space required for export can also
be sizeable. Plan on maintaining 60 to 70% of the size of the database
for the export file.
To back up the database:
1. Start the Database Dashboard (see page 150).
2. In the Database Dashboard window, select the Administration
tab.
3. In the navigation column of the Administration tab, select
AdministrationExport Database.
4. In the Full Database Backup settings, click Browse, navigate to
the desired location, type a name for the exported file, then click
Open.
5. Click Export and wait for the software to complete the operation.
The software displays the progress of the export operation in the Log
Viewer field.
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Chapter 6
Restoring the
Database
After exporting the database tables, you can import the resulting
*.dmp file using the Import utility of the Database Dashboard.
To restore the database from an exported file:
1. Start the Database Dashboard (see page 150).
2. In the Database Dashboard window, select the Administration
tab.
3. In the navigation column of the Administration tab, select
AdministrationImport Database.
4. In the Full Database Restore settings, click Browse, navigate to
the desired location, select the file, then click Open.
5. Click Import.
Wait for the Database Dashboard to complete the operation. The
software displays the progress of the export operation in the Log
Viewer field.
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Chapter 6
Generating a Database Report
About the
Report Tab
Distributing the
Report
The Report tab displays a comprehensive report that characterizes
nearly all aspects of the Oracle® database and the resident
applications. Advanced users with prior knowledge of Oracle®
databases can use the information displayed by the report to assess
and optimize database and application performance. In the event of a
malfunction, the report can provide database error information which
can be used to troubleshoot the problem.
1. In the Database Dashboard window, select the Report tab.
2. In the Report tab, to:
Print the report, click Print.
Save the report as an HTML or tab-delimited text file:
a. Click Save.
b. In the Save dialog box, navigate to the desired destination
directory.
c. Type a name for the exported file,
d. Select the desired file format (HTML or tab-delimited
text),
e. Click Save.
Email the report:
a. Click E-mail.
b. Type the address of a valid email account, then click OK.
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Appendix A
Troubleshooting the Installation
This appendix covers:
■ Troubleshooting Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . .
162
■ Uninstalling the Software. . . . . . . . . . . . . . . . . . . . . . . . . .
164
■ Troubleshooting Checklist . . . . . . . . . . . . . . . . . . . . . . . . .
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161
Appendix A
Troubleshooting Tasks
IMPORTANT! If you have trouble installing the GeneMapper®
Software on your computer, perform the following tasks in the order
given below.
Task
Collect the
Installation
Log File
See page
1. Collect the installation log file.
162
2. Check the Oracle® database installation.
162
3. If necessary, uninstall the software.
164
1. Go to x:\AppliedBiosystems\GeneMapper, where x is the
drive on which the GeneMapper® Software is installed.
2. Copy and save the GMInstall.log file.
You may need to send the GMInstall.log file to
Life Technologies Technical Support if the troubleshooting
procedures in this appendix do not solve the installation
problem.
Check the
Database
Installation
Oracle®
Check to see if the Oracle® database instance was installed correctly.
1. Select StartAll ProgramsAccessories
Command Prompt.
2. Type sqlplus, then press Enter.
3. Type the user name system, then press Enter.
4. Type the password manager, then press Enter.
• If a “Connected to:” message is displayed, the Oracle®
database was installed correctly. Proceed to “Uninstalling
the Software” on page 164.
• If the Oracle® database was not installed correctly,
complete Table A-1, “Troubleshooting checklist,” on
page 170, then contact Technical Support.
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Appendix A
Check the
Oracle Services
®
After installation, if you have trouble connecting to the default
database, perform the following tasks:
• Check the Oracle® Services
• Check to see if the Oracle® services are running.
IMPORTANT! Make sure that the GeneMapper® Software is closed.
1. Right-click Computer and select Manage.
2. Expand Services and Applications and select Services.
3. Scroll to OracleServicesIFA and OracleIFAListener and
check if they have started.
4. If they are not listed as “Started” under the Status column,
right-click the service name and select Start.
5. After the services have started, restart the GeneMapper®
Software.
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Appendix A
Uninstalling the Software
Uninstall
Tasks
164
To uninstall the GeneMapper® Software, perform the following
tasks:
Task
See page
1. Verify that you are logged in as a user with administrator
privileges.
165
2. If you are uninstalling an co-installation configuration of
the GeneMapper® Software, start the Data Collection
Software.
166
3. Uninstall the software.
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Appendix A
Verifying
that You Are
a User with
Administrator
Privileges
Note: Administrator privileges means you have complete and
unrestricted access to the local computer.
1. In the desktop, select StartControl Panel.
2. In the Control Panel window, double-click User Accounts.
3. In the Users tab of the User Accounts dialog box, verify that the
user account you are using belongs to the Administrators group
and to the domain with the same name as the computer name.
Example:
Belongs to the
Administrators
Domain is the same
as the computer
name
4. Click OK.
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Appendix A
Starting the
Data Collection
Services
Before you uninstall co-installation configuration of the
GeneMapper® Software, start the Data Collection services.
To start the Data Collection services:
1. Select StartAll ProgramsApplied Biosystems
Data CollectionRun <Data Collection version>, where
<Data Collection version> is one of the following:
• 3730/3730xl Data Collection v3.1
• 3130/3130xl Data Collection v3.1
After the Service Console opens, wait until all four symbols
change to green squares.
Note: If the services do not start automatically, click Start All.
2. If the Data Collection Software requires a password, a login
dialog box displays. Type the Login Name and Password, then
click OK.
Note: If you do not know the Login Name or Password, contact
the administrator.
3. Confirm that Data Service started without errors:
a. In the Service Console, right-click the square next to Data
Service and select Show Console to display the Data
Service output window.
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Appendix A
Right-click here
b. Confirm that no errors are displayed in the lower pane of
the window, then close the Data Service output window.
No errors
displayed
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Appendix A
Uninstall the
Software
This procedure removes the GeneMapper® Software and the Oracle®
Database Standard Edition.
To uninstall the GeneMapper® Software:
1. Ensure that the Data Collection software is open (see page 166).
2. Close all other applications (including the GeneMapper®
Software) and windows before proceeding with the uninstall.
Note: If you do not close the GeneMapper® Software before
proceeding with the uninstall, the uninstall will fail. The next
time you attempt to uninstall the GeneMapper® Software, the
operating system performs a disk check. If inconsistencies are
found during the disk check, you may be required to correct
issues involving some GeneMapper® Software files.
3. Select StartControl Panel.
4. Double-click Add or Remove Programs.
Note: If you receive the message stating that you need
administrator rights or privileges, log off of the computer, then
log on again as a user with administrator privileges.
5. Select the GeneMapper® Software.
6. Click Change/Remove. The InstallShield Wizard starts up.
7. In the Welcome window, select Remove, then click Next.
8. At the prompt, click OK to confirm the uninstall.
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Appendix A
9. If you are uninstalling an instrument configuration, the message
below appears. Be sure Data Collection services is open, then
click OK to start the uninstall.
10. When the Maintenance Complete window appears, finish the
uninstallation process:
IMPORTANT! If you are upgrading an instrument configuration,
stop the Data Collection services before restarting your
computer by clicking Stop All in the Service Console for the
Data Collection Software:
Stop All
a. Select Yes, I want to restart my computer now.
b. Click Finish.
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Appendix A
Troubleshooting Checklist
IMPORTANT! Complete the Troubleshooting Checklist before
contacting Life Technologies Technical Support for assistance.
Table A-1
Troubleshooting checklist
Check
Information for Technical Support
Summarize the problem:
Have you been able to repeat the problem?
If yes, list the steps that you perform:
1.
2.
3.
4.
5.
6.
7.
Life Technologies personnel that you have contacted:
❏
❏
❏
❏
❏
❏
Field Applications Specialist
Field Service Engineer
Technical Support
Sales Representative
Order Administration
Other
Computer specifications:
• Operating system:
• Version:
• Processor
• Memory
• Hard disk space:
• Hard disk configuration:
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Appendix A
Table A-1
Troubleshooting checklist (Continued)
Check
Information for Technical Support
Software installed:
❏
❏
❏
❏
Data Collection Software version:
Status of Data Collection services:
GeneMapper® Software version:
Other Life Technologies software:
Computer login information:
• User privileges:
• Local or networked domain:
Software configuration installed:
❏ Instrument
❏ Stand-alone
❏ Client
Instrument and instrument computer information:
• Model:
• Data Collection Software version:
• Status of Data Collection services:
• Other Life Technologies software:
• Capillary length:
• Capillary lot number:
• Run module:
• Dye set:
Chemistry kit or reagent, with version number:
Be prepared to send to Technical Support:
• Installation log file (page 162)
• Exported panels
• Exported bins
• Exported size standard definition
• Exported analysis method
• Sample (.fsa) files
• GeneMapper_log.txt
• PanelImportLog.txt
• Printed results
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Appendix A
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Appendix B
Operating the Software
from a Command Line
This appendix covers:
■ Operating the Software from a Command Line . . . . . . . . .
174
■ Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
179
■ Command Line Arguments . . . . . . . . . . . . . . . . . . . . . . . .
183
GeneMapper® Software 5 Installation and Administration Guide
173
Appendix B
Operating the Software from a Command Line
Overview
This appendix explains how to analyze, import, and export data from
the command line interface of the GeneMapper® Software.
IMPORTANT! Life Technologies supports the use of the command
line interface only as it is explained in this manual.
Note: If you are unfamiliar with Microsoft DOS, Life Technologies
recommends running the application from the user interface.
About the
Interface
Command Syntax
The primary advantage of the GeneMapper® Software command line
interface is that it can automate most software operations without
using the graphic user interface. If incorporated as part of a batch file
or a scripted sequence, the commands can eliminate most of the
repetitive, data-entry tasks associated with project analysis. Use of
the command line interface is intended for advanced users (such as
systems administrators, bioinformaticians, and network
administrators) who choose to operate the application using a
scripting language.
Commands are issued to the GeneMapper® Software command line
interface via the MS DOS shell of the Windows operating system.
The basic formula for all commands is as follows:
<GeneMapper.exe> -commandline <arguments>
where:
• <GeneMapper.exe> is the path and filename of the executable
file for the GeneMapper® Software.
• -commandline is the argument that placed the software into
command line mode.
• <arguments> is the series of arguments that specify the
operation(s) to be performed.
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Appendix B
Creating a Batch
File to Run the
GeneMapper®
Software
This section explains how to use the command line interface of the
GeneMapper® Software by creating a common batch file for the
Windows® operating system. The use of batch files is a convenient
method to author and submit command line commands to the
GeneMapper® Software; however, use of the command line interface
is not limited to the method demonstrated here.
To create the batch file:
1. In the desktop, open the Windows Notepad accessory
(StartAll Programs Accessories Notepad).
2. In the Notepad window, type @ECHO OFF to instruct the
operating system to hide the batch file commands as they are
executed.
Note: If you want the operating system to display each
command in the MD DOS prompt as it is executed, replace
@ECHO OFF with @ECHO ON. The @ECHO ON command
can be useful when troubleshooting batch file errors. If the
software encounters an error when executing the commands in
the batch file, you can review the contents of the batch file to
identify the offending command.
3. Press Enter to create a new line.
4. In the Notepad window, type the following:
@echo off
“GeneMapper” -commandline -option h -username “user” -password
“password” -project “project”
where:
• GeneMapper is the directory path for the GeneMapper®
Software executable (enclosed in double quotes).
• user is the name of a user account with privileges
sufficient to perform the desired functions (enclosed in
double quotes).
• password is the password of the user account (enclosed in
double quotes).
• project is the name of the project to create or analyze
(enclosed in double quotes).
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Appendix B
For example:
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gm” -password “password” –project “snpProject”
5. Following the -project argument, type any additional
arguments to instruct the GeneMapper® Software to perform the
desired functions. See “Command Line Arguments” on
page 183 for a complete list of all arguments.
IMPORTANT! Follow the guidelines below when entering
commands:
• Add arguments to the command in any order.
• Type all arguments on the same line of text (the command
cannot contain hard or soft returns)
• Enclose the user-defined component of arguments in
double quotes (for example: -project “my project”)
• Separate all arguments using a space (ASCII character 32).
6. (Optional) After typing the last argument in the command,
repeat steps 3 through 5 to enter additional commands.
Note: The operating system executes the commands in the
order that they appear in the batch file (from top to bottom).
7. (Optional) After typing the last command:
a. Press Enter to create a new line.
b. Type ECHO Batch file operation complete.
c. Press Enter to create a new line.
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Appendix B
Example batch file:
@ECHO off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gm” -password “password” –project “snpProject” analysismethod “snpAM” -sizestandard “snpSS” -panel “snpPanel”
–snpset “snpSet1” -folder “D:\populationStudy\asian D:\
populationStudy\caucasian” -ladder “D:\populationStudy\asian
ladder1.fsa ladder2.fsa” -ladder “D:\populationStudy\caucasian
ladder.fsa” -exportall “D:\populationStudy\genemapper_export.txt”
ECHO Batch file operation complete.
Note: See “Example #2: SNPlex® System Analysis” on
page 180 for an explanation of the example batch file.
8. When finished, carefully review the text of the batch file for any
errors or typos.
9. When satisfied with the content of the file, save the text as a
batch file:
a. Select FileSave.
b. In the File name field, type a name for the batch file that
terminates in the .bat file extension.
For example: mybatchfile.bat or GManalysis.bat
c. Click Save.
10. Select FileExit to close the batch file.
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Appendix B
To run the batch file, double-click the file icon and wait for the
computer to run the scripted command. While the GeneMapper®
Software executes the command(s) in the batch file, the operating
system displays a command prompt window. When the operating
system has finished processing the batch file, the command prompt
window displays Press any key to continue.
Do not close the command prompt window before
it displays “Press any key to continue.” Doing so prematurely
terminates the command(s) executed by the batch file and could
result in loss of data.
Note: Depending on the speed of your computer and the number of
commands included in your batch file, the operating system may take
several minutes to a number of hours to process the batch file.
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Appendix B
Example Commands
Example
Commands in
This Section
■ Example #1: Basic Sample File Analysis . . . . . . . . (see below)
■ Example #2: SNPlex® System Analysis . . . . . . . . . . . . . . . 180
■ Example #3: Sample File Analysis with Named Ladders . . 181
■ Example #4: Export of Project Data . . . . . . . . . . . . . . . . . . 182
Example #1: Basic Sample File Analysis
Purpose
Description
This command was written to analyze sample files that have been
configured with the appropriate analysis method, size standard,
panel, SNP set, and ladder using the Data Collection Software (the
default options can also be used to perform the analysis).
The command logs into the GeneMapper® Software using the default
user account and password (gm and password) and analyzes the
sample files located in the d:\mouseStudy\mouseTrait directory. After
the analysis, the command instructs the software to save the project
as Mouse Project.
Example File
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gm” -password “password” –project
“Mouse Project” -folder “d:\mouseStudy\mouseTrait”
ECHO Batch file operation complete.
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179
Appendix B
Example #2: SNPlex® System Analysis
Purpose
Description
This command was written to perform a SNPlex® System analysis.
This command logs into the GeneMapper® Software using the default
user account and password (gm and password) and analyzes the
sample files located in the d:\populationStudy\asian and d:\
populationStudy\caucasian directories using the snpAM analysis
method, the snpSS size standard, the snpPanel panel, and the snpSet1
SNP set. The command also instructs the software to use the
ladder1.fsa and ladder2.fsa sample files located in the d:\
populationStudy\asian directory, and the ladder.fsa sample file
located in the d:\populationStudy\caucasian directory as allelic
ladders for the analysis. Following the analysis, the command
instructs the software to save the project as SNP Project, and then to
export the Samples and Genotypes tables to the d:\populationStudy\
folder as the genemapper_export.txt file.
Example File
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gm” -password “password” –project “SNP Project”
-analysismethod “snpAM” -sizestandard “snpSS” -panel “snpPanel”
–snpset “snpSet1” -folder “d:\populationStudy\asian d:\
populationStudy\caucasian” -ladder “d:\populationStudy\
asian ladder1.fsa ladder2.fsa” -ladder “d:\populationStudy\
caucasian ladder.fsa” -exportall “d:\populationStudy\
genemapper_export.txt”
ECHO Batch file operation complete.
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Appendix B
Example #3: Sample File Analysis with Named Ladders
Purpose
Description
This command was written to analyze sample files that have been
configured with the appropriate analysis method, size standard, panel,
SNP set, and ladder using the Data Collection Software (the default
options can also be used to perform the analysis).
The command logs into the GeneMapper® Software using the default
user account and password (gm and password) and analyzes the sample
files located in the e:\dog project\dog trait. The command also
instructs the software to use the dog ladder1.fsa and dog ladder2.fsa
sample files located in the e:\dog project\dog trait directory as the
allelic ladders for the analysis. After the analysis, the command
instructs the software to save the project as Dog Project before closing
the application.
Example File
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline option h –username “gm” –password “password” –project “Dog Project”
–folder “e:\dog project\dog trait” –ladder “e:\dog project\dog
trait” “dog ladder1.fsa” “dog ladder2.fsa”
ECHO Batch file operation complete.
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Appendix B
Example #4: Export of Project Data
Purpose
Description
This command was written to export the sizing data and analyzed
electropherogram data for the sample files of an existing project.
The command logs into the GeneMapper® Software using the default
user account and password (gm and password) and exports the sizing
data and analyzed electropherogram data of the California Orange
project as the g:\orange project\size map.txt and g:\orange project\
analyzed eps.txt files.
Example File
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline option h –username “gm” –password “password” –project
“California Orange” –exportsizemap “g:\orange project\size map.txt”
-exportanalyzedeps “g:\orange project\analyzed eps.txt”
ECHO Batch file operation complete.
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Appendix B
Command Line Arguments
Conventions
This section uses the following text conventions:
• “italic text” – Italic text appearing between double
quotation marks (“”) must be substituted with custom values
when entered as part of a command.
IMPORTANT! Always enclose italic text in double quotes (“This
is an example”). The quotations allow the software to
accommodate spaces in the user-defined text.
• bold text – Bold text must be typed exactly as it appears.
• Greyed text – Grey table cells indicate the required elements
of all commands issued via the command line interface.
Commands
Table B-1 contains a summary of all parameters for the command
line interface.
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184
Table B-1
Summary of arguments for the GeneMapper® Software command line interface
Argument
Action/Definition
Usage
-analysismethod “method”
-commandline
Configures the GeneMapper® Software
to operate in command line mode.
-commandline
-deleteproject
Deletes the specified project(s).
-deleteproject “project1” “project2” …
where method is the name of the analysis
method.
where project1 and project2 are the names
of the projects to be deleted.
GeneMapper® Software 5 Installation and Administration Guide
-deletesnpset
Deletes the specified SNP sets.
-deletesnpset “snpset1” “snpset2” …
where snpset1 and snpset2 are the names of
the SNP sets to be deleted.
-exportall
-exportanalyzedeps
-exportbinoffsettable
-exportclustergenotypetable
Exports the combined contents of the
Samples and Genotypes tables of the
specified project as a tab-delimited text
file of the specified name.
-exportall “filename”
Exports the analyzed electropherogram
data for the samples of the specified
project as a tab-delimited text file of the
specified name.
-exportanalyzedeps “filename”
Exports the bin offsets for the specified
project as a tab-delimited text file of the
specified name.
-exportbinoffsettable “filename”
Exports the Genotypes table of the
Cluster Plot Manager for the specified
project as a tab-delimited text file of the
specified name.
-exportclustergenotypetable “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
where filename is the long path (file name
appended to the export directory path) of the
exported file.
where filename is the long path (file name
appended to the export directory path) of the
exported file.
where filename is the long path (file name
appended to the export directory path) of the
exported file.
Appendix B
Specifies the name of the analysis
method to use in the analysis of the
specified project.
-analysismethod
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Table B-1
Summary of arguments for the GeneMapper® Software command line interface (Continued)
Argument
-exportgenotypetable
-exportplotsampletable
-exportsampletable
-exportsizemap
-exportsnptable
-folder
Action/Definition
Usage
Exports the Genotypes table for the
specified project as a tab-delimited text
file of the specified name.
-exportgenotypetable “filename”
Exports the Samples table of the
Samples plot for the specified project
as a tab-delimited text file of the
specified name.
-exportplotsampletable “filename”
Exports the Samples table for the
specified project as a tab-delimited text
file of the specified name.
-exportsampletable “filename”
Exports the sizing data for the specified
project as a tab-delimited text file of the
specified name.
-exportsizemap “filename”
Exports the specified SNP table for the
specified project as a tab-delimited text
file of the specified name.
-exportsnptable “filename”
Specifies the names of the affected run
folders in the project:
-folder “folder1” “folder2” …
• If analyzing by project, the argument
specifies the run folders of interest in
the specified project.
where filename is the long path (file name
appended to the export directory path) of the
exported file.
where filename is the long path (file name
appended to the export directory path) of the
exported file.
where filename is the long path (file name
appended to the export directory path) of the
exported file.
where filename is the long path (file name
appended to the export directory path) of the
exported file.
where folder1 is always required. The
following folders are needed only if analyzing by
project (not used when analyzing by run).
Appendix B
• If analyzing by run, the argument
specifies the run folder of interest
where filename is the long path (file name
appended to the export directory path) of the
exported file.
185
186
Table B-1
Summary of arguments for the GeneMapper® Software command line interface (Continued)
Argument
Action/Definition
Usage
Prints a summary of the commands for
the command-line interface.
-help
-importanalysismethod
Imports the specified file as an analysis
method.
-importanalysismethod “filename”
where filename is the long path (file name
appended to the import directory path) of the
imported file.
IMPORTANT! The specified file must be formatted as an XML file that uses GeneMapperspecific syntax and contains the necessary analysis method data in the format identical to
that of an exported analysis method.
GeneMapper® Software 5 Installation and Administration Guide
-importproject
Imports the project or projects stored
by the specified file.
-importproject “filename”
where filename is the long path (file name
appended to the import directory path) of the
imported file.
IMPORTANT! The specified file must be an exported project file (*.) created by the export
function of the GeneMapper Manager.
-importsizestandard
Imports the specified file as a size
standard.
-importsizestandard “filename”
where filename is the long path (file name
appended to the import directory path) of the
imported file.
IMPORTANT! The specified file must be formatted as an XML file that uses GeneMapperspecific syntax and contains the necessary size standard data in the format identical to that
of an exported size standard.
-importsnpset
Imports the specified file as a SNP set.
-importsnpset “filename”
where filename is the long path (file name
appended to the import directory path) of the
imported file.
IMPORTANT! The specified file must be formatted as an XML file that uses GeneMapperspecific syntax and contains the necessary SNP set data in the format identical to that of an
exported SNP set.
Appendix B
-help
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Table B-1
Summary of arguments for the GeneMapper® Software command line interface (Continued)
Argument
-ladder
Action/Definition
Instructs the software to use the
specified samples as allelic ladders in
the analysis of the specified project.
Usage
-ladder “folder” “ladder1” “ladder2” …
where:
• folder is the name of the project folder that
contains the negative control samples.
• ladder1 and ladder2 … are the names of
the allelic ladder sample files separated by a
space.
-negcontrol
Instructs the software to use the
specified samples as negative controls
in the analysis of the specified project.
-negcontrol “folder” “ctrl1” “ctrl2” …
where:
• folder is the name of the project folder that
contains the negative control samples.
• ctrl1 and ctrl2 … are the names of the
negative control sample files separated by a
space.
-option
Specifies the options for the exported
data.
-option “option”;“option”;…;“option”
where option is any of the following option
letters:
• b – Attaches bin names to the exported
Genotype table
• h – Hides the user interface
-panel
-password
Specifies the name of the panel to use
in the analysis of the specified project.
-panel “panel”
Specifies the password for the user
account defined by the -username
argument.
-password “password”
where panel is the name of the panel.
where password is the password for the user
account.
Appendix B
• p “port” – Specifies the monitoring TCP/IP
port number (default is 8393)
187
188
Table B-1
Summary of arguments for the GeneMapper® Software command line interface (Continued)
Argument
Usage
Instructs the software to use the
specified samples as positive controls
in the analysis of the specified project.
-poscontrol “folder” “ctrl1” “ctrl2” …
where:
• folder is the name of the project folder that
contains the positive control samples.
• ctrl1 and ctrl2 … are the names of the
positive control sample files separated by a
space.
-project
GeneMapper® Software 5 Installation and Administration Guide
-sizestandard
-snpset
-username
Specifies the name of the project to
create or analyze.
-project “project”
Specifies the name of the size standard
to use in the analysis of the specified
project.
-sizestandard “standard”
Specifies the name of the SNP set to
use in the analysis of the specified
project.
-snpset “snpset”
Specifies the user account with which
to perform the actions of command.
-username “user”
where project is the name of project.
where standard is the name of the size
standard.
where snpset is the name of the SNP set.
where user is the name of a user account.
IMPORTANT! The user account that you use must have privileges sufficient to perform the
desired function(s).
Appendix B
-poscontrol
Action/Definition
Appendix C
Migrating Data Using the
GeneMapper® Database
Utility Wizard
When to use
Use the utility wizard to export the database from the GeneMapper®
Software installed on a Windows XP computer.
Use this procedure to export the database from a Windows XP
computer with the following GeneMapper® Software configuration:
• Stand-alone (not co-installed with Data Collection software)
• Co-installed on a 3500 Series computer (the 3500 Series Data
Collection software does not store data in a database)
IMPORTANT! This procedure exports the entire database. For
computers with a GeneMapper® Software co-installation that share
the database with the Data Collection software (3730 Series, 3130
Series, 3100, or 310 computers), follow the procedure in
Appendix D, Migrating Data Manually.
The GeneMapper® Database Utility Wizard is included on the
GeneMapper® Software v5 Full Installation DVD.
Procedure
1. Insert the Full Installation DVD.
2. In the launcher window, click Software Extras, then click
GeneMapper Database Utility Wizard.
3. In the GeneMapper Database Utility Wizard window, select
MIGRATE.
Note: The MIGRATE option only exports the database to a
.dmp file; it does not actually migrate the GeneMapper®
Software. When you perform a full installation of the software
(described on page 35), the software prompts you to import the
.dmp file.
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189
Appendix C
4. Click Next and follow the instructions in the wizard.
Note: Exporting or importing the database may take a while to
complete. You can check the progress by opening the minimized
command prompt window.
5. Click Finish.
6. Perform a full installation (page 35). The full installation
prompts you to import the .dmp file.
Other functions
The wizard also includes the following functions. These
functions are for use to export and import on the same computer.
Note: Do not use the IMPORT function to import the .dmp file
into the GeneMapper® Software on the Windows 7 computer.
When you perform a full installation of the software (described
on page 35), the software prompts you to import the .dmp file.
• EXPORT makes a copy of the database and saves it to the
folder that you specify.
Note: Exporting a database may require more disk space
than is available. You may need to export the database
temporarily to a different hard drive.
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Appendix C
• IMPORT restores the exported database to the upgraded
software. This is done automatically by the upgrade
installer during installation. However, you can use this
option to manually import the GeneMapper database.
Log File
The wizard log file is written to: <C>:\AppliedBiosystems\
logs\GeneMapper41_DB_Utility\wizard.log
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Appendix C
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Appendix D
Migrating Data Manually
When to use
Use this procedure to:
• Export GeneMapper® Software components from the database
on a Windows XP computer co-installed with 3730 Series, 3130
Series, 3100, or 310 Data Collection Software. In these
co-installation configurations, the GeneMapper® Software and
the Data Collection Software share the database.
• Import GeneMapper® Software components into the database on
a Windows 7 computer co-installed with 3730 Series, 3130
Series, 3100, or 310 Data Collection Software.
Note: For computers with a GeneMapper® Software co-installation
on a stand-alone or a 3500 Series computer, follow the procedure in
Appendix C, Migrating Data Using the GeneMapper® Database
Utility Wizard.
Export procedure
1. Export projects elements:
a. In the GeneMapper main window, select
ToolsGeneMapper Manager.
b. Select a tab:
•
•
•
•
•
•
•
•
•
Projects
Analysis Methods
Table Settings
Plot Settings
Cluster Plot Settings
Matrices
Size Standards
SNP Sets
Report Settings
c. Select the object(s) you want to export. Press and hold
Shift or Ctrl to select multiple objects.
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193
Appendix D
d. Click Export.
e. Repeat for all remaining tabs.
2. Export projects elements:
a. In the GeneMapper main window, select
ToolsGeneMapper Manager.
b. Select a tab:
•
•
•
•
•
•
•
•
•
Projects
Analysis Methods
Table Settings
Plot Settings
Cluster Plot Settings
Matrices
Size Standards
SNP Sets
Report Settings
c. Select the object(s) you want to export. Press and hold
Shift or Ctrl to select multiple objects.
d. Click Export.
e. Repeat for all remaining tabs.
3. Export studies:
a. In the GeneMapper main window, select ToolsStudy
Manager.
b. Select FileManage Study.
c. Select the studies, then click Export.
4. Export security settings:
a. In the GeneMapper main window, select
ToolsSecurity Manager.
b. In the Access Control Administration window, select
FileExport Database.
c. In the Save dialog box, type a file name for the exported
file, select Access Control files (.acc), then click Save to
export the security settings as an .acc file.
d. In the Export Users dialog box, click OK.
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Appendix D
5. Export audit records:
a. In the GeneMapper main window, select
ToolsAudit ManagerBackup Audit Records.
b. In the Save dialog box, type a file name for the exported
file, then click OK.
6. Copy all exported data to the computer on which you installed
the new version of software.
Import procedure
Import the data in the following order:
1. Security settings
2. Audit records
3. Analysis methods, Table Settings, Plot Settings, Cluster Plot
Settings, SNP Sets, Report Settings, Matrix, Kits, Panels, Bin
Sets
4. Projects
5. Studies
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Appendix D
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Glossary
ABB (Automatic
Bin Builder)
The first step in accurate allele assignment. After sample files are
collected, bins are created by the ABB based on the chosen panel
information and successive allele calls from sample file collection.
As each sample file in the collection is processed, the bin definitions
are refined to reflect the actual data.
access control list
(See security group)
Admin profile
A pre-configured profile that cannot be removed and that has execute
access to all functions. Initially associated with the “admin” user. (A
user must always have an assigned profile.)
admin security
group
A pre-configured security group that cannot be removed. This
security group has been granted all rights to all data, to provide a way
for at least one user to have “admin” access to all data.
admin user group
A pre-configured user group that cannot be removed and that is
always associated with the Admin security group.
administrator user
A pre-configured user that cannot be removed and that is always
associated with the Admin user group.
ADO
Allele Display Overflow PQV
AE
Allele Edit PQV
AFLP
Amplified Fragment Length Polymorphism. A DNA fingerprinting
technique that allows the comparison of the DNA from different
organisms. DNA fragments of varying lengths are created by
cleaving an organism’s DNA with restriction enzymes; a specific
subset of these fragments are amplified and analyzed for comparison
purposes.
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197
algorithm
A set of ordered steps for solving a problem, such as a mathematical
formula or the instructions in a program. The terms algorithm and
logic are synonymous, where both refer to a sequence of steps to
solve a problem. However, an algorithm is an expression that solves a
complex problem rather than the overall input-process-output logic
of typical business programs.
all user group
A user group that contains all users. A user cannot be disassociated
from the user group.
allele
One of two or more alternate forms of a marker or gene.
Reference alleles are all alleles or bins created in a bin set in the
GeneMapper Software. They are denoted by a red cross hatch
in
the Panel Manager.
Project alleles are all alleles detected in sample data in a project in
the GeneMapper Software. They are denoted by a blue asterisk in the
Panel Manager.
allele call
Identification of the specific allelic form of a marker.
allele-calling
Identification of alleles based on bin definitions; genotyping;
GeneMapper® Software analysis
allelic ladder
A sample of DNA containing most possible alleles for a specific
marker or set of markers. Used to create a sample file that the
GeneMapper Software can use to genotype or make allele calls on
sample data.
Within the GeneMapper Software, you select a Sample Type of
Allelic Ladder for the sample file generated using an allelic ladder.
AN
Allele Number PQV
analysis method
A collection of user-defined parameters that determine the bin set and
analysis algorithms.
analysis
parameters
A collection of user-defined settings (including analysis method, size
standard, and panel) that determine the sizing and genotyping
algorithms used by the GeneMapper Software to analyze all sample
files in a project. Also called project settings.
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association
Two identifiers combined are said to be associated. A user can be
associated with a user group. A user group associated with a security
group yields a set of data rights.
audit event
A single permanent change to one or more attributes of an object.
Includes creating a new instance of an object or deleting an exiting
one.
audit map
An object associated with an object type; used to tell the audit
component how to audit an object type.
audit object
A collection of data defined by an application. Also referred to as an
object.
audit record
The description of a single audit event.
autopanelizer
A feature that uses reference data generated by the Primer Focus kit
to quickly define new SNP markers and bin sets.
BD
Broad Peak PQV
bin
Within the GeneMapper Software, a fragment size (bp) or basepair
range and dye color that define an allele within a marker. You create
a bin for each possible allele associated with a marker.
BIN
Out of Bin Allele PQV
bin set
Within the GeneMapper Software, a collection of bins (allele
definitions), typically specific to a set of experimental conditions,
usually an instrument. Bin sets are available inside a kit.
cache
An “in memory” representation of the access control data. The
Admin Tool modifies the data in the cache. When the Admin Tool or
Admin API issues the “save” command, the data in the cache are
written to the data store.
CC
Control Concordance PQV
challenge
A term from user authentication indicating that the user is asked to
provide identification (typically by entering a password).
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199
chromosome
A long stretch of coiled strands of DNA and proteins containing
many genes. Human DNA is contained within 23 pairs of
chromosomes.
control
See “positive control” on page 203.
See “negative control” on page 202.
control security
group
The security group assigned to an Access Control administrative
identifier (user, user group, security group, profile). This security
group is used to determine access by a user to the administrative data
in the Administrative GUI and API.
data access control
The part of access control that administers access to user data.
data group
(See security group)
data rights
Properties that define the type of access a user has to a piece of data.
database
One form of offline storage.
diploid
Having two sets of chromosomes and, therefore, having two alleles
per marker or gene. Human cells (other than egg and sperm cells) are
diploid.
DP
Double Peak PQV
dye set
A set of four to five different colored dyes. A specific dye set is used
to label DNA fragments or markers in matrix standards, installation
standards, and chemistry kits.
electropherogram
A graphical representation of the intensity (y-axis) of bands produced
in a single gel lane or capillary as a function of time (x-axis).
electrophoresis
A technique used to separate molecules by using an electric field to
pass those molecules through a porous matrix.
gene
The basic unit of heredity that carries the genetic information for a
given RNA molecule or protein.
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genome
All the DNA contained in an organism or cell, including both the
chromosomes in the nucleus and the DNA in the mitochondria.
genotype
The set of allele calls for specific markers or genes within an
organism. (noun)
To determine the allele calls for specific markers or genes within an
organism. (verb)
GQ
Genotype Quality PQV
haploid
Having one set of chromosomes and, therefore, having one allele per
marker or gene. Human egg and sperm cells are haploid.
heterozygous
Having two different alleles for a specific marker or gene.
homozygous
Having two identical alleles for a specific marker or gene.
installation
standard
A collection of known genetic markers, labeled with dyes from a
specific dye set, used to test the function of a genetic analyzer.
kit
Within the GeneMapper Software, a group of panels.
LMS
Linkage Mapping Set; Life Technologies chemistry using
dinucleotide repeat microsatellite markers
locus
The chromosomal location of a genetic marker or gene.
LPH
Low Peak Height PQV
marker
A known segment of DNA that has two or more allelic forms. A
marker exists at a known chromosomal loci and can be a gene or a
non-gene. See also microsatellite and SNP.
Within the GeneMapper Software:
A microsatellite marker is defined by a name, fragment size range
(bp), dye color, and repeat length.
A SNaPshot® kit analysis marker is defined by a name and fragment
size range (bp).
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201
matrix standard
A collection of known DNA fragments, labeled with four to five
different colored dyes from a specific dye set. The matrix standard is
run on a genetic analyzer and used for spectral calibration of sample
fragments that are run on the same instrument and labeled with the
same dye set.
microsatellite
Microsatellite markers, also known as short tandem repeats (STRs),
are polymorphic DNA loci consisting of a repeated nucleotide
sequence. The repeat sequence can be from 2 to 7 base pairs long.
The number of repeat units varies within a population, thereby
creating multiple alleles for a microsatellite locus.
MNF
Matrix Not Found
NB
Narrow Bin PQV
negative control
A blank sample that contains no DNA, but all other reagents used in
the experiment. It can indicate if any contamination came from
sample preparation.
In the Sample tab of GeneMapper Software, you select a Sample
Type of Negative Control for the sample file generated from the
negative control. Additionally, in the Panel Manager you define the
negative control when creating markers.
OBA
One Basepair Allele PQV
OS
Offscale PQV
OVL
Overlap PQV
panel
A group of markers. Within the GeneMapper Software, you associate
a panel with a bin set to provide bin definitions for the markers.
phenotype
The physical manifestation of a genotype.
PHR
Peak Height Ratio PQV
polymorphism
Differences between organisms’ or individuals’ DNA. Variations of
allele calls.
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positive control
A sample that contains DNA with known alleles for specific markers.
Its purpose is to verify that the PCR amplification, electrophoresis,
and GeneMapper® Software analysis worked correctly.
In the Sample tab of GeneMapper Software, you select a Sample
Type of Positive Control for the sample file generated from the
positive control. Additionally, in the Panel Manager you define the
positive control when creating markers.
PQV
Process Component-Based Quality Values reported by data analysis
and are an aid to finding and fixing problems in sample preparation
and analysis.
primer
A single-stranded piece of DNA or RNA that anneals to a
complementary section of DNA and serves as a starting point for
chain extension by DNA polymerase.
Primer Focus® kit
An Life Technologies kit containing reagents used to create and
amplify all four possible alleles of any SNP marker. The kit allows
you to take advantage of the Auto Panel feature in the GeneMapper
Software to automatically create bins for each allele in a SNaPshot
kit analysis.
probe
A DNA or RNA fragment that has been labeled in some way (for
example, fluorescent or radioactive), then used in a molecular
hybridization assay to identify DNA or RNA sequences that are the
same or closely related to it in sequence.
profile
An identifier that gives an administrator the ability to grant or revoke
access to functions.
project
Within the GeneMapper Software, a collection of sample files and
the analysis parameters for genotyping them.
project settings
See “analysis parameters” on page 198.
project settings
Parameters set by the user to prepare a project for analysis.
reference samples
All or a subset of the actual samples. The reference samples typically
contain all of the alleles present in the sample set and are used to
create a bin for each allele within the GeneMapper® Software.
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203
rights
Properties that define whether a user has access to data or a function.
security group
An identifier that can be associated with a user group to confer a set
of data rights.
security ID
The universal identifier of the security group and the preferred name
of the column in an application table that holds the security group ID.
SFN
Sample File Normalization
SFNF
Sample File Not Found
SHP
Sharp Peak PQV
silent auditing
Automatic audit record creation (without prompting of the user).
size match editor
A window in GeneMapper® Software that allows users to examine
size-standard electropherograms, edit the identification of sizestandard peaks, and view the size-calling curve.
size standard
A collection of DNA fragments of known lengths within a range (for
example, 50 to 400 bp) all tagged with the same dye. The size
standard is co-injected into the genetic analyzer capillary with the
sample, then used to size the sample data. All Life Technologies size
standards are labeled with a red or orange dye.
SNaPshot® kit
An Life Technologies kit containing reagents used to PCR amplify
any SNP markers, using single-base-extension technology. Sample
files can then be sized and genotyped by using a SNaPshot analysis
in the GeneMapper Software.
SNaPshot® System
Multiplex Analysis
Primer extension-based chemistry for SNP validation
SNF
Size Standard Not Found
SNP
Single Nucleotide Polymorphism. A marker consisting of a single
base pair that varies, thereby creating up to four alleles of the marker.
In this document, SNP refers to SNaPshot® system markers and
SNPlex® systems
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SNPlex® System
High-throughput assay for genotyping.
SP
Split Peak PQV
SPA
Single Peak Artifact PQV
SPU
Spectral Pull-Up PQV
SQ
Sizing Quality
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Index
A
ABB (automatic bin builder), definition 197
Access Control Administration Software 64
access control list, definition 197
action maps 126
activating
auditing system 107
electronic signature system 125
user accounts 93
admin profile, definition 197
admin security group, definition 197
admin user group, definition 197
admin user, definition 197
Administrator
default user account 84
default user profile 83
administrator privileges 27
verifying 27, 165
administrator, role 150
ADO PQV column 197
Adobe Acrobat Reader 27
AE PQV column 197
algorithm, definition 198
all user group, definition 198
Allele audit map object 110
ALLELE audit map object attribute 112
allele-calling, definition 198
allelic ladders, specifying in a command line
analysis 187
allocating, disk space 154
AN PQV column 198
Analysis Method audit map object 110
analysis methods
definition 198
import via a command line 186
specifying in a command line 184
analysis methods, backing up 144
analysismethod argument 184
API support 147
applications, managing 78
Applied Biosystems 3500 series genetic
analyzers 17
arguments (command line interface)
about 183
analysismethod 184
commandline 184
deleteproject 184
deletesnpset 184
exportall 184
exportanalyzedeps 184
exportbinoffsettable 184
exportclustergenotypetable 184
exportgenotypetable 185
exportplotsampletable 185
exportsampletable 185
exportsizemap 185
exportsnptable 185
folder 185
help 186
importanalysismethod 186
importsizestandard 186
importsnpset 186
ladder 187
negcontrol 187
option 187
panel 187
password 187
poscontrol 188
project 188
sizestandard 188
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207
snpset 188
username 188
association, definition 199
assumptions for using this guide 7
Audit Data table 152
audit event, definition 199
audit map
configuring 107
Audit Map Configuration Software
about 100
global auditing setting 107
starting 101
audit map definition 199
audit map object attributes
about 109
states 108
audit map objects
about 109
states 107
Audit Map Viewer Software
about 114
starting 115
audit maps 102, 109
about 102
configuring 107
viewing the history 114
audit object attributes 102
audit object, definition 199
audit records
archiving 118
backing up 118
filtering 116
removing 118
viewing 115
audit records, definition 199
audit state inheritance 103
auditing 63, 97
auditing setting (global) 107
auditing system
about 100
maintaining 101
setup 100
Auto Extend 152
208
autoanalysis not supported 16
automatic notification 66
automating software operations 174
autopanelizer, definition 199
B
backing up
analysis methods 144
audit records 118
bin sets 144
cluster plot settings 144
database 158
kits 143
matrices 144
panels 143
plot settings 144
projects 138
report settings 144
size standards 144
SNP sets 144
studies 140
table settings 144
batch file, creating for command line
operation 175
BD PQV column 199
Bin audit map object 110
BIN audit map object attribute 111
bin offsets, export via a command line 184
BIN PQV column 199
bin sets, backing up 144
BinSet audit map object 110
BINSET audit map object attribute 110
bold text, when to use 7
C
cache, definition 199
CAUTION, description 12
CC PQV column 199
challenge, definition 199
changing, user password 92
checklist, troubleshooting 170
GeneMapper® Software 5 Installation and Administration Guide
Checksum settings 125
client configuration
installing client 50
client configuration (stand-alone)
description 48
installation tasks 48
Cluster Plot Genotypes table, export via a
command line 184
cluster plot settings, backing up 144
command line interface
about 174
arguments 183
example commands 179
hiding the user interface 187
specifying allelic ladders 187
specifying analysis methods 184
specifying negative controls 187
specifying panels 187
specifying port setting 187
specifying positive controls 188
specifying size standards 188
specifying SNP sets 188
specifying the project 188
commandline argument 184
compatibility matrix 26
computer requirements
full installation 23
verifying minimum 24
Configuration tab settings 125
configurations, new installation
instrument 36
stand-alone 33, 43
configuring
action maps 126
audit map 107
automatic notification 66
electronic signature system 125
connecting to a new host 60
control security group, definition 200
controlling access to the software 63, 97
conventions
bold text 7
for describing menu commands 7
IMPORTANTS! 8
italic text 7
Notes 8
safety 12
user attention words 8
creating
security profiles 81
user accounts 89
user profiles 81
D
DANGER, description 12
data
archiving 133, 145
export via a command line 184
data access control, definition 200
Data Collection services
starting on local computer 37
Data Collection Software
installing with locally 36
starting 37, 166
stopping 42, 169
data compatibility 26
data group, definition 200
data rights, definition 200
Data Service output window 38
Data Service, checking if started without
errors 38, 166
database
API support 147
backing up 158
SQL support 146
statistics, viewing 151
Database Dashboard software
about 149
logging into for the first time 57
database utilities
Audit Configuration Tool 100
Audit Map Viewer Software 114
Electronic Signature Software 122
database, definition 200
deactivating
auditing system 107
electronic signature system 125
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209
user accounts 93
default user name 55
deleteproject argument 184
deletesnpset argument 184
deleting, user accounts 91
destination folder, selecting 40, 44, 51
disk space, allocating 154
documentation, related 9
domain name, verifying 28, 165
DOS window, during installation 41, 47, 51
DP PQV column 200
E
editing
security profiles 82
user account 92
user accounts 91
user profiles 82
Electronic Signature Challenge Text 127
electronic signature records
about 124
viewing 128
electronic signature system
about 122
configuring 125
maintaining 123
Electronic Signature Verification dialog
box 124
electropherogram data, export via a command
line 184
enabling
auditing 107
electronic signatures 125
ergonomics, safety 14
eSig software. See electronic signature system
exportall argument 184
exportanalyzedeps argument 184
exportbinoffsettable argument 184
exportclustergenotypetable argument 184
exportgenotypetable argument 185
210
exporting
analysis methods 144
bin sets 144
cluster plot settings 144
database 158
Database Utility Wizard 189
kits 143
matrices 144
panels 143
plot settings 144
projects 138
reference data 142
report settings 144
security settings 96
size standards 144
SNP sets 144
studies 140
table settings 144
exportplotsampletable argument 185
exportsampletable argument 185
exportsizemap argument 185
exportsnptable argument 185
F
filtering
audit records 116
record data 116
folder argument 185
full installation
computer requirements 23
G
GeneMapper® Database Utility Wizard 189
GeneMapper® Software
logging out 61
registering after new installation 54
uninstalling 168
Genotypes table (Cluster Plot), export via a
command line 184
Genotypes table, export via a command
line 184
gm, default user name 55
GQ PQV column 201
GeneMapper® Software 5 Installation and Administration Guide
guidelines
Audit Map Configuration Software 107
Electronic Signature Software 122
H
hazard symbols. See safety symbols, on
instruments
help argument 186
help, online, accessing 10
history
auditing (viewing) 114
electronic signature (viewing) 128
History Viewer tab settings 128
how to use this guide 7, 12
I
importanalysismethod argument 186
importing
analysis methods (via a command
line) 186
projects 139
security settings 96
size standard definition (via a command
line) 186
SNP sets (via a command line) 186
studies 141
importsizestandard argument 186
importsnpset argument 186
inheritance, audit state 103
installation DVDs 28
installation process workflow 22
installation tasks
client configuration (stand-alone) 48
instrument configuration 36
stand-alone configuration 43
installation, troubleshooting 162
installed elements 83
installer, starting 39, 43, 50
installing software
instrument configuration 39
instrument compatibility 26
instrument configuration
description 36
installation tasks (new installation)
installing (new installation) 39
italic text, when to use 7
36
K
Kit audit map object 110
kits, backing up 143
L
ladder argument 187
license agreement, Oracle® database 18
Life Technologies
contacting 10
Technical Support 10
LIMS, linking the software using the command
line interface 174
LMS, definition 201
log file, collecting 162
log on requirements 27
logging out of the GeneMapper®
Software 59
LPH PQV column 201
M
maintaining
auditing system 100, 101
database 153
electronic signature system 123
security system 65
software and database 132
maintenance schedule 132
managing
software and database 132
user accounts 88
user profiles 78
Marker audit map object 111
MARKER audit map object attribute 111
matrices, backing up 144
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211
Matrix audit map object 111
menu commands, conventions for
describing 7
migrating data 193
migration utility. See GeneMapper® Database
Utility Wizard 189
minimum requirements for computer 24
MNF PQV column 202
monitor requirements 23
moving and lifting, safety 13
MSDSs, obtaining 10
N
NB PQV column 202
negative controls, specifying in a command line
analysis 187
negcontrol argument 187
new host, connecting to 60
new installation
instrument configuration 39
registering the software 54
O
OBA PQV column 202
OIR (Override Inherited Rights) 79
online help, accessing 10
operating system
requirements 23
Operator default user account 84
option argument 187
Oracle® database
checking installation of 162
maintenance 132
tools, use of 147
viewing statistics 151
Oracle® database license agreement 18
OS PQV column 202
OverrideGQ audit map object attribute 112
OverrideSQ audit map object attribute 112
212
OverrideStatus audit map object attribute
OVL PQV column 202
113
P
panel argument 187
Panel audit map object 111
PANEL audit map object attribute 110
panels
backing up 143
specifying in a command line
analysis 187
password argument 187
password policies
about 66
Max Login Attempts 66
Minimum Password Width 69
Password Grace Logins 68
Password kept per usage 68
Password Lifetime 68
Password Reuse Period 68
Send log message 67
Set User State 67
passwords
changing 55, 57, 92
default user accounts 88
PHR PQV column 202
plot settings, backing up 144
poscontrol argument 188
positive controls, specifying in a command line
analysis 188
Primer Focus® kit, definition 203
primer, definition 203
procedural workflow, GeneMapper®
Software 19
profile, definition 203
project argument 188
Project audit map object 111
PROJECT audit map object attribute 113
Project Data table 152
project settings, definition 203
ProjectAdded audit map object attribute 113
GeneMapper® Software 5 Installation and Administration Guide
ProjectRemoved audit map object
attribute 113
projects
backing up 138
deletion via a command line 184
importing 139
specifying in a command line
analysis 188
R
Reason(s) For Change dialog box 105
recommended maintenance schedule 132
Reference Data table 152
reference data, exporting 142
registering the GeneMapper® Software
new installation 54
registration code 54
removing
audit records 118
the GeneMapper Software 168
repetitive motion, safety 14
report settings, backing up 144
Require UserID? setting 125
requirements
log on 27
user accounts 27
verifying minimum computer 24
verifying user account 27
restoring
audit records 118
projects 139
security settings 96
studies 141
rights, definition 204
Run audit map object 112
RUN audit map object attribute 111
run folder, specifying in a command line
analysis 185
RunAnalyzed audit map object attribute 113
S
safety
before operating the instrument 13
conventions 12
ergonomic 14
moving/lifting 13
repetitive motion 14
workstation 14
Sample audit map object 112
SAMPLE audit map object attribute 112
sample data file compatibility 26
Samples table, export via a command
line 184
Scientist default user account 84
Scientist default user profile 83
scripting software operations 174
security group, definition 204
security ID, definition 204
security log 94
security profiles
creating 81
editing 82
security settings
exporting 96
importing 96
security system
about 64
maintenance 65
reporting 94
setup 65
Service Console 37, 166
setting
action maps 126
audit map object attribute states 108
audit map object states 107
electronic signature settings 125
global auditing setting 107
password policies 66
setting up
auditing system 100
electronic signature system 125
security system 65
Show EULA option 89
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213
SHP PQV column 204
signatures (electronic) enabling 125
silent auditing, definition 204
size match editor, definition 204
Size Standard audit map object 112
size standard definition, import via a command
line 186
size standards
backing up 144
specifying in a command line
analysis 188
sizestandard argument 188
Sizing table (Samples Plot), export via a
command line 185
SNaPshot® analysis, definition 204
SNF PQV column 204
SNP sets
deletion via a command line 184
import via a command line 186
specifying in a command line
analysis 188
SNP sets, backing up 144
SNPlex® system analysis, definition 205
snpset argument 188
software
Access Control Administration 64
Audit Map Configuration Software 100
Audit Map Viewer Software 114
controlling access to 64
maintenance 132
SP PQV column 205
SPA PQV column 205
SPU PQV column 205
SQ PQV column 205
SQL support 146
stand-alone configuration
description 33
installation tasks (new installation) 43
installing (new installation) 43
starting
Access Control Administration
Software 64
214
Audit Map Configuration Software 101
Audit Map Viewer Software 115
Esig Administration Software 123
studies
backing up 140
importing 141
Study audit map object 113
suspending, user accounts 93
T
table settings, backing up 144
Technical Support
contacting 10
information needed before contacting
Technician default user profile 83
training, information on 10
troubleshooting checklist 170
troubleshooting tasks 162
170
U
uninstalling the GeneMapper Software
user accounts 88
activating 93
Administrator 84
changing password 92
creating 89
deactivating 93
deleting 91
editing 91, 92
Operator 84
requirements 27
Scientist 84
status 89
suspending 93
User Accounts dialog box 27, 165
user attention words, defined 8
user guide
attention words 8
audience 7
how to use 7, 12
purpose of 7
text conventions 7
168
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user name, default 55
user privileges 84
user profiles
about 78
creating 81
default privileges 83
editing 82
username argument 188
V
verifying
administrator privileges 27, 165
computer minimum requirements 24
domain name 28, 165
user account 27
viewing
audit history 114
audit record details 116
audit records 115, 118
database statistics 151
electronic signature records 128
security log 94
W
WARNING, description 12
workflow
GeneMapper® Software 19
installation process overview
workstation safety 14
22
GeneMapper® Software 5 Installation and Administration Guide
215
Headquarters
5791 Van Allen Way | Carlsbad, CA 92008 USA
Phone +1 760 603 7200 | Toll Free in USA 800 955 6288
For support visit www.lifetechnologies.com/support
www.lifetechnologies.com
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