Thermo Fisher Scientific GeneMapper Software Guide

GeneMapper® Software Version 4.1
Installation and
Administration Guide
Getting Started
Installation
Requirements
and Software
Compatibility
Performing a
New Installation
of the
GeneMapper®
Software
Upgrading a
Previous Version
of the
GeneMapper®
Software
Managing
Database Security
and User Access
Managing the
Auditing and
Electronic
Signature
Systems
Managing the
Software and
Database
Application
GeneMapper® Software Version 4.1
Installation and
Administration Guide
Getting Started
Installation
Requirements
and Software
Compatibility
Performing a
New Installation
of the
GeneMapper®
Software
Upgrading a
Previous Version
of the
GeneMapper®
Software
Managing
Database Security
and User Access
Managing the
Auditing and
Electronic
Signature
Systems
Managing the
Software and
Database
Application
For Research Use Only. Not for use in diagnostic procedures.
Information in this document is subject to change without notice.
APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR
PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED BIOSYSTEMS 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, WHETHER OR NOT
FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
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 Applied Biosystems, 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:
Applied Biosystems, AB (Design), ABI PRISM, GeneMapper, GeneScan, LIZ, Primer Focus, and SNaPshot are registered
trademarks, and GeneScan and SNPlex are trademarks of Applied Biosystems or its affiliates in the U.S. and/or certain other
countries.
AFLP is a registered trademark of Keygene N.V.
This product includes software developed by the Apache Software Foundation (http://www.apache.org/). Copyright © 1999-2000
The Apache Software Foundation. All rights reserved.
This product includes software developed by the ExoLab Project.
JNIRegistry is Copyright © 1997 Timothy Gerard Endres, ICE Engineering, Inc., http://www.trustice.com.
Microsoft and Windows are registered trademarks of Microsoft Corporation. Windows Vista is a registered trademark of Microsoft
Corporation in the United States and/or other countries.
Oracle is a registered trademark of Oracle Corporation.
All other trademarks are the sole property of their respective owners.
© Copyright 2009, Life Technologies Corporation. All rights reserved.
Part Number 4403614 Rev. A
04/2009
GeneMapper® Software Version 4.1 Installation and Administration Guide
Contents
Preface
ix
How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . xi
How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Safety Information
xiii
Safety Conventions Used in This Document . . . . . . . . . . . . . . . . xiv
General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvi
Chapter 1
Getting Started
1
Start Here: Getting the Most Out of This Guide . . . . . . . . . . . . . . . . 2
New Features in the GeneMapper® Software Version 4.1 . . . . . . . . 4
For Applied Biosystems 3500 Series Genetic Analyzers . . . . . . . . . 5
Oracle® Database License Agreement . . . . . . . . . . . . . . . . . . . . . . . 6
GeneMapper® Software Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2
Installation Requirements
and Software Compatibility
9
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Computer Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Instrument, Software, and Data Compatibility . . . . . . . . . . . . . . . . 14
User Account Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
GeneMapper® Software Installation DVDs . . . . . . . . . . . . . . . . . . . 18
GeneMapper® Software Version 4.1 Installation and Administration Guide
iii
Contents
Chapter 3
Performing a New Installation
of the GeneMapper® Software
19
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Selecting a Configuration for a New Installation . . . . . . . . . . . . . . 21
Section 3.1: Full Installation Procedures . . . . . . . . . . . . . . . . . . . 25
Full Installation Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Instrument Configuration Procedures . . . . . . . . . . . . . . . . . . . . . . 27
Remote Autoanalysis Configuration Procedures . . . . . . . . . . . . . 33
Stand-alone Configuration Procedures . . . . . . . . . . . . . . . . . . . . . 40
Section 3.2: Client-Server Installation Procedures . . . . . . . . . . . 45
Client-Server Installation Workflow . . . . . . . . . . . . . . . . . . . . . . . . 45
Server Configuration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . 47
Client Configuration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Section 3.3: Software Login Procedures . . . . . . . . . . . . . . . . . . . 59
Registering the Software After a New Installation . . . . . . . . . . . . . 60
Logging In to the Software for the First Time
After a New Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Logging In to the Database Dashboard for the First Time . . . . . . 63
What Next? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Logging In to and Out of the Software . . . . . . . . . . . . . . . . . . . . . 65
Chapter 4
Upgrading a Previous Version
of the GeneMapper® Software
69
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Upgrade Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Upgrading from GeneMapper® Software Version 3.7 or earlier . . 72
Backing Up Your Data (Version 4.0 Only) . . . . . . . . . . . . . . . . . . . 73
Determining the Appropriate Upgrade Procedure for Your
Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Instrument Configuration Upgrade . . . . . . . . . . . . . . . . . . . . . . . . 77
Remote Autoanalysis Configuration Upgrade . . . . . . . . . . . . . . . . 80
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GeneMapper® Software Version 4.1 Installation and Administration Guide
Contents
Stand-alone Configuration Upgrade . . . . . . . . . . . . . . . . . . . . . . . 83
Client-Server Configuration Upgrade . . . . . . . . . . . . . . . . . . . . . . . 84
Upgrading the GeneMapper® Software . . . . . . . . . . . . . . . . . . . . . 85
Registering the Software After Upgrading . . . . . . . . . . . . . . . . . . . 88
Logging In to the Software for the First Time After Upgrading . . . 89
What Next After Upgrading? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Logging In to and Out of the Software . . . . . . . . . . . . . . . . . . . . . . 91
Chapter 5
Managing Database Security
and User Access
95
About GeneMapper® Software Security . . . . . . . . . . . . . . . . . . . . 96
Configuring the Password Policies . . . . . . . . . . . . . . . . . . . . . . . . 98
Managing User and Security Groups . . . . . . . . . . . . . . . . . . . . . . 102
Setting Up User and Security Groups . . . . . . . . . . . . . . . . . . 107
Managing Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Managing Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Managing User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Exporting and Importing the Security Settings . . . . . . . . . . . . . . 128
Chapter 6
Managing the Auditing and
Electronic Signature Systems
129
About the Data Tracking Systems . . . . . . . . . . . . . . . . . . . . . . . . 130
Section 6.1: Setting Up the Auditing System . . . . . . . . . . . . . . . 131
About the Auditing System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Audit Maps, Objects, and Attributes . . . . . . . . . . . . . . . . . . . . . . 134
Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Managing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Viewing the Audit History . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Backing Up, Removing, and Restoring Audit Data . . . . . . . . 149
GeneMapper® Software Version 4.1 Installation and Administration Guide
v
Contents
Section 6.2: Setting Up the Electronic Signature System . . . . 151
About the Electronic Signature System . . . . . . . . . . . . . . . . . . . . 152
About Electronic Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Configuring the Electronic Signature Settings . . . . . . . . . . . . . . 155
Configuring the GeneMapper® Software Action Map . . . . . . . . . 156
Viewing the Electronic Signature History . . . . . . . . . . . . . . . . . . 158
Chapter 7
Maintaining the Software
and Database Application
161
Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Section 7.1: Managing Study, Project, and Sample Data . . . . . 163
Exporting Data Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Exporting GeneMapper Data Objects . . . . . . . . . . . . . . . . . . . . . 167
Exporting and Importing Projects . . . . . . . . . . . . . . . . . . . . . 167
Exporting and Importing Studies . . . . . . . . . . . . . . . . . . . . . 170
Exporting and Importing Reference Data . . . . . . . . . . . . . . . . . . 172
Exporting Kits, Panels, and Bin Sets . . . . . . . . . . . . . . . . . . 173
Exporting All Other Reference Data . . . . . . . . . . . . . . . . . . . 174
Section 7.2: Managing the Database. . . . . . . . . . . . . . . . . . . . . 175
Using the Oracle® Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
About the Dashboard Software . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . . . . . . 180
Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Viewing Project Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Generating a Database Report . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Appendix A
Troubleshooting the Installation
189
Troubleshooting Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Uninstalling the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Troubleshooting Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
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GeneMapper® Software Version 4.1 Installation and Administration Guide
Contents
Appendix B
Operating the Software
from a Command Line
201
Operating the Software from a Command Line . . . . . . . . . . . . . . 202
Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Example #1: Basic Sample File Analysis . . . . . . . . . . . . . . . . 207
Example #2: SNPlex™ System Analysis . . . . . . . . . . . . . . . . 208
Example #3: Sample File Analysis with Named Ladders . . . . 209
Example #4: Export of Project Data . . . . . . . . . . . . . . . . . . . 210
Command Line Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Appendix C
Appendix D
Migrating Data Using the GeneMapper®
Database Utility Wizard
217
Software Warranty Information
221
Computer Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Limited Product Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Glossary
225
Index
235
GeneMapper® Software Version 4.1 Installation and Administration Guide
vii
Contents
viii
GeneMapper® Software Version 4.1 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 Version 4.1.
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 xi.
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 Version 4.1 Installation and Administration Guide
ix
Preface
How to Use This Guide
User Attention
Words
Two user attention words appear in Applied Biosystems 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.
x
GeneMapper® Software Version 4.1 Installation and Administration Guide
Preface
How to Obtain More Information
How to Obtain More Information
Related
Documentation
The following related documents are shipped with the software:
• GeneMapper® Software Version 4.1 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 Applied Biosystems 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 Version 4.1 Online Help – Describes
the GeneMapper Software and provides procedures for common
tasks. Access online help by pressing F1, selecting Help
Contents and Index, or clicking
in the toolbar of the
GeneMapper window.
• GeneMapper® Software Version 4.1 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 Version 4.1 Reference and
Troubleshooting Guide (PN 4403673) – Provides reference
information such as theory of operation and includes
troubleshooting information.
Portable document format (PDF) versions of this guide and the other
documents are available on the GeneMapper Software Version 4.1
Documentation CD.
Note: For additional documentation, see “How to Obtain Support”
on page xii.
GeneMapper® Software Version 4.1 Installation and Administration Guide
xi
Preface
How to Obtain Support
Obtaining
Information from
the Online Help
The GeneMapper Software features an online help system that
describes how to use each feature of the user interface. Access online
help by clicking
in the toolbar of the GeneMapper window,
selecting HelpContents and Index, or pressing F1.
Using the online help, you can:
• Search for a specific topic
• View Adobe® Acrobat® versions of all documents of the
GeneMapper Software Version 4.1 documentation set.
Send Us Your
Comments
Applied Biosystems welcomes your comments and suggestions for
improving its user documents. You can e-mail your comments to:
[email protected]
How to Obtain Support
For the latest services and support information for all locations, go to
http://www.appliedbiosystems.com, then click the link for
Support.
At the Support page, you can:
• Search through frequently asked questions (FAQs)
• Submit a question directly to Technical Support
• Order Applied Biosystems user documents, MSDSs, certificates
of analysis, and other related documents
• Download PDF documents
• Obtain information about customer training
• Download software updates and patches
In addition, the Support page provides access to worldwide telephone
and fax numbers to contact Applied Biosystems Technical Support
and Sales facilities.
xii
GeneMapper® Software Version 4.1 Installation and Administration Guide
Safety Information
This section covers:
■ Safety Conventions Used in This Document . . . . . . . . . . . . xiv
■ General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . .
xv
■ Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvi
GeneMapper® Software Version 4.1 Installation and Administration Guide
xiii
Safety Information
Safety Conventions Used in This Document
Safety Conventions Used in This Document
Safety Alert
Words
Four safety alert words appear in Applied Biosystems 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.
xiv
GeneMapper® Software Version 4.1 Installation and Administration Guide
Safety Information
General Instrument Safety
General Instrument Safety
PHYSICAL INJURY HAZARD. Use this
product only as specified in this document. Using this instrument in a
manner not specified by Applied Biosystems 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 Version 4.1 Installation and Administration Guide
xv
Safety Information
Workstation Safety
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.
xvi
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 1
Getting Started
Chapter 1
Getting Started
Chapter 2
Installation
Requirements and
Software Compatibility
This chapter covers:
■ Start Here: Getting the Most Out of This Guide . . . . . . . . . .
2
■ New Features in the GeneMapper® Software Version 4.1 . . .
4
■ For Applied Biosystems 3500 Series Genetic Analyzers. . . .
5
■ Oracle® Database License Agreement . . . . . . . . . . . . . . . . . .
6
■
GeneMapper®
Software Workflow . . . . . . . . . . . . . . . . . . . . 7
Chapter 3
Performing a
New Installation of the
GeneMapper® Software
Chapter 4
Upgrading a
Previous Version of the
GeneMapper® Software
Chapter 5
Managing
Database Security
and User Access
Chapter 6
Managing the
Auditing and Electronic
Signature Systems
Chapter 7
Maintaining the
Software and
Database Application
GeneMapper® Software Version 4.1 Installation and Administration Guide
1
Chapter 1 Getting Started
Start Here: Getting the Most Out of This Guide
Start Here: Getting the Most Out of This Guide
The GeneMapper® Software Version 4.1 Installation and
Administration Guide describes how to install the GeneMapper®
Software Version 4.1 and manage the software, database, and
auditing functions.
Installation
To get the most out of this guide, Applied Biosystems recommends
that you:
1. Read through this chapter to familiarize yourself with the:
• New features in the GeneMapper® Software Version 4.1
• 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. Be sure to follow the
appropriate procedures for your particular instrument/software
setup:
• For a new installation (no previous versions of the
GeneMapper Software are on your computer), see
Chapter 3.
• For an upgrade installation, see Chapter 4.
4. Log in to and configure the GeneMapper Software:
• For a new installation, see Chapter 3.
• For an upgrade installation, see Chapter 4.
Administration
2
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
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 1 Getting Started
Start Here: Getting the Most Out of This Guide
Maintenance
Troubleshooting
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
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 190.
2. If you continue to have problems, complete the Troubleshooting
Checklist on page 198, then contact Technical Support
(page xii).
GeneMapper® Software Version 4.1 Installation and Administration Guide
3
Chapter 1 Getting Started
New Features in the GeneMapper® Software Version 4.1
New Features in the GeneMapper® Software
Version 4.1
In addition to a number of user interface and feature improvements,
the GeneMapper Software v4.1 includes the following new features:
• Oracle® database – GeneMapper Software v4.1 uses an
Oracle® 11g 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.
GeneMapper Software v4.1 also includes enhancements to
SQL*Plus® requests.
• Autosave – In the option menu, you can now customize the
project Autosaving frequency.
• 6th dye – GeneMapper Software v4.1 allows the analysis of
6th dye data generated from the Applied Biosystems 3500 and
3500xL instrument systems.
• Data normalization – GeneMapper Software v4.1 enables size
standard normalization of data generated from the Applied
Biosystems 3500 and 3500xL instrument systems.
• Sizing quality – In the analysis method, you can now define a
linearity range. This feature is especially useful for large
fragment analysis (>1000 bp).
• Size standard – The new GeneScan™ 600 LIZ® Size Standard
and GeneScan™ 1200 LIZ® Size Standard are now installed with
GeneMapper Software v4.1.
• SNPlex – The default 3130xl analysis settings,
“SNPlex_Rules_3130” analysis method, and the
“SNPlex_48plex_3130” kit are now installed with GeneMapper
Software v4.1
The GeneMapper Software v4.1 provides:
• Continued support of security and audit features to assist with
21CFR11 (phase 1) requirements.
• Coinstallation and autoanalysis with Data Collection Software
v3.1 on the Microsoft® Windows® XP or Windows Vista®
operating systems.
4
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 1 Getting Started
For Applied Biosystems 3500 Series Genetic Analyzers
• Coinstallation and autoanalysis with 3500, 3500xL Data
Collection Software v1.0 on the Windows Vista operating
system.
GeneMapper Software v4.1 also maintains GeneMapper Software
v4.0 features such as client-server functionality, universal markers,
and marker-specific analysis.
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
• Setting up remote autoanalysis
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 Version 4.1 Installation and Administration Guide
5
Chapter 1 Getting Started
Oracle® Database License Agreement
Oracle® Database License Agreement
About the
Database
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.
Database Access
Applied Biosystems does not support access to the Oracle database
through any means other than the GeneMapper Software.
User Access
6
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 Applied Biosystems
agreement with the Oracle corporation.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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
Import/
export
Create,
import,
or edit
Apply
Cluster plot
Table settings
Plot settings
Import/
export
Samples plot
Genotypes plot
Table settings
Plot settings
Archive
Log
CD
Secondary
database
Delete
Auditing
7
Export to
*.ser, *.txt
Print
Chapter 1 Getting Started
Analysis methods
Size standards
SNP sets
Samples table
Genotypes table
Analysis methods
Size standards
SNP sets
GeneMapper Manager
GeneMapper® Software Workflow
GeneMapper® Software Version 4.1 Installation and Administration Guide
GeneMapper® Software Workflow
Chapter 1 Getting Started
GeneMapper® Software Workflow
8
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 2
Installation Requirements
and Software Compatibility
Chapter 1
Getting Started
This chapter covers:
■ Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
■ Computer Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 2
Installation
Requirements and
Software Compatibility
■ Instrument, Software, and Data Compatibility. . . . . . . . . . .
14
■ User Account Requirements. . . . . . . . . . . . . . . . . . . . . . . . .
16
■
GeneMapper®
Software Installation DVDs . . . . . . . . . . . . . 18
Chapter 3
Performing a
New Installation of the
GeneMapper® Software
Chapter 4
Upgrading a
Previous Version of the
GeneMapper® Software
Chapter 5
Managing
Database Security
and User Access
Chapter 6
Managing the
Auditing and Electronic
Signature Systems
Chapter 7
Maintaining the
Software and
Database Application
GeneMapper® Software Version 4.1 Installation and Administration Guide
9
Chapter 2 Installation Requirements and Software Compatibility
Overview
Overview
This chapter specifies the requirements for installing the
GeneMapper® Software Version 4.1.
Figure 2-1 shows an overview of the installation process. For more
information about any part of the workflow, see the specified chapter.
Chapter 2, Installation Requirements and Software Compatibility
Verify that the computer meets requirements.
Verify that you have Administrator privileges on the computer.
Is a previous version of the
GeneMapper® Software
installed on the computer?
YES
NO
Chapter 3, Performing a
New Installation of the
GeneMapper® Software
NO
Do you want to set up a
client-server network?
Perform a
full installation.
YES
Chapter 4,
Upgrading a
Previous
Version of the
GeneMapper®
Software
Perform a
client-server installation.
Register and log in to the
GeneMapper® Software.
Figure 2-1
10
Perform an
upgrade installation.
Register and log in to the
GeneMapper® Software.
Installation workflow overview
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 2 Installation Requirements and Software Compatibility
Computer Requirements
Computer Requirements
Computer
Configuration
Table 2-1 shows the computer specifications that Applied Biosystems
recommends for use with the GeneMapper Software Version 4.1.
Even though you can install the GeneMapper Software on a computer
containing the minimum supported RAM, Applied Biosystems highly
recommends using 2 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.
Note: GeneMapper Software v4.1 has not been tested on a computer
with server-type hardware or server operating systems
Table 2-1
GeneMapper® Software computer requirements
Recommended
Configuration
Component
Computer
•
Dell®
OptiPlex™
755 PLUS
Minitower, Intel Core™2
Duo Processor,
E8400/3.0 GHz
®
Monitor
Minimum Configuration ‡
Full or Server Installation
•
Dell®
OptiPlex™
755
STANDARD Minitower,
Intel® Core™2 Duo
Processor,
E4500/2.2 GHz
Client Installation
• Dell® 270 Workstation,
Intel® Pentium® 4
Processor, 2.8 GHz
• 512 MB of RAM
• 2 GB of RAM, Non-ECC,
667 MHz DDR2 2 × 1 GB
• 1 GB of RAM
• 1 × 80 GB EIDE hard
drive
• 320 GB SATA hard drive,
3.0 Gb/s and 8 MB Data
Burst Cache
• 160 GB SATA hard
drive, 3.0 Gb/s and
8 MB Data Burst Cache
• 16✕/48✕ IDE
DVD/CD-ROM Drive
• 16✕ DVD +/- RW IDE
Combo Drive
• 16✕ DVD +/- RW IDE
Combo Drive
• 10/100 NIC network
card with RWU
(internal)
• 1280 × 1024 or higher pixel resolution
• 17-inch color monitor
Operating
System
One of the following operating systems:
• Microsoft® Windows® XP Professional operating system, Service Pack 2 or 3
• Microsoft® Windows Vista® Business edition operating system, 32-bit, 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 client-server environment.
GeneMapper® Software Version 4.1 Installation and Administration Guide
11
Chapter 2 Installation Requirements and Software Compatibility
Computer Requirements
Verifying that
Your Computer
Meets the
Minimum
Requirements
For the Windows® XP operating system
1. In the desktop, right-click My Computer, then select
Properties.
2. In the General tab of the System Properties dialog box, verify
that your computer meets the minimum requirements for the
operating system, processor, and memory as shown in
“Computer Requirements” on page 11.
Operating System
(OS)
OS version
Latest Service Pack
installed
Computer model
Microprocessor
type and speed
Installed memory
12
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 2 Installation Requirements and Software Compatibility
Computer Requirements
For the Windows Vista® operating system
1. In the desktop, right-click Computer (Windows Vista), 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 11.
Operating System
(OS)
Latest Service Pack
installed
Computer model
Microprocessor
type and speed
Installed memory
GeneMapper® Software Version 4.1 Installation and Administration Guide
13
Chapter 2 Installation Requirements and Software Compatibility
Instrument, Software, and Data Compatibility
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 15.
Table 2-2
Compatibility matrix
Genetic Analysis
Instrument
Compatible Data Collection Software
and Operating System
Applied Biosystems
3500/3500xL
Genetic Analyzer
• Data Collection v1.0
• Windows Vista® Business edition,
32-bit, SP1
Sample Data
Compatibility
• Sample files
• Co-installation
• Automation
• Data Collection v1.0
• Windows® 2000, SP 2
• Data Collection v2.0
• Windows® 2000, SP 3 and 4
Applied Biosystems
3730/3730xl
DNA Analyzer
Applied Biosystems
3130/3130xl
Genetic Analyzer
14
• Sample files
• Data Collection v3.0
• Windows® XP Professional, SP 1 and 2
• Data Collection v3.1
• Windows® XP Professional, SP 2 and 3
• Windows Vista® Business edition,
32-bit, SP1
• Sample files
• Co-installation
• Automation
• Data Collection v3.0
• Windows® XP Professional, SP 1 and 2
• Sample files
• Data Collection v3.1
• Windows® XP Professional, SP 2 and 3
• Windows Vista® Business edition,
32-bit, SP1
• Sample files
• Co-installation
• Automation
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 2 Installation Requirements and Software Compatibility
Instrument, Software, and Data Compatibility
Table 2-2
Compatibility matrix (continued)
Genetic Analysis
Instrument
Compatible Data Collection Software
and Operating System
ABI PRISM ® 3100
Genetic Analyzer
Sample Data
Compatibility
• Data Collection v1.0/1.0.1/1.1
• Windows® NT, SP 5
• Data Collection v2.0
• Windows® 2000, SP 3 and 4
• Sample files
ABI PRISM ®
3100-Avant
Genetic Analyzer
• Data Collection v1.0
• Windows® NT, SP 5
• Data Collection v2.0
• Windows® 2000, SP 3 and 4
• Data Collection v1.0/1.0.1/1.1/3.0
• Windows® NT 4.0, SP 3, 4, 5, and 6a
• Sample files
ABI PRISM ® 310
Genetic Analyzer
• Data Collection v3.0
• Windows® 2000, SP 3 and 4
• Data Collection v3.1
• Windows® XP Professional, SP 2 and 3
• Data Collection v3.1 Vista Patch
• Windows Vista® Business edition,
32-bit, SP1
• Sample files
• Co-installation
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.
GeneMapper® Software Version 4.1 Installation and Administration Guide
15
Chapter 2 Installation Requirements and Software Compatibility
User Account Requirements
• 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.
• Automation – The software can automatically retrieve and
analyze data generated by the specified combination of the Data
Collection Software and Windows operating system.
GeneMapper®
Software
You can install GeneMapper Software as:
• A new installation
• An upgrade from a previous version (version 4.0 only)
Note: The GeneMapper Software cannot be upgraded directly
from v3.7 or earlier to v4.1; you must first back up your data,
uninstall the earlier version of GeneMapper Software, then
install the full version of v4.1
You cannot co-install the GeneMapper Software Version 4.1 on a
computer running a previous version of the GeneMapper Software.
PDF File Reader
To open the user documentation included on the GeneMapper®
Software Version 4.1 Documentation CD, use the Adobe® Acrobat®
Reader® software available from:
• www.adobe.com
• www.appliedbiosystems.com/support/software
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.
16
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 2 Installation Requirements and Software Compatibility
User Account Requirements
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.
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 or server 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 Version 4.1 Installation and Administration Guide
17
Chapter 2 Installation Requirements and Software Compatibility
GeneMapper® Software Installation DVDs
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 …
18
Use the DVD …
A full installation
GeneMapper® Software v4.1 Full Installation
A server installation
GeneMapper® Software v4.1 Installer for Server
A client installation
GeneMapper® Software v4.1 Installer for Client
An upgrade
GeneMapper® Software v4.1 Upgrade Software
v4.0 to v4.1
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3
Performing a New Installation
of the GeneMapper® Software
Chapter 1
Getting Started
This chapter covers:
■ Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
20
■ Selecting a Configuration for a New Installation. . . . . . . . .
21
Section 3.1: Full Installation Procedures . . . . . . . . . . . . . . . . 25
Chapter 2
Installation
Requirements and
Software Compatibility
Chapter 3
Performing a
New Installation of the
GeneMapper® Software
Chapter 4
Upgrading a
Previous Version of the
GeneMapper® Software
■ Full Installation Workflow . . . . . . . . . . . . . . . . . . . . . . . . . .
25
■ Instrument Configuration Procedures . . . . . . . . . . . . . . . . .
27
■ Remote Autoanalysis Configuration Procedures . . . . . . . . .
33
■ Stand-alone Configuration Procedures. . . . . . . . . . . . . . . . .
40
Section 3.2: Client-Server Installation Procedures . . . . . . . . 45
■ Client-Server Installation Workflow . . . . . . . . . . . . . . . . . .
45
■ Server Configuration Procedures . . . . . . . . . . . . . . . . . . . . .
47
■ Client Configuration Procedures . . . . . . . . . . . . . . . . . . . . .
51
Section 3.3: Software Login Procedures. . . . . . . . . . . . . . . . . 59
■ Registering the Software After a New Installation . . . . . . .
Chapter 5
Managing
Database Security
and User Access
Chapter 6
60
■ Logging In to the Software for the First Time
After a New Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
■ Logging In to the Database Dashboard for the First Time. .
63
■ What Next?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
64
■ Logging In to and Out of the Software . . . . . . . . . . . . . . . .
65
Managing the
Auditing and Electronic
Signature Systems
Chapter 7
Maintaining the
Software and
Database Application
GeneMapper® Software Version 4.1 Installation and Administration Guide
19
Chapter 3 Performing a New Installation of the GeneMapper® Software
Overview
Overview
This chapter describes how to perform a new installation of the
GeneMapper® Software Version 4.1. To perform a new installation,
you cannot have a previous version of the GeneMapper Software on
your computer.
Note: If you have a previous version of the GeneMapper Software
on your computer, go to Chapter 4, “Upgrading a Previous Version of
the GeneMapper® Software.”
20
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3 Performing a New Installation of the GeneMapper® Software
Selecting a Configuration for a New Installation
Selecting a Configuration for a New Installation
When you perform a new installation of the GeneMapper Software,
you can select one the following configurations:
• Instrument
• Remote autoanalysis
• Stand-alone
• Client-server
In Table 3-1, find the configuration that best suits your needs, then go
to the referenced page for the appropriate installation procedures.
Table 3-1
GeneMapper® Software configurations
Configuration
Description
Instrument
See page
Local computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
27
Autoanalysis
GeneMapper ®
Software
The Data Collection Software and the GeneMapper Software are
installed on the same computer.
In an instrument configuration, you can set up both software products
so that the GeneMapper Software:
• Obtains sample files from the local Data Collection Software
database.
• Performs analysis of the generated sample files automatically
(autoanalysis).
GeneMapper® Software Version 4.1 Installation and Administration Guide
21
Chapter 3 Performing a New Installation of the GeneMapper® Software
Selecting a Configuration for a New Installation
Table 3-1
GeneMapper® Software configurations (continued)
Configuration
Description
Remote
autoanalysis
See page
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Local
computer
33
Remote
autoanalysis
GeneMapper ®
Software
The Data Collection Software and the GeneMapper Software are
installed on separate computers.
In a remote autoanalysis configuration, you can set up both software
products so that the GeneMapper Software:
• Connects to a remote computer running the Data Collection
Software.
• Obtains sample files from the remote Data Collection Software
database.
• Performs analysis of the generated sample files automatically
(remote autoanalysis).
Stand-alone
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Local
computer
40
Data
transfer
GeneMapper ®
Software
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.
Note: In stand-alone configuration, the GeneMapper Software
does not interact with the Data Collection Software for autoanalysis
or remote autoanalysis.
22
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3 Performing a New Installation of the GeneMapper® Software
Selecting a Configuration for a New Installation
Table 3-1
GeneMapper® Software configurations (continued)
Configuration
Client-server
Description
Remote autoanalysis
configuration
Compatible
Applied Biosystems
electrophoresis
instrument
45
Remote
computer
Data
Collection
Software
Client
computer
Remote
autoanalysis
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Stand-alone
configurations
See page
Data
Collection
Software
GeneMapper ®
Software
application
Client
computer
Data
transfer
GeneMapper ®
Software
application
Server
computer
GeneMapper ®
Software
database
Client
computer
GeneMapper ®
Software
application
The GeneMapper Software application is installed on multiple client
computers. The GeneMapper Software database is installed on a
server computer separate from the client computers. The Data
Collection Software is installed on a computer separate from the
clients and server.
In a client-server configuration, you can set up a GeneMapper
Software client to:
• Connect to a remote computer running the Data Collection
Software.
• Obtain sample files from the remote Data Collection Software
database.
• Perform analysis of the generated sample files automatically
(remote autoanalysis).
• Store sample files, panel and bin definitions, analysis methods, size
standards, table and plot settings, and projects on the
GeneMapper Software server computer.
IMPORTANT! The GeneMapper Software server configuration and
the Data Collection Software cannot be installed on the same
computer.
GeneMapper® Software Version 4.1 Installation and Administration Guide
23
Chapter 3 Performing a New Installation of the GeneMapper® Software
Selecting a Configuration for a New Installation
24
GeneMapper® Software Version 4.1 Installation and Administration Guide
Section 3.1
Section 3.1 Full Installation Procedures
This section covers:
■ Full Installation Workflow . . . . . . . . . . . . . . . . . . . . . . . . . .
25
■ Instrument Configuration Procedures . . . . . . . . . . . . . . . . .
27
■ Remote Autoanalysis Configuration Procedures . . . . . . . . .
33
■ Stand-alone Configuration Procedures. . . . . . . . . . . . . . . . .
40
Note: To perform a client-server installation, go to Section 3.2,
“Client-Server Installation Procedures,” on page 45.
IMPORTANT! Be sure you use the GeneMapper® Software v4.1 Full
Installation DVD when performing the installation procedures
described in this section.
Full Installation Workflow
Figure 3-1 on page 26 shows the workflow for performing a full
installation of the GeneMapper Software.
GeneMapper® Software Version 4.1 Installation and Administration Guide
25
Chapter 3 Performing a New Installation of the GeneMapper® Software
Full Installation Workflow
Verify that the computer meets requirements.
(See page 11)
Verify that you have Administrator privileges on the computer.
(See page 16)
Is a previous version of the
GeneMapper® Software installed
on the computer?
YES
Perform an
upgrade of the
previous version.
(Go to Chapter 4)
NO
Do you want to set up a
client-server network?
YES
Perform a
client-server
installation.
(See page 45)
NO
Perform a full installation.
Do you want to
autoanalyze data?
NO
NO
Install the
stand-alone
configuration.
(See page 40)
YES
Is the Data Collection
Software installed
on the computer?
YES
Start the Data Collection services on
the remote Data Collection computer
(See page 33)
Start the Data
Collection services.
(See page 28)
Install the
remote autoanalysis
configuration.
(See page 36)
Install the
instrument
configuration.
(See page 30)
Register and log in to the GeneMapper® Software.
(See pages 60 and 61)
Figure 3-1
26
Full installation workflow
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3 Performing a New Installation of the GeneMapper® Software
Instrument Configuration Procedures
Instrument Configuration Procedures
Install the instrument configuration if:
• The Data Collection Software is installed on the local computer.
• You want to perform analysis of the generated sample files
automatically (autoanalysis).
Local computer
Compatible
Applied Biosystems
electrophoresis
instrument
Figure 3-2
Data
Collection
Software
Autoanalysis
GeneMapper ®
Software
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 remote autoanalysis configuration (see page 33)
• Install the stand-alone configuration (see page 40)
Installation Tasks
for an Instrument
Configuration
Installing the GeneMapper Software in an instrument configuration
requires that you:
Task
See page
1. Start the Data Collection services on the computer.
28
2. Install the GeneMapper Software on the computer.
30
GeneMapper® Software Version 4.1 Installation and Administration Guide
27
Chapter 3 Performing a New Installation of the GeneMapper® Software
Instrument Configuration Procedures
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.
28
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3 Performing a New Installation of the GeneMapper® Software
Instrument Configuration Procedures
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
GeneMapper® Software Version 4.1 Installation and Administration Guide
29
Chapter 3 Performing a New Installation of the GeneMapper® Software
Instrument Configuration Procedures
Installing the
Instrument
Configuration
of the
GeneMapper®
Software
To install the GeneMapper Software Version 4.1 on the same
computer as the Data Collection Software:
Note: For information on installing the GeneMapper Software on the
same computer as the Data Collection Software for the 3500 series
genetic analyzers, refer to the instrument user guide.
1. Insert the GeneMapper® Software v4.1 Full Installation DVD
into the DVD drive to start the installer.
If the installer does not start automatically:
a. Right-click My Computer (Windows® XP) or Computer
(Windows Vista®) and select Explore.
b. Expand the DVD drive, then select the GeneMapper 4.1
folder to display the contents.
c. Double-click
GeneMapper4.1 to start the installer.
2. Be sure that the Data Collection services are running
(see page 28). 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.
30
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3 Performing a New Installation of the GeneMapper® Software
Instrument Configuration Procedures
6. If you want to install the GeneMapper Software to a drive
different from the default drive, select the destination folder:
Note: Applied Biosystems recommends 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.
7. 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.
8. 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.
GeneMapper® Software Version 4.1 Installation and Administration Guide
31
Chapter 3 Performing a New Installation of the GeneMapper® Software
Instrument Configuration Procedures
9. 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.
10. Go to Section 3.3, “Software Login Procedures,” on page 59.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Remote Autoanalysis Configuration Procedures
Remote Autoanalysis Configuration Procedures
Install the remote autoanalysis configuration if:
• You plan to connect to a separate computer running the Data
Collection Software.
• You want to autoanalyze data.
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Figure 3-3
Installation Tasks
for a Remote
Autoanalysis
Configuration
Starting the
Data Collection
Services on the
Remote
Computer
Data
Collection
Software
Local
computer
Remote
autoanalysis
GeneMapper ®
Software
Example of a remote autoanalysis configuration
Installing the GeneMapper Software as a remote autoanalysis
configuration requires that you:
Task
See page
1. Start the Data Collection services on the remote Data
Collection computer.
33
2. Install the GeneMapper Software on the local computer.
36
Before you install the GeneMapper Software, start the Data
Collection services on the remote Data Collection computer.
Note: For information on starting the Data Collection services for
the 3500 series genetic analyzers, refer to the instrument user guide.
1. On the Data Collection computer, select Start
All ProgramsApplied Biosystems Data Collection
Run <Data Collection version>, where <Data Collection
version> is one of the following:
• 3730/3730xl Data Collection v3.1
• 3130/3130xl Data Collection v3.1
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Remote Autoanalysis Configuration Procedures
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.
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
34
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Remote Autoanalysis Configuration Procedures
b. Verify that no errors are displayed in the lower pane of the
window, then close the Data Service output window.
No errors
displayed
4. Obtain the host name:
a. Right-click My Computer (Windows XP) or Computer
(Windows Vista) in the desktop and select Properties.
b. Locate the full computer name. You will need the enter the
name when you install the GeneMapper Software.
Note: The full computer name is the host name.
• Windows XP – Select the Computer Name tab to
view the full computer name.
• Windows Vista
c. Close the dialog box.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Remote Autoanalysis Configuration Procedures
Installing the
Remote
Autoanalysis
Configuration
of the
GeneMapper®
Software
To install the GeneMapper Software Version 4.1 on a computer
separate from the Data Collection computer:
1. Insert the GeneMapper® Software v4.1 Full Installation DVD
into the DVD drive to start the installer.
If the installer does not start automatically:
a. Right-click My Computer (Windows XP) or Computer
(Windows Vista) and select Explore.
b. Expand the DVD drive, then select the GeneMapper 4.1
folder to display the contents.
c. Double-click
GeneMapper4.1 to start the installer.
2. 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. Select Remote Autoanalysis for type of installation, then
click Next.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Remote Autoanalysis Configuration Procedures
6. Type the server name (host name or full computer name) for the
Data Collection computer (see step 4 on page 35), select the
instrument type, then click Next.
7. Read the release notes, then click Next.
8. If you want to install the GeneMapper Software to a drive
different from the default drive, select the destination folder:
a. Verify 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.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Remote Autoanalysis Configuration Procedures
9. If you do not want to import data from a previous GeneMapper
installation, click No.
10. (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 184.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Remote Autoanalysis Configuration Procedures
11. 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.
12. 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.
13. Go to Section 3.3, “Software Login Procedures,” on page 59.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Stand-alone Configuration Procedures
Stand-alone Configuration Procedures
Install the stand-alone configuration if you do not plan to connect to a
computer with Data Collection Software for autoanalysis or remote
autoanalysis.
IMPORTANT! It is not possible to convert from the stand-alone
configuration to the remote autoanalysis configuration.
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Figure 3-4
Installation Tasks
for a Stand-alone
Configuration
Data
Collection
Software
Local
computer
Data
transfer
GeneMapper ®
Software
Example of a stand-alone configuration
Installing the GeneMapper Software as a stand-alone configuration
requires that you:
Task
Install the GeneMapper Software on the local computer.
Installing the
Stand-alone
Configuration
of the
GeneMapper®
Software
See page
40
To install the GeneMapper Software Version 4.1 on a computer
separate from the Data Collection computer without autoanalysis
or remote autoanalysis:
1. Insert the GeneMapper® Software Version 4.1 Full Installation
DVD into the DVD drive to start the installer.
If the installer does not start automatically:
a. Right-click My Computer (Windows XP) or Computer
(Windows Vista) and select Explore.
b. Expand the DVD drive, then select the GeneMapper 4.1
folder to display the contents.
c. Double-click
40
GeneMapper4.1 to start the installer.
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3 Performing a New Installation of the GeneMapper® Software
Stand-alone Configuration Procedures
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.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Stand-alone Configuration Procedures
b. Select a destination folder with at least 7 GB of free space,
then click Next.
7. If you do not want to import data from a previous GeneMapper
installation, click No.
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.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Stand-alone Configuration Procedures
Note: You can allocate more drive space later using the
Database Dashboard. See “Allocating Additional Disk Space”
on page 184.
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 59
GeneMapper® Software Version 4.1 Installation and Administration Guide
43
Chapter 3 Performing a New Installation of the GeneMapper® Software
Stand-alone Configuration Procedures
44
GeneMapper® Software Version 4.1 Installation and Administration Guide
Section 3.2
Section 3.2 Client-Server
Installation Procedures
This section covers:
■ Client-Server Installation Workflow . . . . . . . . . . . . . . . . . .
45
■ Server Configuration Procedures . . . . . . . . . . . . . . . . . . . . .
47
■ Client Configuration Procedures . . . . . . . . . . . . . . . . . . . . .
51
IMPORTANT! Be sure you use the appropriate installation DVD
when performing the procedures described in this section:
• For a server installation, use the GeneMapper® Software v4.1
Installer for Server DVD
• For a client installation, use the GeneMapper® Software v4.1
Installer for Client DVD
Client-Server Installation Workflow
Figure 3-5 on page 46 shows the workflow for performing a
client-server installation of the GeneMapper Software.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Client-Server Installation Workflow
Verify that the computer meets requirements.
(See page 11)
Verify that you have Administrator privileges on the computer.
(See page 16)
Is a previous version of the
GeneMapper® Software installed
on the computer?
YES
Perform an
upgrade of the
previous version.
Go to Chapter 4
NO
Perform a full
installation.
(See page 25)
Do you want to set up a
client-server network?
NO
YES
Perform a client-server installation.
Install the GeneMapper® Software on the server computer.
(See page 47)
Install the GeneMapper® Software on the client computer(s).
(See page 51)
Is the Data Collection Software
installed on the client computer?
YES
NO
NO
Do you want to
autoanalyze data?
YES
Install the stand-alone
configuration.
Start the Data Collection
services on the Data
Collection computer.
(See page 53)
Install the remote
autoanalysis configuration.
Register and log in to the GeneMapper® Software.
(See pages 60 and 61)
Figure 3-5
46
Client-server installation workflow
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Server Configuration Procedures
Server Configuration Procedures
Install the server configuration on a separate computer that serves
multiple client computers.
IMPORTANT! The GeneMapper Software server configuration and
the Data Collection Software cannot be installed on the same
computer.
Remote
Computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Client
computer
Remote
autoanalysis
Remote
Computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
GeneMapper ®
Software
application
Client
computer
Data
transfer
GeneMapper ®
Software
application
Server
computer
GeneMapper ®
Software
database
Client
computer
GeneMapper ®
Software
application
Figure 3-6
Installation Tasks
for a Server
Configuration
Example of a server configuration
Installing the GeneMapper Software as a server configuration
requires that you:
Task
Install the GeneMapper Software database on the server
computer.
GeneMapper® Software Version 4.1 Installation and Administration Guide
See page
48
47
Chapter 3 Performing a New Installation of the GeneMapper® Software
Server Configuration Procedures
Installing
the Server
Configuration
of the
GeneMapper®
Software
To install the GeneMapper Software Version 4.1 as a database
server:
1. Save and close all applications and windows.
2. Insert the GeneMapper® Software Version 4.1 Installer for
Server DVD into the DVD drive to start the installer.
If the installer does not start automatically, then:
a. Right-click My Computer (Windows XP) or Computer
(Windows Vista) and select Explore.
b. Expand the DVD drive, then select the GeneMapper 4.1
folder to display the contents.
c. Double-click
GeneMapper4.1 to start the installer.
3. Close all other applications and windows, then click OK to
close the following message.
4. In the Welcome window, click Next.
5. Review the installation requirements status, then click Next.
6. Read the release notes, then click Next.
7. If you want to install the GeneMapper Software to a different
drive than the default one, select the destination folder:
a. Confirm that the boot drive has at least 200 MB of
available free space.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Server Configuration Procedures
b. Select a destination folder with at least 7 GB of free space,
then click Next.
8. If you do not want to import data from a previous GeneMapper
installation, click No.
9. (Optional) Allocate space for the GeneMapper Software
database, then click Next.
Note: 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.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Server Configuration Procedures
Note: You can allocate more drive space later using the
Database Dashboard. See “Allocating Additional Disk Space”
on page 184.
10. 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.
11. 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.
12. Install the GeneMapper Software application on the client
computers (see page 51).
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Client Configuration 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:
• Stand-alone
• Remote autoanalysis
Stand-alone
Client
Configuration
In stand-alone configuration, the GeneMapper Software client
does not interact with the Data Collection Software for autoanalysis
or remote autoanalysis.
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.
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Client
computer
Data
transfer
GeneMapper ®
Software
application
Server
computer
Client
computer
GeneMapper ®
Software
database
GeneMapper ®
Software
application
Figure 3-7
Remote
Autoanalysis
Client
Configuration
Examples of stand-alone client configurations
In remote autoanalysis configuration, the GeneMapper Software
client can connect to and obtain sample files from a remote computer
with Data Collection Software, then perform analysis of the
generated sample files automatically (remote autoanalysis).
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Client Configuration Procedures
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Figure 3-8
Installation Tasks
for a Stand-alone
Client
Configuration
Installation Tasks
for a Remote
Autoanalysis
Client
Configuration
Obtaining the
GeneMapper®
Software
Server Name
Data
Collection
Software
Client
computer
Remote
autoanalysis
GeneMapper ®
Software
application
Server
computer
GeneMapper ®
Software
database
Example of a remote autoanalysis 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 server computer.
52
2. Install the GeneMapper Software client on the local computer.
56
To install the GeneMapper Software as a remote autoanalysis client
configuration, perform the following tasks:
Task
See
page
1. Obtain the name of the GeneMapper Software server computer.
52
2. Start the Data Collection services on the remote Data Collection
computer.
40
3. Obtain the name of the remote Data Collection computer.
55
4. Install the GeneMapper Software client on the local computer.
56
When installing the GeneMapper Software clients, you need the
name of the GeneMapper Software server computer.
1. Right-click My Computer (Windows XP) or Computer
(Windows Vista) in the desktop and select Properties.
2. Locate the full computer name. You will need the enter the name
when you install the GeneMapper Software.
Note: The full computer name is the host name.
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Client Configuration Procedures
• Windows XP – Select the Computer Name tab to view
the full computer name.
• Windows Vista
3. Close the dialog box.
Starting the
Data Collection
Services on the
Remote
Computer
(For Remote
Autoanalysis
Only)
Before you install the remote autoanalysis configuration of the
GeneMapper Software, start the Data Collection services on the
remote Data Collection computer.
Note: If you are installing a stand-alone configuration, go to
page 56.
Note: For information on setting up remote autoanalysis for the 3500
series genetic analyzers, refer to the instrument user guide.
1. On the Data Collection computer, select Start
All ProgramsApplied Biosystems Data Collection
Run <Data Collection version>, where <Data Collection
version> is one of the following:
• 3730/3730xl Data Collection v3.1
• 3130/3130xl Data Collection v3.1
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Client Configuration Procedures
The software displays the Service Console. 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 appears. 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.
Right-click here
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Client Configuration Procedures
b. Verify that no errors are displayed in the lower pane of the
window, then close the Data Service output window.
No errors
displayed
4. Obtain the name of the Data Collection computer:
a. Right-click My Computer (Windows XP) or Computer
(Windows Vista) in the desktop and select Properties.
b. Locate the full computer name. You will need the enter the
name when you install the GeneMapper Software.
Note: The full computer name is the host name.
• Windows XP – Select the Computer Name tab to
view the full computer name.
• Windows Vista
c. Close the dialog box.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Client Configuration Procedures
Installing
the Client
Configuration
of the
GeneMapper®
Software
To install the GeneMapper Software Version 4.1 as a software
application-only client:
1. Insert the GeneMapper® Software Version 4.1 Installer for
Client DVD into the DVD drive to start the installer.
If the installer does not start automatically, then:
a. Right-click My Computer (Windows XP) or Computer
(Windows Vista) and select Explore.
b. Expand the DVD drive.
c. Select the GeneMapper 4.1 folder to display the contents.
d. Double-click
GeneMapper4.1 to start the installer.
2. In the Welcome window, click Next.
3. Review the installation requirements status, then click Next.
4. Type the server name (host name or full computer name) for the
GeneMapper Software database computer (see page 52), then
click Next.
5. After the installer establishes a connection with the
GeneMapper Software server computer, click OK to continue.
6. Select the type of installation:
• Stand-alone – Select this if you do not want the
GeneMapper client to interact with the Data Collection
Software for autoanalysis or remote autoanalysis
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Client Configuration Procedures
• Remote Autoanalysis – Select this if you want to connect
to and obtain sample files from a remote Data Collection
computer and perform remote autoanalysis of data.
IMPORTANT! If you select Remote Autoanalysis, be sure
that the Data Collection services are running on the remote
Data Collection computer (see page 53).
7. If you are installing a remote autoanalysis configuration, type
the server name (host name or full computer name) for the Data
Collection computer (see step 4 on page 35), select the type of
instrument, then click Next.
8. Read the release notes, then click Next.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Client Configuration Procedures
9. 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.
10. 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.
11. In the InstallShield Wizard Complete window, click Finish.
12. Go to Section 3.3, “Software Login Procedures,” on page 59.
58
GeneMapper® Software Version 4.1 Installation and Administration Guide
Section 3.3
Section 3.3 Software Login Procedures
This section covers:
■ Registering the Software After a New Installation . . . . . . .
60
■ Logging In to the Software for the First Time
After a New Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
■ Logging In to the Database Dashboard for the First Time. .
63
■ What Next?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
64
■ Logging In to and Out of the Software . . . . . . . . . . . . . . . .
65
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Registering the Software After a New Installation
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 189.
1. In the desktop, double-click
GeneMapper v4.1 or
select StartAll ProgramsApplied Biosystems
GeneMapper GeneMapper v4.1.
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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Logging In to the Software for the First Time After a New Installation
Logging In to the Software for the First Time
After a New Installation
Use the following procedure to log in to the GeneMapper Software
for the first time after performing a new installation of the software
or upgrading the software from version 3.7 or older.
To log in for the first time after installing GeneMapper® Software
Version 4.1 as 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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Chapter 3 Performing a New Installation of the GeneMapper® Software
Logging In to the Software for the First Time After a New Installation
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
Applied Biosystems 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 121 for
instructions on adding users.
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Logging In to the Database Dashboard for the First Time
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 or server installation of the
GeneMapper Software.
To log in to the Database Dashboard for the first time:
1. Select StartAll ProgramsApplied Biosystems
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
Applied Biosystems to retrieve it.
5. See “About the Dashboard Software” on page 178 and the
GeneMapper Software Online Help for more information about
using the Database Dashboard to maintain the GeneMapper
Software database.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
What Next?
What Next?
For a New
Installation
64
If you installed the GeneMapper Software Version 4.1 as a new
installation, you can use the software. For user instructions, refer
to the:
• GeneMapper® Software Getting Started Guides
• GeneMapper® Software Version 4.1 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
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 3 Performing a New Installation of the GeneMapper® Software
Logging In to and Out of the Software
Logging In to and Out of the Software
Logging In
1. In the desktop, double-click
GeneMapper v4.1 or select
StartAll ProgramsApplied Biosystems
GeneMapperGeneMapper v4.1.
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! Applied Biosystems recommends changing the
password for the Administrator user account after installing the
software.
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Chapter 3 Performing a New Installation of the GeneMapper® Software
Logging In to and Out of the Software
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 125 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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Logging In to and Out of the Software
a. In the Host Name field, type the server 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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67
Chapter 3 Performing a New Installation of the GeneMapper® Software
Logging In to and Out of the Software
68
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Chapter 4
Upgrading a Previous Version
of the GeneMapper® Software
Chapter 1
Getting Started
This chapter covers:
■ Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
70
■ Upgrade Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
70
®
■ Upgrading from GeneMapper Software Version 3.7
Chapter 2
Installation
Requirements and
Software Compatibility
or earlier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
■ Backing Up Your Data (Version 4.0 Only) . . . . . . . . . . . . .
73
■ Determining the Appropriate Upgrade Procedure
for Your Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Chapter 3
Performing a
New Installation of the
GeneMapper® Software
Chapter 4
Upgrading a
Previous Version of the
GeneMapper® Software
■ Instrument Configuration Upgrade . . . . . . . . . . . . . . . . . . .
77
■ Remote Autoanalysis Configuration Upgrade . . . . . . . . . . .
80
■ Stand-alone Configuration Upgrade. . . . . . . . . . . . . . . . . . .
83
■ Client-Server Configuration Upgrade . . . . . . . . . . . . . . . . .
84
®
■ Upgrading the GeneMapper Software . . . . . . . . . . . . . . . .
85
■ Registering the Software After Upgrading. . . . . . . . . . . . . .
88
■ Logging In to the Software for the First Time
Chapter 5
Managing
Database Security
and User Access
After Upgrading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
■ What Next After Upgrading? . . . . . . . . . . . . . . . . . . . . . . . .
90
■ Logging In to and Out of the Software . . . . . . . . . . . . . . . .
91
Chapter 6
Managing the
Auditing and Electronic
Signature Systems
Chapter 7
Maintaining the
Software and
Database Application
GeneMapper® Software Version 4.1 Installation and Administration Guide
69
Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Overview
Overview
This chapter describes how to upgrade a previous version of the
GeneMapper® Software to Version 4.1.
Note: If you do not have a previous version of the GeneMapper
Software on your computer, go to Chapter 3, “Performing a New
Installation of the GeneMapper® Software.”
Note: Be sure you use the GeneMapper® Software v4.1 Upgrade
Software v4.0 to v4.1 DVD when performing the installation
procedures described in this chapter.
IMPORTANT! The GeneMapper Software cannot be upgraded
directly from v3.7 or earlier to v4.1; you must first back up your data,
uninstall the earlier version of GeneMapper Software, then install the
full version of v4.1.
Upgrade Workflow
Figure 4-1 on page 71 shows the workflow for upgrading a previous
version of the GeneMapper Software to version 4.1.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Upgrade Workflow
Verify that the computer meets requirements.
(See page 11)
Verify that you have Administrator privileges on the computer.
(See page 16)
Perform a new
installation.
Go to Chapter 3
Is a previous version of the
GeneMapper® Software
installed on the computer?
NO
YES
Uninstall
Version 3.7 or earlier,
perform a new installation.
(See page 72)
Is the installed version of
the GeneMapper® Software
Version 4.0?
NO
YES
Perform an upgrade of the previous version.
Back up your data.
(See page 163)
Is the previous
version an
instrument
configuration?
Is the previous
version a remote
autoanalysis
configuration?
NO
YES
YES
Start the Data
Collection services.
(See page 78)
Start the Data Collection services
on the Data Collection computer.
(See page 163)
NO
Is the previous
version a
stand-alone
configuration?
YES
Upgrade the
GeneMapper® Software.
(See page 85)
Register and log in to the GeneMapper® Software.
(See pages 88 and 89)
Figure 4-1
Upgrade installation workflow
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Upgrading from GeneMapper® Software Version 3.7 or earlier
Upgrading from GeneMapper® Software
Version 3.7 or earlier
IMPORTANT! Be sure to back up your data before you upgrade to
GeneMapper Software Version 4.1.
The GeneMapper Software cannot be upgraded directly from v3.7 or
earlier to v4.1; you must:
1. Back up your data.
2. Uninstall the earlier version of GeneMapper Software.
3. Install the full version of v4.1.
Backing Up Your
Data (Version 3.7
or Earlier)
The following steps provide only a brief outline for backing up your
data. For details on how to perform each step, see Section 7.1,
“Managing Study, Project, and Sample Data,” on page 163.
1. If necessary, restore any data that you have archived.
IMPORTANT! You cannot restore archived data from an earlier
version of the GeneMapper software after you upgrade to
GeneMapper Software Version 4.1.
2. Export reference data (such as panels, bin sets, analysis
methods, and size standards).
3. Export projects.
Uninstalling the
Earlier Version of
GeneMapper®
Software
Installing
GeneMapper®
Software
Version 4.1
72
See “Uninstalling the Software” on page 192 for instructions.
See Chapter 3, “Performing a New Installation of the
GeneMapper® Software,”for instructions.
GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Backing Up Your Data (Version 4.0 Only)
Backing Up Your Data (Version 4.0 Only)
IMPORTANT! Be sure to back up your data before you upgrade to
GeneMapper Software Version 4.1.
Use the GeneMapper® Database Utility Wizard to back up your data
before upgrading to GeneMapper® Software v4.1. See Appendix C
on page 217 for more information.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Determining the Appropriate Upgrade Procedure for Your Configuration
Determining the Appropriate Upgrade Procedure
for Your Configuration
When you upgrade to the GeneMapper Software Version 4.1, the
installer automatically selects your existing configuration. For
example, if you installed GeneMapper Software Version 4.0 as an
instrument configuration, GeneMapper Software Version 4.1 will
also be installed as an instrument configuration.
IMPORTANT! You cannot change configurations during an upgrade
installation.
Find your existing configuration in Table 4-1, then go to the
referenced page for the appropriate upgrade procedure.
Table 4-1
GeneMapper® Software configurations for upgrading
Existing
configuration
See
page
Description
Instrument
Local computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
77
Autoanalysis
GeneMapper ®
Software
The Data Collection Software and the GeneMapper Software are
installed on the same computer.
In the instrument configuration, the GeneMapper Software can:
• Obtain sample files from the local Data Collection Software database.
• Perform analysis of the generated sample files automatically
(autoanalysis).
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Determining the Appropriate Upgrade Procedure for Your Configuration
Table 4-1
GeneMapper® Software configurations for upgrading (continued)
Existing
configuration
See
page
Description
Remote
autoanalysis
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Local
computer
80
Remote
autoanalysis
GeneMapper ®
Software
The Data Collection Software and the GeneMapper Software are
installed on separate computers.
In the remote autoanalysis configuration, the GeneMapper Software
can:
• Connect to a remote computer with Data Collection Software.
• Obtain sample files from the remote Data Collection Software
database.
• Perform analysis of the generated sample files automatically (remote
autoanalysis).
Stand-alone
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Local
computer
83
Data
transfer
GeneMapper ®
Software
The Data Collection Software and the GeneMapper Software are
installed on separate computers.
In the stand-alone configuration, you can use the GeneMapper Software
to:
• Add sample files from a remote Data Collection Software database to
a project
• Perform manual analysis of the project.
Note: In stand-alone configuration, the GeneMapper Software does
not interact with the Data Collection Software for autoanalysis or remote
autoanalysis.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Determining the Appropriate Upgrade Procedure for Your Configuration
Table 4-1
GeneMapper® Software configurations for upgrading (continued)
Existing
configuration
Client-server
See
page
Description
Remote autoanalysis
configuration
Compatible
Applied Biosystems
electrophoresis
instrument
84
Remote
computer
Data
Collection
Software
Client
computer
Remote
autoanalysis
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Stand-alone
configurations
Data
Collection
Software
GeneMapper ®
Software
application
Client
computer
Data
transfer
GeneMapper ®
Software
application
Server
computer
GeneMapper ®
Software
database
Client
computer
GeneMapper ®
Software
application
The GeneMapper Software application is installed on multiple client
computers. The GeneMapper Software database is installed on a server
computer separate from the client computers. The Data Collection
Software is installed on a computer separate from the clients and server.
In a client-server configuration, you can set up a GeneMapper Software
client to:
• Connect to a remote computer running the Data Collection Software.
• Obtain sample files from the remote Data Collection Software
database.
• Perform analysis of the generated sample files automatically (remote
autoanalysis).
• Store sample files, panel and bin definitions, analysis methods, size
standards, table and plot settings, and projects on the GeneMapper
Software server computer.
IMPORTANT! The GeneMapper Software server configuration and the
Data Collection Software cannot be installed on the same computer.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Instrument Configuration Upgrade
Instrument Configuration Upgrade
Local computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data Collection
Software and
GeneMapper®
Software
Versions
Data
Collection
Software
Autoanalysis
GeneMapper ®
Software
You can upgrade an instrument configuration only if you are:
• Running Data Collection Software v3.1
• Upgrading from the GeneMapper® Software Version 4.0
Note: If you have another version of the Data Collection Software or
an earlier version of the GeneMapper Software, install GeneMapper
Software Version 4.1as a new installation. See “Uninstalling the
Software” on page 192, then “Instrument Configuration Procedures”
on page 27.
Note: After upgrading to version 4.1, you must recreate any results
groups and plates that were created using the GeneMapper Software
Version 4.0.
Installation Tasks
for Upgrading
an Instrument
Configuration
Upgrading an instrument configuration of the GeneMapper Software
requires that you:
Task
See page
1. Back up your data.
72
2. Start the Data Collection services on the local computer.
78
3. Upgrade the GeneMapper Software on the local
computer.
85
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77
Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Instrument Configuration Upgrade
Starting the
Data Collection
Services on the
Local Computer
(For Instrument
Configuration
Upgrades Only)
Before you upgrade an instrument configuration of 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 are
changed 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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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Instrument Configuration Upgrade
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
4. Go to “Upgrading the GeneMapper® Software” on page 85.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Remote Autoanalysis Configuration Upgrade
Remote Autoanalysis Configuration Upgrade
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
GeneMapper®
Software
Versions
Data
Collection
Software
Local
computer
Remote
autoanalysis
GeneMapper ®
Software
You can upgrade a remote autoanalysis configuration only if you are
upgrading from the GeneMapper® Software Version 4.0.
Note: If you have an earlier version of the GeneMapper Software,
you need to install GeneMapper Software Version 4.1 as a new
installation. See “Uninstalling the Software” on page 192, then
“Remote Autoanalysis Configuration Procedures” on page 33.
Note: After upgrading to version 4.1, you must recreate any results
groups and plates that were created in the GeneMapper Software
Version 4.0.
Installation Tasks
for Upgrading
a Remote
Autoanalysis
Configuration
80
Upgrading a remote autoanalysis configuration of the GeneMapper
Software requires that you:
Task
See page
1. Back up your data.
72
2. Start the Data Collection services on the remote Data
Collection computer.
81
3. Upgrade the GeneMapper Software on the local
computer.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Remote Autoanalysis Configuration Upgrade
Starting the
Data Collection
Services on the
Remote
Computer
(For Remote
Autoanalysis
Upgrades Only)
Before you upgrade the remote autoanalysis configuration of the
GeneMapper Software, start the Data Collection services on the
remote Data Collection computer.
Note: For information on starting the Data Collection services for
the 3500 series genetic analyzers, refer to the instrument user guide.
1. On the remote Data Collection computer, 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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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Remote Autoanalysis Configuration Upgrade
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
4. Go to “Upgrading the GeneMapper® Software” on page 85
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Stand-alone Configuration Upgrade
Stand-alone Configuration Upgrade
Remote
computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Local
computer
Data
transfer
GeneMapper ®
Software
Note: In stand-alone configuration, the GeneMapper Software does
not interact with the Data Collection Software for autoanalysis or
remote autoanalysis.
GeneMapper®
Software
Versions
Installation Tasks
for Upgrading
a Stand-alone
Configuration
You can upgrade a stand-alone configuration only if you are
upgrading from the GeneMapper® Software Version 4.0.
Note: If you have an earlier version of the GeneMapper Software,
you need to install GeneMapper Software Version 4.1 as a new
installation. See “Uninstalling the Software” on page 192, then
“Stand-alone Configuration Procedures” on page 40.
Upgrading a stand-alone configuration of the GeneMapper Software,
requires that you:
Task
See page
1. Back up your data.
72
2. Upgrade the GeneMapper Software on the local
computer.
85
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83
Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Client-Server Configuration Upgrade
Client-Server Configuration Upgrade
Remote
Computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
Client
computer
Remote
autoanalysis
Remote
Computer
Compatible
Applied Biosystems
electrophoresis
instrument
Data
Collection
Software
GeneMapper ®
Software
application
Client
computer
Data
transfer
GeneMapper ®
Software
application
Server
computer
GeneMapper ®
Software
database
Client
computer
GeneMapper ®
Software
application
GeneMapper®
Software
Versions
Installation Tasks
for Upgrading
a Client-Server
Configuration
84
You can upgrade a client-server configuration only if you are
upgrading from the GeneMapper® Software Version 4.0.
Upgrading a client-server configuration of the GeneMapper
Software, requires that you:
Task
See page
1. Back up your data.
72
2. Upgrade the GeneMapper Software on the server
computer.
85
3. Upgrade the GeneMapper Software on the client
computer(s).
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Upgrading the GeneMapper® Software
Upgrading the GeneMapper® Software
Before You
Upgrade the
GeneMapper®
Software
Make sure you complete the appropriate pre-installation tasks before
you upgrade the GeneMapper Software.
Table 4-2
Pre-installation tasks
Before you upgrade the
GeneMapper Software
If you are upgrading …
An instrument configuration
1. Back up your data.
2. Make sure the Data Collection services
are running on the local computer.
A remote autoanalysis
configuration
1. Back up your data.
A stand-alone configuration
Back up your data.
A client-server
configuration
Back up your data.
2. Make sure the Data Collection services
are running on the remote computer
Note: If you are not able to complete the upgrade as it is described,
see Appendix A on page 189.
Upgrading the
GeneMapper®
Software to
Version 4.1
IMPORTANT! Be sure to back up your data before you upgrade to
GeneMapper Software Version 4.1.
IMPORTANT! If you are upgrading a client-server configuration,
upgrade the server computer first, then upgrade the client computers.
1. Insert the GeneMapper® Software v4.1 Upgrade Software v4.0
to v4.1 DVD into the DVD drive to start the installer.
If the installer does not start automatically:
a. Right-click My Computer (Windows® XP) or Computer
(Windows Vista®) and select Explore.
b. Expand the DVD drive, then double-click
GeneMapper4.1 to start the installer.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Upgrading the GeneMapper® Software
c. In the splash screen, click GeneMapper v4.1 <type of
upgrade>, where <type of upgrade> is one of the
following:
• Full Upgrade
• Server Upgrade
• Client Upgrade
d. For the full or server upgrade, make sure the database has
been saved using the GeneMapper Database Utility
Wizard. Click No to start the utility wizard.
2. Close all other applications and windows, then click OK to
close the “Close All” message box.
IMPORTANT! If you are upgrading an instrument configuration,
leave the Data Collection Software running on the local
computer.
3. Carefully read the message in the “Caution: Before you proceed
with the upgrade” window, then:
• If you have not already backed up your data, click Exit,
then return to page 72 for backup procedures.
• If you have already backed up your data, click Accept to
open the InstallShield Wizard Welcome window.
4. Click Next, then follow the instructions in the wizard.
IMPORTANT! During installation, DOS commands are executed
and the DOS window may open. Do not delete, close, or click
the DOS window. If you click it, press the Esc key.
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Upgrading the GeneMapper® Software
5. When the InstallShield Wizard Complete window appears,
finish the installation:
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:
a. Remove the upgrade DVD from the drive.
b. In the InstallShield Wizard Complete window, select Yes, I
want to restart my computer now.
c. Click Finish.
Proceed to “Registering the Software After Upgrading” on page 88.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Registering the Software After Upgrading
Registering the Software After Upgrading
Register the software the first time that you start the software.
Note: If you are not able to register the software as described, see
Appendix A on page 189.
1. In the desktop, double-click
GeneMapper v4.1 or
select StartAll ProgramsApplied Biosystems
GeneMapperGeneMapper v4.1.
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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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Logging In to the Software for the First Time After Upgrading
Logging In to the Software for the First Time After
Upgrading
Use the following procedure to log in to the GeneMapper Software
for the first time after upgrading the software from versions 4.0.
Note: If you upgraded from GeneMapper Software Version 3.7 or
older, follow the log in procedure for a new installation (see page 60).
To log in for the first time after upgrading from GeneMapper®
Software Version 4.0 to GeneMapper® Software Version 4.1:
1. Complete the Login to GeneMapper dialog box:
a. Type your existing user name and password (the user name
and password from your previous version of the
GeneMapper Software).
b. Click OK.
2. Read the license agreement, then click Yes if you are in
agreement with the terms.
3. Review the license agreement and product warranty. You may:
• Click Decline to quit the application.
• Click Service to bypass the agreement and proceed to the
Project window.
Note: 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.
4. If necessary, see “Creating a User Account” on page 121 for
instructions on adding users.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
What Next After Upgrading?
What Next After Upgrading?
For an Upgrade
Installation
If you have upgraded to GeneMapper Software Version 4.1 from a
previous version of the software, you can migrate your existing
projects using the steps listed below.
Note: These steps provide a brief outline only for migrating existing
projects. For details on how to perform each step, see the
GeneMapper® Software Version 4.1 Online Help.
1. Import the reference data and projects into the GeneMapper
Software Version 4.1 database.
2. Associate sample files with the migrated projects. This allows
you to view raw and EPT data, and to analyze projects.
Note: If you export/import only the reference data and projects,
but do not associate sample files, you can view results and make
or edit allele calls, but you cannot reanalyze the projects.
3. Reanalyze the migrated projects. To reanalyze the migrated
projects, make sure that sample files were generated on any of
the following instruments:
• Applied Biosystems 3130 Genetic Analyzer
• Applied Biosystems 3130xl Genetic Analyzer
• Applied Biosystems 3730 DNA Analyzer
• Applied Biosystems 3730xl DNA Analyzer
• ABI PRISM® 3100 Genetic Analyzer
• ABI PRISM® 3100-Avant Genetic Analyzer
• ABI PRISM® 310 Genetic Analyzer
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Logging In to and Out of the Software
Logging In to and Out of the Software
1. In the desktop, double-click
GeneMapper v4.1 or
select StartAll ProgramsApplied Biosystems
GeneMapperGeneMapper v4.1.
2. Select your user name from the User Name drop-down list or, 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 when you click OK.
3. Type your password.
IMPORTANT! Applied Biosystems recommends changing the
password for the Administrator user account after installing the
software.
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Logging In to and Out of the Software
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, you
can either wait out 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 125).
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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Logging In to and Out of the Software
a. In the Host Name field, type the server 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, then restart the
software 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.” The GeneMapper Software closes completely if you use either
the Exit command or the Close button.
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Chapter 4 Upgrading a Previous Version of the GeneMapper® Software
Logging In to and Out of the Software
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Chapter 5
.
Managing Database Security
and User Access
Chapter 1
Getting Started
Chapter 2
Installation
Requirements and
Software Compatibility
Chapter 3
Performing a
New Installation of the
GeneMapper® Software
This chapter covers:
■ About GeneMapper® Software Security . . . . . . . . . . . . . . .
96
■ Configuring the Password Policies . . . . . . . . . . . . . . . . . . .
98
■ Managing User and Security Groups . . . . . . . . . . . . . . . . .
102
■ Managing Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
■ Managing Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
■ Managing User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . .
120
■ Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . .
126
■ Exporting and Importing the Security Settings . . . . . . . . .
128
Chapter 4
Upgrading a
Previous Version of the
GeneMapper® Software
Chapter 5
Managing
Database Security
and User Access
Chapter 6
Managing the
Auditing and Electronic
Signature Systems
Chapter 7
Maintaining the
Software and
Database Application
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About GeneMapper® Software Security
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 6, “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 115) 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 65).
2. In the GeneMapper window, select ToolsSecurity Manager.
3. In the AdminToolAcc dialog box, type a user name and password
for a user account with administrative privileges, then click OK.
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About GeneMapper® Software Security
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 96).
Configure the password policies (see page 98).
Can you use the default profiles provided with the
installation? (see page 116).
No
Yes
Create custom security profiles for your users (see page 113).
Create user accounts for all users of the GeneMapper Software
(see page 121).
If you just installed the GeneMapper Software, change the
passwords for the default Administrator and gm user accounts
(see page 124).
Exit the Access Control Administration Software (see page 96).
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 121).
• Create, modify, or retire security profiles as needed
(see page 113).
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Configuring the Password Policies
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. Applied Biosystems recommends 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 96).
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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Configuring the Password Policies
• 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 126.
• 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 125. 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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Configuring the Password Policies
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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Configuring the Password Policies
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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Managing User and Security Groups
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-server 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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Managing User and Security Groups
Examples
This section illustrates the function of user and security groups
through a series of example scenarios. Figure 5-1 on page 106
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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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 5-1
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Examples of user and security group configurations
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Managing User and Security Groups
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 102 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 109 (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 113.
• Create user accounts for your users as explained in “Creating a
User Account” on page 121.
• 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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Managing User and Security Groups
Creating Security
Groups
1. Start the Access Control Administration Software (see page 96).
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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Managing User and Security Groups
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 5 Managing Database Security and User Access
Managing Applications
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 Applied Biosystems 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. Applied Biosystems recommends 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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Managing Profiles
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 5-2 on page 112 illustrates the concept of the inheritance
hierarchy using the Installed Elements of the GeneMapper
applications group.
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Example of Installed Element Inheritance
Figure 5-2 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 5-2
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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Managing Profiles
Creating a Profile
1. Start the Access Control Administration Software (see page 96).
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 5-1 on page 116 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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Managing Profiles
Editing a Profile
IMPORTANT! Applied Biosystems strongly recommends against
modifying the Admin(istrator) Profile.
1. Start the Access Control Administration Software (see page 96).
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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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 Applied Biosystems products, the Installed Elements
table may contain elements other than those listed in Table 5-1. Most
Applied Biosystems products employ the Access Control
Administration Software and install their elements to the same
location.
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Scientist
Admin Profile
Service
Action)
✓
✓
✓
✓
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 96)
Associate User Groups with Security
Groups
✓
✓
• Editing user accounts (see page 123)
Associate User Groups with Users
✓
✓
• Changing the password policies (see page 98)
Change Password Policies
✓
✓
• Exporting/importing security settings (see page 126)
Import Security Data
✓
✓
Export Security Data
✓
✓
User Groups
✓
✓
Create
✓
✓
Modify
✓
✓
Change Control Security Group
✓
✓
Delete
✓
✓
Default Rights
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Admin Tool Acc(ess)
General
• Editing user groups
Create, delete, or modify user groups (
).
Managing Profiles
Installed Elements
Application/ Action Group/
Chapter 5 Managing Database Security and User Access
(
User groups and privileges
Technician
116
Table 5-1
Admin Profile
Service
Create
✓
✓
Modify
✓
✓
Change Control Security Group
✓
✓
Delete
✓
✓
Applications
✓
✓
Create
✓
✓
Modify
✓
✓
Delete
✓
✓
✓
✓
Create
✓
✓
Modify
✓
✓
Change Control Security Group
✓
✓
Delete
✓
✓
Scientist
✓
Action)
Profiles
Users
—
—
✓
✓
Create
—
— ✓
✓
Modify
—
—
✓
✓
Change Control Security Group
—
—
✓
✓
Security Groups
Grants the user permission(s) to…
Create, delete, or modify user profiles ( ).
User profile
Note: See page 110 for more information on user
profiles.
Create, delete, or modify applications (
).
Application
Note: See page 102 for more information on
applications.
Create, delete, or modify user accounts (
).
User account
Note: See page 120 for more information on user
accounts.
Create, delete, or modify security groups (
).
Managing Profiles
✓
Installed Elements
Application/ Action Group/
Technician
(
User groups and privileges (continued)
Chapter 5 Managing Database Security and User Access
GeneMapper® Software Version 4.1 Installation and Administration Guide
Table 5-1
117
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 180)
and project information (see page 185)
UPDATE_DATABASE_CONGIF(uration)
✓
✓
• Modifying (updating) the disk space allocated for the
GeneMapper Software database (see page 183)
Scientist
✓
Action)
Audit GUI
GeneMapper® Software Version 4.1 Installation and Administration Guide
Audit History Viewer
May Run Application
Map Configuration Tool
Foundation Data Collection
GeneMapper
Database Manager
✓
Note: See page 145 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 138 for more information on the Audit
Map Configuration Software and the auditing system for
the GeneMapper Software.
Managing Profiles
Grants the user permission(s) to…
Installed Elements
Application/ Action Group/
Chapter 5 Managing Database Security and User Access
(
User groups and privileges (continued)
Technician
118
Table 5-1
Admin Profile
Service
✓
✓
✓
✓
✓
✓
READ_SIZE_STANDARD
✓
✓
UPDATE_SIZE_STANDARD
✓
✓
✓
✓
READ_ANALYSIS_METHOD
✓
✓
UPDATE_ANALYSIS_METHOD
✓
✓
✓
✓
✓
✓
READ_PANEL
UPDATE_PANEL
Size Standard
Analysis Method
Study
READ_STUDY
UPDATE_STUDY
Scientist
✓
Panel Manager
Action)
✓
✓
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. ‡
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. ‡
Use the GeneMapper Manager to view (read) and create
or modify (update) the analysis methods stored by the
GeneMapper Software.
Note: For more information on analysis methods or the
GeneMapper Manager, see the online help. ‡
Use the GeneMapper Manager to view (read) and create
or modify (update) the studies stored by the GeneMapper
Software.
Note: For more information on analysis methods or the
GeneMapper Manager, see the online help. ‡
119
‡ 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 xi for more information.
Managing Profiles
✓
Installed Elements
Application/ Action Group/
Technician
(
User groups and privileges (continued)
Chapter 5 Managing Database Security and User Access
GeneMapper® Software Version 4.1 Installation and Administration Guide
Table 5-1
Chapter 5 Managing Database Security and User Access
Managing User Accounts
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 110 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 6, “Managing the Auditing and Electronic Signature Systems.”
Default User
Names and
Passwords
Table 5-2 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, Applied Biosystems
strongly recommends 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 5-2
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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Chapter 5 Managing Database Security and User Access
Managing User Accounts
Creating a
User Account
1. Start the Access Control Administration Software (see page 96).
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 110), the software
assigns the Suspended status to user
accounts that have been subject to multiple
unsuccessful login attempts.
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Chapter 5 Managing Database Security and User Access
Managing User Accounts
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 the user to enter a
password of their choice.
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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in the toolbar).
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Managing User Accounts
Editing a
User Account
1. Start the Access Control Administration Software (see page 96).
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 120). After you delete a user account, you cannot retrieve
or restore it, nor can you create another user account of the same
name. Applied Biosystems recommends 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 125.
To delete a user account:
1. Start the Access Control Administration Software (see page 96).
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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Chapter 5 Managing Database Security and User Access
Managing User Accounts
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,
Applied Biosystems strongly recommends 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 96).
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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in the toolbar).
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Chapter 5 Managing Database Security and User Access
Managing User Accounts
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 98).
To reactivate, deactivate, or suspend the user account:
1. Start the Access Control Administration Software (see page 96).
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 110), 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
GeneMapper® Software Version 4.1 Installation and Administration Guide
in the toolbar).
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Chapter 5 Managing Database Security and User Access
Viewing the Security Report
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 6, “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 5-3
Printing the
Security Log
Security report example records
Note: The security log is regenerated daily.
1. Start the Access Control Administration Software (see page 96).
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
126
(FileReport).
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Chapter 5 Managing Database Security and User Access
Viewing the Security Report
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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Chapter 5 Managing Database Security and User Access
Exporting and Importing the Security Settings
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 96).
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 96).
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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GeneMapper® Software Version 4.1 Installation and Administration Guide
Chapter 6
Managing the Auditing and
Electronic Signature Systems
Chapter 1
Getting Started
This chapter covers:
■ About the Data Tracking Systems . . . . . . . . . . . . . . . . . . .
130
Section 6.1: Setting Up the Auditing System . . . . . . . . . . . . 131
Chapter 2
Installation
Requirements and
Software Compatibility
Chapter 3
Performing a
New Installation of the
GeneMapper® Software
Chapter 4
Upgrading a
Previous Version of the
GeneMapper® Software
■ About the Auditing System . . . . . . . . . . . . . . . . . . . . . . . .
132
■ Audit Maps, Objects, and Attributes . . . . . . . . . . . . . . . . .
134
■ Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . .
138
■ Managing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . .
145
Section 6.2: Setting Up the Electronic Signature System . . 151
■ About the Electronic Signature System . . . . . . . . . . . . . . .
152
■ About Electronic Signatures. . . . . . . . . . . . . . . . . . . . . . . .
154
■ Configuring the Electronic Signature Settings. . . . . . . . . .
155
■ Configuring the
GeneMapper®
Software Action Map. . . . 156
■ Viewing the Electronic Signature History . . . . . . . . . . . . .
158
Chapter 5
Managing
Database Security
and User Access
Chapter 6
Managing the
Auditing and Electronic
Signature Systems
Chapter 7
Maintaining the
Software and
Database Application
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Chapter 6 Managing the Auditing and Electronic Signature Systems
About the Data Tracking Systems
About the Data Tracking Systems
About the Data
Tracking Systems
The GeneMapper® Software Version 4.1 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 6-1 summarizes the functions of the utilities.
Table 6-1
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.
131
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.
151
130
GeneMapper® Software Version 4.1 Installation and Administration Guide
Section 6.1
Section 6.1 Setting Up the Auditing System
This section covers:
■ About the Auditing System . . . . . . . . . . . . . . . . . . . . . . . .
132
■ Audit Maps, Objects, and Attributes . . . . . . . . . . . . . . . . .
134
■ Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . .
138
■ Managing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . .
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Chapter 6 Managing the Auditing and Electronic Signature Systems
About the Auditing System
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 5, “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.
Note: The Audit Map Configuration Software is an integral part of
the GeneMapper Software that cannot be deactivated or uninstalled.
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 133).
Can you use the default settings for the software?
(see page 134)
No
Yes
Configure the audit map settings as needed (see page 138).
Close the software.
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Chapter 6 Managing the Auditing and Electronic Signature Systems
About the Auditing System
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 145).
• Backup/restore audit records (page 149).
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 138).
1. Start and log in to the GeneMapper Software (see “Logging In
to and Out of the Software” on page 65).
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 115) can use the Audit Map Configuration
Software.
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Chapter 6 Managing the Auditing and Electronic Signature Systems
Audit Maps, Objects, and Attributes
Audit Maps, Objects, and Attributes
About the
GeneMapper®
Software
Audit Maps
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 6-1 has the attributes “created, deleted, and modified” because
users can create, delete, or modify analysis methods using the
GeneMapper Software.
Audit Map Objects
(AnalysisMethod selected)
Figure 6-1
Attributes for the
“AnalysisMethod” audit map object
Audit map objects and attributes
Note: Because most Applied Biosystems 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.
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Chapter 6 Managing the Auditing and Electronic Signature Systems
Audit Maps, Objects, and Attributes
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 6-2
displays the locations of the audit state controls in the software.
Audit map setting
Selected audit
map object
(enabled)
Current attribute
state
Possible states
for the selected
attribute
Figure 6-2
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 6-2 shows the result of all possible
combinations of the audit states for the audit map objects and object
attributes.
Table 6-2
Audit state inheritance matrix
State of the
Audit Object
(Enabled)
Audit State of the Attribute
ON
Silent
OFF
(Yes)
ON
Silent
OFF
(No)
OFF
OFF
OFF
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Chapter 6 Managing the Auditing and Electronic Signature Systems
Audit Maps, Objects, and Attributes
Auditing from
the Users
Perspective
When a user changes an audited object attribute, the software
displays the Reason(s) For Change dialog box (see Figure 6-3). 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.
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 6-3
Reason(s) For Change dialog box
Note: Figure 6-3 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
136
Figure 6-4 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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Chapter 6 Managing the Auditing and Electronic Signature Systems
Audit Maps, Objects, and Attributes
Figure 6-4
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 6-4.
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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Chapter 6 Managing the Auditing and Electronic Signature Systems
Configuring the Audit Map
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 133).
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 6-3 on page 141 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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Configuring the Audit Map
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 136). 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 146.
5. When you finish configuring the audit map, select FileExit to
close the software.
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Configuring the Audit Map
About the Audit
Map, Audited
Objects, and
Attributes
140
Table 6-3 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 6-3. Most
Applied Biosystems products employ the Audit Map Configuration
Software and install their audit map objects to the same location.
GeneMapper® Software Version 4.1 Installation and Administration Guide
Elements of the audit map for the GeneMapper® Software
Object
Allele
Analysis Method
Bin
BinSet
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.
Configuring the Audit Map
Kit
Attribute(s)
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Table 6-3
141
142
Table 6-3
Elements of the audit map for the GeneMapper® Software (continued)
Object
Panel
Project
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.
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.
analyzed
Off
created
Off
Represents the project data object that associates analysis
parameters, settings, and sample data for projects.
deleted
Off
modified
Off
RUN
On
When configured for auditing, the software creates a record of the
associated modification(s) made from the GeneMapper window.
Note: When the RUN attribute is activated, the software creates
audit records for edits made to the run folders within projects.
Configuring the Audit Map
GeneMapper® Software Version 4.1 Installation and Administration Guide
Matrix
Default
State
Chapter 6 Managing the Auditing and Electronic Signature Systems
Marker
Attribute(s)
Elements of the audit map for the GeneMapper® Software (continued)
Object
Run
Attribute(s)
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
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
OverrideGQ
Off
OverrideSQ
Off
Note: When the ALLELE attribute is activated, the software creates
audit records for edits made to the alleles of individual samples.
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.
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.
Configuring the Audit Map
Size Standard
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Table 6-3
143
144
Table 6-3
Elements of the audit map for the GeneMapper® Software (continued)
Object
Default
State
Off
created
Off
deleted
Off
OverrideStatus
Off
PROJECT
On
ProjectAdded
Off
ProjectRemoved
Off
RunAnalyzed
Off
Represents the study data object that associates projects for the
analysis of SNPlex™ System data.
When configured for auditing, the software creates a record of the
associated modification(s) made from the Study Manager.
Note: When the PROJECT attribute is activated, the software
creates audit records for edits made to the projects that are attached
to studies.
Configuring the Audit Map
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analyzed
Definition
Chapter 6 Managing the Auditing and Electronic Signature Systems
Study
Attribute(s)
Chapter 6 Managing the Auditing and Electronic Signature Systems
Managing Audit Records
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 . . . . . . . 149
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 115) 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 6-5
Components of the Audit History Viewer window
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Managing Audit Records
Starting the
Audit History
Viewer
IMPORTANT! Only users that belong to the Administrator user group
(see page 115) 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 65).
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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Managing Audit Records
Viewing Audit
Record Details
If you configured an audit object attribute for active auditing
(see step 4c on page 139), 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 6-6 Details of the Audit Record created for the change
shown in Figure 6-3 on page 136
Filtering the
Record Data
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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Managing Audit Records
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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Managing Audit Records
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 180). 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 183, 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 186). 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 65).
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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Managing Audit Records
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 145).
Restoring Audit
Records
1. Start and log in to the GeneMapper Software (see “Logging In
to and Out of the Software” on page 65 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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Section 6.2
Section 6.2 Setting Up the Electronic
Signature System
This section covers:
■ About the Electronic Signature System . . . . . . . . . . . . . . .
152
■ About Electronic Signatures. . . . . . . . . . . . . . . . . . . . . . . .
154
■ Configuring the Electronic Signature Settings. . . . . . . . . .
155
■ Configuring the GeneMapper® Software Action Map. . . .
156
■ Viewing the Electronic Signature History . . . . . . . . . . . . .
158
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About the Electronic Signature System
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 115) 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 153).
Can you use the default settings for the software?
(see page 156)
No
Yes
Configure the eSig settings as needed (see page 156).
Close the software.
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About the Electronic Signature System
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 158).
Semi-annually
Review the electronic signature system settings and
modify them as necessary to meet the regulation
requirements of your laboratory (see page 155).
1. Start and log in to the GeneMapper Software (see “Logging In
to and Out of the Software” on page 65).
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 115) can use the Electronic Signature
Administration Software.
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About Electronic Signatures
About Electronic Signatures
Electronic
Signatures from
the User’s
Perspective
Version 4.1 of 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 6-7). 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 6-7
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
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 153).
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
Configuring the GeneMapper® Software
Action Map
About the Action
Administration
Tab Settings
About the
GeneMapper®
Software
Action Maps
Configuring the
Action Maps
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.
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 6-7 on
page 154).
IMPORTANT! You must enable the electronic signature system as
explained on page 155 and save it before changes to the ESig Action
map can take effect.
1. If necessary, start the Electronic Signature Software (see
page 155).
2. In the ESig Administration window, select the Action
Administration tab.
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Configuring the GeneMapper® Software Action Map
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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Viewing the Electronic Signature History
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 155).
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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Viewing the Electronic Signature History
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 7
Maintaining the Software
and Database Application
Chapter 1
Getting Started
This chapter covers:
■ Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . .
162
Section 7.1: Managing Study, Project, and Sample Data . . 163
Chapter 2
Installation
Requirements and
Software Compatibility
■ Exporting Data Objects . . . . . . . . . . . . . . . . . . . . . . . . . . .
165
■ Exporting GeneMapper Data Objects . . . . . . . . . . . . . . . .
167
■ Exporting and Importing Reference Data . . . . . . . . . . . . .
172
Section 7.2: Managing the Database. . . . . . . . . . . . . . . . . . . 175
Chapter 3
Performing a
New Installation of the
GeneMapper® Software
Chapter 4
Upgrading a
Previous Version of the
GeneMapper® Software
■ Using the Oracle® Database . . . . . . . . . . . . . . . . . . . . . . . .
176
■ About the Dashboard Software . . . . . . . . . . . . . . . . . . . . .
178
■ Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . .
180
■ Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . .
183
■ Viewing Project Information . . . . . . . . . . . . . . . . . . . . . . .
185
■ Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . .
186
■ Generating a Database Report . . . . . . . . . . . . . . . . . . . . . .
188
Chapter 5
Managing
Database Security
and User Access
Chapter 6
Managing the
Auditing and Electronic
Signature Systems
Chapter 7
Maintaining the
Software and
Database Application
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Maintenance Overview
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 7-1, but are explained in Chapters 5 and 6 respectively.
Recommended
Maintenance
Schedule
Table 7-1
IMPORTANT! The maintenance schedule shown in Table 7-1
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 67).
• (Optional) Back up the GeneMapper database application (see page 186).
• Review the statistics for the database (see page 180), and if necessary:
– Export unused projects and data (see page 168).
– Allocate additional disk space (see page 183).
Monthly
• Defragment the computer hard drive.
• If using the auditing system, review the audit report (see page 145).
• If using the electronic signature system, review the history (see page 158).
Semi-annually
(6 months)
• Visit the Applied Biosystems website and check for software upgrades
• If using the auditing system, review the audit map and modify the settings as
necessary (see page 138).
• If using the electronic signature system, review the electronic signature settings
and modify them as necessary (see page 155).
As Needed
162
Export projects (see page 168), studies (see page 170), and audit records (see
page 149).
GeneMapper® Software Version 4.1 Installation and Administration Guide
Section 7.1
Section 7.1 Managing Study, Project, and
Sample Data
This section covers:
■ Exporting Data Objects . . . . . . . . . . . . . . . . . . . . . . . . . . .
165
■ Exporting GeneMapper Data Objects . . . . . . . . . . . . . . . .
167
■ Exporting and Importing Reference Data . . . . . . . . . . . . .
172
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Maintenance Overview
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 7-2 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 7-2
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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Chapter 7 Maintaining the Software and Database Application
Exporting Data Objects
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 7-2 lists the exportable data objects of the GeneMapper
Software.
Table 7-3
Exportable data objects of the GeneMapper® Software
Data Object(s)
• Analysis Method
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.
174
Audit Records
An *.aud file containing the metadata equivalents of the
audit records generated by the GeneMapper Software
149
Bin Set
An *.xml file containing the metadata equivalents of the
base pair ranges of all bins in the bin set
173
Panel
An *.xml file containing the metadata equivalents of the kit,
panel, and marker definitions
173
Projects
A *.ser file containing all of the analyzed data for a
project ‡
167
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).
128
Study
A *.ser file containing all of the analyzed data for a study
and associated projects ‡
170
• 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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Exporting Data Objects
Export Formats
166
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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Chapter 7 Maintaining the Software and Database Application
Exporting GeneMapper Data Objects
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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Chapter 7 Maintaining the Software and Database Application
Exporting GeneMapper Data Objects
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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Exporting GeneMapper Data Objects
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 173)
• Supporting data such as analysis methods, table settings, plot
settings, cluster plot settings, matrices, size standard definitions,
SNP sets, or report settings (see page 174)
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 7 Maintaining the Software and Database Application
Exporting GeneMapper Data Objects
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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Exporting GeneMapper Data Objects
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 173)
• Supporting data such as analysis methods, table settings, plot
settings, cluster plot settings, matrices, size standard definitions,
SNP sets, or report settings (see page 174)
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 7 Maintaining the Software and Database Application
Exporting and Importing Reference Data
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 7-4
Exportable reference data
Reference Data
• Kits
• Panels
Exported
from the…
See
Page
Panel
Manager
173
GeneMapper
Manager
174
• Bin sets
172
• Analysis methods
• Report settings
• Cluster plot
settings
• Size standard
definitions
• Matrices
• SNP sets
• Plot settings
• Table settings
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Chapter 7 Maintaining the Software and Database Application
Exporting and Importing Reference Data
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 173 and “Exporting Bin Sets” on
page 174.
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 173.
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 7 Maintaining the Software and Database Application
Exporting and Importing Reference Data
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 173.
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 7.2
Section 7.2 Managing the Database
This section covers:
■ Using the Oracle® Database . . . . . . . . . . . . . . . . . . . . . . . .
176
■ About the Dashboard Software . . . . . . . . . . . . . . . . . . . . .
178
■ Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . .
180
■ Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . .
183
■ Viewing Project Information . . . . . . . . . . . . . . . . . . . . . . .
185
■ Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . .
186
■ Generating a Database Report . . . . . . . . . . . . . . . . . . . . . .
188
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Chapter 7 Maintaining the Software and Database Application
Using the Oracle® Database
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
Applied Biosystems 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
Applied Biosystems does not support the use of SQL (using
SQLMGR or SQL*Plus) to query or modify the tables of the
GeneMapper database application.
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.
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Using the Oracle® Database
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
version 4.1 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 Applied
Biosystems’ agreement with the Oracle corporation.
IMPORTANT! Applied Biosystems 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. Applied Biosystems does not
support the use of the Oracle utilities and recommends against their
use by anyone other than a certified Oracle database administrator.
Oracle®
Documentation
Additional documentation for the Oracle 11g Database is available
from the Oracle web site:
www.oracle.com
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Chapter 7 Maintaining the Software and Database Application
About the Dashboard Software
About the Dashboard Software
Overview
The Database Dashboard utility that installs with the full version and
the server 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 Applied Biosystems software products, the
Database Dashboard utility may contain additional tabs for the
administration of the related applications.
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About the Dashboard Software
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. Applied Biosystems 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,
Applied Biosystems 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 multi-user environment,
you can avoid most problems caused by usage conflicts.
Note: Ideally, Applied Biosystems 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 115) can use the software.
1. In the desktop, select StartAll Programs
Applied BiosystemsDatabase 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 7 Maintaining the Software and Database Application
Reviewing the Database Statistics
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 7-1
180
Database Statistics table of the Dashboard Software
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Chapter 7 Maintaining the Software and Database Application
Reviewing the Database Statistics
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
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 7 Maintaining the Software and Database Application
Reviewing the Database Statistics
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 179).
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 183, 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 183.
If Available Space on the computer is
insufficient for disk allocation, export
data and delete it from the
GeneMapper database application.
< 80%
182
n/a
No maintenance required
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Chapter 7 Maintaining the Software and Database Application
Allocating Disk Space
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 7-5 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 180 to view
the table size statistics.
Table 7-5
Table spaces and related exportable data objects
Table
Approaching
Limit
Audit Data
Export and Remove
Audit records
See Page
149
Project Data
Projects and studies
167 / 170
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 7 Maintaining the Software and Database Application
Allocating Disk Space
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 179 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 181 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.
8. Click Allocate.
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Viewing Project Information
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 179).
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 7 Maintaining the Software and Database Application
Backing Up the Database
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
Applied Biosystems recommends 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 128 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 179).
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 7 Maintaining the Software and Database Application
Backing Up the Database
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 179).
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 7 Maintaining the Software and Database Application
Generating a Database Report
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
190
■ Uninstalling the Software. . . . . . . . . . . . . . . . . . . . . . . . . .
192
■ Troubleshooting Checklist . . . . . . . . . . . . . . . . . . . . . . . . .
198
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189
Appendix A Troubleshooting the Installation
Troubleshooting Tasks
Troubleshooting Tasks
IMPORTANT! If you have trouble installing the GeneMapper®
Software Version 4.1 on your computer, perform the following tasks
in the order given below.
Task
See page
1. Collect the installation log file.
®
Collect the
Installation
Log File
190
2. Check the Oracle database installation.
190
3. If necessary, uninstall the software.
192
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 Applied
Biosystems Technical Support if the troubleshooting procedures
in this appendix do not solve the installation problem.
Check the
Oracle® Database
Installation
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 192.
• If the Oracle database was not installed correctly, complete
Table A-1, “Troubleshooting checklist,” on page 198, then
contact Technical Support.
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Appendix A Troubleshooting the Installation
Troubleshooting Tasks
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 My Computer (Windows® XP) or Computer
(Windows Vista®) 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 Troubleshooting the Installation
Uninstalling the Software
Uninstalling the Software
Uninstall
Tasks
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.
193
2. If you are uninstalling an instrument or remote
autoanalysis configuration of the GeneMapper Software,
start the Data Collection Software.
194
• Instrument configuration – Start the Data Collection
Software on the local computer.
• Remote autoanalysis configuration – Start the Data
Collection Software on the remote Data Collection
computer.
3. Uninstall the software.
192
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Appendix A Troubleshooting the Installation
Uninstalling the Software
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 Troubleshooting the Installation
Uninstalling the Software
Starting the
Data Collection
Services
Before you uninstall an instrument or remote autoanalysis
configuration of the GeneMapper Software, start the Data Collection
services.
• If you are uninstalling an instrument configuration of the
GeneMapper Software, start the Data Collection services on the
local computer.
• If you are uninstalling a remote autoanalysis configuration, start
the Data Collection services on the remote Data Collection
computer.
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.
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Appendix A Troubleshooting the Installation
Uninstalling the Software
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.
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 Troubleshooting the Installation
Uninstalling the Software
Uninstall the
Software
This procedure removes the GeneMapper Software and the Oracle®
Database Standard Edition.
Note: If you installed the GeneMapper Software server, then
installed the client on the same computer, uninstall each one
separately.
To uninstall the GeneMapper Software:
1. If you are uninstalling an instrument configuration or a remote
autoanalysis configuration, be sure that the Data Collection
software is open (see page 194).
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 Troubleshooting the Installation
Uninstalling the Software
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.
Note: If you are uninstalling a remote autoanalysis configuration,
you will not receive the message above; however, be sure the
Data Collection services are open on the remote Data Collection
computer.
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 the Installation
Troubleshooting Checklist
Troubleshooting Checklist
IMPORTANT! Complete the Troubleshooting Checklist before
contacting Applied Biosystems 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.
Applied Biosystems 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 Troubleshooting the Installation
Troubleshooting Checklist
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 Applied Biosystems software:
Computer login information:
• User privileges:
• Local or networked domain:
Software configuration installed:
❏
❏
❏
❏
Instrument
Remote autoanalysis
Stand-alone
Client-server
Instrument and instrument computer information:
• Model:
• Data Collection Software version:
• Status of Data Collection services:
• Other Applied Biosystems 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 190)
• 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 Troubleshooting the Installation
Troubleshooting Checklist
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Appendix B
Operating the Software
from a Command Line
This appendix covers:
■ Operating the Software from a Command Line . . . . . . . . .
202
■ Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
207
■ Command Line Arguments . . . . . . . . . . . . . . . . . . . . . . . . . 211
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201
Appendix B Operating the Software from a Command Line
Operating the Software from a Command Line
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! Applied Biosystems supports the use of the command
line interface only as it is explained in this manual.
Note: If you are unfamiliar with Microsoft DOS, Applied Biosystems
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 Operating the Software from a Command Line
Operating the Software from a Command Line
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 Operating the Software from a Command Line
Operating the Software from a Command Line
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 211 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 Operating the Software from a Command Line
Operating the Software from a Command Line
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 208 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 Operating the Software from a Command Line
Operating the Software from a Command Line
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 Operating the Software from a Command Line
Example Commands
Example Commands
Example
Commands in
This Section
■ Example #1: Basic Sample File Analysis . . . . . . . . (see below)
■ Example #2: SNPlex™ System Analysis . . . . . . . . . . . . . . . 208
■ Example #3: Sample File Analysis with Named Ladders . . 209
■ Example #4: Export of Project Data . . . . . . . . . . . . . . . . . . 210
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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Appendix B Operating the Software from a Command Line
Example Commands
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 Operating the Software from a Command Line
Example Commands
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 Operating the Software from a Command Line
Example Commands
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 Operating the Software from a Command Line
Command Line Arguments
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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212
Table B-1 Summary of arguments for the GeneMapper® Software command line interface
Argument
Action/Definition
Usage
-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.
GeneMapper® Software Version 4.1 Installation and Administration Guide
where project1 and project2 are the names
of the projects to be deleted.
-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.
Command Line Arguments
-analysismethod “method”
Appendix B Operating the Software from a Command Line
Specifies the name of the analysis
method to use in the analysis of the
specified project.
-analysismethod
Argument
-exportgenotypetable
-exportplotsampletable
-exportsampletable
-exportsizemap
-exportsnptable
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 run, the argument
specifies the run folder of interest
• 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 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).
Command Line Arguments
-folder
Action/Definition
Appendix B Operating the Software from a Command Line
GeneMapper® Software Version 4.1 Installation and Administration Guide
Table B-1 Summary of arguments for the GeneMapper® Software command line interface (continued)
213
214
Table B-1 Summary of arguments for the GeneMapper® Software command line interface (continued)
Argument
Action/Definition
Usage
-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.
GeneMapper® Software Version 4.1 Installation and Administration Guide
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.
-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.
Command Line Arguments
Prints a summary of the commands for
the command-line interface.
Appendix B Operating the Software from a Command Line
-help
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:
• h – Hides the user interface
• p “port” – Specifies the monitoring TCP/IP
port number (default is 8393)
-panel
-password
215
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.
Command Line Arguments
• b – Attaches bin names to the exported
Genotype table
Appendix B Operating the Software from a Command Line
GeneMapper® Software Version 4.1 Installation and Administration Guide
Table B-1 Summary of arguments for the GeneMapper® Software command line interface (continued)
216
Table B-1 Summary of arguments for the GeneMapper® Software command line interface (continued)
Argument
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.
GeneMapper® Software Version 4.1 Installation and Administration Guide
• ctrl1 and ctrl2 … are the names of the
positive control sample files separated by a
space.
-project
-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).
Command Line Arguments
Usage
Appendix B Operating the Software from a Command Line
-poscontrol
Action/Definition
Appendix C
Migrating Data Using the
GeneMapper® Database
Utility Wizard
The GeneMapper® Database Utility Wizard is included on the:
• GeneMapper® Software v4.1 Full Installation DVD
• GeneMapper® Software v4.1 Installer for Server DVD
• GeneMapper® Software v4.1 Upgrade Software v4.0 to v4.1
DVD
Use the utility wizard to export/import your data when upgrading to
GeneMapper® Software v4.1.
1. Insert the full installation, server, or upgrade DVD into the DVD
drive.
2. In the launcher window, start the GeneMapper Database Utility
Wizard:
• For the full or server installation DVD – Click Software
Extras, then click GeneMapper Database Utility
Wizard.
• For the upgrade DVD – Select GeneMapper v4.1 Full
Upgrade or GeneMapper v4.1 Server Upgrade, then
click GeneMapper Database Utility Wizard.
3. In the GeneMapper Database Utility Wizard window, select the
task you want to perform:
• 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.
• 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.
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217
Appendix C Migrating Data Using the GeneMapper® Database Utility Wizard
Other tasks you can perform with the utility wizard are:
• UPGRADE gives a detailed description of the steps
required to perform the upgrade and exports the database
from the currently-installed GeneMapper Software version.
Note: The UPGRADE option only exports the database; it
does not actually upgrade the GeneMapper Software.
• MIGRATE provides a workflow detailing how to migrate
the GeneMapper Software and database from one computer
to another and exports the database from the
currently-installed GeneMapper Software version.
Note: The MIGRATE option only exports the database; it
does not actually migrate the GeneMapper Software.
• RECOVER describes the workflow needed to restore the
database after a failed attempt to upgrade or migrate data.
This option will import the database into the version of the
GeneMapper Software that was installed prior to the
upgrade/migration attempt.
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Appendix C Migrating Data Using the GeneMapper® Database Utility Wizard
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.
Log File
The wizard log file is written to: <C>:\AppliedBiosystems\
logs\GeneMapper41_DB_Utility\wizard.log
GeneMapper® Software Version 4.1 Installation and Administration Guide
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Appendix C Migrating Data Using the GeneMapper® Database Utility Wizard
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Appendix D
Software Warranty Information
This appendix covers:
■ Computer Configuration . . . . . . . . . . . . . . . . . . . . . . . . . .
222
■ Limited Product Warranty . . . . . . . . . . . . . . . . . . . . . . . . .
222
GeneMapper® Software Version 4.1 Installation and Administration Guide
221
Appendix D Software Warranty Information
Computer Configuration
Computer Configuration
Applied Biosystems supplies or recommends certain configurations
of computer hardware, software, and peripherals for use with its
instrumentation. Applied Biosystems reserves the right to decline
support for or impose extra charges for supporting nonstandard
computer configurations or components that have not been supplied
or recommended by Applied Biosystems. Applied Biosystems also
reserves the right to require that computer hardware and software be
restored to the standard configuration prior to providing service or
technical support. For systems that have built-in computers or
processing units, installing unauthorized hardware or software may
void the Warranty or Service Plan.
Limited Product Warranty
Limited Warranty
222
Applied Biosystems warrants that for a period of ninety (90) days
from the date the warranty period begins, its GeneMapper® Software
will perform substantially in accordance with the functions and
features described in its accompanying documentation when properly
installed on the instrument system for which it is designated, and that
for a period of ninety (90) days from the date the warranty period
begins, the tapes, diskettes, or other media bearing the software
product will be free of defects in materials and workmanship under
normal use. If buyer believes that it has discovered a failure of the
software to satisfy the foregoing warranty, and if buyer notifies
Applied Biosystems of such failure in writing during the ninety (90)
day warranty period, and if Applied Biosystems is able to reliably
reproduce such failure, then Applied Biosystems, at its sole option,
will either (i) provide any software corrections or “bug-fixes” of the
identified failure, if and when they become commercially available,
to buyer free of charge, or (ii) notify buyer that Applied Biosystems
will accept a return of the software from the buyer and, upon such
return and removal of the software from buyer's systems, terminate
the license to use the software and refund the buyer's purchase price
for the software. If there is a defect in the media covered by the above
warranty and the media is returned to Applied Biosystems within the
ninety (90) day warranty period, Applied Biosystems will replace the
GeneMapper® Software Version 4.1 Installation and Administration Guide
Appendix D Software Warranty Information
Limited Product Warranty
defective media. Applied Biosystems does not warrant that the
software will meet buyer's requirements or conform exactly to its
documentation, or that operation of the software will be
uninterrupted or error free.
Warranty Period
Effective Date
Any applicable warranty period under these sections begins on the
earlier of the date of installation or ninety (90) days from the date of
shipment for software installed by Applied Biosystems personnel.
For all software installed by the buyer or anyone other than
Applied Biosystems, the applicable warranty period begins the date
the software is delivered to the buyer.
Warranty Claims
Warranty claims must be made within the applicable warranty period.
Warranty
Exceptions
The above warranties do not apply to defects resulting from misuse,
neglect, or accident, including without limitation: operation outside
of the environmental or use specifications, or not in conformance
with the instructions for the instrument system, software, or
accessories; improper or inadequate maintenance by the user;
installation of software or interfacing, or use in combination with
software or products, not supplied or authorized by
Applied Biosystems; and modification or repair of the product not
authorized by Applied Biosystems.
THE FOREGOING PROVISIONS SET FORTH
APPLIED BIOSYSTEMS' SOLE AND EXCLUSIVE
REPRESENTATIONS, WARRANTIES, AND OBLIGATIONS
WITH RESPECT TO ITS PRODUCTS, AND
APPLIED BIOSYSTEMS MAKES NO OTHER WARRANTY
OF ANY KIND WHATSOEVER, EXPRESSED OR IMPLIED,
INCLUDING WITHOUT LIMITATION, WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE, WHETHER ARISING FROM A STATUTE OR
OTHERWISE IN LAW OR FROM A COURSE OF DEALING
OR USAGE OF TRADE, ALL OF WHICH ARE EXPRESSLY
DISCLAIMED.
Warranty
Limitations
The remedies provided herein are the buyer's sole and exclusive
remedies. Without limiting the generality of the foregoing, in no
event shall Applied Biosystems be liable, whether in contract, tort,
warranty, or under any statute (including without limitation any trade
practice, unfair competition, or other statute of similar import) or on
GeneMapper® Software Version 4.1 Installation and Administration Guide
223
Appendix D Software Warranty Information
Limited Product Warranty
any other basis, for direct, indirect, punitive, incidental, multiple,
consequential, or special damages sustained by the buyer or any other
person or entity, whether or not foreseeable and whether or not
Applied Biosystems is advised of the possibility of such damages,
including without limitation, damages arising from or related to loss
of use, loss of data, failure or interruption in the operation of any
equipment or software, delay in repair or replacement, or for loss of
revenue or profits, loss of good will, loss of business, or other
financial loss or personal injury or property damage.
No agent, employee, or representative of Applied Biosystems has
any authority to modify the terms of this Limited Warranty Statement
or to bind Applied Biosystems to any affirmation, representation, or
warranty concerning the product that is not contained in this Limited
Warranty Statement, and any such modification, affirmation,
representation, or warranty made by any agent, employee, or
representative of Applied Biosystems will not be binding on
Applied Biosystems unless in a writing signed by an executive
officer of Applied Biosystems.
This warranty is limited to the buyer of the product from
Applied Biosystems and is not transferable.
Some countries or jurisdictions limit the scope of or preclude
limitations or exclusion of warranties, of liability, such as liability for
gross negligence or willful misconduct, or of remedies or damages,
as or to the extent set forth above. In such countries and jurisdictions,
the limitation or exclusion of warranties, liability, remedies or
damages set forth above shall apply to the fullest extent permitted by
law, and shall not apply to the extent prohibited by law.
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GeneMapper® Software Version 4.1 Installation and Administration Guide
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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225
Glossary
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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Glossary
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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227
Glossary
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 231.
See “negative control” on page 230.
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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Glossary
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; Applied Biosystems 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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229
Glossary
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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Glossary
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 Applied Biosystems 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 226.
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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231
Glossary
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 Applied Biosystems
size standards are labeled with a red or orange dye.
SNaPshot® kit
An Applied Biosystems 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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Glossary
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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Glossary
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GeneMapper® Software Version 4.1 Installation and Administration Guide
Index
A
ABB (automatic bin builder), definition 225
Access Control Administration Software 96
access control list, definition 225
action maps 156
activating
auditing system 138
electronic signature system 155
user accounts 125
admin profile, definition 225
admin security group, definition 225
admin user group, definition 225
admin user, definition 225
Administrator
default user account 116
default user profile 115
administrator privileges 16
verifying 17, 193
administrator, role 179
ADO PQV column 225
Adobe Acrobat Reader 16
AE PQV column 225
algorithm, definition 226
all user group, definition 226
Allele audit map object 141
ALLELE audit map object attribute 143
allele-calling, definition 226
allelic ladders, specifying in a command line
analysis 215
allocating, disk space 183
AN PQV column 226
Analysis Method audit map object 141
analysis methods
definition 226
import via a command line 214
specifying in a command line 212
analysis methods, backing up 174
analysismethod argument 212
API support 176
applications, managing 110
Applied Biosystems
contacting xii
customer feedback on documentation xii
Information Development department xii
Technical Support xii
Applied Biosystems 3500 series genetic
analyzers 5
arguments (command line interface)
about 211
analysismethod 212
commandline 212
deleteproject 212
deletesnpset 212
exportall 212
exportanalyzedeps 212
exportbinoffsettable 212
exportclustergenotypetable 212
exportgenotypetable 213
exportplotsampletable 213
exportsampletable 213
exportsizemap 213
exportsnptable 213
folder 213
help 214
importanalysismethod 214
importsizestandard 214
importsnpset 214
ladder 215
negcontrol 215
option 215
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235
Index
panel 215
password 215
poscontrol 216
project 216
sizestandard 216
snpset 216
username 216
association, definition 227
assumptions for using this guide ix
Audit Data table 181
audit event, definition 227
audit map
configuring 138
Audit Map Configuration Software
about 132
global auditing setting 138
starting 133
audit map definition 227
audit map object attributes
about 140
states 139
audit map objects
about 140
states 138
Audit Map Viewer Software
about 145
starting 146
audit maps 134, 140
about 134
configuring 138
viewing the history 145
audit object attributes 134
audit object, definition 227
audit records
archiving 149
backing up 149
filtering 147
removing 149
viewing 146
audit records, definition 227
audit state inheritance 135
auditing 95, 129
auditing setting (global) 138
236
auditing system
about 132
maintaining 133
setup 132
Auto Extend 181
automatic notification 98
automating software operations
autopanelizer, definition 227
202
B
backing up
analysis methods 174
audit records 149
bin sets 174
cluster plot settings 174
data 72
database 186
kits 173
matrices 174
panels 173
plot settings 174
projects 168
report settings 174
size standards 174
SNP sets 174
studies 170
table settings 174
batch file, creating for command line
operation 203
BD PQV column 227
Bin audit map object 141
BIN audit map object attribute 142
bin offsets, export via a command line 212
BIN PQV column 227
bin sets, backing up 174
BinSet audit map object 141
BINSET audit map object attribute 141
bold text, when to use ix
C
cache, definition 227
CAUTION, description
xiv
GeneMapper® Software Version 4.1 Installation and Administration Guide
Index
CC PQV column 227
challenge, definition 227
changing, user password 124
checklist, troubleshooting 198
Checksum settings 155
client configuration (remote autoanalysis)
description 51
installation tasks 52
client configuration (stand-alone)
description 51
installation tasks 52
client-server configuration
description 23, 76
installing client 56
installing server 48
client-server installation workflow 45
Cluster Plot Genotypes table, export via a
command line 212
cluster plot settings, backing up 174
command line interface
about 202
arguments 211
example commands 207
hiding the user interface 215
specifying allelic ladders 215
specifying analysis methods 212
specifying negative controls 215
specifying panels 215
specifying port setting 215
specifying positive controls 216
specifying size standards 216
specifying SNP sets 216
specifying the project 216
commandline argument 212
compatibility matrix 14
computer
configuration requirement 222
Technical Support for altered
configuration 222
computer requirements
full installation 11
verifying minimum 12
Configuration tab settings 155
configurations, determining existing 74
configurations, new installation
client-server 23, 45, 76
instrument 27
remote autoanalysis 22, 33
stand-alone 22, 40
configurations, upgrade
instrument 77
remote autoanalysis 80
stand-alone 83
configuring
action maps 156
audit map 138
automatic notification 98
electronic signature system 155
connecting to a new host 66, 92
control security group, definition 228
controlling access to the software 95, 129
conventions
bold text ix
for describing menu commands ix
IMPORTANTS! x
italic text ix
Notes x
safety xiv
user attention words x
creating
security profiles 113
user accounts 121
user profiles 113
customer feedback, on Applied Biosystems
documents xii
D
DANGER, description xiv
data
archiving 163, 175
backing up before upgrading software 72
export via a command line 212
data access control, definition 228
Data Collection services
starting on local computer 28
starting on remote computer 33
GeneMapper® Software Version 4.1 Installation and Administration Guide
237
Index
Data Collection Software
connecting to remotely 33
installing with locally 27
starting 28, 33, 53, 78, 81, 194
stopping 32, 87, 197
data compatibility 14
data group, definition 228
data rights, definition 228
Data Service output window 29, 34, 35, 54
Data Service, checking if started without
errors 29, 34, 54, 79, 82, 195
database
API support 176
backing up 186
SQL support 176
statistics, viewing 180
Database Dashboard software
about 178
logging into for the first time 63
database utilities
Audit Configuration Tool 132
Audit Map Viewer Software 145
Electronic Signature Software 152
database, definition 228
deactivating
auditing system 138
electronic signature system 155
user accounts 125
default user name 61
deleteproject argument 212
deletesnpset argument 212
deleting, user accounts 123
destination folder, selecting 31, 37, 41, 48, 58
disk space, allocating 183
documentation, related xi
domain name, verifying 17, 193
DOS window, during installation 31, 39, 43,
50, 58, 86
DP PQV column 228
238
E
editing
security profiles 114
user account 124
user accounts 123
user profiles 114
Electronic Signature Challenge Text 157
electronic signature records
about 154
viewing 158
electronic signature system
about 152
configuring 155
maintaining 153
Electronic Signature Verification dialog
box 154
electropherogram data, export via a command
line 212
enabling
auditing 138
electronic signatures 155
ergonomics, safety xvi
eSig software. See electronic signature system
exportall argument 212
exportanalyzedeps argument 212
exportbinoffsettable argument 212
exportclustergenotypetable argument 212
exportgenotypetable argument 213
exporting
analysis methods 174
bin sets 174
cluster plot settings 174
database 186
kits 173
matrices 174
panels 173
plot settings 174
projects 168
reference data 172
report settings 174
security settings 128
size standards 174
SNP sets 174
GeneMapper® Software Version 4.1 Installation and Administration Guide
Index
studies 170
table settings 174
exportplotsampletable argument 213
exportsampletable argument 213
exportsizemap argument 213
exportsnptable argument 213
history
auditing (viewing) 145
electronic signature (viewing) 158
History Viewer tab settings 158
host name, obtaining 35
how to use this guide ix, xiv
F
I
filtering
audit records 147
record data 147
folder argument 213
full computer name. See host name
full installation
computer requirements 11
workflow 25
importanalysismethod argument 214
importing
analysis methods (via a command
line) 214
projects 169
security settings 128
size standard definition (via a command
line) 214
SNP sets (via a command line) 214
studies 171
importsizestandard argument 214
importsnpset argument 214
Information Development department,
contacting xii
inheritance, audit state 135
installation DVDs 18
installation process workflow 10
installation tasks
client configuration (remote
autoanalysis) 52
client configuration (stand-alone) 52
instrument configuration 27
instrument configuration (upgrade) 77
remote autoanalysis configuration 33
stand-alone configuration 40
installation tasks, upgrading
remote autoanalysis configuration 80
stand-alone configuration 83
installation workflow
client-server 45
full 25
upgrade 70
installation, troubleshooting 190
installed elements 115
35
G
GeneMapper® Database Utility Wizard 73,
217
GeneMapper® Software
logging out 67, 93
new features in v4.1 4
registering after new installation 60
registering after upgrade 88
uninstalling 196
Genotypes table (Cluster Plot), export via a
command line 212
Genotypes table, export via a command
line 212
gm, default user name 61
GQ PQV column 229
guidelines
Audit Map Configuration Software 138
Electronic Signature Software 152
H
hazard symbols. See safety symbols, on
instruments
help argument 214
help, online, accessing xi
GeneMapper® Software Version 4.1 Installation and Administration Guide
239
Index
K
Marker audit map object 142
MARKER audit map object attribute 142
matrices, backing up 174
Matrix audit map object 142
menu commands, conventions for
describing ix
migration utility. See GeneMapper® Database
Utility Wizard 217
minimum requirements for computer 12
MNF PQV column 230
monitor requirements 11
moving and lifting, safety xv
MSDSs, obtaining xii
Kit audit map object 141
kits, backing up 173
N
installer, starting 30, 36, 40, 48, 56, 85
installing software
instrument configuration 30
remote autoanalysis configuration 36
instrument compatibility 14
instrument configuration
description 27
installation tasks (new installation) 27
installing (new installation) 30
instrument configuration, upgrade
installation tasks 77
italic text, when to use ix
L
ladder argument 215
license agreement, Oracle® database 6
LIMS, linking the software using the command
line interface 202
LMS, definition 229
log file, collecting 190
log on requirements 16
logging out of the GeneMapper®
Software 65, 91
LPH PQV column 229
M
maintaining
auditing system 132, 133
database 182
electronic signature system 153
security system 97
software and database 162
maintenance schedule 162
managing
software and database 162
user accounts 120
user profiles 110
240
NB PQV column 230
negative controls, specifying in a command line
analysis 215
negcontrol argument 215
new features, GeneMapper® Software v4.1 4
new host, connecting to 66, 92
new installation
instrument configuration 30
registering the software 60
remote autoanalysis configuration 36
O
OBA PQV column 230
OIR (Override Inherited Rights) 111
online help, accessing xi
operating system
requirements 11
Operator default user account 116
option argument 215
Oracle® database
checking installation of 190
maintenance 162
tools, use of 177
viewing statistics 180
Oracle® database license agreement 6
GeneMapper® Software Version 4.1 Installation and Administration Guide
Index
OS PQV column 230
OverrideGQ audit map object attribute 143
OverrideSQ audit map object attribute 143
OverrideStatus audit map object
attribute 144
OVL PQV column 230
P
panel argument 215
Panel audit map object 142
PANEL audit map object attribute 141
panels
backing up 173
specifying in a command line
analysis 215
password argument 215
password policies
about 98
Max Login Attempts 98
Minimum Password Width 101
Password Grace Logins 100
Password kept per usage 100
Password Lifetime 100
Password Reuse Period 100
Send log message 99
Set User State 99
passwords
changing 61, 63, 124
default user accounts 120
PHR PQV column 230
plot settings, backing up 174
poscontrol argument 216
positive controls, specifying in a command line
analysis 216
Primer Focus® kit, definition 231
primer, definition 231
procedural workflow, GeneMapper®
Software 7
profile, definition 231
project argument 216
Project audit map object 142
PROJECT audit map object attribute 144
Project Data table 181
project settings, definition 231
ProjectAdded audit map object attribute 144
ProjectRemoved audit map object
attribute 144
projects
backing up 168
deletion via a command line 212
importing 169
specifying in a command line
analysis 216
R
Reason(s) For Change dialog box 136
recommended maintenance schedule 162
Reference Data table 181
reference data, exporting 172
registering the GeneMapper® Software
for upgrade installation 88
new installation 60
registration code 60, 88
remote autoanalysis configuration
description 22
installation tasks (new installation) 33
installation tasks (upgrade) 80
installing (new installation) 36
removing
audit records 149
the GeneMapper Software 196
repetitive motion, safety xvi
report settings, backing up 174
Require UserID? setting 155
requirements
log on 16
user accounts 16
verifying minimum computer 12
verifying user account 17
restoring
audit records 149
projects 169
security settings 128
GeneMapper® Software Version 4.1 Installation and Administration Guide
241
Index
studies 171
rights, definition 232
Run audit map object 143
RUN audit map object attribute 142
run folder, specifying in a command line
analysis 213
RunAnalyzed audit map object attribute 144
S
safety
before operating the instrument xv
conventions xiv
ergonomic xvi
moving/lifting xv
repetitive motion xvi
workstation xvi
Sample audit map object 143
SAMPLE audit map object attribute 143
sample data file compatibility 14
Samples table, export via a command
line 212
Scientist default user account 116
Scientist default user profile 115
scripting software operations 202
security group, definition 232
security ID, definition 232
security log 126
security profiles
creating 113
editing 114
security settings
exporting 128
importing 128
security system
about 96
maintenance 97
reporting 126
setup 97
Service Console 28, 34, 54, 78, 81, 194
setting
action maps 156
242
audit map object attribute states 139
audit map object states 138
electronic signature settings 155
global auditing setting 138
password policies 98
setting up
auditing system 132
electronic signature system 155
security system 97
Show EULA option 121
SHP PQV column 232
signatures (electronic) enabling 155
silent auditing, definition 232
size match editor, definition 232
Size Standard audit map object 143
size standard definition, import via a command
line 214
size standards
backing up 174
specifying in a command line
analysis 216
sizestandard argument 216
Sizing table (Samples Plot), export via a
command line 213
SNaPshot® analysis, definition 232
SNF PQV column 232
SNP sets
deletion via a command line 212
import via a command line 214
specifying in a command line
analysis 216
SNP sets, backing up 174
SNPlex™ system analysis, definition 233
snpset argument 216
software
Access Control Administration 96
Audit Map Configuration Software 132
Audit Map Viewer Software 145
controlling access to 96
maintenance 162
SP PQV column 233
SPA PQV column 233
GeneMapper® Software Version 4.1 Installation and Administration Guide
Index
SPU PQV column 233
SQ PQV column 233
SQL support 176
stand-alone configuration
description 22
installation tasks (new installation) 40
installation tasks (upgrade) 83
installing (new installation) 40
starting
Access Control Administration
Software 96
Audit Map Configuration Software 133
Audit Map Viewer Software 146
Esig Administration Software 153
studies
backing up 170
importing 171
Study audit map object 144
suspending, user accounts 125
T
table settings, backing up 174
Technical Support
contacting xii
for computers with altered
configuration 222
information needed before
contacting 198
Technician default user profile 115
training, information on xii
troubleshooting checklist 198
troubleshooting tasks 190
U
uninstalling the GeneMapper Software 196
upgrade installation
registering the software 88
upgrade installation workflow 70
user accounts 120
activating 125
Administrator 116
changing password 124
creating 121
deactivating 125
deleting 123
editing 123, 124
Operator 116
requirements 16
Scientist 116
status 121
suspending 125
User Accounts dialog box 17, 193
user attention words, defined x
user guide
attention words x
audience ix
how to use ix, xiv
purpose of ix
text conventions ix
user name, default 61
user privileges 116
user profiles
about 110
creating 113
default privileges 115
editing 114
username argument 216
V
verifying
administrator privileges 17, 193
computer minimum requirements 12
domain name 17, 193
user account 17
viewing
audit history 145
audit record details 147
audit records 146, 149
database statistics 180
electronic signature records 158
security log 126
W
WARNING, description xiv
warranty
GeneMapper® Software Version 4.1 Installation and Administration Guide
243
Index
claims 223
exceptions 223
for computers with altered
configuration 222
limitations 223
period 222
warranty period, effective date 223
workflow
client-server installation 45
full installation 25
GeneMapper® Software 7
installation process overview 10
upgrade installation 70
workstation safety xvi
244
GeneMapper® Software Version 4.1 Installation and Administration Guide
Part Number 4403614 Rev. A 04/2009
Applied Biosystems
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Phone 650.638.5800 | Toll Free 800.345.5224
www.appliedbiosystems.com
Technical Resources and Support
For the latest technical resources and
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please refer to our Web site at
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