Thermo Fisher Scientific GeneMapper™ Software Installation guide

DRAFT

September 5, 2003 10:35 am, 4344950.fm

GeneMapper™ Software v3.5

Installation Instructions

This document includes:

Before You Install v3.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Installing the Instrument Configuration . . . . . . . . . . . . . . . . . . . . . . 6

Installing the Remote Autoanalysis Configuration. . . . . . . . . . . . . 14

Installing the Standalone Configuration . . . . . . . . . . . . . . . . . . . . . 22

Upgrading Previous Versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Starting GeneMapper Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Migrating Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Troubleshooting Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Contacting Applied Biosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Audience and

Assumptions

This guide is intended for customers installing GeneMapper™

Software v3.5 on a computer that meets or exceeds the requirements.

It is assumed that you have:

• A working knowledge of the Windows® 2000 operating system

• Administrative privileges on the computer

• Access to information about the network environment

The following related documents are shipped with the software:

•GeneMapper™ Software v3.5 User Guide – Describes the

software and provides information on controlling access and

auditing, archiving, and software functions.

•GeneMapper™ Software v3.5 Online Help – Describes the

software and provides procedures for common tasks.

Portable document format (PDF) versions of this document and the

GeneMapper™ Software v3.5 User Guide are also available on the

GeneMapper™ Software v3.5 software installation CD.

Note: For additional documentation, see “How to Obtain Services

and Support” on page 44.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

2 GeneMapper Software v3.5 Installation Instructions

New Features in

v3.5

• Access control and auditing

• Automated analysis with ABI PRISM® 3100/3100-Avant Genetic

Analyzers

• New features and functions for analysis using the SNPlex™

Genotyping System:

– Cluster plot analysis and display for SNP genotyping

– Process (Component-Based) Quality Values (PQVs)

• OLA Analysis analysis method for certain oligo ligation assay

(OLA)-based mutation analysis

• Improved analysis and post-analysis functions:

– Improved performance of plot displays

– Improved printing speeds and views

• Drag-and-drop marker management

• Database archiving

Before You Install v3.5

Computer

Requirements

For optimal performance, install the software on a computer with:

• 2.4 GHz Intel® Pentium® 4 processor

•1 GB of RAM

• Two 120 GB hard drives

• 20/48x IDE CD-ROM

• 10/100 NIC with RWU (internal)

• 17" color monitor

• Microsoft® Windows® 2000 Professional operating system,

Service Pack 3

Note: Applied Biosystems ships the Dell Precision™ Workst a tion

340. The Dell 340 computer that shipped with the

Applied Biosystems 3730/3730xl DNA Synthesizers Data Collection

Software v1.0 is sufficient but does not provide optimal performance.

Note: GeneMapper software is not compatible with dual-processors

or with Intel Xeon® processors.

Note: For optimal performance of GeneMapper software, partition

the hard drives on your computer.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Before You Install v3.5

GeneMapper Software v3.5 Installation Instructions 3

Supported

Instruments

The GeneMapper™ Software v3.5 supports data generated on the

following instruments:

• Applied Biosystems 3730 DNA Analyzer

• Applied Biosystems 3730xl DNA Analyzer

•ABI P

RISM® 3100 Genetic Analyzer

•ABI P

RISM® 3100-Avant Genetic Analyzer

Data Collection

Software

Compatibility

Functional compatibility between GeneMapper Software v3.5 and

Data Collection Software v1.0 and v2.0:

Supported

Fragment

Analysis

Chemistry Kits

The GeneMapper™ Software v3.5 is designed to analyze the data

generated using several fragment analysis chemistry kits on the 3730,

3730xl, 3100, and/or 3100-Avant systems.

Kits Supported Using the 3730 or 3730xl Systems

•ABI PRISM® GeneScan™ Size Standards (LIZ® dye only)

•ABI P

RISM® Linkage Mapping Set v2.5

•ABI P

RISM® Mouse Mapping Primers v1.0

•SNPlex

™ Genotyping Systema

• Custom microsatellites (G5 dye set only)

Note: Analysis of non-STR applications, including AFLP, SSCP, and

polyploidy data, is not supported.

Data Collection

Software Version

Sample File

Compatibility

Installation on the

Same Computer Autoanalysis

2.0 Yes Yes Yes

1.0 Yes No No

a. New for v3.5.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

4 GeneMapper Software v3.5 Installation Instructions

Kits Supported Using the 3100 or 3100-Avant Systems

•ABI PRISM® GeneScan™ Size Standards (ROX™ dye and LIZ®

dye)

•ABI P

RISM® Linkage Mapping Set v2.5

•ABI P

RISM® Mouse Mapping Primers v1.0

•ABI P

RISM® SNaPshot® Multiplex Kit

•ABI P

RISM® SNaPshot® Primer Focus Kit

•SNPlex

™ Genotyping Systema

•StockMarks

® Animal Parentage Typing Kits

• Custom microsatellites

• Certain oligo ligation assay (OLA)-based mutation analysis

assaysa

Note: Analysis of non-STR applications, including AFLP, SSCP, and

polyploidy data, is not supported.

What Gets

Installed

The installer on the CD installs:

• GeneMapper™ Software v3.5

•Oracle

® Database Standard Edition v8.1.7

• Size standard definitions

• Example data: sample files, reference sample files, and panels

•GeneMapper™ Software v3.5 User Guide (*.pdf) (PN 4343790)

•GeneMapper™ Software v3.5 Installation Instructions (*.pdf)

(PN 4344950)

•GeneMapper™ Software v3.5 Online Help

a. New for v3.5.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Before You Install v3.5

GeneMapper Software v3.5 Installation Instructions 5

Supported

Configurations

If you have no previous versions of GeneMapper software, you can

install GeneMapper software v3.5 as one of three configurations.

Configuration Description See Page

Instrument In the instrument configuration, Data Collection software and

GeneMapper software are installed on the same computer. You

can set up both software products so that GeneMapper software:

1. Obtains sample files from the local Data Collection Software

database.

2. Performs analysis of the generated sample files automatically

(autoanalysis).

6

Remote

autoanalysis

In the remote autoanalysis configuration, Data Collection

software and GeneMapper software are installed on separate

computer. You can set up Data Collection software and

GeneMapper software v3.5 so that GeneMapper software:

1. Connects to a remote computer with Data Collection software.

2. Obtains sample files from the remote Data Collection Software

database.

3. Performs analysis of the generated sample files automatically

(remote autoanalysis).

14

Standalone In the standalone configuration, Data Collection softwareand

GeneMapper software are installed on separate computers. You

can use GeneMapper software to add sample files from a remote

Data Collection software database to a project and perform

manual analysis of the project. GeneMapper software does not

interact with Data Collection software for autoanalysis or remote

autoanalysis.

22

DRAFT

September 5, 2003 10:35 am, 4344950.fm

6 GeneMapper Software v3.5 Installation Instructions

Installing the Instrument Configuration

Overview Install the instrument configuration if Data Collection Software v2.0

is installed on the local computer.

Workflow 1. Log onto the local domain of your computer as a user with

administrative privileges (below).

2. Confirm that your computer meets requirements (page 6).

3. Start Data Collection services (page 7).

4. Install the instrument configuration (page 9).

5. Register and log into the software (page 33).

Logging Onto the

Computer

Installing the GeneMapper software v3.5 on the computer requires

that you log onto the computer:

• As a user with administrative privileges, with complete and

unrestricted access to the computer/domain

• Onto the local domain

IMPORTANT! Do not log onto the network.

Confirming That

Your Computer

Meets

Requirements

IMPORTANT! For optimal performance, confirm that your computer

meets requirements.

To confirm that your computer meets requirements:

1. View the system properties:

a. Right-click My Computer on the desktop and choose

Properties.

b. Confirm that the properties meet requirements:

• Operating System: Microsoft Windows® 2000

Professional

• Ve r s i o n : Service Pack 3

• Processor: Intel Pentium® 4, 2.4 GHz

• Memory: at least 1 GB RAM

Note: GeneMapper software is not compatible with dual-

processors or with Intel Xeon® processors.

c. Close the System Properties box.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Installing the Instrument Configuration

GeneMapper Software v3.5 Installation Instructions 7

2. View the hard disk properties:

a. Right-click My Computer on the desktop and choose

Explore.

b. Confirm that the hard drive is partitioned.

Note: For optimal performance, partition the hard drives on

your computer.

c. Right-click one local disk, choose Properties, and confirm

that the hard disk is at least 120 GB and that there is at least

164 MB of free space.

d. Right-click another local disk, choose Properties, and

confirm that the hard disk is at least 120 GB and that there

is at least 2 GB of free space.

e. Click OK.

Starting Data

Collection

Services

Start Data Collection services before installing GeneMapper

software.

If you do not have Data Collection software on the computer, quit the

installer and do one of the following:

• Install Data Collection software before proceeding

• Install the remote analysis configuration (page 14)

• Install the standalone configuration (page 22)

To start Data Collection services:

1. Choose Start > Programs > Applied Biosystems > Data

Collection > Data Collection v2.0 to display the Service

Console and wait until all four symbols are changed to green

squares.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

8 GeneMapper Software v3.5 Installation Instructions

Note: If the services do not start automatically, click Start All.

2. If the Data Collection software requires a password, a login

dialog box appears. Enter the Login Name and Password and

then click OK.

Note: If you do not know the Login Name or Password, contact

the administrator.

3. Confirm that Data Services started without errors:

a. From the Service Console, right-click the square next to

Data Service and select Show Console to display Data

Service output, a Java applet.

b. Confirm that no errors are displayed in the lower pane of

the Data Service output and close the applet.

Right-click here

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Installing the Instrument Configuration

GeneMapper Software v3.5 Installation Instructions 9

Installing the

Software

(Instrument

Configuration)

Instrument configuration installation takes approximately 5 minutes.

Note: If you are not able to complete the installation as it is

described, then go to “Troubleshooting Installation” on page 38.

To install the instrument configuration:

1. Insert the GeneMapper™ Software v3.5 CD into the CD drive

and start the installer.

Note: If the installer does not start, then:

a. Right-click My Computer and choose Explore.

b. Expand the CD drive.

c. Select the GeneMapper v3.5 folder to display the contents.

d. Double-click setup.exe to start the installer.

2. Click Install GeneMapper Software v3.5 to open a Welcome

window.

No errors

displayed

DRAFT

September 5, 2003 10:35 am, 4344950.fm

10 GeneMapper Software v3.5 Installation Instructions

3. Make sure that Data Collection Software v2.0 is open and save

and close all other applications and windows before proceeding

with the installation.

4. On the Welcome window, click Next. The installer checks your

computer to confirm that your system meets the requirements.

Note: If your system does not meet the requirements, you

receive a warning message that if you proceed with the

installation, your system will not have optimal performance.

5. Click Next. The installer checks your system for Data

Collection software versions.

The installer presents a message that your computer has Data

Collection software installed. If you do not get this message,

start Data Collection services (page 7).

6. Click Next if Data Collection services is started.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Installing the Instrument Configuration

GeneMapper Software v3.5 Installation Instructions 11

7. Select the install drive:

a. Confirm that the boot drive has at least 164 MB of free

space.

b. Select an install drive with at least 5000 MB (5 GB) of free

space.

c. Click Next.

8. View the amount of disk space that is preallocated for the

GeneMapper database and click Next.

Note: You cannot change the values shown, but you can allocate

more disk space later using the Database Manager from within

GeneMapper software. For instructions, access the

GeneMapper™ Software v3.5 Online Help from within the

GeneMapper software.

Note: The amount of disk space that is preallocated varies

according to your computer configuration.

9. Read the license agreement, select I accept the terms of the

license agreement, and click Next to continue with the

installation.

10. Read the release notes and click Next.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

12 GeneMapper Software v3.5 Installation Instructions

11. Read the installation preview and click Next to start the

installation.

IMPORTANT! During installation, DOS commands are executed

and a DOS windows open. Do not delete, close, or click in the

windows. If you click in one, press the Esc key.

After the installer completes the installation, it presents an

Installation Successful window.

12. Click Next to continue.

13. Select No, I will restart my system at a later time and then

click Finish.

Restarting the

System

Stop Data Collection Services before restarting the system.

1. On the Service Console for Data Collection Software v2.0, click

Stop All.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Installing the Instrument Configuration

GeneMapper Software v3.5 Installation Instructions 13

2. Press Ctrl+Alt+Delete and select Shut Down.

3. Select Restart and click OK to restart the system.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

14 GeneMapper Software v3.5 Installation Instructions

Installing the Remote Autoanalysis Configuration

Overview Install the remote autoanalysis configuration for GeneMapper

software if you plan to connect to a remote computer with Data

Collection Software v2.0.

Workflow 1. Log onto the local domain of your computer as a user with

administrative privileges (below).

2. Confirm that your computer meets requirements (page 14).

3. Set up the remote computer (page 15).

4. Install the remote autoanalysis configuration (page 17):

5. Register and log into the software (page 33).

Logging Onto the

Computer

Installing the GeneMapper software v3.5 on the computer requires

that you log onto the computer:

• As a user with administrative privileges, with complete and

unrestricted access to the computer/domain

• Onto the local domain

IMPORTANT! Do not log onto the network.

Confirming That

Your Computer

Meets

Requirements

IMPORTANT! For optimal performance, confirm that your computer

meets requirements.

To confirm that your computer meets requirements:

1. View the system properties:

a. Right-click My Computer on the desktop and choose

Properties.

b. Confirm that the properties meet requirements:

• Operating System: Microsoft Windows® 2000

Professional

• Ve r s i o n : Service Pack 3

• Processor: Intel Pentium 4, 2.4 GHz

• Memory: at least 1 GB RAM

Note: GeneMapper software is not compatible with dual-

processors or with Intel Xeon® processors.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Installing the Remote Autoanalysis Configuration

GeneMapper Software v3.5 Installation Instructions 15

c. Close the System Properties box.

2. View the hard disk properties:

a. Right-click My Computer on the desktop and choose

Explore.

b. Confirm that the hard drive is partitioned.

Note: For optimal performance of GeneMapper software,

partition the hard drives on your computer.

c. Right-click one local disk, choose Properties, and confirm

that the hard disk is at least 120 GB and that there is at least

164 MB of free space.

d. Right-click another local disk, choose Properties, and

confirm that the hard disk is at least 120 GB and that there

is at least 2 GB of free space. Click OK.

Setting Up the

Remote

Computer

Set up the remote Data Collection computer before installing

GeneMapper software on the local computer.

To set up the remote computer:

1. On the remote Data Collection computer, choose Start >

Programs > Applied Biosystems > Data Collection > Data

Collection v2.0 to start Data Collection Software v2.0.

The software displays the Service Console. Wait until all four

symbols are changed to green squares.

Note: If the services do not start automatically, click Start All.

2. If the Data Collection software requires a password, a login

dialog box appears. Enter the Login Name and Password and

then click OK.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

16 GeneMapper Software v3.5 Installation Instructions

Note: If you do not know the Login Name or Password, contact

the administrator.

3. Confirm that Data Services started without errors:

a. From the Service Console, right-click the square next to

Data Service and select Show Console to display Data

Service output, a Java applet.

b. Confirm that no errors are displayed in the lower pane of

the Data Service output and close the applet.

4. Obtain the host name:

Right-click here

No

errors

in

lower

pane

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Installing the Remote Autoanalysis Configuration

GeneMapper Software v3.5 Installation Instructions 17

a. Right-click My Computer on the desktop and choose

Properties.

b. Select the Network Identification tab to view the full

computer name. The full computer name is the host name.

c. Write down the full computer name and save it for later.

d. Close the Properties dialog box.

Installing the

Software (Remote

Autoanalysis

Configuration)

Remote autoanalysis configuration installation takes approximately

45 minutes.

Note: If you are not able to complete the installation as it is

described, then go to “Troubleshooting Installation” on page 38.

To install the remote autoanalysis configuration:

1. Insert the GeneMapper™ Software v3.5 CD into the CD drive

and start the installer.

Note: If the installer does not start, then:

a. Right-click My Computer and choose Explore.

b. Expand the CD drive.

c. Select the GeneMapper v3.5 folder to display the contents.

d. Double-click setup.exe to start the installer.

2. Click Install GeneMapper Software v3.5 to open a Welcome

window.

3. Save and close all applications and windows before proceeding

with the installation.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

18 GeneMapper Software v3.5 Installation Instructions

4. On the Welcome window, click Next. The installer checks your

computer to confirm that your system meets the requirements.

Note: If your system does not meet the requirements, you

receive a warning message that if you proceed with the

installation, your system will not have optimal performance.

5. Click Next. The installer checks your system for Data

Collection software versions.

If your computer does not have Data Collection software

installed, you are presented with a choice between the remote

autoanalysis and standalone configurations.

If you have a previous version of Data Collection software

installed, quit the installation and either go to page 6 to install

the instrument configuration or uninstall the Data Collection

software and repeat the installation of the remote autoanalysis

configuration of GeneMapper software (start at page 15).

6. Select Remote autoanalysis, enter the Computer ID (host

name) for the remote computer (see step 4 on page 16), and

click Next.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

Installing the Remote Autoanalysis Configuration

GeneMapper Software v3.5 Installation Instructions 19

The installer checks your system for previous versions of Oracle

software and GeneMapper software. If no previous versions are

found, the installer presents a message that your computer has a

clean configuration.

7. Click Next if you are presented with the message that your

computer has a clean configuration.

8. Select the install drive:

a. Confirm that the boot drive has at least 164 MB of free

space.

b. Select an install drive with at least 5000 MB of free space.

c. Click Next.

DRAFT

September 5, 2003 10:35 am, 4344950.fm

20 GeneMapper Software v3.5 Installation Instructions

9. Allocate disk space for the GeneMapper database and click

• Increase the disk allocation in increments of 5 GB.

Note: You can allocate more disk space later using the Database

Manager from within GeneMapper software. For instructions,

access the GeneMapper™ Software v3.5 Online Help from

within the GeneMapper software.

10. Read the license agreement, select I accept the terms of the

license agreement, and click Next to continue with the

installation.

11. Read the release notes and click Next.

12. Read the installation preview and click Next to start the

installation.

IMPORTANT! During installation, DOS commands are executed

and DOS windows open. Do not delete, close, or click in the

windows. If you click in one, press the Esc key.

After the installer completes the installation, it presents an

Installation Successful window.

Page is loading ...

Thermo Fisher Scientific GeneMapper™ Software Installation guide

Thermo Fisher Scientific GeneMapper™ Software Installation guide

Related papers

Other documents