GeneMapper Software v3.5

Transcription

1 GeneMapper Software v3.5 Installation Instructions This document includes: Before You Install v Installing the Instrument Configuration Installing the Remote Autoanalysis Configuration Installing the Standalone Configuration Upgrading Previous Versions Starting GeneMapper Software Migrating Projects Troubleshooting Installation Contacting Applied Biosystems Index Audience and Assumptions Related Documentation 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.

2 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 Workstation 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. 2 GeneMapper Software v3.5 Installation Instructions

3 Before You Install v3.5 Supported Instruments Data Collection Software Compatibility The GeneMapper Software v3.5 supports data generated on the following instruments: Applied Biosystems 3730 DNA Analyzer Applied Biosystems 3730xl DNA Analyzer ABI PRISM 3100 Genetic Analyzer ABI PRISM 3100-Avant Genetic Analyzer Functional compatibility between GeneMapper Software v3.5 and Data Collection Software v1.0 and v2.0: Data Collection Software Version Sample File Compatibility Installation on the Same Computer Autoanalysis 2.0 Yes Yes Yes 1.0 Yes No No 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 PRISM Linkage Mapping Set v2.5 ABI PRISM Mouse Mapping Primers v1.0 SNPlex Genotyping System a Custom microsatellites (G5 dye set only) Note: Analysis of non-str applications, including AFLP, SSCP, and polyploidy data, is not supported. a. New for v3.5. GeneMapper Software v3.5 Installation Instructions 3

4 Kits Supported Using the 3100 or 3100-Avant Systems ABI PRISM GeneScan Size Standards (ROX dye and LIZ dye) ABI PRISM Linkage Mapping Set v2.5 ABI PRISM Mouse Mapping Primers v1.0 ABI PRISM SNaPshot Multiplex Kit ABI PRISM SNaPshot Primer Focus Kit SNPlex Genotyping System a StockMarks Animal Parentage Typing Kits Custom microsatellites Certain oligo ligation assay (OLA)-based mutation analysis assays a 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 ) GeneMapper Software v3.5 Installation Instructions (*.pdf) (PN ) GeneMapper Software v3.5 Online Help a. New for v GeneMapper Software v3.5 Installation Instructions

5 Before You Install v3.5 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 Remote autoanalysis Standalone 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). 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). 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 GeneMapper Software v3.5 Installation Instructions 5

6 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 Confirming That Your Computer Meets Requirements 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. 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 Version: Service Pack 3 Processor: Intel Pentium 4, 2.4 GHz Memory: at least 1 GB RAM Note: GeneMapper software is not compatible with dualprocessors or with Intel Xeon processors. c. Close the System Properties box. 6 GeneMapper Software v3.5 Installation Instructions

7 Installing the Instrument Configuration 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. GeneMapper Software v3.5 Installation Instructions 7

8 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. Right-click here b. Confirm that no errors are displayed in the lower pane of the Data Service output and close the applet. 8 GeneMapper Software v3.5 Installation Instructions

9 Installing the Instrument Configuration No errors displayed 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. GeneMapper Software v3.5 Installation Instructions 9

10 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. 10 GeneMapper Software v3.5 Installation Instructions

11 Installing the Instrument Configuration 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. GeneMapper Software v3.5 Installation Instructions 11

12 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. 12 GeneMapper Software v3.5 Installation Instructions

13 Installing the Instrument Configuration 2. Press Ctrl+Alt+Delete and select Shut Down. 3. Select Restart and click OK to restart the system. GeneMapper Software v3.5 Installation Instructions 13

14 Installing the Remote Autoanalysis Configuration Overview Workflow Install the remote autoanalysis configuration for GeneMapper software if you plan to connect to a remote computer with Data Collection Software v 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 Confirming That Your Computer Meets Requirements 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. 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 Version: Service Pack 3 Processor: Intel Pentium 4, 2.4 GHz Memory: at least 1 GB RAM Note: GeneMapper software is not compatible with dualprocessors or with Intel Xeon processors. 14 GeneMapper Software v3.5 Installation Instructions

15 Installing the Remote Autoanalysis Configuration 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. GeneMapper Software v3.5 Installation Instructions 15

16 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. Right-click here b. Confirm that no errors are displayed in the lower pane of the Data Service output and close the applet. No errors in lower pane 4. Obtain the host name: 16 GeneMapper Software v3.5 Installation Instructions

17 Installing the Remote Autoanalysis Configuration 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. GeneMapper Software v3.5 Installation Instructions 17

18 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. 18 GeneMapper Software v3.5 Installation Instructions

19 Installing the Remote Autoanalysis Configuration 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. GeneMapper Software v3.5 Installation Instructions 19

20 9. Allocate disk space for the GeneMapper database and click Next: Allocate at least 3 GB of disk space. 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. 20 GeneMapper Software v3.5 Installation Instructions

21 Installing the Remote Autoanalysis Configuration 13. Click Next to continue. 14. Select Yes, restart my system and then click Finish. Remove the installation CD from the drive. GeneMapper Software v3.5 Installation Instructions 21

22 Installing the Standalone Configuration Overview Workflow Install the standalone configuration if you do not plan to connect to a computer with Data Collection Software v2.0 for autoanalysis or remote autoanalysis. Note: It is not possible to convert from the standalone configuration to the remote autoanalysis configuration. 1. Log onto the local domain of your computer as a user with administrative privileges (below). 2. Confirm that your computer meets requirements (page 22). 3. Install the standalone configuration (page 24): 4. Register and log into the software (page 33). Logging Onto the Computer Confirming That Your Computer Meets Requirements 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. 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 Version: Service Pack 3 Processor: Intel Pentium 4, 2.4 GHz Memory: at least 1 GB of RAM Note: GeneMapper software is not compatible with dualprocessors or with Intel Xeon processors. 22 GeneMapper Software v3.5 Installation Instructions

23 Installing the Standalone Configuration 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, 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. GeneMapper Software v3.5 Installation Instructions 23

24 Installing the Software (Standalone Configuration) Standalone configuration installation takes approximately 45 minutes. Note: If you are not able to complete the installation as it is described, go to Troubleshooting Installation on page 38. To install the standalone 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. Make sure that you have saved and closed all 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. 24 GeneMapper Software v3.5 Installation Instructions

25 Installing the Standalone Configuration 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 go to page 6 to install the instrument configuration. 6. Select Standalone and click Next. GeneMapper Software v3.5 Installation Instructions 25

26 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. 26 GeneMapper Software v3.5 Installation Instructions

27 Installing the Standalone Configuration 9. Allocate disk space for the GeneMapper database and click Next: Allocate at least 3 GB of disk space. 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. GeneMapper Software v3.5 Installation Instructions 27

28 13. Click Next to continue. 14. Select Yes, restart my system and then click Finish. Remove the installation CD from the drive. 28 GeneMapper Software v3.5 Installation Instructions

29 Upgrading Previous Versions Upgrading Previous Versions Overview Workflow Exporting Reference Data and Projects You can upgrade previous versions of GeneMapper software (v2.0 or v3.0) if your computer meets the requirements listed on page Export reference data and projects. 2. Log onto the local domain of your computer as a user with administrative privileges (below). 3. Confirm that your computer meets requirements (page 30). 4. Upgrade the software (page 31). 5. Register and log onto the software (page 33). Export reference data and projects before you upgrade the GeneMapper software to create a backup of your data. To export reference data and projects: 1. Export the panels and bins for all of the kits in the GeneMapper database: a. From the Panel Manager, choose File > Export All Kits to open the Export All Kits dialog box. b. Select a folder where you want to save the exported files and click Export All Kits. The software exports the panels and bins *.txt files for all of the kits to the selected folder. The names of the files correspond to the name of the panel and bin set used in the GeneMapper database. 2. Export analysis methods: a. From the GeneMapper Manager, select the Analysis Methods tab and select a project to export. b. Click Export to open the Export Analysis Method dialog box. c. Select the folder where you want to save the exported panel file(s), enter a file name, and click Export. Note: The only file type available for exported analysis methods files is *.xml. GeneMapper Software v3.5 Installation Instructions 29

30 3. Export projects as Java serialized (*.ser) files: a. From the GeneMapper Manager, select the Projects tab and select a project to export. b. Click Export and complete the Export Project dialog box: Check the Auto name checkbox to Check the Overwrite existing files checkbox to Check the Export reference data to export the panels, bins, size standards, and SNP sets used by the project Select the folder where you want to save the exported project file. Enter a name for the exported project file. c. Click Export. Note: The only file type available for exported project files is *.ser. Logging Onto the Computer Confirming That Your Computer Meets Requirements 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. 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 Version: Service Pack 3 Processor: Intel Pentium 4, 2.4 GHz 30 GeneMapper Software v3.5 Installation Instructions

31 Upgrading Previous Versions Memory: at least 1 GB RAM Note: GeneMapper software is not compatible with dualprocessors or with Intel Xeon processors. 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. You should see Local Disk (C:) and Local Disk (D:) in the directory. c. Right-click Local Disk (C:), 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 Local Disk (D:), 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. Installing the Upgrade to v3.5 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 upgrade to v3.5: 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. GeneMapper Software v3.5 Installation Instructions 31

32 Installer reports the version that is installed 3. Continue with the installation as described: Configuration See Page Instrument 6 Remote autoanalysis 14 Standalone 22 Note: When upgrading previous versions of GeneMapper software to v3.5, the Allocate Disk Space window does not appear. 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. 32 GeneMapper Software v3.5 Installation Instructions

33 Starting GeneMapper Software Starting GeneMapper Software Registering the Software Register the software the first time that you start the software. Note: If you are not able to register the software as described, then go to Troubleshooting Installation on page Choose Start > Programs > Applied Biosystems > GeneMapper > GeneMapper v3.5 to start the software. 2. Complete the Registration dialog box: Note: The registration code is located on the registration card packaged with the software. Keep your registration code where you can retrieve it easily. If you need to reinstall the software, you will be prompted for the registration code. 3. Click OK. Logging In for the First Time The first time that you log into the software, use the default user name and change the password. See the GeneMapper Software v3.5 User Guide (P/N ) for instructions on adding users. Note: The default password for v3.5 is different from previous versions. To log in: 1. Enter the password password for the default user name gm and click OK. GeneMapper Software v3.5 Installation Instructions 33

34 2. Click OK when the software prompts you to change the password: 3. Type a new password, retype the new password to confirm, and click OK. Note: Enter a password that is 6 to 10 alphanumeric characters. IMPORTANT! Keep the new password for the default user gm where you can retrieve it easily. If you forget or lose your password for the default user gm, it is not possible for Applied Biosystems to retrieve it. 4. Read the license agreement and click Yes if you are in agreement with the terms. 34 GeneMapper Software v3.5 Installation Instructions

35 Starting GeneMapper Software 5. Review the license agreement and product warranty. You may: Click Decline to quit the application. Click Service to bypass the agreement and proceed to the Project window. Note: You can click Service and bypass the agreement up to three times before you are locked out of the software. After you make this selection one or two times, you are presented with the license agreement and product warranty the next time that you log into the software. Click Print to print the agreement. Click Accept to accept the terms of the agreement and open a new, untitled Project window: GeneMapper Software v3.5 Installation Instructions 35

36 Migrating Projects Overview Data Migration Requirements Reanalysis Requirements Exporting and Importing You can migrate projects from previous versions of GeneMapper database to the GeneMapper Software v3.5 database to view results and to make or edit allele calls. Before migrating the projects, migrate reference data: 1. Panels and bins 2. Analysis methods 3. Size standards To reanalyze migrated projects, make sure that sample files: Are associated with the projects Were generated on the 3100 instrument, the 3100-Avant instrument, or the 3730/3730xl instrument Note: Projects associated with sample files generated on the ABI PRISM 310 Genetic Analyzer or the ABI PRISM 377 DNA Sequencer can be viewed using GeneMapper Software v3.5 but cannot be reanalyzed. In the export/import only workflow, you can view results and make or edit allele calls, but you cannot reanalyze unless you associate sample files with the project. Note: For specific instructions on how to perform each step, access the GeneMapper Software v3.5 Online Help from within the GeneMapper software. To export and import: 1. Export the reference data from the original GeneMapper database: a. Panels and bins b. Analysis methods c. Size standard definitions 2. Import the reference data into the GeneMapper v3.5 database. 3. Export the project from the original GeneMapper database. 36 GeneMapper Software v3.5 Installation Instructions

37 Migrating Projects 4. Import the project into the GeneMapper v3.5 database. 5. Open the project to view results and to make or edit allele calls. Associating Sample Files If you associate sample files with imported projects, you can view raw data, view EPT data, and reanalyze projects. Note: For specific instructions on how to perform each step, access the GeneMapper Software v3.5 Online Help from within the GeneMapper software. To associate sample files: 1. Open the project. 2. In the Samples table on the project window, select the samples to associate. Note: The SFNF (Sample File Not Found) column displays (Check) if the sample file is not associated with the project. 3. Choose File > Associate Samples. 4. In the Associate Samples dialog box: a. Locate the folder containing the sample files and select it. b. Click Select. Note: The SFNF (Sample File Not Found) column displays (Pass) if the sample file is associated with the project. GeneMapper Software v3.5 Installation Instructions 37

38 Troubleshooting Installation Overview Collecting Installation Log Files Checking the Oracle Database Installation To expedite proper installation of GeneMapper software on your computer, perform the following procedures before contacting Technical Support: 1. Collect installation log files. 2. Check the Oracle database installation. 3. Collect information about the installation. To collect installation log files: 1. Go to X:\AppliedBiosystems\GeneMapper\install, where X is the drive where the GeneMapper software is installed. 2. Double-click the file buildlog.bat to generate a log file. 3. Save the log file install_log.jar. Check to see if the Oracle database instance was installed correctly. To check the Oracle database installation: 1. Choose Start > Programs > Accessories > Command Prompt. 2. Type sqlplus and press Enter. 3. Type the user-name system and press Enter. 4. Type the password manager and press Enter. If: A Connected to: message is displayed, the Oracle database was installed correctly. Proceed with Configuring the Database Manually. If the Oracle database was not installed correctly, complete Table 1, Troubleshooting Checklist, on page 42 and then contact Technical Support. 38 GeneMapper Software v3.5 Installation Instructions

39 Troubleshooting Installation Configuring the Database Manually Perform the following steps in the Command Prompt window to configure the database manually if the Oracle database was installed correctly. To configure the database: 1. At the SQL prompt, type exit to exit the SQL Plus application. 2. At the drive prompt, type cd/d x:\genemapper\database, where x is the drive letter where GeneMapper software is installed. 3. At the drive prompt, type ifadb x:\oraclegm\oradata\ifa, where x is the drive letter where GeneMapper software is installed, and press Enter. If Succeeded messages are displayed, the database is configured correctly. Proceed with Registering the Software on page 33. If Error messages are displayed, the database is not configured correctly. Repeat the instructions for configuring the database. Uninstalling GeneMapper Software If the software installation is not successful, you may need to uninstall GeneMapper software and then perform the installation procedures again. This procedure removes GeneMapper software and the Oracle Database Standard Edition v To uninstall GeneMapper software: 1. If you have Data Collection software installed on your computer, start Data Collection services (see page 7) before proceeding. 2. Select Start > Settings > Control Panel. 3. Double-click Add/Remove Programs. 4. Select ABI Prism GeneMapper and click Change/Remove. Select ABI Prism GeneMapper Click Change/Remove GeneMapper Software v3.5 Installation Instructions 39

40 5. Click Next to proceed. Note: Make sure that you export and save all data from the GeneMapper database before you proceed. 6. Click Next to view what will be uninstalled and to start uninstallation. 7. After successful uninstallation, click Next to continue. 40 GeneMapper Software v3.5 Installation Instructions

41 Troubleshooting Installation 8. Select Yes, restart my system and click Finish. Troubleshooting Uninstallation If the uninstallation procedure does not remove GeneMapper software and the Oracle Database Standard Edition v8.1.7 completely, then: 1. Complete the Troubleshooting checklist (page 42). 2. Contact Technical Support for assistance (page 44). GeneMapper Software v3.5 Installation Instructions 41

42 Troubleshooting Checklist Complete the troubleshooting checklist before contacting Technical Support: Table 1 Check Troubleshooting Checklist Information for Technical Support Summarize the problem: Have you been able to repeat the problem? If yes, list the steps that you perform: Applied Biosystems personnel that you have contacted: Field Applications Specialist Field Service Engineer Technical Support Sales Representative Order Administration Other Computer specifications: Operating system: Version: Processor Memory Hard disk space: Hard disk configuration: 42 GeneMapper Software v3.5 Installation Instructions

43 Troubleshooting Installation Table 1 Check Troubleshooting Checklist (continued) Information for Technical Support Software installed: Data Collection Software version: Status of Data Collection Services: GeneMapper Software version: Other Applied Biosystems software: Computer login information: User privileges: Local or networked domain: Software configuration installed: Instrument Remote autoanalysis Standalone Instrument and instrument computer information: Model: Data Collection Software version: Status of Data Collection Services: Other Applied Biosystems software: Capillary length: Capillary lot number: Run module: Dye set: Chemistry kit or reagent, with version number: Be prepared to send to Technical Support: Installation log files (page 38) Exported panels Exported bins Exported size standard definition Exported analysis method Sample (.fsa) files GeneMapper_log.txt PanelImportLog.txt Printed results GeneMapper Software v3.5 Installation Instructions 43

44 Contacting Applied Biosystems How to Obtain Services and Support Send Us Your Comments For the latest services and support information for all locations, go to then click the link for Support. At the Support page, you can: Search through frequently asked questions (FAQs) Submit a question directly to Technical Support Order Applied Biosystems user documents, MSDSs, certificates of analysis, and other related documents Download PDF documents Obtain information about customer training Download software updates and patches In addition, the Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities. Applied Biosystems welcomes your comments and suggestions for improving user documents. You can your comments to: techpubs@appliedbiosystems.com 44 GeneMapper Software v3.5 Installation Instructions

45 Index A analysis methods, exporting 29 Associate Samples function, using 37 B bins, exporting 29 C chemistry kits supported 3 computer ID 18 computer requirements, confirming 6, 14, 22, 30 configurations instrument 6 remote autoanalysis 14 standalone 24 supported 5 D Data Collection Software compatibility with 3 connecting to remotely 14 installing with locally 6 starting 7, 15 stopping 12 Data Services, checking if started without errors 8, 16 database checking installation of 38 configuring manually 39 default login 33 documentation, related to this document 1 DOS window, during installation 12, 20, 27 drive recommendation for partitioning 2 selecting 11, 19, 26 E exporting reference data 29 F features, new in v3.5 2 G gm, default user name 33 H hard disk, viewing properties of 7, 15, 23, 31 host name entering for remote autoanalysis 18 obtaining 16 I installer, starting 9, 17, 24 installing software instrument configuration 9 remote autoanalysis configuration 17 standalone configuration 24 upgrade to v instrument configuration description 6 time required for installing 9 instruments supported 3 GeneMapper Software v3.5 Installation Instructions 45 September 5, :36 am, _GM35installIX.fm

46 K kits exporting 29 supported using the 3100 or 3100-Avant systems 4 supported using the 3730 or 3730xl systems 3 L log file, collecting 38 logging in 33 M memory requirement 6, 14, 22, 31 migrating projects 36 N new features 2 O operating system requirement 6, 14, 22, 30 Oracle database checking installation of 38 configuring manually 39 P password, changing 34 processor requirement 6, 14, 22, 30 projects exporting 30 migrating 36 requirements confirming 6, 14, 22, 30 system 2 S sample files, associating 37 Service Console 15 service pack requirement 6, 14, 22, 30 SFNF (Sample File Not Found) column 37 standalone configuration description 24 selecting during installation 25 time required for installing 24 system, viewing properties of 6, 14, 22, 30 T Technical Support contacting 44 information needed before contacting 42 time required for installing instrument configuration 9 remote autoanalysis configuration 17 standalone configuration 24 troubleshooting 38 U uninstalling 39 upgrading previous versions 29 user name, default 33 V v3.5 new features 2 R reference data, exporting 29 registration code 33 remote autoanalysis configuration description 17 selecting during installation 18 time required for installing GeneMapper Software v3.5 Installation Instructions September 5, :36 am, _GM35installIX.fm

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48 Copyright 2003, Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic procedures. NOTICE TO PURCHASER: PLEASE REFER TO THE GENEMAPPER SOFTWARE V3.5 USER GUIDE FOR LIMITED LABEL LICENSE OR DISCLAIMER INFORMATION. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document. TRADEMARKS: ABI PRISM, Applied Biosystems, SNaPshot, and StockMarks are registered trademarks and AB (Design), Applera, GeneMapper, GeneScan, and SNPlex are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries. 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. Headquarters 850 Lincoln Centre Drive Foster City, CA USA Phone: Toll Free (In North America): Fax: 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 Applera Corporation 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. Printed in the United States, 09/2003 Part Number Rev. B