Thermo Fisher Scientific GeneMapper® ID-X Software Owner's Manual

Administrator’s Guide
GeneMapper® ID-X Software
Version 1.0
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Administrator’s Guide
Setting Up
User Accounts
and User Access
GeneMapper® ID-X
Software
Version 1.0
Managing the
Auditing System
Managing the
E-Signature System
Maintaining the
Software and
Database
Application
© Copyright 2007, Applied Biosystems. All rights reserved.
For Research Use Only. Not for use in diagnostic procedures.
Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that
may appear in this document.
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. 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.
Notice to Purchaser: License Disclaimer.
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 Applera Corporation,
either expressly, or by estoppel.
Applera, Applied Biosystems, AB (Design), and GeneMapper are registered trademarks of Applera Corporation or its subsidiaries
in the U.S. and/or certain other countries.
This product includes software developed by the Apache Software Foundation.
This product includes software developed by the ExoLab Project.
JNIRegistry is copyrighted © by ICE Engineering, Inc.
Microsoft and Windows are registered trademarks of Microsoft Corporation.
Oracle is a registered trademark of Oracle Corporation.
All other trademarks are the sole property of their respective owners.
Part Number 4376327 Rev. A
09/07
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Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . ix
How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Chapter 1
Setting Up User Accounts and User Access. . . . . . . . 1
GeneMapper® ID-X Software Electronic Data Chain-of-Custody
Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Overview of the Security System . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Default User Accounts, Profiles, User Groups, and Security Groups
..................................................... 5
Default Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Default Security Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Default User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Default User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Starting the Security Manager . . . . . . . . . . . . . . . . . . . . . . . . 12
Setting Password Policies . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Setting Up User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Using Default User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . 16
Creating New User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . 18
Creating a User Account for Autoanalysis . . . . . . . . . . . . . . . 21
Using Security Groups to Control Data Access . . . . . . . . . . . . . . 24
Customizing Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Creating Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Editing or Deleting Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Profile Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Customizing User and Security Groups . . . . . . . . . . . . . . . . . . . . 34
Creating User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
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Creating Security Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Maintaining User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Editing User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Changing the Password for a User Account . . . . . . . . . . . . . 39
Deleting a User Account . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Activating, Deactivating, and Suspending User Accounts . . 40
Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Exporting and Importing the Security Settings . . . . . . . . . . . . . . 44
Chapter 2
Managing the Auditing System . . . . . . . . . . . . . . . . . 45
Overview of the Audit System . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Default Audit Map Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Using the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Starting the Audit Manager . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Printing an Audit Map Settings Report . . . . . . . . . . . . . . . . . 53
Audit Map Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Viewing Audit History Records . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Starting the Audit History Viewer . . . . . . . . . . . . . . . . . . . . . . 57
Creating Audit Record Queries . . . . . . . . . . . . . . . . . . . . . . . 58
Performing Audit Record Queries and Viewing Audit Records
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Example Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Printing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Backing Up, Removing, and Restoring Audit Records . . . . . . . . 63
Chapter 3
Managing the E-Signature System . . . . . . . . . . . . . . 65
Overview of the Electronic Signature (E-Signature) System . . . . 66
Default E-Signature Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Configuring the E-Signature System . . . . . . . . . . . . . . . . . . . . . . 67
Starting the E-Signature Manager . . . . . . . . . . . . . . . . . . . . . 68
Enabling the E-Signature Function . . . . . . . . . . . . . . . . . . . . 68
Configuring E-Signature Actions . . . . . . . . . . . . . . . . . . . . . . 70
E-Signature Action Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
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Viewing E-Signature Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Specifying E-Signature Queries . . . . . . . . . . . . . . . . . . . . . . . 72
Performing E-Signature Queries and Viewing E-Signature
Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Printing E-Signature Records . . . . . . . . . . . . . . . . . . . . . . . . . 74
Backing Up, Removing, and Restoring E-Signature Records . . . 74
Chapter 4
Maintaining the Software and Database Application 75
Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Recommended Maintenance Schedule . . . . . . . . . . . . . . . . . 76
Using and Maintaining the Oracle® Database . . . . . . . . . . . . . . . 77
Database Access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Maintaining the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Using the Database Dashboard Software . . . . . . . . . . . . . . . . . . 79
Dashboard Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Setting a Dashboard Password
. . . . . . . . . . . . . . . . . . . . . . 80
Starting the Database Dashboard . . . . . . . . . . . . . . . . . . . . . 80
Reviewing the Database Statistics
. . . . . . . . . . . . . . . . . . . . . . . 81
Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Options for Creating More Disk Space . . . . . . . . . . . . . . . . . 83
Allocating Additional Disk Space . . . . . . . . . . . . . . . . . . . . . . 84
Viewing Project Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
When to Back Up the Oracle Database . . . . . . . . . . . . . . . . . 87
Backing Up (Exporting) the Database . . . . . . . . . . . . . . . . . . 87
Restoring (Importing) the Database . . . . . . . . . . . . . . . . . . . . 88
Generating a Database Report . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Appendix A
Operating the Software from a Command Line . . . . 91
Operating the Software from a Command Line . . . . . . . . . . . . . . 92
Creating a Batch File to Run the Command-Line Interface . . 93
Example Batch File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Running the Batch File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
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Example #1: Analyze Sample Files . . . . . . . . . . . . . . . . . . . . 97
Example #2: Analyze Sample Files with Named Ladders . . . 98
Example #3: Export Project Data . . . . . . . . . . . . . . . . . . . . . . 99
Example #4: Export Sample Plot to PDF . . . . . . . . . . . . . . . . 99
Command-Line Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
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Preface
How to Use This Guide
Purpose of
This Guide
This guide describes the procedures for configuring and maintaining
the following administrative tools of the GeneMapper® ID-X
Software Version 1.0 (v1.0) after it is installed:
• Security Manager (Chapter 1) −Use this tool to control a user’s
access to the GeneMapper ID-X Software, to functions in the
software, and to data (projects, plot settings, table settings, kits
and panels, report settings, size standards, analysis methods).
• Audit Manager (Chapter 2) −Use this tool to configure the
auditing system to create and record an audit trail for changes
(create/modify/delete) to data.
• Esig Administrator (Chapter 3) − Use this tool to configure
the electronic signature system that requires users to sign-off on
changes to data.
• Database Dashboard (Chapter 4) −Use this tool to monitor
real-time information about database performance, space
utilization, and operating systems usage. You can also allocate
additional disk space and back up the database.
Note: For instructions on configuring the software to prepare for
analysis, see the GeneMapper® ID-X Software v1.0 Human
Identification Getting Started Guide.
Audience
Assumptions
This guide is written for laboratory personnel responsible for
configuring and maintaining the GeneMapper ID-X Software.
This guide assumes that you have a working knowledge of the
Microsoft® Windows® operating system.
GeneMapper® ID-X Software v1.0 Administrator’s Guide
vii
Preface
How to Use This Guide
Text Conventions
This guide uses the following conventions:
• Bold indicates user action. For example:
Enter 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.
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.
viii
GeneMapper® ID-X Software v1.0 Administrator’s Guide
Preface
How to Obtain More Information
How to Obtain More Information
Related
Documentation
The following related documents are shipped with the software:
• GeneMapper® ID-X Software Version 1.0 Installation Guide –
Describes how to install the software.
• GeneMapper® ID-X Software Version 1.0 Human
Identification Getting Started Guide – Explains how to set up
the software, configure software settings, create projects,
analyze example data provided with the GeneMapper ID-X
Software, and view, interpret, and export results.
• GeneMapper® ID-X Software Version 1.0 Online Help –
Describes specific software features and provides procedures
for common tasks.
• GeneMapper® ID-X Software Version 1.0 Reference Guide –
Describes peak detection and allele calling algorithms, quality
values, and software optimization, validation, and verification.
• GeneMapper® ID-X Software Version 1.0 Quick Reference
Guide – Provides basic workflows and compatibility
information for use while using the software.
Portable document format (PDF) versions of this guide and the other
documents are available on the GeneMapper® ID-X Software
Version 1.0 Documentation CD.
Note: For additional documentation, see “How to Obtain Support”
on page x.
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]
GeneMapper® ID-X Software v1.0 Administrator’s Guide
ix
Preface
How to Obtain Support
How to Obtain Support
For HID support, you can send an e-mail to
[email protected] or call 888-821-4443
option 1.
For HID support outside North America, contact your local support
office.
For the latest services and support information for all locations, go to
http://www.appliedbiosystems.com, then click Support. At the
Support page, you can:
• Access worldwide telephone and fax numbers to contact
Applied Biosystems Technical Support and Sales facilities.
• 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.
x
GeneMapper® ID-X Software v1.0 Administrator’s Guide
Chapter 1
Setting Up User Accounts
and User Access
Chapter 1
Setting Up User
Accounts and User
Access
This chapter covers:
■ GeneMapper® ID-X Software Electronic Data Chain-of-
Custody Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
■ Overview of the Security System . . . . . . . . . . . . . . . . . . . . . . . 3
■ Default User Accounts, Profiles, User Groups, and Security
Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
■ Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
■ Setting Up User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Chapter 2
■ Using Security Groups to Control Data Access . . . . . . . . . . . 24
Managing the
Auditing System
■ Customizing Profiles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
■ Customizing User and Security Groups . . . . . . . . . . . . . . . . . 34
■ Maintaining User Accounts. . . . . . . . . . . . . . . . . . . . . . . . . . . 39
■ Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . . . . . 42
■ Exporting and Importing the Security Settings . . . . . . . . . . . . 44
Chapter 3
Managing the
E-Signature System
Chapter 4
Maintaining the Software
and Database Application
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Chapter 1 Setting Up User Accounts and User Access
GeneMapper® ID-X Software Electronic Data Chain-of-Custody Systems
GeneMapper® ID-X Software Electronic Data
Chain-of-Custody Systems
The GeneMapper® ID-X Software contains three systems that assist
with chain-of-custody of electronic data. These systems can be
custom-configured or turned off by the GeneMapper ID-X Software
System administrator as needed:
• Security system – Controls user access to software functions
and data, and allows custom configuration that meets the datasharing needs of your laboratory (described in this chapter)
• Auditing system – Tracks changes and provides audit history
reports (described in Chapter 2)
• E-signature system – Requires user-authentication before
changes are saved (described in Chapter 3)
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Chapter 1 Setting Up User Accounts and User Access
Overview of the Security System
Overview of the Security System
The GeneMapper® ID-X Software security system allows you to
control user behavior by specifying:
• What data a user can access, based on the user and security
Group(s) the user belongs to.
• What functions a user can perform, based on the user profile.
A user with an Admin profile sets up user accounts, profiles, user
groups, and security groups using wizards in the Access Control
Administration window.
Security System
Components
Table 1
The four components of the security system are defined below.
Components of the security system
Component
Description
User Account
All users log in to the GeneMapper® ID-X Software with a user account created by
the GeneMapper ID-X system administrator.
Profile
A profile defines the set of software functions that a user is allowed to perform. For
example, profiles can allow or deny a user the right to view, create, edit, delete
analysis methods, or analyze data.
The system administrator configures profiles, or uses default profiles provided with
the software. When the system administrator creates a user account, the
administrator assigns a profile to the user.
Users can have only one profile.
User Group
User groups are associated with security groups, which control the data a user can
access. Users can access data assigned to a security group only if their user group
is associated with the security group.
The system administrator defines user groups or uses default user groups provided
with the software.
When a user account is created, the user must be assigned to at least one user
group, but the user can be assigned to several groups.
Security
Group
Security groups determine the data that user groups can access. A user group must
be associated with at least one security group, but can be associated with several.
A user can access only data (for example, analysis methods, panels, size standards,
matrices, or projects) that have been saved with a security group that is associated
with one of the user groups to which the user belongs.
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Chapter 1 Setting Up User Accounts and User Access
Overview of the Security System
In summary:
• Each user has only one profile.
• Each user belongs to one or more user groups and each user
group is associated with one or more security groups.
• Security groups associated with a user group and data
determine the data a user can access.
Therefore:
• A user can access the data in a security group that is associated
with any of the user groups to which the user belongs.
• A user can perform any of the software functions permitted by
the user’s profile.
User
A user can perform actions
allowed by the user’s profile
Profile
User Group
Security Group
Security Group
A
C
Data
cannot
access
Users
A
Security Groups B
Data Access
Control
Users in a user group can access
the data of the security groups
associated with the user group
Security groups control access to any of the following items:
•
•
•
•
Projects
Plot settings
Table settings
Panels and bin sets
•
•
•
•
Report settings
Size standards
Analysis methods
Matrix files
Items are associated with a security group when a user creates or
edits, then saves the item (described on the next page).
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Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Associating a
Security Group
with an Item
Whenever users save an item, they must select a security group from
a drop-down list in the Save or Save As dialog box. Users can select
the GeneMapper ID-X Security Group (available to everyone) or any
other security group that they are allowed to use (see below).
For example, the figure below shows the drop-down list that appears
when a user with access only to the Casework and GeneMapper ID-X
security groups saves a new project.
Bypassing
Security Group
Access Control
If you do not want to control access to data in your laboratory,
instruct all users to specify the GeneMapper ID-X security group
when creating projects and settings. All users have access to items
associated with the GeneMapper ID-X security group.
Default User Accounts, Profiles, User Groups, and
Security Groups
Applied Biosystems provides default user accounts, profiles, user
groups, and security groups so that you can use the security system
with minimal set up. You can use the defaults without changes or as a
starting point to customize your own security system.
Note: If your GeneMapper ID-X Software system administrator has
modified the default user accounts, profiles, user groups, and/or
security groups, the tables in this section may no longer be accurate.
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Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
The discussion in this section covers the default profiles, user
groups, and security groups provided by the GeneMapper ID-X
Software. With these defaults, a system administrator can quickly
create a working security system.
Duplicating
Defaults Before
Modifying
Before modifying a default component of the security system,
duplicate it and save it under a new name.
To duplicate any default component, open the Security Manager,
select the default, then select EditDuplicate.
You will need to duplicate the default user accounts multiple times to
provide each user with an account that has a unique or
laboratory-specific login name.
Relationship
Between User
Accounts,
Profiles, and User
Groups
A user’s account determines what the user can do (profile) and
access (user groups). Profiles and user groups must exist before any
user accounts are created, so they are presented in this section before
user accounts.
The GeneMapper ID-X Software system administrator is responsible
for maintaining profiles and user groups. The administrator can:
• Use default profiles and user groups provided by the
GeneMapper ID-X Software.
• Create custom profiles and user groups.
• Use a combination of defaults and custom profiles, user groups,
and security settings.
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Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Default Profiles
The profile that is specified in a user account determines the
software functions a user can perform. Four default profiles are
provided by Applied Biosystems.
Note: If your GeneMapper ID-X Software system administrator has
modified or customized the default profiles, they may differ from the
defaults described in Table 2.
Table 2
Default profiles – actions allowed and not allowed
Profile
Technician/
Read Only
Analyst
Actions Allowed
Actions Not Allowed
• Open, view, and export projects,
analysis methods, panels, matrices, and
size standards associated with the
security groups that the user is
permitted to access
• Generate reports
• Create, edit, delete, export, and import
table settings, plot settings, and report
settings associated with the security
groups the user is permitted to access
• Use of the CODIS Export Manager
• Create projects
• Add samples to projects
• Create, edit, or change settings in a
project (analysis method, panel, size
standard, matrix)
• Analyze data
• Override GQ, CGQ, or SQ
• Edit allele labels
• Perform Remote Shutdown
• Add profiles to the Profile Manager
• Access and manage the Security, Audit
Trail, and E-signature systems
All actions allowed to the Technician/Read • Create a new analysis method
Only profile, plus:
• Edit analysis method parameters other
than sizing range and analysis range
• Create, import, edit, or delete projects,
panels, matrices, and size standards
• Add profiles to the Profile Manager
associated with the security groups that • Access and manage the Security, Audit
the user is permitted to access
Trail, and E-signature systems
• Edit sizing range and analysis range in
analysis methods
• Save or Save As analysis methods
• Add samples to projects
• Change selections in a project (analysis
method, panel, size standard, matrix)
• Analyze data
• Edit alleles
• Override SQ, GQ, and CGQ
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Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Table 2
Default profiles – actions allowed and not allowed (continued)
Profile
Scientist
Actions Allowed
All actions allowed to the Analyst profile,
plus:
Actions Not Allowed
Access and manage the Security, Audit
Trail, and E-signature systems
• Create or modify/save analysis methods
• Add profiles to Profile Manager
Admin
Profile
All possible actions, which include:
None
• Access and manage the Security, Audit
Trail, and E-signature systems
• All GeneMapper ID-X Software
functions
Default Security Groups
The security groups specified in a user account determine the:
• Specific data (for example, analysis methods, panels, size
standards, matrices, and projects) a user can access.
• The Read (view or select) or Update (create, edit, delete,
analyze) privileges allowed for the data.
The Read/Update privileges associated with a security group can
clash with the actions permitted in user profiles (profiles also define
read/write privileges). For this reason, all the default security groups
defined by Applied Biosystems have both Read and Update
privileges.
IMPORTANT! There are software functions (for example, changing
table or plot settings) that are not covered in profiles. You can use
security group Update privileges to control use of these functions.
The software contains three default security groups:
• GeneMapper ID-X (read and update)
• Casework (read and update)
• Databasing (read and update)
When users create or edit and then save an item, they select a
security group from a drop-down list in the Save dialog box. Users
can select any of the three default security groups to which they have
access.
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Default User Accounts, Profiles, User Groups, and Security Groups
Security group definitions are just names. Their significance
depends entirely on the user groups they are associated with. When a
user saves an item and assigns it a security group, it means that:
• Any user in any user group that is associated with that security
group can access the data.
• Users who are only in user groups that are not associated with
the selected security group cannot access the data.
Default User Groups
Four default user groups are associated with the default security
groups:
Note: If your GeneMapper ID-X Software system administrator has
modified or customized the default user groups, they may differ from
the defaults described in Table 3.
Table 3
Default user groups and associated security groups
Default User
Group Name
Security Group/Privileges ‡
Accessible Data
Read = View or select
Update = Create, edit, delete, analyze
All Users
GeneMapper ID-X /read+update
Data assigned to the GeneMapper ID-X
security group
Casework
Users
Casework/read+update
Private data assigned to the Casework
security group
GeneMapper ID-X/read+update
Data assigned to the GeneMapper ID-X
security group
Databasing
Users
Databasing/read+update
GeneMapper ID-X/read+update
Private data assigned to the Databasing
security group
Data assigned to the GeneMapper ID-X
security group
Administrators
Casework/read+update
All data
Databasing/read+update
GeneMapper ID-X/read+update
Admin/read+update
‡ A Practice user group and a Practice security group are also provided for use with the Getting Started
Guide.
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Default User Accounts, Profiles, User Groups, and Security Groups
Default User Accounts
IMPORTANT! If you migrate to the GeneMapper® ID-X Software
from GeneMapper ID Software v3.1 or 3.2, user accounts from v3.1
or 3.2 are deleted and not available in the GeneMapper ID-X
Software. You must create new user accounts in the GeneMapper IDX Software.
Nine default user accounts are provided with the software. Each of
these accounts has a profile and one or more user groups assigned.
Table 4 shows the characteristics of the type of user who is intended
for each of the nine accounts.
Note: If your GeneMapper ID-X Software system administrator has
modified or customized the default user accounts, they may differ
from the defaults described in Table 4.
Table 4
Default user accounts
Default User Account
Name ‡
Casework Tech
Databasing Tech
Casework Analyst
Databasing Analyst
Casework Tech Lead
Databasing Tech Lead
Intended User
User who requires read-only access to the software. This user account
does not allow analysis or changes to the software but does allow viewing,
reporting, printing, and exporting of data.
User who requires access to analyze (with limited ability to change analysis
settings), view, edit, report, and print data.
User who requires full access to all functions of the software: analyze, view,
edit, report, and print data; and all administrative functions: Security
Manager, Audit Manager, and E-Sig Manager.
gmidx
Default user account with full access to all functions of the software:
analyze, view, edit, report, and print data; and all administrative functions:
Security Manager, Audit Manager, and E-Sig Manager.
Administrator
For Applied Biosystems use only.
‡ A Practice user account with Scientist Profile is also provided for use with the Getting Started Guide.
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Default User Accounts, Profiles, User Groups, and Security Groups
To add a new account for a user that matches one of these
descriptions, duplicate the appropriate user account, rename it for
that specific user, then assign a new password.
Applied Biosystems cannot retrieve passwords.
Do not lose the new password for the gmidx account. This account
can be used to reset passwords for other accounts. Applied
Biosystems cannot reset the password for this account if it is lost.
For more detail about the profiles, user groups, and security groups
for the default user accounts, see Table 5.
Note: If your GeneMapper ID-X Software system administrator has
modified or customized the default user accounts, profiles, user
groups, and/or security groups, user access may differ from the
defaults described in Table 5.
Table 5
Default user accounts – data access allowed
User Account ‡
Casework Tech
Profile
Technician/
Read Only
Casework
Analyst
Analyst
Casework Tech
Lead
Admin Profile
Databasing Tech
User Groups Belonged
To
Security Group/Privileges
Read = View or select
Update = Create, edit, delete, analyze
All Users
GeneMapper ID-X/read+update
Casework User Group
Casework/read+update
All Users
GeneMapper ID-X/read+update
Casework User Group
Casework/read+update
All Users
GeneMapper ID-X/read+update
Casework User Group
Casework/read+update
Technician/
Read Only
All Users
GeneMapper ID-X/read+update
Databasing User Group
Databasing/read+update
Databasing
Analyst
Analyst
All Users
GeneMapper ID-X/read+update
Databasing User Group
Databasing/read+update
Databasing Tech
Lead
Admin Profile
All Users
GeneMapper ID-X/read+update
Databasing User Group
Databasing/read+update
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Getting Started
Table 5
Default user accounts – data access allowed (continued)
User Account ‡
gmidx
Administrator
Profile
Admin Profile
User Groups Belonged
To
Security Group/Privileges
Read = View or select
Update = Create, edit, delete, analyze
All Users
GeneMapper ID-X/read+update
Casework User Group
Casework/read+update
Databasing User Group
Databasing/read+update
Administrators
Admin
‡ A Practice user account with Scientist Profile is also provided for use with the Getting Started Guide. It
is associated with the Practice user group and Practice security group.
Getting Started
When you set up the security system for the first time, open the
Security Manager and set password policies.
Starting the Security Manager
Note: User names are not case-sensitive. Passwords are
case-sensitive.
To access the Security Manager, you must use an account that
belongs to the Administrator user group and has an Admin profile,
for example, the gmidx account.
1. Select StartAll ProgramsApplied Biosystems
GeneMapper GeneMapper ID-X v1.0, then log in.
2. In the Login to GeneMapper ID-X dialog box, enter or select the
following administrator account user name and password, then
click OK:
– gmidx, temporary password is password
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3. When prompted, specify a new password. Keep a record of the
new password. The gmidx account requires that you set a new
password when you log in for the first time. If you follow this
procedure after first log in, the password for the account may be
different from password.
Applied Biosystems cannot retrieve
passwords. Do not lose the new password for the gmidx account.
This account can be used to reset passwords for other accounts.
Applied Biosystems cannot reset the password for this account
if it is lost.
4. In the GeneMapper ID-X main window, select
AdminSecurity Manager.
5. In the AdminToolAcc dialog box, log in with the gmidx account
listed in step 2, then click OK. The Access Control
Administration window opens (below):
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Getting Started
The FileNew Application command and the
Applications entry in the navigation pane are for Applied
Biosystems only. Using these functions interferes with proper
software operation.
Setting Password Policies
Password policies apply to all user accounts.
1. Start the Security Manager (see page 12).
2. Select SettingsPassword Policies.
3. In the Password Policies dialog box (below), specify the
password settings (see Table 6), then click Save Changes.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
4. Close and restart the GeneMapper ID-X Software to apply the
changed settings.
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Getting Started
Table 6
Password policies settings
Setting
Description
Attempts
Max Login
Attempts
Enter the number of failed login attempts that the software allows before
suspending the user account. Works in conjunction with the User State.
Send log
message
Records the failed login attempts to the security log.
Set User State
– Remain active
Disables the “Maximum Login Attempts” setting. A user is allowed unlimited
attempts to log in.
Set User State
– Suspend for
___ min(s)
Suspends the user account for the specified number of minutes after a user
exceeds the maximum login attempts. The user must wait for the specified
number of minutes to elapse before attempting another login.
The security information for the GeneMapper ID-X Software is written to the
<drive>:\AppliedBiosystems\ GeneMapperID-X\GeneMapper_Log.txt file.
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 40.
Password
Password
Lifetime
Retires the password of each user account after the specified number of days
elapses. If this parameter is not selected, passwords do not expire.
Note: After retiring a password, the software automatically prompts the user to
create a new password at the next login.
Password
Grace Logins
Enter the number of times that a user can delay changing the password after the
software prompts the user to change it. After a user exceeds the number of
specified grace logins, the software requires the user to change the password.
Password Reusability
Password
Reuse Period
Allows a user to reuse a former password after the specified number of days has
elapsed since its last use.
Passwords kept
per user
Enter the number of former passwords per user that the Security Manager should
store.
Password Format
Minimum
Password width
Enter the minimum number of characters required in the password (alphanumeric,
not case-sensitive).
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Setting Up User Accounts
Setting Up User Accounts
After setting password policies, you can:
• Accept and use all the default settings by duplicating a default
user account, renaming it, and using it without further
modification,
or
• Create an entirely new user account, using any combination of
defaults and your own custom settings.
Using Default User Accounts
To set up your security system using the defaults for user accounts,
profiles, user groups, and security groups, follow these steps:
1. Start the Security Manager (see page 12).
2. Select the default user account type that fits the new user (see
Table 2, “Default profiles – actions allowed and not allowed,”
on page 7), for example, Casework Analyst.
3. Select EditDuplicate to open the User Properties dialog box
(shown on the next page).
4. In the Name field in the General section, replace the name
“Clone of Casework Analyst(1)” with the login name for the
new account (for example, User1). The login name is not casesensitive and must be ≤ 30 characters.
Note: You cannot create a user account with the same name as a
user account that has been previously deleted.
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Setting Up User Accounts
5. Set other values:
• (Optional) Enter a description in the Description field in
the General section (≤ 1023 characters).
• In the User Details section, enter the user’s real name in the
Full Name field.
• (Optional) Select Show EULA if you want the software to
display the End User License Agreement (EULA) when
the user logs in.
• Leave Status set to Active.
• (Optional) Select Pre-Expire, if you want to ensure that a
user logging in to an account for the first time is prompted
to change the password.
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Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
6. Click Set Password.
7. In the Change Password dialog box, enter a new password twice,
then click OK.
8. Without making any other changes in the Access Control
Administration window, select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
The new user account has the same profile and group associations as
the default Casework Analyst user account.
Creating New User Accounts
Preparing to Use
Custom Settings
If you will use the default profiles, user groups, and/or security
groups, skip to “Creating the User Account” on page 18.
If you want to use custom profiles, user groups, and/or security
groups, you must create them before creating new user accounts.
To create any custom:
• Profiles that you want to use, see “Customizing Profiles” on
page 26.
• User groups and security groups that you want to use, see
“Customizing User and Security Groups” on page 34.
• User group/security group associations that you want to use, see
“Creating a New User Group” on page 35.
Creating the User
Account
After you create any custom profiles, user groups, and/or security
groups that you want to use:
1. Start the Security Manager (see page 12).
2. Select FileNew User.
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Setting Up User Accounts
3. In the Create User wizard, click Next to open the Name page.
4. In the Name field in the General section, enter the login name
for the new account (for example, User1). The login name is not
case-sensitive and must be ≤ 30 characters.
Note: You cannot create a user account with the same name as a
user account that has been previously deleted.
5. Set other values:
• (Optional) Enter a description in the Description field in
the General section (≤ 1023 characters).
• In the User Details section, enter the user’s real name in the
Full Name field.
• (Optional) Select Show EULA if you want the software to
display the End User License Agreement (EULA) when
the user logs in.
• Leave Status set to Active.
• (Optional) Select Pre-Expire, if you want to ensure that a
user logging in to an account for the first time is prompted
to change the password.
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Setting Up User Accounts
6. Click Set Password.
7. In the Change Password dialog box, enter a new password twice,
then click OK.
8. In the Control Properties section, select the profile for the user.
9. Click Next to open the User Groups page (below).
10. Select the user groups for the user. If you have previously
associated user groups and security groups (see “Preparing to
Use Custom Settings” on page 18), this selection also
designates the security groups for this user.
11. Click Next to see a summary of the account, then click Finish.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
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Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
Creating a User Account for Autoanalysis
If you perform autoanalysis (the system is configured to
automatically collect data, then create, analyze, and save a project),
you must create a user account for autoanalysis.
IMPORTANT! When you set up the data collection computer for
autoanalysis, you are asked to create an autoanalysis user account.
You must enter a user name, password, and host computer. For the
host computer, enter the name of the GeneMapper ID-X database
host, not a client computer. For information on autoanalysis, see the
GeneMapper® ID-X Software Version 1.0 Installation Guide and the
GeneMapper® ID-X Software Help.
1. Start the Security Manager (see page 12).
2. Select FileNew User.
3. In the Create User wizard, click Next to open the Name page.
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Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
4. In the Name field in the General section, enter the login name
for the new account (for example, Auto1). The login name is
not case-sensitive and must be ≤ 30 characters.
Note: You cannot create a user account with the same name as a
user account that has been previously deleted.
5. Set other values:
• (Optional) Enter a description in the Description field in
the General section (≤ 1023 characters).
• In the User Details section, enter Autoanalysis in the Full
Name field.
• Deselect Show EULA.
• Leave Status set to Active.
• Deselect Pre-Expire.
6. Click Set Password.
7. In the Change Password dialog box, enter a new password twice,
then click OK.
8. In the Control Properties section, select the Scientist profile.
Note: If you create custom profiles for your system and do not
choose to use the Scientist profile, use a profile for autoanalysis
with the following minimum privileges: Read privileges for
Panel Manager, Size Standard, Analysis Method; Read and
Update privileges for creating and analyzing projects.
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Setting Up User Accounts
9. Click Next to open the User Groups page.
10. Associate the user account with any user group. The project that
autoanalysis creates, analyzes, and saves is associated with the
GeneMapper ID-X security group, which is accessible by all
user groups.
11. Click Next to see a summary of the account you just created,
then click Finish.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
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Chapter 1 Setting Up User Accounts and User Access
Using Security Groups to Control Data Access
Using Security Groups to Control Data Access
In the GeneMapper® ID-X Software, a user associates Security
groups with data items (such as analysis methods, table settings, plot
settings, matrices, size standards, or report settings) when the user
saves a data item to which he or she has access. Only users in user
groups associated with that security group can later access the data
items.
Using Open
Access
Using Access
Control
Changing the
Security Group
Default
If you want all users to have access to all data, instruct your users to
select the GeneMapper ID-X security group when they save data.
The data associated with this security group are accessible to every
user.
If you want to restrict user access to data, instruct users to select a
security group associated with their user group. For example, you
can instruct the users in the Casework user group to select the
Casework security group when they save items.
The security groups that a user can select to associate with a data
item (when saving the data item) include the GeneMapper ID-X
security group as the default. However, any user can change the
security group that appears as the default choice when he or she
saves a data item.
1. In the In the GeneMapper ID-X main window, select
FileProject Options to open the Options dialog box.
2. Select the General tab.
3. In the drop-down list box in the Data Access Control pane,
select the new default.
4. Click OK.
The new security group default applies only to the user who reset the
default, unless the default is reset by a user who is a member of only
one user group (other than the All Users group). In this case, the
default applies to all other users who have identical group
membership.
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Using Security Groups to Control Data Access
For example, if you use accounts like those listed on page 11, and a
Casework Tech sets Casework as the new security group default, that
will also become the default for Casework Analysts and Casework
Tech Leads. All other users continue to have the GeneMapper ID-X
security group as default.
Changing the
Security Group
Association for a
Data Item
In the GeneMapper ID-X Software, a user can change the security
group associated with one or more data items if the user’s profile
allows changing the data items.
To change the security group associated with a data item:
1. In the GeneMapper ID-X main window, select
ToolsGeneMapper ID-X Manager to open the GeneMapper
ID-X Manager.
2. Select the appropriate tab, then select the item to change.
3. Click Open.
4. Change the Security Group setting (for items that contain
multiple tabs, the Security Group setting is in the General tab).
5. Click OK.
Changing the
Security Group
Association for a
Project
A user can change the security group associated with a project if the
user’s profile allows the user to change the project. However, you
must save the project with a new name.
1. In the GeneMapper ID-X main window, select
ToolsGeneMapper ID-X Manager to open the
GeneMapper ID-X Manager.
2. Select the Projects tab.
3. Select the project to change.
4. Click Save As.
5. Enter a new name for the project, select a new security group,
then click OK.
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Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Customizing Profiles
Profiles determine the software functions that a user can perform.
Applied Biosystems recommends that you use the default profiles
described in “Default Profiles” on page 7, even if you use custom
user and/or security groups.
However, if the default profiles do not suit your needs, you can create
custom profiles.
This section describes:
• Creating Profiles
• Editing or Deleting Profiles
• Profile Elements
Creating Profiles
To create a custom profile, you can:
• Duplicate an existing default profile, then edit it to meet your
requirements.
• Create a new profile.
Applied Biosystems recommends that you duplicate a default
profile, rename it, and then customize it, rather than change the
default profile.
Duplicating and
Editing a Default
Profile
To base a new profile on an existing default profile (see Table 2,
“Default profiles – actions allowed and not allowed,” on page 7):
1. Start the Security Manager (see page 12).
2. In the navigation pane of the Access Control Administration
window, select the profile to duplicate.
3. Right-click, then select Duplicate (or select EditDuplicate).
4. Select the Clone of .... profile in the navigation pane.
5. In the Profile Properties section, change the profile’s name and
modify the settings as desired.
6. Select FileSave.
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Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Creating a Profile
1. Start the Security Manager (see page 12).
2. Select FileNew Profile.
3. In the Create Profile wizard, click Next.
4. Enter a Name (≤ 30 characters) and Description (≤ 1023
characters) for the new profile.
5. In the Installed Elements table (shown on the next page), assign
permissions to the new profile for the GeneMapper ID-X
module based on the actions allowed in profiles, as described in
Table 7 on page 30 and Table 8 on page 32:
a. For the GeneMapper ID-X module, select OIR (Override
Inherited Rights), then select Execute. All functions are
automatically set to Execute. See page 28 for an
explanation of OIR.
b. For each function you want to disable, select OIR
(Override Inherited Rights), then deselect Execute.
6. When you finish, click Next, then click Finish to complete the
profile setup.
7. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
When you create a profile, do not set the
FoundationDataCollection module, which is for use by Applied
Biosystems only.
IMPORTANT! To perform autoanalysis (see “Creating a User
Account for Autoanalysis” on page 21), a user account requires a
Scientist profile or equivalent. For a custom profile that permits
autoanalysis functions, ensure that its rights are at least equivalent to
those of the Scientist profile.
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Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Do not set
Select OIR, then
Execute, to
automatically enable all
actions.
To disable an action,
select OIR for the action,
then deselect Execute.
Override Inherited
Rights (OIR)
The permissions listed in the Installed Elements tables can be
“inherited” in one of two ways:
• All actions ( ) are children of either an action group ( ) or an
application ( ).
• Action groups ( ) are children of applications ( ).
• Whenever a parent is enabled for the first time, all its children
are automatically enabled through “inheritance” and displayed
in the Installed Elements Table Execute column with a gray
check mark (disabled).
• To individually set the state of a child element, select OIR to
enable the Execute box.
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Customizing Profiles
Editing or Deleting Profiles
IMPORTANT! Do not modify the Admin(istrator) profile.
1. Start the Security Manager (see page 12).
2. In the navigation pane of the Access Control Administration
window, select the profile to edit or to delete.
• In the Installed Elements table, to edit the rights for the profile:
– For each function you want to enable, select OIR (Override
Inherited Rights) and Execute (see “Override Inherited
Rights (OIR)” on page 28).
– For each function you want to disable, select OIR (Override
Inherited Rights) and deselect Execute.
Note: Table 7 on page 30 and Table 8 on page 32 describe the
functions displayed in the Installed Elements table.
• To delete the profile, select EditDelete, then click Yes.
3. When you finish, click Next, then click Finish to complete the
profile setup.
4. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
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Customizing Profiles
Profile Elements
If the GeneMapper ID-X Software is installed on a computer that
contains other Applied Biosystems software products, the Installed
Elements table may contain elements in addition to those listed in
Table 7 on page 30 and Table 8 on page 32.
All users with an administrator profile have all the permissions in
Table 7. These permissions include:
• Managing user accounts, user groups, security groups, and
profiles
• Using the Audit Manager
• Using the ESig Manager
• All GeneMapper ID-X Software functions (described in Table 8
on page 32)
Table 7
(
Profile elements – actions allowed in admin profiles
Installed Elements
Application/ Action
Group/ Action)
Permissions
Default Rights
Determines the default value (all or none) for all elements.
Admin Tool Acc(ess)
All aspects of the Security Manager (Access Control
Administration tool).
Does not affect functions in the
GeneMapper ID-X Software.
General
May Run Application
Use the general functions of the Security Manager (Access
Control Administration tool).
Add User to User Group
Associate User Groups with
Security Groups
Associate User Groups
with Users
Change Password Policies
Import Security Data
Export Security Data
30
User Groups
Create, modify, or delete user groups (
).
Profiles
Create, modify, or delete user profiles ( ).
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Customizing Profiles
Table 7
(
Profile elements – actions allowed in admin profiles (continued)
Installed Elements
Application/ Action
Group/ Action)
Applications
Permissions
IMPORTANT! Do not change. For Applied Biosystems use
only.
Users
Create, modify, or delete user accounts (
Security Groups
Create or modify security groups (
Audit GUI
Does not affect functions in the
GeneMapper ID-X Software.
ESig GUI
).
).
All aspects of the Audit Manager, including Audit Map
Configuration tool and Audit History Viewer.
All aspects of the ESig Administration tool.
Does not affect functions in the
GeneMapper ID-X Software.
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Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
All users have permissions to use some of the GeneMapper ID-X
functions. Table 8 lists the defaults for each profile.
Scientist
Admin Profile
Installed Elements
Application/ Action
Group/ Action)
Analyst
(
Technician/Read Only
Table 8 Profile elements – actions allowed in technician, analyst, scientist, and admin
profiles
—
✓
✓
✓
GeneMapper
✓
✓
✓
—
✓
✓
✓
—
✓
✓
✓
READ_PANEL
✓
✓
✓
✓
UPDATE_PANEL
—
✓
✓
✓
—
✓
✓
✓
✓
✓
✓
✓
—
✓
✓
✓
Remote Shutdown
Panel Manager
Size Standard
READ_SIZE_ STANDARD
UPDATE_SIZE_
STANDARD
32
All aspects of the GeneMapper ID-X
Software.
For information on the elements listed in this
column, see GeneMapper® ID-X Software
v1.0 Help.
—
Administration
Permissions
Use the remote shutdown function.
Use the functions of the Panel Manager
including:
• Viewing panels, binsets, and bin
definitions
• Creating/modifying panels, binsets, and
bins
View and create or modify the size standard
definitions stored by the GeneMapper ID-X
Software.
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Customizing Profiles
Analyst
Scientist
Admin Profile
(
Technician/Read Only
Table 8 Profile elements – actions allowed in technician, analyst, scientist, and admin
profiles (continued)
Analysis Method
—
✓
✓
✓
READ_ANALYSIS_
METHOD
✓
✓
✓
✓
UPDATE_ANALYSIS_
METHOD
—
—
✓
✓
UPDATE_ANALYSIS_
RANGE
—
✓
✓
✓
—
✓
✓
✓
SAVE_AS_ANALYSIS_
METHOD
—
✓
✓
✓
Project
—
✓
✓
✓
READ_PROJECT
✓
✓
✓
✓
UPDATE_PROJECT
—
✓
✓
✓
—
—
—
✓
READ_PROFILE
✓
✓
✓
✓
UPDATE_PROFILE
—
—
✓
✓
—
✓
✓
✓
READ_MATRIX
✓
✓
✓
✓
UPDATE_MATRIX
—
✓
✓
✓
Installed Elements
Application/ Action
Group/ Action)
UPDATE_SIZING_RANGE
Profile Manager
Matrix
Permissions
View and create or modify the analysis
methods stored by the GeneMapper ID-X
Software.
View and create or modify the projects stored
by the GeneMapper ID-X Software.
Create, edit, and delete custom reference and
control profiles.
View and create or modify the matrices
stored by the GeneMapper ID-X Software.
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Chapter 1 Setting Up User Accounts and User Access
Customizing User and Security Groups
Customizing User and Security Groups
This section describes:
• Creating User Groups
• Creating Security Groups
IMPORTANT! Before using the security groups and user groups you
create, test them by creating, modifying, deleting, and viewing data
using the appropriate user accounts.
User groups, with their associated security groups, determine the
data a user can access (described on page 3). Applied Biosystems
recommends that you use the default user groups and security groups
described in “Default User Groups” on page 9 and “Default Security
Groups” on page 8.
If the default user or security groups do not suit your needs, you can
create custom groups.
Creating User Groups
To create a custom user group, you can:
• Duplicate an existing default user group, then edit it to meet
your requirements,
or
• Create a new user group.
Note: Applied Biosystems recommends that you duplicate a default
user group, rename it, and then customize it, rather than change the
default user group.
Duplicating and
Editing a Default
User Group
To base a new user group on an existing default user group
(see “Default User Groups” on page 9):
1. Start the Security Manager (see page 12).
2. In the navigation pane of the Access Control Administration
window, select the user group to duplicate.
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Customizing User and Security Groups
3. Right-click, then select Duplicate (or select EditDuplicate).
4. Select the Clone of .... user group in the navigation pane.
5. In the User Group Properties section, modify the settings for the
selected user group.
6. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
Creating a New
User Group
1. In the Security Manager, select FileNew User Group.
2. In the Create User Group wizard, click Next.
3. Enter a Name (≤ 30 characters) and Description
(≤ 1023 characters) for the new user group.
4. Select both Read and Update in the Default rights when
associated with a Security Group section.
Note: This is a default setting applied to the security groups
that you add to a user group. You can override the default setting
in the Security Group tab. See step 7.
5. Click Next.
6. Select Associate for each user account that you want to associate
with the new user group, then click Next.
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Customizing User and Security Groups
7. Associate security groups for this user group:
Note: You can associate a security group with a user group at
any time.
a. Select Associate for each security group that you want to
associate with the user group.
b. For each associated security group, select:
IMPORTANT! Applied Biosystems recommends that you
change Read and Update rights in the profile only and
always enable both Read and Update rights in the
user/security group.
• Read – Allows the user to view or select the data
(projects, plot settings, table settings, panels and bin
sets, report settings, size standards, analysis methods,
and matrix files) associated with the security group
associated with the user group.
• Update – Allows the user to create/modify/delete
/analyze the data associated with the security groups
associated with the user group (consistent with the
user’s profile).
c. Click Next.
8. Click Finish to complete the user group setup.
9. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
Deleting User
Groups
36
You can delete a user group by selecting EditDelete.
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Customizing User and Security Groups
Creating Security Groups
To create a custom security group, you can:
• Duplicate an existing default security group, then edit it to meet
your requirements,
or
• Create a new security group.
Note: Applied Biosystems recommends that you duplicate a default
security group, rename it, and then customize it, rather than change
the default security group.
Duplicating and
Editing Default
Security Groups
To base a new security group on an existing default security group
(see “Default Security Groups” on page 8):
1. Start the Security Manager (see page 12).
2. In the navigation pane, select the security group to duplicate.
3. Right-click, then select Duplicate (or select EditDuplicate).
4. Select the Clone of .... security group in the navigation pane.
5. In the Security Group Properties section, modify the settings for
the selected security group.
6. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
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Chapter 1 Setting Up User Accounts and User Access
Customizing User and Security Groups
Creating a New
Security Group
1. Start the Security Manager (see page 12).
2. In the Security Manager, select FileNew Security Group.
3. In the Create Security Group wizard, click Next.
4. Enter a Name (≤ 30 characters) and Description
(≤ 1023 characters) for the new security group.
5. Click Next.
6. Associate user groups for this security group:
Note: You can associate a security group with a user group at
any time.
a. Select Associate for each user group that you want to
associate with the security group.
b. For each associated user group, select Read and/or Update
to grant rights for the relationship to the security group.
IMPORTANT! Applied Biosystems recommends that you
control functional access through the profile only and that
you enable both Read and Update rights for all security
groups.
c. Click Next.
7. Click Finish to complete the setup.
8. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
Deleting Security
Groups
38
You cannot delete a security group.
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Maintaining User Accounts
Maintaining User Accounts
Applied Biosystems cannot retrieve passwords.
Do not lose the new password for the gmidx account. This account
can be used to reset passwords for other accounts. Applied
Biosystems cannot reset the password for this account if it is lost.
Editing User Accounts
Note: Applied Biosystems recommends that you duplicate a default
user account, rename it, and then customize it, rather than change the
default user account.
1. Start the Security Manager (see page 12).
2. In the navigation pane, select the user account of interest.
3. Modify the settings for the selected user account.
4. If you are changing an account name, enter the new name in the
Name field.
5. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper® ID-X Software.
Changing the Password for a User Account
1. Start the Security Manager (see page 12).
2. In the navigation pane, select the user account.
3. In the User Properties section, set click Set Password.
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Chapter 1 Setting Up User Accounts and User Access
Maintaining User Accounts
4. In the Change Password dialog box, enter a password in the
Type and Retype fields. The password is not case-sensitive and
can contain up to 17 alphanumeric and special characters.
5. Click OK.
6. Select or deselect Pre-Expire. If Pre-Expire is selected, the
software prompts the user to enter a new password at the next
log in. If Pre-Expire is deselected, the user continues to use the
password you entered in step 4.
7. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
Deleting a User Account
After you delete an account, you cannot retrieve
or restore the deleted account, and you cannot create another user
account with the same name.
An alternative to deleting a user account is to deactivate or suspend
the account, as explained in the next section.
To delete a user account:
1. In the navigation pane of the Access Control Administration
window, select the user account you want to delete.
2. Select EditDelete.
Activating, Deactivating, and Suspending User Accounts
You can change the status of a user account if:
• 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.
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Maintaining User Accounts
1. Start the Security Manager (see page 12).
2. In the navigation pane, select the user account of interest.
3. In the Status drop-down list of the User Details section (see
below), select the appropriate account status for the user
account.
Select the
desired status.
Select the
desired user
account.
Table 9
Account statuses
Status
Description
Active
The user can log in to and use the software.
Inactive
The user cannot log in. Set by a user with an
Admin profile.
Suspended
The user cannot log in. Set by the software
when a user exceeds the limit of unsuccessful
login attempts.
4. Select FileSave.
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software.
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Chapter 1 Setting Up User Accounts and User Access
Viewing the Security Report
Viewing the Security Report
About the
Security Report
The security report summarizes the current Security Manager
settings.
You can print a summary of one or more components of the security
system (such as access rights for a particular user). See below.
Note: The Security Manager does not monitor login attempts or
other user activity (such as creating projects). To monitor and record
user activity, configure the auditing system (see Chapter 2,
Managing the Auditing System, on page 45).
Printing the
Security Report
1. Start the Security Manager (see page 12).
2. In the navigation pane, select a user account or profile.
3. Select FileReport.
4. In the Print Access Control Identifiers dialog box, select options
to specify the content of the report.
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Viewing the Security Report
• Entire Access Control – Prints a summary of all user accounts,
applications, and profiles.
• Selection only – Prints a report of the selected user account,
application, or profile selected in the navigation pane of the
Security Manager.
• Print checked objects below – Prints a report of one or more of
the following elements that you select:
– Users – A report of all user accounts.
– Applications – A report of all applications.
– User Groups – A report of all user groups.
– Security Groups – A report of all security groups.
– Profiles – A report of all profiles.
5. Click Preview to view a preview of the report (see below).
6. Click Print. Otherwise, click Close, then repeat step 4 to
modify the report settings as desired.
7. Click Cancel to close the Print Access Control Identifiers
dialog box.
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Chapter 1 Setting Up User Accounts and User Access
Exporting and Importing the Security Settings
Exporting and Importing the Security Settings
Transferring
Security Settings
Between
Computers
You can export a summary of all security settings to back up or
transfer to another computer. The exported security file contains
password policies, user accounts, profiles, user groups, and security
groups.
IMPORTANT! The GeneMapper® ID-X Software does not
automatically back up the security data when you back up the
database. You must back up manually by exporting a file. Applied
Biosystems recommends that you back up security settings after you
make any change to the system. For more information on backing up,
see Chapter 4, Maintaining the Software and Database Application,
on page 75.
Exporting the
Security Settings
1. Start the Security Manager (see page 12).
2. Select FileExport Database.
3. In the Save dialog box, enter 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 security settings.
1. Start the Security Manager (see page 12).
2. Select FileImport Database.
3. In the Save dialog box, navigate to the appropriate location,
select the desired .acc file, then click Open.
4. In the Import Users dialog box, click OK.
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Chapter 2
Managing the
Auditing System
Chapter 1
Setting Up User
Accounts and User
Access
■ Overview of the Audit System . . . . . . . . . . . . . . . . . . . . . . . . 46
■ Default Audit Map Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . 48
■ Using the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
■ Viewing Audit History Records . . . . . . . . . . . . . . . . . . . . . . . 57
■ Backing Up, Removing, and Restoring Audit Records. . . . . . 63
Chapter 2
Managing the
Auditing System
Chapter 3
Managing the
E-Signature System
Chapter 4
Maintaining the Software
and Database Application
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Chapter 2 Managing the Auditing System
Overview of the Audit System
Overview of the Audit System
Use the GeneMapper® ID-X Software audit system to specify the
types of actions you want to audit (for example, allele edits) and the
auditing mode (silent, or requiring the user to enter a reason for
change).
The components of the audit system are defined in Table 10.
Table 10
Components of the audit system
Component
Audit Map
(open in GeneMapper ID-X
Software by selecting
Admin
Audit ManagerSetting...)
Auditing in the GeneMapper
ID-X Software
Definition
Set of instructions specified by the GeneMapper ID-X Software
system administrator that defines the types of data to audit, the
actions to audit, and whether auditing is On (prompts the user for a
Reason for Change) or Silent (tracks the change, but does not prompt
the user).
The cumulative record of changes to all audited objects. When a user
creates or deletes an audited item, the change is tracked. If auditing is
On instead of Silent, the user must enter a reason for the change in the
Reason(s) for Change dialog box (see figure on next page). When a
user changes an audited item (instead of creating or deleting), the
dialog box also includes an Apply To All option that applies the reason
for change to future changes of the same type, until the project is
saved (for example, when editing alleles, the same reason is used for
all future edits of alleles until you save the project).
IMPORTANT! Audit records are saved only when a user saves the
project, analysis method, size standard, or other object being
changed. Audit records are not saved when a user clicks OK in the
Reasons for Change dialog box. If a user clicks Cancel without saving
the change, the software discards all possible audit records.
Action
Name of the affected
audit object attribute
Former (Old) and current
(New) values of the audit
object (if applicable)
Reason for the change
entered by user
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Chapter 2 Managing the Auditing System
Overview of the Audit System
Table 10
Components of the audit system (continued)
Component
Audit History Viewer
(open with
AdminAudit
ManagerReport...)
Audit Record Backup
(open from Admin menu)
Example
Configuration
Definition
The tool that provides the GeneMapper ID-X Software system
administrator with advanced query options for retrieving and reporting
audit records. Described in “Viewing Audit History Records” on
page 57.
Allows the GeneMapper ID-X Software system administrator to back
up, remove, and restore audit records. Described in “Backing Up,
Removing, and Restoring Audit Records” on page 63.
The figure below displays the settings for the Allele audit object. In
the example configuration, the audit trail:
• Does not track the change when a user creates an allele label
(Audit State for Created is set to Off).
• Displays the Reason(s) for Change dialog box when a user
deletes an allele label and saves the changes to the project
(Audit State for Deleted is set to On).
• Silently creates a record when a user changes an allele label and
saves the changes to the project (Audit State for Modified is set
to Silent).
Does not track change
Tracks change and
prompts for reason
Tracks change
When Audit
Records Are
Saved
Audit records for actions related to a project (for example, editing
alleles) are saved when the user saves the project.
Audit records for actions not related to a project (for example,
creating analysis methods or panels) are saved when the user clicks
OK to save the item, then returns to the Project window.
IMPORTANT! Audit records are saved only when a user saves the
item being changed. Audit records are not saved when a user clicks
OK in the Reasons for Change dialog box. If a user clicks Cancel
without saving the change, the software discards all possible audit
records.
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Chapter 2 Managing the Auditing System
Default Audit Map Settings
Default Audit Map Settings
By default:
• Allele Edit is set to “On” and the software prompts for a Reason
for Change for allele edits. You can change the state to “Silent”
(tracks the change but does not prompt for a Reason for
Change) or “Off ” (does not track the change).
• All other audited items (primitive, parent items) are set to “Off,”
except for those that are children of other auditable items.
Auditable items are related hierarchically. For example, a Kit
contains (is a parent of) Panels and Binsets, Panels contain Markers,
and Markers contain Bins.
In the example above, the attributes named PANEL, BINSET,
MARKER, and BIN have their states set to “On.” This does not mean
that they are set to be audited because they are not primitive types
(parent items); only primitive object attributes can be selected for
auditing.
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Default Audit Map Settings
PANEL, BINSET, MARKER, and BIN have their attribute states set
to “On” to allow one of their primitive types to be enabled for
auditing. For example, you can set the “modified” attribute of the
Bin object to “On” because this attribute is a primitive type.
modified
attribute is a
primitive
type and
can be
audited
If the BIN attribute states of all parent objects are not set to “On,”
then the Bin auditing does not occur.
All the child Attributes are set to “On” by default. You do not need to
set them to “On” to audit an object with parents.
In Table 11, “Elements of the audit map,” on page 54, none of the
Attributes that are “On” are primitive types, except for Allele. This
means that the only object being audited by default is Allele.
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Chapter 2 Managing the Auditing System
Using the Audit Map
Using the Audit Map
This section describes:
•
•
•
•
Starting the Audit Manager
Configuring the Audit Map
Printing an Audit Map Settings Report
Audit Map Elements (with their defaults)
Note: The audit trail does not track printing or exporting.
Starting the Audit Manager
1. Start the GeneMapper® ID-X Software
(StartAll ProgramsApplied Biosystems
GeneMapper GeneMapper ID-X v1.0), then log in.
2. In the GeneMapper ID-X main window, select
AdminAudit Manager Setting.
3. In the AuditMapConfiguration dialog box, log in with an
administrative user name and password (for example, gmidx).
4. Click OK. The Audit Map Configuration window opens.
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Using the Audit Map
Note: The settings on the Auditing menu in this window apply to
changes made in the Audit Map Configuration window. If you select
On and you make a change in the Audit Map Configuration window,
you are prompted for a Reason for Change. If you select Silent,
changes are tracked, but without a prompt. You cannot turn auditing
of the Audit Map Configuration off.
Saving Changes
When you close the Audit Map Configuration window, your changes
to the audit map are saved. Settings are not applied until you close
and restart the GeneMapper ID-X Software.
Configuring the Audit Map
IMPORTANT! Each audited item generates an audit record that takes
up space in the database. Instead of enabling auditing for an action
such as modifying an analysis method, consider creating a set of
analysis methods with expected settings to minimize the number of
audit records that are generated.
IMPORTANT! Applied Biosystems recommends that you review the
audit map configuration every 6 months and modify them as needed.
For more information on routine maintenance, see Chapter 4,
Maintaining the Software and Database Application.
1. Start the Audit Manager (see page 50).
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Using the Audit Map
2. In the Audit Map Configuration window (in the Audit Map
Objects pane) select the enabled check box of each object audit.
(enabled) – Audits all object attributes (created,
modified, deleted, and so on) according to their individual
attribute states.
Note: An object is not audited unless the Enabled check box is
selected, even if the State in Attributes list is set to On.
3. For each audit map object that you enable for auditing (only
primitive objects can be audited), change its attribute states, as
needed:
a. Select the audit map object.
b. Click the cell in the State
column for each attribute you
want to modify. A drop-down
list appears.
c. In the drop-down list, select
the attribute state that
determines the software behavior when a user performs the
action associated with the attribute:
•
On – Creates an audit record and prompts the user
for the reasons for change. (see page 46).
•
Silent – Creates an audit record, but does not
prompt the user for reasons.
•
Off – Does not create an audit record.
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Using the Audit Map
Note: If you disable an audit map object, the attribute
states for the object are shown in italic text and have no
effect on the audit status of the object.
Note: If you run autoanalysis, auditing for objects set to
On is automatically performed in Silent mode (because no
user is available to be prompted for Reason for Change).
4. Repeat step 3 for each audit map object that you enable.
5. Close the Audit Map Configuration window.
6. Restart the GeneMapper ID-X Software to apply the settings.
Printing an Audit Map Settings Report
1. Start the Audit Manager (see page 50).
2. In the Audit Map Configuration window, select FileReport.
You are prompted for formatting information, then the report
prints.
Audit Map Elements
Table 11 lists all potential audit map objects, their attributes, the
default settings for each attribute, and the audit category to which
they belong (items in the same audit category are related to each
other). If the GeneMapper ID-X Software is installed on a computer
that contains other Applied Biosystems products, the audit map may
contain elements additional to those listed in Table 11.
Note: The Allele object is the only object enabled by default for
auditing. All other audited objects are set to “Off,” except for those
that are children of other auditable items (for example, RUN under
the Project object is set to “On.” Only primitive objects (objects
listed in lower case) can be audited.
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Chapter 2 Managing the Auditing System
Using the Audit Map
Table 11
Elements of the audit map
Object
Project
Attribute
Default
State
analyzed
Off
created
Off
deleted
Off
modified
Off
RUN
On
Action Recorded When State Is
On or Silent
Creating, deleting, or changing a project in
the Project window, or renaming a project in
the Projects tab of the GeneMapper IDX
Manager.
When RUN is activated, auditing for the
Run object (described below) is allowed
(you must also enable the Run object and
set its attributes).
Audit category: ProjectT
Run
IMPORTANT! To
audit the Run object,
you must enable the
Project object and
set the Project RUN
attribute to On or
Silent (described
above).
Sample
IMPORTANT! To
audit the Sample
object, you must
enable the Run
object and set the
Run SAMPLE
attribute to On or
Silent (described
above).
created
Off
deleted
Off
SAMPLE
On
Adding samples from a new run folder, or
deleting all samples in a run folder from a
project.
When SAMPLE is activated, auditing for the
Sample object (described below) is allowed
(you must also enable the Sample object
and set its attributes).
Audit category: ProjectT
ALLELE
On
created
Off
deleted
Off
modified
Off
OverrideGQ
Off
OverrideCGQ
Off
OverrideSQ
Off
Adding, deleting, or modifying samples
(change the sample name) in the Project
window, or deleting samples from the
Samples plot.
When ALLELE is activated, auditing for the
Allele object (described below) is allowed
(you must also enable the Allele object and
set its attributes).
When OverrideGQ or Override CGQ is
activated, creates a record when a user
overrides the GQ PQV or CGQ PQV in the
Samples or Genotypes plot.
When OverrideSQ is activated, creates a
record when a user overrides the SQ PQV in
the Size Match Editor.
Audit category: ProjectT
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Chapter 2 Managing the Auditing System
Using the Audit Map
Table 11
Elements of the audit map (continued)
Object
Allele
IMPORTANT! To
audit the Allele
object, you must
enable the Sample
object and set the
Sample ALLELE
attribute to On or
Silent (described
above).
Analysis Method
Kit
BinSet
IMPORTANT! To
audit the BinSet
object, you must
enable the Kit object
and set the Kit
BINSET attribute to
On or Silent
(described above).
Attribute
Default
State
Action Recorded When State Is
On or Silent
created
On
Modifying allele labels in the Samples or
Genotypes plot.
deleted
On
modified
On
created
Off
deleted
Off
modified
Off
BINSET
On
created
Off
deleted
Off
modified
Off
PANEL
On
Audit category: KitT
created
Off
Creating or deleting bin sets using the
Panel Manager.
deleted
Off
Audit category: ProjectT
Creating, deleting, or modifying an analysis
method.
Audit category: Analysis MethodT
Creating, deleting, or modifying a kit in the
Panel Manager.
When BINSET or PANEL is activated,
auditing for the BinSet or Panel object
(described below) is allowed (you must also
enable the BinSet or Panel object and set
its attributes).
Audit category: KitT
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Using the Audit Map
Table 11
Elements of the audit map (continued)
Object
Panel
IMPORTANT! To
audit the Panel
object, you must
enable the Kit object
and set the Kit
PANEL attribute to
On or Silent
(described above).
Marker
IMPORTANT! To
audit the Marker
object, you must
enable the Panel
object and set the
Panel MARKER
attribute to On or
Silent (described
above).
Bin
IMPORTANT! To
audit the Bin object,
you must enable the
Marker object and
set the Marker BIN
attribute to On or
Silent (described
above).
Matrix
Size Standard
56
Attribute
Default
State
created
Off
deleted
Off
MARKER
On
modified
Off
Action Recorded When State Is
On or Silent
Creating, deleting, or modifying panels in
the Panel Manager, the Samples plot, or the
Genotypes plot.
When MARKER is activated, auditing for
the Marker object (described below) is
allowed (you must also enable the Marker
object and set its attributes).
Audit category: KitT
BIN
On
created
Off
deleted
Off
modified
Off
Creating, deleting, or modifying markers of
a panel in the Panel Manager, the Samples
plot, or the Genotypes plot.
When BIN is activated, auditing for the Bin
object (described below) is allowed (you
must also enable the Bin object and set its
attributes).
Audit category: KitT
created
Off
deleted
Off
Creating, deleting, or modifying individual
bins of the bin sets in the Panel Manager,
the Samples plot, or the Genotypes plot.
modified
Off
Audit category: KitT
created
Off
Creating, deleting, or modifying matrices
using the GeneMapper ID-X Manager.
deleted
Off
modified
Off
created
Off
deleted
Off
Creating, deleting, or modifying size
standard definitions using the GeneMapper
ID-X Manager.
modified
Off
Audit category: SizeStandardT
Audit category: MatrixT
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Chapter 2 Managing the Auditing System
Viewing Audit History Records
Viewing Audit History Records
This section describes:
•
•
•
•
•
Starting the Audit History Viewer
Creating Audit Record Queries
Performing Audit Record Queries and Viewing Audit Records
Example Audit Records
Printing Audit Records
Starting the Audit History Viewer
1. Select StartAll ProgramsApplied Biosystems
GeneMapper GeneMapper ID-X v1.0, then log in.
2. In the Login to GeneMapper ID-X dialog box, log in with your
user name and password, then click OK.
3. In the GeneMapper ID-X main window, select
AdminAudit ManagerReport.
4. In the AuditHistoryViewer dialog box, log in with an
administrative user name and password (for example, gmidx or
Lab Manager).
5. Click OK. The Audit History Viewer window opens (page 58).
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Chapter 2 Managing the Auditing System
Viewing Audit History Records
User-defined
queries
Audit objects
Audit records for
selected object
Details for selected
Audit record
Creating Audit Record Queries
1. Open the Audit History Viewer window (see above).
2. Select FileNew Query to display the New Query dialog box.
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Chapter 2 Managing the Auditing System
Viewing Audit History Records
3. Complete the fields in the New Query dialog box, as needed.
You can:
• Leave a field blank to find all records for a field.
• Enter a partial string in any field. For example, if you enter
“modified” or “Allele” in the Audit Record field, the query
finds all modified records or all records that relate to
Allele edits.
• Enter a full string in any field to limit the query to specific
records.
Field
Query Name
Description
Name of the query.
Example
Full Audit History
IMPORTANT! To create a query that
lists all audit records, enter a Query
Name and leave the remaining fields
blank.
Old Value
Original value before the item is changed.
22
[KitT.AmpFLSTR_Panels_v1.PANEL.
Identifiler_v1.MARKER.D2S1338.
BASEPAIR.336.33.SAMPLE.Sample
3.PEAK_ID.1911.ANALYSIS_ID.44]
New Value
New value after the item is changed.
new variant
[KitT.AmpFLSTR_Panels_v1.PANEL.
Identifiler_v1.MARKER.D2S1338.
BASEPAIR.336.33.SAMPLE.Sample
3.PEAK_ID.1911.ANALYSIS_ID.44]
Instance
Name of the item.
ID_Control
Type
Audit category
SizeStandardT
Full Name
Full name of user who made the change
Audit Record
Audit record entry.
RUN.identifiler data
files.SAMPLE.ID_Control.fsa.
ALLELE.new.created
Reason
Reason for the change that is specified, if
audit state was set to On.
Change allele label
Date From and
To
Dates for the record.
12/10/2006
4. Click OK. The query is listed in the Queries pane of the Audit
History Viewer.
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Chapter 2 Managing the Auditing System
Viewing Audit History Records
Performing Audit Record Queries and Viewing Audit
Records
1. Open the Audit History Viewer window (see page 57).
2. Select a query in the Queries pane.
3. Click
in the toolbar.
4. In the Audit Objects pane, select the audited item to view
records for.
5. To view details for an audit record:
a. Click
(Audit Record Details icon) in the toolbar to
display the Audit Records Details section.
b. In the Audit Records section, select a record of interest.
c. Examine the Old Value, New Value, and Reason for
Change in the Audit Records Details section.
6. (Optional) To show or hide columns, right-click a column
header, then specify the columns to show or hide.
7. (Optional) To sort the audit history records in the Audit Records
list, click one of the column headers. A triangle (▲) appears
inside the column header to indicate the direction of the sort.
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Viewing Audit History Records
Example Audit Records
Table 12
Example audit records
Audit
Category
ProjectT
Objects
With audit
Records
Project
Example Audit Records
analyzed
deleted
Run
RUN.identifiler data files.created
RUN.identifiler data files.deleted
Sample
RUN.identifiler data files.SAMPLE.ID_Sample3.fsa.OverrideSQ
RUN.identifiler data files.SAMPLE.ID_Sample3.fsa.OverrideGQ
RUN.identifiler data files.SAMPLE.ID_Neg_cntrl.fsa.deleted
Allele
Analysis
MethodT
KitT
MatrixT
SizeStandardT
Analysis
Method
RUN.identifiler data files.SAMPLE.ID_Control.fsa.ALLELE.new.created
modified
Kit
deleted
Panel
PANEL.Blue_V1.deleted
BinSet
BINSET.YFilerBinSetTest.created
Marker
PANEL.Yfiler_v2.MARKER.Y_DYS392.deleted
Bin
PANEL.Identifiler_CODIS_v1.MARKER.CSF1PO.BIN.7.modified
Matrix
created
Size
Standard
created
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Chapter 2 Managing the Auditing System
Viewing Audit History Records
Printing Audit Records
You can print audit record reports for each object.
IMPORTANT! Review audit reports every month. For more
information on routine maintenance, see Chapter 4, Maintaining the
Software and Database Application.
1. In the Audit History Viewer window, select the object to print
from the Audit Objects list.
2. Select FilePrint Preview. The Select Columns dialog box
opens.
3. Select the columns to display in the report, then click OK. The
Preview Audit History Records window opens.
4. Click Print to print the report.
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Chapter 2 Managing the Auditing System
Backing Up, Removing, and Restoring Audit Records
Backing Up, Removing, and Restoring Audit
Records
This section describes:
•
•
•
•
When to Back Up
and Remove
Audit Records
When to Back Up and Remove Audit Records
Backing Up and Removing Audit Records
Storing Audit Records
Restoring Audit Records
Routinely review the amount of database space occupied by audit
records using the Database Dashboard (see “Reviewing the Database
Statistics” on page 81). As the amount of occupied disk space
approaches the maximum limit defined in the software, you must:
• Increase the amount of disk space, as explained in “Allocating
Disk Space” on page 82,
or
• Back up and remove the audit records, as explained below.
Backing Up and
Removing
Audit Records
IMPORTANT! The GeneMapper® ID-X Software automatically
backs up the audit data when you back up the database (see “Backing
Up the Database” on page 87). Use this function to selectively back
up, then remove audit records to free up space in the database.
1. Select StartAll ProgramsApplied Biosystems
GeneMapper GeneMapper ID-X v1.0.
2. Log in with an administrative account (for example, gmidx).
3. In the GeneMapper ID-X Software main window, select
AdminAudit ManagerBackup Audit Records.
4. In the Backup Audit Records dialog box:
a. Navigate to the location to which you want to export the
audit data.
b. Enter a name for the exported audit file (*.aud).
c. Click Backup.
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Chapter 2 Managing the Auditing System
Backing Up, Removing, and Restoring Audit Records
5. In the GeneMapper ID-X Software main window, select
AdminAudit Manager Delete All Audit Records.
6. In the Delete All Audit Records dialog box, click Yes.
Storing Audit
Records
Restoring Audit
Records
After exporting the audit records file, move the GeneMapper ID-X
Software audit file (*.aud) to a storage medium for archiving. If you
need to view the archived records, restore the records as explained
below, then view them using the Audit History Viewer (see “Viewing
Audit History Records” on page 57).
1. Select StartAll ProgramsApplied Biosystems
GeneMapper GeneMapper ID-X v1.0.
2. Log in with an administrative account (for example, gmidx).
3. In the main window, select AdminAudit Manager
Restore Audit Records.
4. In the Backup Audit Records dialog box, navigate to, then select
the desired GeneMapper ID-X Software audit file (*.aud).
5. Click Restore.
Note: Restoring audit records does not erase any current records. It
adds the restored records to the current records in the audit trail.
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Chapter 3
Managing the
E-Signature System
Chapter 1
Setting Up User
Accounts and User
Access
This chapter covers:
■ Overview of the Electronic Signature (E-Signature) System . 66
■ Default E-Signature Settings . . . . . . . . . . . . . . . . . . . . . . . . . . 67
■ Configuring the E-Signature System . . . . . . . . . . . . . . . . . . . 67
■ Viewing E-Signature Records . . . . . . . . . . . . . . . . . . . . . . . . . 72
■ Backing Up, Removing, and Restoring E-Signature Records. 74
Chapter 2
Managing the
E-Signature System
Chapter 3
Managing the
E-Signature System
Chapter 4
Maintaining the Software
and Database Application
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Chapter 3 Managing the E-Signature System
Overview of the Electronic Signature (E-Signature) System
Overview of the Electronic Signature (E-Signature)
System
The GeneMapper® ID-X Software electronic signature (E-Signature)
system ensures that only authorized users are allowed to make
certain changes (create, modify, or delete) in the GeneMapper ID-X
Software. You can configure the types of actions that require user
authentication (for example, analyze projects). A user must provide
his or her GeneMapper ID-X Software user name and password
before changes are saved.
The GeneMapper ID-X Software E-Signature system also keeps
track of who made certain changes. By comparison, the Audit
Manager keeps track of only what was done.
The components of the E-Signature system are defined in Table 13.
Table 13
Components of the E-Signature system
Component
Definition
Esig
Administrator
Configured by the GeneMapper ID-X Software system administrator to identify
the actions that require a signature.
Electronic
Signature
Verification
When a user performs actions (for example, deleting analysis methods) that have
been specified for electronic signature, the GeneMapper® ID-X Software
automatically displays the Electronic Signature Verification dialog box (see figure
on next page).
A user authenticates or “signs” for an action by entering his or her GeneMapper
ID-X user name and password.
If a user enters the correct password, the GeneMapper ID-X Software performs
the requested action and records the electronic signature transaction.
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Chapter 3 Managing the E-Signature System
Default E-Signature Settings
Table 13
Components of the E-Signature system (continued)
Component
Definition
Electronic
Signature
Verification
(continued)
A default warning that
indicates the action
that prompted
signature verification
An additional custom
message to the user
User enters user
name
User enters password
Default E-Signature Settings
By default, all E-Signature actions are disabled.
Configuring the E-Signature System
Note: The E-Signature system does not track printing or exporting
of object types.
This section describes:
•
•
•
•
Starting the E-Signature Manager
Enabling the E-Signature Function
Configuring E-Signature Actions
E-Signature Action Maps
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Chapter 3 Managing the E-Signature System
Configuring the E-Signature System
Starting the E-Signature Manager
1. Select StartAll ProgramsApplied Biosystems
GeneMapper GeneMapper ID-X v1.0, then log in.
2. In the GeneMapper ID-X main window, select Admin
Esig Administrator.
3. In the EsigAdministration dialog box, log in with an
administrative user name and password (for example, gmidx).
4. Click OK. The ESig Manager (Administration) window opens.
Enabling the E-Signature Function
The E-Signature Configuration settings apply to all users. A user
with an Admin profile can change settings for all users at any time.
1. Start the E-Signature Manager (see above).
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Chapter 3 Managing the E-Signature System
Configuring the E-Signature System
2. The ESig Administration window opens by default to the
Configuration tab.
3. For “Is Electronic Signature Required?”, select Yes.
4. For Method, select UsernamePassword.
5. (Optional) To require the user to enter a user name as part of the
electronic signature, select the Require UserID? check box.
Otherwise, the software fills the user name field with the name
of the user who is currently logged in to the software.
6. (Optional) In the Description field, enter comments for internal
use (for example, “Configured by Admin”).
7. Select FileSave to save the settings.
Configure each E-Signature action as described in the next section.
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Chapter 3 Managing the E-Signature System
Configuring the E-Signature System
Configuring E-Signature Actions
Note: Settings are not applied until you close and restart the
GeneMapper ID-X Software. By default, all E-Signature actions are
disabled.
1. Start the E-Signature Manager (see page 68).
2. In the ESig Administration window, select the Action
Administration tab.
Enable Esig (disabled)
Selected object type
Custom message displayed to
users when signature requested
Actions for the selected
actions group
Definition text displayed to users
when signature requested
3. In the ESig Action Maps pane, define actions that require
electronic signature:
a. Select a GM_object type. The actions you specify for
electronic signature (creating, modifying, deleting) are
grouped together, unlike the actions in the Audit Manager,
where you can specify actions individually.
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Configuring the E-Signature System
b. To require electronic signatures for the actions displayed in
the Action List, select the Enable Esig check box.
Note: You may need to resize the ESig Administration
window to see the Enable Esig check box.
c. (Optional) In the Electronic Signature Challenge Text box,
enter a custom message to the user that displays (for this
object type) every time an electronic signature is requested
(for example, “By entering your user name and password,
you are signing this action”).
4. Repeat step 3 for each object type in the ESig Action Maps
pane.
5. Select FileSave to save the settings.
IMPORTANT! Applied Biosystems recommends that you review the
E-Signature administration settings every 6 months, and modify
them as needed. For more information on routine maintenance, see
Chapter 4, Maintaining the Software and Database Application, on
page 75.
E-Signature Action Maps
Table 14 lists the actions that can be tracked by E-signature.
Table 14
E-Signature action maps
Object
Default
State
Actions Requiring an E-signature (When Enabled)
Default Action Group
NA
Not used in GeneMapper® ID-X Software.
GM_PROJECT
Disabled
A project is created, modified, or deleted.
GM_CHEMISTRY_ KIT
Disabled
A chemistry kit is created, modified, or deleted.
GM_ANALYSIS_ METHOD
Disabled
An analysis method is created, modified, or deleted.
GM_SIZE STANDARD
Disabled
A size standard is created, modified, or deleted.
GM_MATRIX
Disabled
A matrix is created, modified, or deleted.
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Chapter 3 Managing the E-Signature System
Viewing E-Signature Records
Viewing E-Signature Records
This section describes:
• Specifying E-Signature Queries
• Performing E-Signature Queries and Viewing E-Signature
Records
• Printing E-Signature Records
Specifying E-Signature Queries
1. Start the E-Signature Manager (see page 68).
2. In the ESig Administration window, select the History Viewer
tab.
3. To view all records, leave blank all fields in the Query
Electronic Signature Events section, then click Find.
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Viewing E-Signature Records
4. To refine the query of electronic signature records, in the Query
Electronic Signature Events pane, enter parameter values:
Note: Enter parameter values only in those fields that are
relevant to your search.
• Object Name – Enter the name of an object. For example,
entering Analysis Method 123 in this field retrieves all
events for the analysis method named “Analysis Method
123.”
• Object Type – Enter the object type. For example,
entering analysis method in the Object Type field retrieves
events for all analysis methods.
• 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, modified, or deleted 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 GroupGM_ANALYSIS_METHOD, selecting
ActionDELETE_ANALYSIS_METHOD retrieves all
events created in which a user deleted an analysis method.
• Event Date/Time – Enter a date or dates to display records
created in a specific time period.
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Chapter 3 Managing the E-Signature System
Backing Up, Removing, and Restoring E-Signature Records
Performing E-Signature Queries and Viewing E-Signature
Records
1. After specifying E-Signature queries in the History View tab of
the ESig Administration window, click Find.
Note: The Server Time is the local time on the database
computer at which the action occurred. The Client Time is the
local time on the software computer at which the action
occurred. (Typically, these times are similar. However, if you
make a change on a client computer in one time zone and the
database computer is in another time zone, the times may
differ.)
Note: The Version field is not used in the GeneMapper® ID-X
Software.
2. (Optional) In the Events list, select an event to view the Event
Details.
3. If you want to run another query, click Clear, then repeat
step 1 through step 2.
Sorting
The GeneMapper® ID-X Software 1.0 does not support sorting of
E-signature records.
Printing E-Signature Records
The GeneMapper® ID-X Software 1.0 does not support printing
E-signature records.
Backing Up, Removing, and Restoring E-Signature
Records
The GeneMapper® ID-X Software 1.0 does not support backing up,
removing, or restoring E-signature records.
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Chapter 4
Maintaining the Software
and Database Application
Chapter 1
Setting Up User
Accounts and User
Access
This chapter covers:
■ Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
■ Using and Maintaining the Oracle® Database. . . . . . . . . . . . . 77
■ Using the Database Dashboard Software . . . . . . . . . . . . . . . . 79
■ Reviewing the Database Statistics. . . . . . . . . . . . . . . . . . . . . . 81
■ Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
■ Viewing Project Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
■ Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Chapter 2
Managing the
Auditing System
■ Generating a Database Report. . . . . . . . . . . . . . . . . . . . . . . . . 90
Chapter 3
Managing the
E-Signature System
Chapter 4
Maintaining the Software
and Database
Application
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Chapter 4 Maintaining the Software and Database Application
Maintenance Overview
Maintenance Overview
The GeneMapper® ID-X Software requires regular maintenance to
provide:
• Optimal performance of the software and database application
• Protection against data loss (due to hardware or software
failure)
Recommended Maintenance Schedule
The maintenance schedule in Table 15 contains general
recommendations for routine maintenance of the GeneMapper ID-X
Software.
Table 15
Database maintenance activities
Frequency
Tasks
Weekly
• Exit the GeneMapper ID-X Software and restart the computer.
• Review the statistics for the database (see page 81), and, if necessary:
– Export unused projects and data (see GeneMapper ID-X Software v1.0 Online
Help) and then delete them.
– Allocate additional disk space (see page 84).
• (Optional) Back up the GeneMapper ID-X Software database (see page 87).
Monthly
• Defragment the computer hard drive.
As Needed
• Review password policies, and modify them as necessary (see page 14).
• If using the auditing system, review the audit map configuration, and modify as
needed (see page 50).
• If using the electronic signature system, review the electronic signature settings,
and modify as needed (see page 67).
•
•
•
•
•
Manage user accounts (see page 39).
Manage security groups (see page 37).
Manage user groups (see page 34).
Manage profiles (see page 29).
Back up security settings after making any change to the security system (see
page 44).
• Back up, remove, and restore audit records (see page 63).
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Using and Maintaining the Oracle® Database
Using and Maintaining the Oracle® Database
This section describes:
• Database Access
• Maintaining the Database
• Oracle Documentation
Database Access
The Database Dashboard Software provides tools for maintaining
and evaluating the performance of the GeneMapper® ID-X Software
database application. The software is installed with the full version
(co-installation, remote autoanalysis, and stand-alone
configurations) of the GeneMapper ID-X Software.
Do not install any other database applications on
the computer running the GeneMapper ID-X Software. If
co-installed with the GeneMapper ID-X Software, other database
applications can produce unexpected results, including loss of data
and corruption of the GeneMapper ID-X Software database
application.
IMPORTANT! The Oracle Database included in the
GeneMapper® ID-X Software package should serve as a data
repository for this software product only and should not be used for
other data storage purposes.
Applied Biosystems does not support access to the Oracle Database
through any means other than the GeneMapper ID-X Software and
associated tools (Database Dashboard, Security Manager, Audit
Manager, and E-signature Manager).
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 ID-X Software database application.
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Using and Maintaining the Oracle® Database
API Support
The GeneMapper ID-X Software does not include an application
programming interface (API) for linking the GeneMapper ID-X
Software database application with a LIMS. However, the
GeneMapper ID-X Software can export data from the database in a
variety of formats, many of which can be imported by major
third-party data storage and analysis applications.
Note: The GeneMapper ID-X Software includes 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 using a scripting language or batch file so that
most maintenance and data-entry tasks can be minimized or
eliminated. For more information, see Appendix A, “Operating the
Software from a Command Line,” on page 91.
Maintaining the Database
Use the Database Dashboard software (described on page 79) to
perform routine maintenance. You do not need Oracle training to use
the Database Dashboard software. However, Applied Biosystems
recommends that the maintenance of the Oracle Database be
performed by a certified Oracle Database Administrator.
Advanced Oracle
Database Tools
Oracle
Documentation
78
The Oracle Corporation provides tools to optimize the performance
of the Oracle Database. Applied Biosystems recommends use of
these tools only by a certified Oracle database administrator.
Additional documentation for the Oracle Database is available at
www.oracle.com.
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Chapter 4 Maintaining the Software and Database Application
Using the Database Dashboard Software
Using the Database Dashboard Software
The Database Dashboard Software installed with the full version of
the GeneMapper ID-X Software (software and database) provides
tools for maintaining the GeneMapper ID-X Software database that
reside in the Oracle Database.
Note: The Database Dashboard software is not installed on client
computers.
This section describes:
• Dashboard Features
• Setting a Dashboard Password
Dashboard Features
The Database Dashboard includes the:
• Dashboard tab – Provides information about
database performance, space utilization, and
operating systems usage. The traffic light displays
the current state of the database.
• Report tab – Provides a comprehensive view for
troubleshooting the Oracle Database database. The top of the
report provides a list of potential problems that the Database
Dashboard software identifies.
• Administration tab – Provides a limited set of database
administration functions.
• GeneMapper ID-X tab – Provides statistical summaries and
tools for the GeneMapper ID-X Software database.
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Using the Database Dashboard Software
Setting a Dashboard Password
On all multi-user database computers, log in to the Database
Dashboard and set a password to ensure that only authorized users
can access the Database Dashboard software.
Note: The Database Dashboard software is not installed on client
computers.
1. Select StartAll ProgramsApplied Biosystems
Database DashboardDashboard.
2. Click Yes when asked if you want to set a password.
3. Enter the password: password.
4. Click OK.
IMPORTANT! Do not lose the password for the Database
Dashboard software. Applied Biosystems cannot retrieve
passwords.
Starting the Database Dashboard
Note: You must log in to GeneMapper ID-X Software at least once
before starting the Database Dashboard for the first time.
1. Select StartAll Programs
Applied BiosystemsDatabase DashboardDashboard.
2. Enter the password specified by the GeneMapper ID-X
Software system administrator after the software was installed.
IMPORTANT! Do not lose the password for the Database
Dashboard software. Applied Biosystems cannot retrieve the
passwords.
Note: To change or set the password at any other time, select
DatabaseSet Password.
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Chapter 4 Maintaining the Software and Database Application
Reviewing the Database Statistics
Reviewing the Database Statistics
Review database statistics weekly to determine if database
maintenance is required.
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the GeneMapper
ID-X tab.
3. Select the Database Statistics tab (see below).
The Database Statistics table displays statistics for the
GeneMapper ID-X Software database. The statistics are
approximate values that are calculated based on the space that is
allocated for the database, including tables and indexes.
The columns of the Database Statistics table provide storage
space information on the three tables (Audit Data, Project Data,
and Reference Data) used by the GeneMapper ID-X Software
database to store data.
Table Name
Stored Content
Audit Data
Audit records generated from changes made to
the software (if auditing is turned on).
Project Data
Projects, including samples and results data.
Reference Data
Supporting data (analysis methods, size
standards, panels, bin sets, matrices, and so
on).
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Allocating Disk Space
4. Review the content of the Database Statistics table for each
category of data and determine whether or not database
maintenance is required, based on the instructions in the
following table:
Used(%)
Value
(Used/
Allocated)
Auto
Extend
Value
>80%
Yes
Required Action
Allocate more space for data as
explained in “Allocating Additional
Disk Space” on page 84, if:
• Used (MB) is approaching
Allocated (MB), or
• Free disk space on the current
drive is low. Allocate space on
another drive.
<80%
No
Allocate more space for data, as
explained in “Allocating Additional
Disk Space” on page 84.
N/A
No maintenance required
Allocating Disk Space
This section describes:
• Options for Creating More Disk Space
• Allocating Additional Disk Space
The Database Dashboard allows you to allocate additional space on
the hard drive of a a computer that does not contain Data Collection
Software.
The Allocation feature is not available if the GeneMapper® ID-X
Software is co-installed with the Data Collection Software.
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Allocating Disk Space
Options for Creating More Disk Space
When the Used (%) value of any database table approaches 80%:
• Allocate additional hard disk space for the GeneMapper ID-X
Software database,
or
• Export and delete existing data objects to provide more room
for new projects and settings.
Note: If available space on the computer’s hard disk is insufficient
for allocation, you must export and remove data.
Table 16 indicates the data objects that you can export to increase the
free space of the corresponding GeneMapper ID-X Software
database tables.
Table 16
Exportable data objects
Table Name
Exportable Data Objects
Audit Data
Audit records
Project Data
Projects
Reference Data
•
•
•
•
•
•
•
•
Analysis methods
Binsets
Matrices
Kits, panels, and markers
Plot settings
Size-standard definitions
Report settings
Table settings
To export audit data, see “Backing Up, Removing, and Restoring
Audit Records” on page 63.
To export project data and reference data, see the
GeneMapper® ID-X Software Help.
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Allocating Disk Space
Allocating Additional Disk Space
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Dashboard tab.
3. In the Connections pane, determine if any users (clients) are
logged on to the GeneMapper ID-X Software.
4. Before you continue, instruct all users to log off the
GeneMapper ID-X Software.
5. Select the GeneMapper tab, then select the Database
Statistics tab.
6. At the bottom of the Database Dashboard, select the Default
Allocation tab.
Note: The Allocation feature is not available if the
GeneMapper® ID-X Software is co-installed with the Data
Collection Software.
7. In the Available Drives drop-down list, select a drive.
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Chapter 4 Maintaining the Software and Database Application
Allocating Disk Space
8. In the Table Space drop-down list, select a database table.
Note: The Project Data table has three subdivisions that can be
allocated separately in the Custom Allocation tab to optimize
allocation. For information on refining the allocation of the
Project Data tables, see the Database Dashboard Help.
9. In the Add Disk Space (MB) scroll box, click the up (down)
arrow to increase (decrease) the disk space for the selected table
space. You can also enter a number.
IMPORTANT! After disk space has been allocated by clicking
Allocate, the disk space cannot be reduced. You can use the
allocation feature at a later date to increase the allocated space
further, but you cannot undo a previous disk space allocation.
10. Click Allocate.
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Chapter 4 Maintaining the Software and Database Application
Viewing Project Statistics
11. In the Alert dialog box, click Yes.
IMPORTANT! Allocating disk space cannot be undone.
12. 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 updated the
Database Statistics table.
Viewing Project Statistics
Use the Database Dashboard Software to view summary statistics for
the projects that are stored by the GeneMapper® ID-X Software
database.
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the GeneMapper
tab.
3. Select the Project Statistics tab to display the project types and
number of samples for each project type.
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Chapter 4 Maintaining the Software and Database Application
Backing Up the Database
Backing Up the Database
This section describes:
• When to Back Up the Oracle Database
• Backing Up (Exporting) the Database
• Restoring (Importing) the Database
When to Back Up the Oracle Database
Applied Biosystems recommends that you back up the Oracle
Database onto an external storage medium (for example, 4-mm tape)
frequently, depending on software use.
Note: The Security Manager settings are not backed up when you
back up the database. Back up Security Manager settings separately
as an exported file. See “Exporting and Importing the Security
Settings” on page 44 for more information.
Backing Up (Exporting) the Database
IMPORTANT! The disk space required for backup can be 60 to 70%
of the size of the database. The database size is the Allocated Space
displayed in the Dashboard tab.
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Dashboard tab.
3. In the Tablespace pane (lower left of the tab), note the Allocated
Table Space.
4. Review your backup medium to ensure that you have space
available to back up at least 60 to 70 percent of the Allocated
Table Space noted in step 3.
5. In the Connections pane, determine if any users (clients) are
logged on to the GeneMapper ID-X Software.
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Backing Up the Database
6. Before you continue, request and ensure that all users are
logged off the GeneMapper ID-X Software.
7. In the Database Dashboard window, select the Administration
tab.
8. In the navigation column of the Administration tab, select
AdministrationExport Database.
9. In the Full Database Backup pane, click Browse, navigate to the
desired location, enter a name for the backup file, then click
Open.
Note: Ensure that you have available for backup at least 60 to
70% of the Allocated Table Space indicated in the Dashboard
tab.
10. Click Export, then wait for the software to complete the
operation. The software displays the progress of the export
operation in the Log View field.
Restoring (Importing) the Database
IMPORTANT! When you restore the database, you erase the current
data and recreate the database. You lose all existing data when you
import the data from the exported *.dmp file.
After backing up (exporting) the database, you can import the
resulting *.dmp file to recreate the database.
The target computer that you restore the database to must have a
configuration identical to the computer from which the database was
backed up. For example, if you back up a database with 250 MB
allocations on the C, D, and G drives, you can restore the database
only on a computer that contains at least 250 MB on its C, D, and G
drives.
Note: The restore procedure does not restore the database directly. It
creates a batch file that you run to restore the database.
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Backing Up the Database
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Administration
tab.
3. In the navigation column of the Administration tab, select
AdministrationImport Database.
4. Click Browse, navigate to the desired location, select the correct
.dmp file, then click Open.
5. In the Full Database Restore settings, click Check. The
Database Dashboard Software runs a check to ensure that the
.dmp file you are importing matches your system configuration.
If the software displays an error message, the drive partitions of
your computer do not match the original configuration, or they
cannot support the amount of data you are attempting to restore.
The software displays the required structure in the import log
(the field below the Import controls). Click OK, correct the
problem, then import again.
6. Click Import.
The software displays a message indicating the location of the
batch file it creates to perform the import.
7. Make a note of the location of the batch file, then click OK.
8. Exit the Database Dashboard Software.
9. In Windows Explorer, navigate to the batch file, then
double-click the file to run it. The software runs SQL scripts to
import the data into the database.
10. Restart your computer.
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Generating a Database Report
Generating a Database Report
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Report tab.
3. To print the report, click Print.
4. To e-mail the report, click E-mail, enter the e-mail address, then
click OK.
5. To 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. Enter a name for the exported file.
d. Select the desired file format (HTML or tab-delimited
text).
e. Click Save.
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Appendix A
Operating the Software
from a Command Line
This appendix covers:
■ Operating the Software from a Command Line . . . . . . . . . . . 92
■ Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
■ Command-Line Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . 100
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Appendix A 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® ID-X Software.
IMPORTANT! Applied Biosystems supports the use of the
command-line interface only as it is explained in this appendix.
Note: If you are unfamiliar with Microsoft DOS,
Applied Biosystems does not recommend using the command-line
interface. Use the command-line interface only if you are an
advanced user (systems administrator, bioinformatician, network
administrator).
About the
Command-Line
Interface
Command Syntax
The GeneMapper ID-X Software command-line interface can
automate most software operations without using the graphic user
interface. Commands can automate data-entry tasks associated with
project analysis (for example, creating a project adding samples, and
specifying analysis parameters).
Commands are issued to the GeneMapper ID-X Software
command-line interface in the MS DOS shell of the Windows
operating system. The basic formula for all commands is:
<GeneMapper.exe> -commandline <arguments>
where:
• <GeneMapper.exe> is the path and filename of the
executable file for the GeneMapper ID-X Software.
• -commandline is the argument that places the software into
command-line mode.
• <arguments> is the series of arguments that specify the
operations to be performed.
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.
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Appendix A Operating the Software from a Command Line
Operating the Software from a Command Line
Creating a Batch File to Run the Command-Line Interface
1. In the desktop, select
StartAll Programs Accessories Notepad.
2. In the Notepad window, enter @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 MS 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, enter the following:
@echo off
“GeneMapper.exe” -commandline -option h -username “user” -password
“password” -project “project”
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.
where:
• GeneMapper.exe is the directory path for the
GeneMapper ID-X Software executable (enclosed in
double quotes).
• –commandline signals the exe to run the command line.
• –option h instructs the command line to execute without
displaying the GeneMapper® ID-X Software user interface.
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Appendix A Operating the Software from a Command Line
Operating the Software from a Command Line
• –username and –password instruct the command line to log
in with user and password, a user account with
privileges sufficient to perform the desired functions
(enclosed in double quotes).
IMPORTANT! User names and passwords are casesensitive. That is, “User1” is considered different from
“user1.”
• –project instructs the software to create or analyze a
project named project (enclosed in double quotes).
For example:
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gmidx” -password “password” –project “myProject”
5. After the -project argument, enter any additional arguments
to instruct the GeneMapper ID-X Software to perform the
desired functions. See “Command-Line Arguments” on
page 100 for a complete list of all arguments.
When you enter arguments:
• Add them to the command in any order.
• Enter 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 entering 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 in which they appear in the batch file (from top to
bottom).
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Appendix A Operating the Software from a Command Line
Operating the Software from a Command Line
7. (Optional) After entering the last command:
a. Press Enter to create a new line.
b. Enter ECHO Batch file operation complete.
c. Press Enter to create a new line.
Note: See “Example #2: Analyze Sample Files with Named
Ladders” on page 98 for an explanation of the example batch
file.
8. 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, enter a name for the batch file with a
.bat file extension.
For example: mybatchfile.bat or GMIDXanalysis.bat
c. Click Save.
10. Select FileExit to close the batch file.
Example Batch File
@ECHO off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gmidx” -password “password” –project “myProject”
-analysismethod “myMethod” -sizestandard “mySS” -panel “myPanel” folder “D:\casework\case01 -ladder “D:\casework\case01 ladder1.fsa”
-exportall “D:\casework\case01\case01_export.txt”
ECHO Batch file operation complete.
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Appendix A Operating the Software from a Command Line
Operating the Software from a Command Line
Running the Batch File
Close the GeneMapper® ID-X Software before you run the batch file.
Run the batch file containing the command-line arguments from an
MS DOS command prompt window. Wait for the computer to run the
scripted command. When the operating system finishes processing
the batch file, the command prompt window displays “Press any key
to continue”.
IMPORTANT! The Batch File Complete message is displayed, even
if the command does not generate the expected output file (for
example, if the project name specified does not exist). If you do not
find the expected output files after running a command-line
command, review the .bat file to ensure that all commands are valid.
Do not close the command prompt window
before it displays “Press any key to continue.” Doing so prematurely
terminates the commands 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 A Operating the Software from a Command Line
Example Commands
Example Commands
This section covers:
Example #1: Analyze Sample Files
Example #2: Analyze Sample Files with Named Ladders
Example #3: Export Project Data
Example #4: Export Sample Plot to PDF
Example #1: Analyze Sample Files
This example analyzes sample files generated by the Data Collection
software using the analysis method, size standard, panel, and ladder
specified by the Data Collection Software.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gmidx” -password “password” –project
“Case01 Project” -folder “d:\Casework\Case01”
ECHO Batch file operation complete.
Description
The example batch file logs in to the GeneMapper ID-X Software
using the default user account, gmidx, and analyzes the sample files
in the d:\Casework\Case01 directory. Each executed step of the batch
file is not displayed in the command prompt window (–option h).
After the analysis, the command instructs the software to save the
project as Case01 Project, then display “Batch file operation
complete” in the command prompt window.
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Appendix A Operating the Software from a Command Line
Example Commands
Example #2: Analyze Sample Files with Named Ladders
This example analyzes sample files generated by the Data Collection
software using the analysis method, size standard, panel, and ladder
specified by the Data Collection Software.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline
–username “gmidx” –password “password” –project “Casework02 Project”
–folder “e:\Casework\Case02” –ladder “e:\Casework\Case02”
“ladder1.fsa” “ladder2.fsa”
ECHO Batch file operation complete.
Description
98
The example logs in to the GeneMapper ID-X Software using the
default user account, gmidx, and analyzes the sample files in the e:\
Casework\Case02. The command also instructs the software to use the
ladder1.fsa and ladder2.fsa sample files in the e:\Casework\Case02
directory as the allelic ladders for the analysis. After the analysis, the
command instructs the software to save the project as Casework02
Project, then display “Batch file operation complete” in the
command prompt window. Each executed step of the batch file is
displayed in the command prompt window.
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Appendix A Operating the Software from a Command Line
Example Commands
Example #3: Export Project Data
This example exports the sizing data and analyzed electropherogram
data for the sample files of an existing project.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline option h –username “gmidx” –password “password” –project “Case03”
–exportsizemap “g:\Case03\size map.txt” -exportanalyzedeps “g:\
Case03\analyzed eps.txt”
ECHO Batch file operation complete.
Description
The example logs in to the GeneMapper ID-X Software using the
default user account, gmidx, exports the sizing data and analyzed
electropherogram data of the Case03 project as the g:\Case03\size
map.txt and g:\Case03\analyzed eps.txt files, then displays “Batch
file operation complete” in the command prompt window. Each
executed step of the batch file is not displayed in the command
prompt window (–option h).
Example #4: Export Sample Plot to PDF
This example exports the sample plot of an existing project to a PDF
file.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline option h –username “gmidx” –password “password” –project “Case04”
–exportsampleplot “g:\Case04\Case04SamplePlot.PDF”
ECHO Batch file operation complete.
Description
The example logs in to the GeneMapper ID-X Software using the
default user account, gmidx, exports the sample plot of the Case04
project as the g:\Case04\Case04SamplePlot.PDF, then displays
“Batch file operation complete” in the command prompt window.
Each executed step of the batch file is not displayed in the command
prompt window (–option h).
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Appendix A 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.
• Grayed text – Gray table cells indicate the required elements
of all commands issued via the command-line interface.
Commands
100
Table 17 contains a summary of all arguments for the command-line
interface.
GeneMapper® ID-X Software v1.0 Administrator’s Guide
CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
Summary of arguments for the GeneMapper® ID-X Software command-line interface
Argument
-analysismethod
Action/Definition
Usage
Specifies the name of the analysis
method to use in the analysis of the
specified project.
-analysismethod “method”
-commandline
Configures the GeneMapper ID-X
Software to operate in command-line
mode.
-commandline
-deleteproject
Deletes the specified project(s).
-deleteproject “project1” “project2” …
where method is the name of the analysis method.
where project1 and project2 are the names of
the projects to be deleted.
-exportall
-exportanalyzedeps
-exportbinoffsettable
Exports the analyzed
electropherogram data for the
samples of the specified project as a
tab-delimited text file of the specified
name.
Exports the bin offsets for the
specified project as a tab-delimited
text file of the specified name.
Exports the Genotypes table for the
specified project as a tab-delimited
text file of the specified name.
-exportall “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
-exportanalyzedeps “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
-exportbinoffsettable “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
-exportgenotypetable “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
Command-Line Arguments
-exportgenotypetable
Exports the combined contents of
the Samples and Genotypes tables of
the specified project as a tabdelimited text file of the specified
name.
Appendix A Operating the Software from a Command Line
GeneMapper® ID-X Software v1.0 Administrator’s Guide
CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
Table 17
101
102
Table 17
Summary of arguments for the GeneMapper® ID-X Software command-line interface (continued)
Argument
GeneMapper® ID-X Software v1.0 Administrator’s Guide
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-exportsampletable
-exportsizemap
-folder
Exports the Sample plot for the
specified project to a PDF file.
Exports the Samples table for the
specified project as a tab-delimited
text file of the specified name.
Exports data point/base pair data for
the specified project as a tabdelimited text file of the specified
name.
Specifies the names of the affected
run folders in the project:
• 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.
-help
Prints a summary of the commands
for the command-line interface.
-exportplotsampletable “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
-exportsampleplot “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
-exportsampletable “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
-exportsizemap “filename”
where filename is the long path (file name
appended to the export directory path) of the
exported file.
-folder “folder1” “folder2” …
where folder1 is always required. Additional
folders are needed only if analyzing by project (not
used when analyzing by run).
-help
Appendix A Operating the Software from a Command Line
-exportsampleplot
Exports the Sizing table of the
Samples plot for the specified project
as a tab-delimited text file of the
specified name.
Usage
Command-Line Arguments
-exportplotsampletable
Action/Definition
Summary of arguments for the GeneMapper® ID-X Software command-line interface (continued)
Argument
-importanalysismethod
Action/Definition
Imports the specified file as an
analysis method.
Usage
-importanalysismethod “filename”
where filename is the long path (file name
appended to the import directory path) of the
imported file.
IMPORTANT! The specified file must be formatted as an XML file that uses GeneMapper
ID-X Software-specific 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 (*.ser) created by the
export function of the GeneMapper ID-X 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 GeneMapper
ID-X Software-specific syntax and contains the necessary size standard data in the format
identical to that of an exported size standard.
Instructs the software to use the
specified samples as allelic ladders in
the analysis of the specified project.
-ladder “folder” “ladder1” “ladder2” …
where:
• folder is the name of the project folder that
contains the ladder samples.
• ladder1 and ladder2 … are the names of the
allelic ladder sample files separated by a space.
Command-Line Arguments
-ladder
Appendix A Operating the Software from a Command Line
GeneMapper® ID-X Software v1.0 Administrator’s Guide
CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
Table 17
103
104
Table 17
Summary of arguments for the GeneMapper® ID-X Software command-line interface (continued)
Argument
Instructs the software to use the
specified samples as negative
controls in the analysis of the
specified project.
-negcontrol “folder” “ctrl1” “ctrl2” …
Specifies the options for the exported
data.
-option “option”;“option”;…;“option”
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.
GeneMapper® ID-X Software v1.0 Administrator’s Guide
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where option is any of the following option letters:
• b – Attaches bin names to the exported
Genotype table.
• h – Hides the user interface.
• p “port” – Specifies the monitoring TCP/IP
port number (default is 8393).
-panel
-password
Specifies the name of the panel to
use in the analysis of the specified
project.
-panel “panel”
Specifies the password for the user
account defined by the -username
argument.
-password “password”
where panel is the name of the panel.
where password is the password for the user
account.
IMPORTANT! Passwords are case-sensitive. That
is, “User1” is considered different from “user1.”
-poscontrol
Instructs the software to use the
specified samples as positive
controls in the analysis of the
specified project.
-poscontrol “folder” “ctrl1” “ctrl2” …
where:
• folder is the name of the project folder that
contains the positive-control samples.
• ctrl1 and ctrl2 … are the names of the
positive-control sample files separated by a
space.
Appendix A Operating the Software from a Command Line
-option
Usage
Command-Line Arguments
-negcontrol
Action/Definition
Summary of arguments for the GeneMapper® ID-X Software command-line interface (continued)
Argument
-project
-sizestandard
-username
Action/Definition
Usage
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 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 user is the name of a user account.
IMPORTANT! The user account that you use must have privileges sufficient to perform
the specified actions. For information, see Chapter 1, “Setting Up User Accounts and User
Access.”.
IMPORTANT! User names are case-sensitive. That is, “User1” is considered different from
“user1.”
Command-Line Arguments
Appendix A Operating the Software from a Command Line
GeneMapper® ID-X Software v1.0 Administrator’s Guide
CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
Table 17
105
Appendix A Operating the Software from a Command Line
Command-Line Arguments
106
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CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
Index
A
action maps 70
activating user accounts 40
Admin user account 10
intended user 10
profile and actions allowed 8
administrator’s guide
attention words viii
audience vii
how to use vii
purpose of vii
text conventions viii
Allele audit map object 55, 61
ALLELE audit map object attribute 54
allelic ladders, specifying in a command line
analysis 103
allocating, disk space 82
Analysis Method audit map object 55, 61, 71
analysis methods
import via a command line 103
specifying in a command line 101
analysismethod argument 101
API support 78
Applied Biosystems
contacting x
customer feedback on documentation ix
Information Development department ix
Technical Support x
assumptions for using this guide vii
Audit Data table 81
Audit History records
creating queries 58
examples 61
printing 62
running queries 60
viewing 57, 60
audit map
configuring 51
definition 46
elements 53
example configuration 47
viewing the history 58
when records are saved 47
audit map objects
Allele 55, 61
Analysis Method 55, 61
Bin 56, 61
BinSet 55, 61
Kit 55, 61
Marker 56, 61
Matrix 56, 61
Panel 56, 61
Project 54, 61
Run 54, 61
Sample 54, 61
Size Standard 56, 61
audit records
archiving 63
backing up 63
for autoanalysis 53
removing 63
restoring 64
storing 64
Audit Trail System
components 46
defaults 48
enabling 51
overview 46
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107
Index
autoanalysis
see also GeneMapper ID-X Installation
Guide and GeneMapper ID-X Help
auditing 53
Scientist profile required 27
user account 21
automating software operations 92
B
backing up
audit records 63
database 87
E-Sig records 74
batch file, creating for command line
operation 93
Bin audit map object 56, 61
BIN audit map object attribute 56
bin offsets, export via a command line 101
BinSet audit map object 55, 61
BINSET audit map object attribute 55
bold text, when to use viii
C
Casework Analyst user account
intended user 10
profile and actions allowed 7
Casework Tech Lead user account
intended user 10
profile and actions allowed 8
Casework Tech user account
intended user 10
profile and actions allowed 7
chain-of-custody of electronic data 2
changing password 39
command line arguments
about 100
analysismethod 101
deleteproject 101
exportall 101
exportanalyzedeps 101
108
exportbinoffsettable 101
exportgenotypetable 101
exportplotsampletable 102
exportsampletable 102
exportsizemap 102
folder 102
help 102
importanalysismethod 103
importsizestandard 103
ladder 103
negcontrol 104
option 104
panel 104
password 104
poscontrol 104
project 105
sizestandard 105
username 105
command line interface
about 92
arguments 100
example commands 97
hiding the user interface 104
specifying allelic ladders 103
specifying analysis methods 101
specifying negative controls 104
specifying panels 104
specifying port setting 104
specifying positive controls 104
specifying size standards 105
specifying the project 105
configuring
audit map 51
configuring E-Sig actions 70
controlling access to the software 45, 65
conventions
bold text viii
for describing menu commands viii
IMPORTANTS! viii
italic text viii
Notes viii
user attention words viii
GeneMapper® ID-X Software v1.0 Administrator’s Guide
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Index
creating
audit queries 58
Database Dashboard Software
password 80
profiles 26
security groups 37
user accounts 16
user groups 34
customer feedback, on Applied Biosystems
documents ix
customizing user and security groups 34
D
data export via a command line 101
database
backing up 87
exporting 87
importing 87
statistics, viewing 81
Database Dashboard Software
about 79
generating a report 90
maintaining database 80
setting password 80
viewing project statistics 86
Databasing Analyst user account
intended user 10
profile and actions allowed 7
Databasing Tech Lead user account
intended user 10
profile and actions allowed 8
Databasing Tech user account
intended user 10
profile and actions allowed 7
deactivating user accounts 40
deleteproject argument 101
deleting
security groups 38
user accounts 40
user groups 36
disclaimer, license ii
disk space, allocating 82
disk space, creating more 83
documentation, related ix
E
editing
profiles 29
security groups 37
user accounts 39
electronic data tracking systems, overview 2
Electronic Signature Challenge Text 71
electropherogram data, export via a command
line 101
enable/disable audit object 52
enabling
auditing 51
E-Sig History Viewer
printing records 74
running queries 74
specifying queries 72
viewing records 74
E-Sig records
archiving 74
backing up 74
removing 74
E-Sig System
action maps 71
components 66
configuring actions 70
default settings 67
enabling 68
starting 68
exportall argument 101
exportanalyzedeps argument 101
exportbinoffsettable argument 101
exportgenotypetable argument 101
exporting
database 87
security settings 44
exportplotsampletable argument 102
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109
Index
exportsampletable argument 102
exportsizemap argument 102
LIMS, linking the software using the
command line interface 92
F
M
folder argument 102
GeneMapper ID-X Software, starting 12
Genotypes table, export via a command
line 101
gmidx user account
intended user 10
profile and actions allowed 8
maintaining software and database 76
maintenance schedule 76
Marker audit map object 56, 61
MARKER audit map object attribute 56
Matrix audit map object 56, 61, 71
Max Login Attempts 15
menu commands, conventions for
describing viii
MSDSs, obtaining x
H
N
help argument 102
how to use this guide vii
negative controls, specifying in a command
line analysis 104
negcontrol argument 104
New Application command, do not use 14
G
I
importanalysismethod argument 103
importing
analysis methods (command line) 103
database 87
security settings 44
size standard definition (command
line) 103
importsizestandard argument 103
Information Development department,
contacting ix
intended user 10
italic text, when to use viii
K
Kit audit map object 55, 61, 71
L
O
option argument 104
Oracle® database
accessing 77
API support 78
maintaining 77
maintenance 76
SQL support 77
tools, use of 78
using 77
viewing statistics 81
Override Inherited Rights (OIR), meaning
of 28
OverrideCGQ audit map object attribute 54
OverrideGQ audit map object attribute 54
OverrideSQ audit map object attribute 54
overview, Audit Trail System 46
ladder argument 103
license disclaimer ii
110
GeneMapper® ID-X Software v1.0 Administrator’s Guide
CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
Index
P
panel argument 104
Panel audit map object 56, 61
PANEL audit map object attribute 55
panel, specifying in a command line
analysis 104
password
see also password policies
automatic notification 15
case-sensitive 12
changing 39
Database Dashboard software 80
password argument 104
password policies
about 14
Max Login Attempts 15
Minimum Password Length 15
Password Grace Logins 15
Password Lifetime 15
Password Reuse Period 15
Passwords Kept per User 15
Send Log Message 15
Set User State - Remain Active 15
Set User State - Suspend 15
setting 14
table of settings 15
poscontrol argument 104
positive controls, specifying in a command
line analysis 104
Practice user account 10, 12
Practice user group and security group 9
pre-expire, user account 17, 19, 22
profile
Admin, default actions allowed 8
Analyst, default actions allowed 7
creating 26
customizing 26
defaults 7
definition 3
editing 29
elements 30
Scientist, default actions allowed 8
Technician/Read-Only, default actions
allowed 7
project argument 105
Project audit map object 54, 61, 71
Project Data table 81
projects
deletion via a command line 101
specifying in a command line analysis 105
R
read/write privileges in user and security
groups 8
Reference Data table 81
removing
audit records 63
E-Sig records 74
Require UserID? setting 69
restoring
audit records 63
E-Sig records 74
security settings 44
Run audit map object 54, 61
RUN audit map object attribute 54
run folder, specifying in a command line
analysis 102
S
Sample audit map object 54, 61
SAMPLE audit map object attribute 54
Samples table, export via a command line 101
Scientist profile, actions allowed 8
scripting software operations 92
security groups
associating with data 5
bypassing 5
changing assignment for a data item 25
changing association for a project 25
creating 37
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111
Index
creating based on defaults 37
creating new 38
customizing 34
default, associating 5
defaults provided 9
definition 3
deleting 38
editing 37
read/write privileges 8
security log 42
Security Manager, starting 12
security settings
exporting 44
importing 44
security system
overview 3
reporting 42
setting up 16
setting up with custom settings,
preliminary steps 18
setting
action maps 70
password policies 14
Show EULA option 17, 19, 22
Size Standard audit map object 56, 61, 71
size standard definition, import via a command
line 103
size standard, specifying in a command line
analysis 105
sizestandard argument 105
Sizing table (Samples Plot), export via a
command line 102
software maintenance 76
software password, creating for Database
Dashboard 80
SQL support 77
statistics, reviewing 81
suspending user accounts 40
112
T
Technical Support, contacting x
Technician/Read-Only profile. see profiles
training, information on x
U
user accounts
activating 40
autoanalysis 21
deactivating 40
default accounts provided 10
definition 3
deleting 40
editing 39
pre-expire 17, 19, 22
status 17, 19, 22
suspending 40
user attention words, defined viii
user groups
actions and data access allowed by
default 11
creating 34
creating based on defaults 34
creating new 35
customizing 34
defaults provided 9
definition 3
deleting 36
read/write privileges 8
user name, not case-sensitive 12
username argument 105
V
viewing
Audit History records 57
audit records 63
database statistics 81
E-Sig history 74
E-Sig records 74
security log 42
GeneMapper® ID-X Software v1.0 Administrator’s Guide
CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
Worldwide Sales and Support
Applied Biosystems vast distribution and
service network, composed of highly trained
support and applications personnel,
reaches 150 countries on six continents.
For sales office locations and technical support,
please call our local office or refer to our
Web site at www.appliedbiosystems.com.
Applera is committed to providing the
world’s leading technology and information
for life scientists. Applera Corporation
consists of the Applied Biosystems and
Celera Genomics businesses.
Headquarters
850 Lincoln Centre Drive
Foster City, CA 94404 USA
Phone: +1 650.638.5800
Toll Free (In North America): +1 800.345.5224
Fax: +1 650.638.5884
09/07
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Part Number 4376327 Rev. A
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