ABI PRISM 310 Genetic Analyzer

ABI PRISM 310 Genetic Analyzer Upgrading Data Collection Software to the Windows Platform Software Installation Guide May 12, 2004 4:24 pm, Title.fm

Copyright 2004 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. 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. 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. TRADEMARKS: Applied Biosystems, ABI PRISM, GeneMapper, and GeneScan are registered trademarks and AB (Design), Applera, and Celera Genomics are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries. Dell is a trademark of Dell Inc. Macintosh is a registered trademark of Apple Computer, Inc. Windows is a registered trademark of Microsoft Corporation in the United States and/or other countries. All other trademarks are the sole property of their respective owners. Part Number 4326553 Rev. B 05/2004 May 12, 2004 4:24 pm, Title.fm

Upgrading 310 Data Collection Software to the Windows 2000 Platform This software installation guide describes how to install and configure the Dell computer, convert from a Macintosh to a Windows operating system, and install the software used with the ABI PRISM 310 Genetic Analyzer. Audience Overview Users of the ABI PRISM 310 Genetic Analyzer who must convert from a Macintosh to a Windows operating system. Upgrading to the Windows platform involves the following steps: 1. Deinstall the Macintosh computer. 2. Configure the Dell computer: Unpack and connect the computer. Install the Windows 2000 operating system. Install Roxio. Create a user account. 3. Install AB software: 310 Data Collection (install first) Genescan GeneMapper Sequence Analysis v5.1 Adobe Acrobat 310 Diagnostic software 4. Set defaults in Data Collection software: Parameters Folder Locations 5. Create matrix files. Upgrading Data Collection Software to the Windows Platform 1

This software installation guide includes the following topics: Deinstalling the Macintosh Computer...................... 3 Configuring the Computer................................ 4 Installing Software...................................... 9 Setting Up the Data Collection Software.................... 12 Creating Matrix Files................................... 16 2 Upgrading Data Collection Software to the Windows Platform

Deinstalling the Macintosh Computer Deinstalling the Macintosh Computer Before Disconnecting the Macintosh Computer Before disconnecting the Macintosh computer: 1. Power on the 310 instrument and launch the 310 Data Collection software. 2. From the Window drop-down menu, select Manual Control to access the Manual Control window: 3. From the Fxn Name pop up, select and record the following values: CCD Pixel Position X CCD Pixel Position Y Syringe Pump Force Syringe Max Travel Note: You may need to enter these values again after connecting the Dell computer. 4. Quit the Data Collection software. 5. Power down the Macintosh computer. 6. Power down the 310 instrument. 7. Disconnect the serial cable (P/N 200800) from the back of the Macintosh computer and from the control/data port of the 310 instrument. Upgrading Data Collection Software to the Windows Platform 3

Configuring the Computer Setting Up the Computer To set up the computer: 1. Unpack the two boxes containing the Dell computer, monitor, and accessories. 2. Verify the contents of the boxes with the packing lists and note any missing or damaged items on the quality postcard. 3. Place the computer and monitor on the bench next to the instrument. 4. Configure the voltage switch on the rear panel of the computer. Country Voltage US / Japan 115 Europe/Australia 230! CAUTION Always check the voltage configuration at the rear of the computer to ensure that it matches your site voltage. Failure to properly set the voltage switch can cause damage to the computer. 5. Follow the procedure in the computer manufacturer s documentation to connect the cables between the computer, monitor, mouse, and keyboard. 6. Connect the serial cable (P/N 4316489) from the COM1 port of the computer to the control/data port of the 310 instrument. Verifying the Operating System The Dell GX270 computer arrives preconfigured with the Windows XP operating system. Install the Windows 2000 operating system to use the Applied Biosystems applications and the 310 instrument with this computer. Use the provided image CD in the computer packing kit to change to the correct operating system. 4 Upgrading Data Collection Software to the Windows Platform

Configuring the Computer Changing to Windows 2000 To install the Windows 2000 Operating System using the ABI Windows 2000 SP3 Image CD: 1. Power on the Dell computer. 2. Insert the image CD into the computer CD-ROM drive and reboot the computer by pressing CTRL+ALT+DEL. 3. When the Dell splash screen appears, press F12 on the keyboard. 4. In the Boot Device Menu, select the number for the IDE CDROM Device. Type the appropriate number and press Enter on the keyboard. Once the computer boots from the CD, a partition selection screen comes up. 5. Select 1 to create an 8GB boot partition (C:/) with the balance of the HDD formatted to NTFS. (Required partition scheme for Applied Biosystems software.) 6. Press Enter to proceed. 7. When the WARNING screen appears, press any key on the keyboard to begin the image installation. 8. After you receive a message that the operation completed successfully, remove the CD. 9. Reboot the computer pressing CTRL+ALT+DEL. 10. Log onto the computer using the default user name with no password. Note: A message may appear that a new device has been found. You may need to reboot the computer again to let the installation of the device driver take effect. Follow the steps to reboot the computer. Upgrading Data Collection Software to the Windows Platform 5

Installing the Roxio Easy CD Creator Software Install the Roxio Easy CD Creator software to save data onto CDs. To install the software: 1. Insert the Roxio Easy CD Creator disk into the CD-ROM drive. The CD autolaunches. 2. Follow the on-screen instructions: Screen Selection Dialog box Choose Setup Language dialog box Welcome to the InstallShield Wizard for Easy CD Creator 5 Basic Setup Type Ready to Install the Program screen InstallShield Wizard Completed Yes Select the language, click OK Click Next Click Next Click Install Click Finish 3. In the Easy CD Creator 5 Basic - InstallShield Wizard dialog box, click Yes to restart the computer. Remove the CD from the drive. Creating a User Account You must have administrator rights to install Applied Biosystems software applications and any future software updates. To create a 310 User account: 1. Right-click My Computer, then select Manage. 2. In the Computer Management window, select Systems Tools in the Tree tab, then Local Users and Groups folder. 6 Upgrading Data Collection Software to the Windows Platform

Configuring the Computer Click here 3. Click the Users folder to open it. 4. In the Action menu, select New User. 5. Configure New User as follows: User Name: 310_User Full Name: Do Not Delete Description: For 310 User Password: 310user Confirm password: 310user Select Password never expires, deselect all other options. Upgrading Data Collection Software to the Windows Platform 7

6. Click Create, then click Close. 7. Click Groups in the Tree tab to open the folder. 8. Double-click Administrators, then click Add... in the Administrator Properties dialog box to bring up the Select Users or Groups screen. 9. Scroll down and double-click on 310_User, then click OK. The 310 user account is added to the administrators member list. 10. Click OK, then close the Computer Management screen. 11. Restart the computer. 12. Log in as User Name: 310_User using the password 310user. 8 Upgrading Data Collection Software to the Windows Platform

Installing Software Installing Software Installing the 310 Data Collection Software You need 30 MB of disk space to complete the installation process. Install the 310 Data Collection software before installing any other Applied Biosystems software packages. To install the 310 Data Collection software: 1. Exit any currently running programs. 2. Insert the 310 Data Collection CD into the computer s CD- ROM drive. 3. When the main installer window opens, follow the instructions, clicking Next at each window. When the final window opens, click Finish. 4. The installer looks for the folder AppliedBio on the D drive of the computer. If it does not find this folder, it creates it and then installs into it. 5. Fill out the registration card included in the software package and mail it to Applied Biosystems. Installing the GeneScan Analysis Software You need 40MB of disk space to complete the GeneScan Analysis Software installation. 1. Exit any currently running programs. 2. Insert the Analysis Software CD into your computer s CD- ROM drive. 3. Start the Setup program by double-clicking the following icons: My Computer > CD-ROM icon > Setup.exe. a. When the main installer window opens, follow the instructions clicking Next at each window. b. Set the destination location by typing (or navigate to the file via the Browse button) D:\ApplieBio. c. In the Select Instrument dialog box, select 310, then click Next. d. In the Start Copying Files dialog box, click Next and when the installation is complete, click Finish. 4. Restart the computer to ensure all changes take effect. Upgrading Data Collection Software to the Windows Platform 9

5. Fill out the registration card included in the software package and mail it to Applied Biosystems. Installing GeneMapper Software Installing Sequence Analysis Software v5.1 When installing the GeneMapper Software, you must log in to the local computer (not a network domain) and have administrator privileges. Total installation time required is about 60 minutes. 1. Exit any currently running programs. 2. Insert the GeneMapper Software CD into your computer s CD- ROM drive. The installer autolaunches and the install splash screen appears. 3. Select Install GeneMapper to begin installation of the software. The GeneMapper installer prompts you through the installation. When prompted, select a target drive with sufficient free space to receive the installation. The default drive is the D drive. The rest of the installation is automatic. Installation takes about 60 minutes. 4. When the installation is complete, click Finish. 5. Restart the computer to ensure all changes take effect. 6. Fill out the registration card included in the software package and mail it to Applied Biosystems. When installing the Sequence Analysis Software, you need to log on to the local computer (not a network domain) and have administrator privileges. To install the sequence analysis software: 1. Exit any currently running programs. 2. Insert the Sequencing Analysis Software v5.1 for Windows XP or Windows 2000 platform CD into your computer s CD-ROM drive. The installer autolaunches and the install splash screen appears. The installer prompts you through the installation. Accept all the installer defaults. 3. When the installation is complete, click Finish. 4. Restart the computer to ensure all changes take effect. 5. Fill out the registration card included in the software package and mail it to Applied Biosystems. 10 Upgrading Data Collection Software to the Windows Platform

Installing Software Installing Adobe Acrobat Installing the 310 Diagnostic Software After Installing All Software The online help system requires Adobe Acrobat Reader with Search. To install the Adobe Acrobat software: 1. Exit any currently running programs. 2. Insert the Analysis Software CD into your computer s CD-ROM drive. 3. Start the Acrobat Setup program by double-clicking the following icons: My Computer CD-ROM Adobe AcRS4ENU.exe 4. Follow the install instructions, clicking Next to take you through the dialog boxes. Install the 310 Diagnostic System Software into the Service Tools folder on the D drive. To install the 310 Diagnostic System Software: 1. Exit any currently running programs. 2. Insert the 310 Service Tools for NT CD into your computer s CD-ROM drive. 3. Navigate to the 310 Tools Setup folder on the CD drive. 4. Double-click on the Service_Tools_Installer.exe to launch the installer. After you have completed installing the various software packages: 1. Exit all programs. 2. Restart the Dell computer. Upgrading Data Collection Software to the Windows Platform 11

Setting Up the Data Collection Software Registering the Data Collection Software Enter the 310 Data Collection software registration code on the computer to use the software. To enter the registration code: 1. Select Start > Applied Biosystems > 310 Data Collection. 2. Locate the registration code that came with the 310 Data Collection software and fill out the Product Registration dialog box. 3. Fill out the Software Registration Card that came with the 310 Data Collection software, and mail the card. Setting Default Parameters If you use the same information repeatedly to fill out the various sample sheets or injection lists, you can automatically add this information to the form to save time. Choose or type this information using the Preferences option. To set the default parameters: (continued) 1. In the Window menu, select Preferences and then select File Names from the Page drop-down menu. The Preferences window opens. 12 Upgrading Data Collection Software to the Windows Platform

Setting Up the Data Collection Software 2. For Sample File name, select the tube number with a sample name as a suffix. 3. In the Page drop-down menu, select either: Sequence Sample Sheet Defaults or GeneScan Sample Sheet Defaults Upgrading Data Collection Software to the Windows Platform 13

4. Set the sample sheet preferences. For Sequencing: In the DyeSet/Primer drop-down menu, select the file appropriate to your chemistry application. In the Matrix drop-down menu, select <none>. You will change the matrix preference after you have made a new matrix. For GeneScan: Leave the default settings that should be correct for most chemistries. 5. In the Page drop-down menu, select either: Sequence Injection List Defaults, or GeneScan Injection List Defaults 6. To set the injection list preferences in the: Module drop-down menu, select the module used most often. AutoAnalyze drop-down menu, navigate to: For Sequence Analysis: D:\AppliedBio\SeqAnal\Bin\ AnalyzeSampleFile.bat For GeneScan Analysis: D:\AppliedBio\GeneScan\ Bin\AnalyzeGSSample.bat 7. In the GeneScan Injection List preferences, leave the AutoAnalyze with selection at the default if you are using the GeneMapper software. GeneMapper will not autoanalyze 310 sample files. 14 Upgrading Data Collection Software to the Windows Platform

Setting Up the Data Collection Software 8. Leave at the default values: General Settings Dye Indicators 9. Click OK when finished. Setting the Folder Locations Verify that items are located in their proper storage folder to set the computer s path to look for, retrieve, or place information. The Folder Locations tab in the Preferences window is shown below. Match folders and items as follows: Folder Name Sample Sheet Module Run Folders Firmware File Sequence Analysis Settings GeneScan Analysis Settings Name and path of Folder D:\AppliedBio\310\Sample Sheets D:\AppliedBio\310\Modules D:\AppliedBio\310\Runs D:\AppliedBio\310\Firmware Folder D:\AppliedBio\Shared\Analysis\Basecaller D:\AppliedBio\Shared\Analysis\Sizecaller Upgrading Data Collection Software to the Windows Platform 15

Creating Matrix Files After the upgrade, run matrix standards on the 310 instrument and create the necessary matrix files. For further information regarding related Applied Biosystems software applications or creating matrix files, please see the user guides that shipped with the software package. In some cases, these user guides are in the Help menu of the software application. 16 Upgrading Data Collection Software to the Windows Platform

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 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 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 USA, 05/2004 Part Number 4326553 Rev. B