Section 1 Installation Procedures. Applied Biosystems GeneMapper ID
GeneMapper ID is a software for analyzing genetic profiles from the AmpFlSTR® Yfiler™ PCR Amplification Kit. It allows you to quickly identify peaks visually and perform a size precision test. The software can also export data in the Export Combined Table format, which allows you to track all samples in an electrophoresis run.
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Section 1 Installation Procedures
Section 1 Installation Procedures
This section covers:
Supported Instruments and AmpF lSTR Kits . . . . . . . . . . . . . . . . . . 4
Installation Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Installation Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Installation Procedures and New Features for GeneMapper ® ID Software v3.2
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GeneMapper ® ID Software
Supported Instruments and AmpFlSTR Kits
Instruments
GeneMapper ID Software v3.2 is compatible with the instruments, operating systems, and Data Collection software listed in the table below. Compatibility is defined as the ability of the GeneMapper ID software to perform at least one of the following functions:
A. Analyze sample files generated from the instrument
B. Coexist with the instrument’s Data Collection software
C. Run concurrently with the instrument’s Data Collection software
D. Work with the automation feature (that is, autoanalysis) in the instrument’s Data Collection software
Instrument
Computer Operating
System
Data
Collection
Software
Functions (as listed above)
A B C D
ABI P
DNA Sequencer
ABI P
RISM
RISM
®
®
377
310
Genetic Analyzer
Macintosh ® a
Microsoft ® Windows NT ®
Macintosh ® a
Microsoft ® Windows NT ®
Microsoft ® Windows ® 2000
2.6
3.0
2.1
v3.0
X
X
X
X
—
X
—
X
—
X
—
X
—
—
—
— v3.0
X X X —
ABI P RISM
® 3100
Genetic Analyzer
Microsoft ® Windows NT ®
Microsoft ® Windows ® 2000 v1.1
X — — — v2.0
X X X X
ABI P RISM
®
3100-Avant
Genetic Analyzer
Microsoft ® Windows NT ® v1.0
X — — —
Microsoft ® Windows ® 2000 v2.0
X X X X a. Data generated from a 310 Genetic Analyzer or 377 DNA Sequencer using a Macintosh ® platform must be converted to a Microsoft ® Windows ® -based format before they can be used with the GeneMapper ID software. For information on converting Macintosh ® sample files, refer to the GeneMapper ™ ID Software
Version 3.1 Human Identification Analysis User Guide (PN 4338775).
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Supported Instruments and AmpF l STR Kits
Chemistry Kits
GeneMapper ID Software v3.2 is specifically designed to work with the following AmpF lSTR ® kits:
• AmpF lSTR ®
Yfiler
™
PCR Amplification Kit
• AmpF lSTR ® Identifiler ® PCR Amplification Kit
• AmpF lSTR ®
SGM Plus
®
PCR Amplification Kit
• AmpF lSTR ® Profiler Plus ® ID PCR Amplification Kit
• AmpF lSTR ®
Profiler Plus
®
PCR Amplification Kit
• AmpF lSTR ® COfiler ® PCR Amplification Kit
• AmpF lSTR ®
SEfiler
™
PCR Amplification Kit
• AmpF lSTR ® Profiler ® PCR Amplification Kit
• AmpF lSTR Blue ™
PCR Amplification Kit
• AmpF lSTR Green ™ I PCR Amplification Kit
Installation Procedures and New Features for GeneMapper ® ID Software v3.2
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GeneMapper ® ID Software
Installation Requirements
Computer
Specifications
The computer specifications for GeneMapper ID Software v3.2 are listed in the table below. Please note the following:
• The Minimum Requirements column lists the lowest specifications that permit the installer to install the
GeneMapper ID software. The minimum requirements may not provide optimal performance.
• The Recommended Requirements column lists the requirements that are recommended by Applied Biosystems.
System
Component
Computer
Minimum Requirements Recommended Requirements
Monitor
Operating System
• Intel Pentium
• 256 MB of RAM
• 2-GB hard drive (free space)
800
540 MHz
® III processor,
× 600 pixels size
17-inch monitor
Microsoft Windows NT ® version 4.0
(Service Pack 5 or higher)
Ethernet Capability • Network card for Oracle ® installation
• TCP/IP must be installed prior to
Oracle installation
• Intel Pentium ® IV processor,
≥2.8 GHz
• 512 MB of RAM
• 40-GB EIDE hard drive
• 20/48X IDE CD-ROM
• 10/100 NIC with RWV (internal)
1024 × 768 or higher pixels size
19-inch or larger monitor
• Microsoft Windows ® 2000
Professional (Service Pack 4)
• Microsoft Windows ® XP
Professional (Service Pack 1)
• Network card for Oracle ® installation
• TCP/IP must be installed prior to
Oracle installation
Special Considerations
• The GeneMapper ID software does not run correctly on dualprocessor Pentium ® computers. A single-processor computer is required.
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Installation Requirements
Compatibility with Oracle
Databases
• GeneMapper ID Software v3.2 runs on Windows NT ® ,
Windows ® 2000, and Windows ® XP platforms only. Conversion utilities are included for analyzing data from Macintosh ® -based sample files. For conversion procedures, refer to the
GeneMapper ™ ID Software Version 3.1 Human Identification
Analysis User Guide (PN 4338775).
• The GeneMapper ID Software v3.2 automated installer operates only on computers running Microsoft Internet Explorer. If you are using another browser, you will need to manually launch the
installer; instructions are provided in step 2 on page 12 .
The GeneMapper ID software uses an Oracle
®
database.
GeneMapper ID Software v3.2 is compatible only with the Oracle database installed with ABI P RISM
®
3100/3100-Avant Genetic
Analyzers Data Collection Software v2.0.
Be sure there is no other Oracle client or Oracle server on the computer. GeneMapper ID Software v3.2 is not supported on any other Oracle client or server configurations.
Special Considerations
• The version of the Oracle database in GeneMapper ID Software v3.2 is an embedded license for use by five named users.
IMPORTANT!
To accommodate more than five users, additional
GeneMapper ID software or Oracle database licenses must be purchased.
• TCP/IP has to be installed before installing GeneMapper ID
Software v3.2.
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GeneMapper ® ID Software
Compatibility with 3100/3100-
Avant Genetic
Analyzers
The table below describes compatibility of GeneMapper ID
Software v3.2 with the Data Collection software for the
ABI P RISM
® 3100/3100-Avant Genetic Analyzers.
3100 Genetic
Analyzer
Data Collection
Version
3100-Avant
Genetic Analyzer
Data Collection
Version
Compatible with
Instrument Computer?
1.1
—
—
1.0
No.
a
2.0
2.0
Yes a. GeneMapper ID Software v3.2 can only exist with the Oracle database installed by 3100/3100-Avant Genetic Analyzer Data Collection Software v2.0.
IMPORTANT!
To install GeneMapper ID Software v3.2 on a computer connected to a 3100/3100-Avant Genetic Analyzer that uses Data Collection Software v2.0, the Data Collection software must be running. If the Data Collection software is not running, the
GeneMapper ID software does not register with the Data Service software.
Login
Requirements
When installing GeneMapper ID Software v3.2, you must:
• Have Administrator privileges on the local computer (that is, have complete and unrestricted access to the local computer)
• Log in to the local computer (not a network domain)
• Be sure there is no other Oracle client or Oracle server on the computer. GeneMapper ID Software v3.2 is not supported on these configurations.
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User Bulletin
Installation Requirements
PDF File Reader
To open the user documentation included on the GeneMapper ® ID
Software v3.2 installation CD, use a program that reads PDF files, such as the Adobe Acrobat ® Reader software.
The GeneMapper ID Software v3.2 installer does not install Acrobat
Reader. If you do not have a program that reads PDF files, you can download Acrobat Reader from either the Adobe or Applied
Biosystems websites:
• www.adobe.com
• www.appliedbiosystems.com/support/software.
Installation Procedures and New Features for GeneMapper ® ID Software v3.2
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GeneMapper ® ID Software
Installation Procedures
What Gets
Installed
The installer on the GeneMapper ® ID Software v3.2 CD installs:
• GeneMapper
®
ID Software v3.2
• Oracle ® database
• Panel folder that contains AmpF lSTR ®
kit panels and bins
• Microsatellite and SNP genotyping example data
• Electronic (PDF) versions of the user guide and tutorial
• Size standard folder that contains various size standards
• Default plot and table settings
Before You Begin the Installation
Before you begin the installation, be sure all requirements are met.
See the references listed below.
•
“Computer Specifications” on page 6
•
“Compatibility with Oracle Databases” on page 7
•
“Compatibility with 3100/3100-Avant Genetic Analyzers” on page 8
•
“Login Requirements” on page 8
•
Installation Time
The total time required to install the GeneMapper ID software is approximately 60 minutes. This time may vary, depending on your system configuration.
Procedure
Flowchart
If necessary, remove previous versions of the
GeneMapper
®
Install or upgrade the GeneMapper ID software
(
).
Installation
Procedures
Register the GeneMapper ID software ( page 14 ).
Launch the GeneMapper ID software (
).
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Installation Procedures
Remove
Non-Validated
GeneMapper
Software
(If Necessary)
If you have either GeneMapper ® Software v3.0 or v3.5 on your computer, you must remove it before installing the GeneMapper ID software.
To remove GeneMapper software v3.0 or v3.5:
1.
Log in to the local computer as an Administrator.
2.
Select Start > Control Panel to open the Control Panel window.
3.
Double-click Add or Remove Programs to open the Add or
Remove Programs dialog box.
4.
Select the GeneMapper software program, then follow the prompts to uninstall/remove the GeneMapper software.
5.
If prompted to do so, restart the computer.
6.
Continue with
Install the
Software
To install GeneMapper ID Software v3.2:
1.
Log in to the local computer as an Administrator.
IMPORTANT!
If you do not have Administrator privileges, log off of the computer and log back in as a user with
Administrator privileges.
Installation Procedures and New Features for GeneMapper ® ID Software v3.2
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GeneMapper ® ID Software
To install GeneMapper ID Software v3.2: (continued)
2.
Insert the GeneMapper ® ID Software v3.2 CD into the CD-
ROM drive.
The installer launches automatically, displaying the Main
Menu.
Note: If the installer does not launch automatically: a. On the desktop, right-click the My Computer icon and select Explore to open the My Computer window.
b. Double-click the CD drive to open the
GeneMapper ID v3.2 folder.
c. Double-click the Setup.exe file to launch the installer.
3.
Click Installation Readme to view the
InstallationReadme.txt file on the GeneMapper ® ID
Software v3.2 CD.
Note: The InstallationReadme.txt file may contain installation information that is more current than the information in this user bulletin.
User Bulletin 12
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Installation Procedures
To install GeneMapper ID Software v3.2: (continued)
4.
Click Install GeneMapper ® ID Software v3.2. to start the
InstallShield ® Wizard.
5.
Follow the onscreen instructions to install the software.
IMPORTANT!
During installation, DOS commands are executed and the DOS window is opened. Do not delete, close, or click in the DOS window. If you click in it, press the
Esc key.
6.
When the installation is complete, click Finish.
7.
If prompted to do so, restart the computer.
8.
Continue with
“Register the Software” on page 14 .
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GeneMapper ® ID Software
Register the
Software
To register GeneMapper ID Software v3.2:
1.
Locate the registration code on the Getting Started Card in the software package.
2.
IMPORTANT!
Keep the registration code in a place where you can easily retrieve it. You will need the registration code the first time you start the GeneMapper ID software (below).
In addition, if you need to reinstall the software at any time, you are prompted for the registration code again.
3.
Complete the registration card and return it to Applied
Biosystems.
4.
Continue with
below.
Start the
Software
To start GeneMapper ID Software v3.2 for the first time:
1.
Log in to the local computer.
2.
On the desktop, click Start > Programs > Applied
Biosystems > GeneMapper > GeneMapper ID v3.2.
The first time you start the GeneMapper ID software, the
Product Registration dialog box opens.
Note: If the GeneMapper ID software fails to start, see
“Troubleshooting the Installation” on page 57 .
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Installation Procedures
To start GeneMapper ID Software v3.2 for the first time:
3.
Register the software: a. In the Product Registration dialog box, enter your name, organization, and registration code.
b. Click OK.
The software verifies the registration code, then displays the
Login dialog box.
Installation Procedures and New Features for GeneMapper ® ID Software v3.2
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GeneMapper ® ID Software
To start GeneMapper ID Software v3.2 for the first time:
4.
The first time you launch the GeneMapper ID software, complete the Login dialog box as follows: a. Leave the User Name as gmid and leave the Password field blank.
b. From the Database Host drop-down list, select the local computer (that is, select the name of the computer you are currently working on).
c. Click OK.
The Enter Password dialog box opens.
5.
Create your password: a. Leave the Old Password field blank.
b. In the Password field, enter a new, user-defined password.
c. Confirm the password.
d. Click OK.
The GeneMapper ID software starts.
User Bulletin 16
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Key features
- Export Combined Table format
- Labeled peak assignments
- Allele calling parameters for different repeat types
- Plus stutter filtering
- HID analysis methods for the Yfiler kit
- Exporting haplotypes