Agilent Genomic Workbench 6.5

Agilent Genomic Workbench 6.5 Installation Guide Quick Start Installation of Agilent Genomic Workbench 6.5 in Windows 3 Flow chart for installation 4 Details and Instructions for Installing Agilent Genomic Workbench 6 Step 1. Prepare for installation 6 a. Check system requirements before you start 6 b. Set up permissions for installer and users 7 c. Create a common storage folder 8 d. Make sure you have a valid earray account 10 e. Create a folder for installation of MySQL 10 f. Disable user account settings for Windows Vista 11 g. Change Windows 7 settings to Never Notify 11 Step 2. Install the database server on a single computer 12 Step 3. Install the user/client software on one or more computers 13 Installation notes for Mac computers 14 Step 4. Start the Agilent Genomic Workbench user/client software 14 Starting Feature Extraction on PCs with Agilent Scanners 19 Upgrading Agilent Genomic Workbench to a New Version 21 To uninstall Agilent Genomic Workbench user/client software 22 To uninstall Agilent Genomic Workbench server without removing database 22 To uninstall Agilent Genomic Workbench server completely 23 To reinstall Agilent Genomic Workbench server with an existing database 23 Contacting Agilent Technical Support 25 To learn about Agilent products and services 25 Agilent Technologies

Agilent Genomic Workbench 6.5 is a comprehensive design and analysis tool for setting up and interpreting your microarray experiments. This guide provides instructions for installing Agilent Genomic Workbench version 6.5. 2 Agilent Genomic Workbench 6.5 Installation Guide

Quick Start Installation of Agilent Genomic Workbench 6.5 in Windows Agilent Genomic Workbench is comprised of two parts: a database with database server software that is usually installed in on a single computer, and one or more copies of the user software (clients) that are installed on any computers that have network access to the database computer. The following flow chart describes the general steps for installing Agilent Genomic Workbench. Make sure to follow the steps in the order they are shown. Detailed instructions for each step are provided later in this guide. Click the See links to jump to the detailed topics. If you want to reinstall, or upgrade to a new revision, read Upgrading Agilent Genomic Workbench to a New Version on page 21 first. Agilent Genomic Workbench 6.5 Installation Guide 3

Flow chart for installation Step 1. Prepare for Installation. See Step 1. Prepare for installation on page 6. a. Make sure computers meet system specifications. See a. Check system requirements before you start on page 6. b. Make sure the person installing the software and users have full administrator permissions on computers. See b. Set up permissions for installer and users on page 7. c. Create a common storage folder, and set permissions so that all users have read/write access to the folder. See c. Create a common storage folder on page 8. d. Make sure you have a registered earray account, and know your user name and password. See d. Make sure you have a valid earray account on page 10. e. If you do not already have MySQL installed, create a folder where Agilent Genomic Workbench will install MySQL. e. Create a folder for installation of MySQL on page 10. f. For Windows Vista computers, turn off the User Account Control. See f. Disable user account settings for Windows Vista on page 11. g. For Windows 7 computers, set User Account Control to Never Notify. See g. Change Windows 7 settings to Never Notify on page 11. h. Make sure you have a working internet connection. 4 Agilent Genomic Workbench 6.5 Installation Guide

Step 2. Install the database server on a single computer. Follow the instructions in the Installation Wizard. See Step 2. Install the database server on a single computer on page 12. Step 3. Install the user/client software on every computer where you want to use Agilent Genomic Workbench. Follow the instructions in the Installation Wizard. See Step 3. Install the user/client software on one or more computers on page 13. Step 4. On one user/client computer, start Agilent Genomic Workbench user software. Default data is downloaded. See Step 4. Start the Agilent Genomic Workbench user/client software on page 14. Step 5. Download your workgroup data to the shared database. See the earray XD User Guide. Figure 1 Flow chart for installing Agilent Genomic Workbench Agilent Genomic Workbench 6.5 Installation Guide 5

Details and Instructions for Installing Agilent Genomic Workbench This section includes more detailed instructions and important notes about each step of the installation process outlined in the installation flow chart shown in Figure 1 on page 5. You can click on the link at the end of each topic to return to the flow chart. Step 1. Prepare for installation a. Check system requirements before you start Check to make sure that your computer system meets the following minimum requirements. The requirements listed here are for Agilent Genomic Workbench Server software components. See Table 2 for a list of system requirements for Agilent Genomic Workbench user/client software. Table 1 System Requirements for Database Server computer Operating system Processor Windows XP-SP2 32 bit (supported but not recommended), Windows XP-SP2 64-bit, Windows Vista Business 32-bit or 64-bit, Windows 7 32-bit (Professional), Windows 7 64-bit (Enterprise) 2 GHz or greater, Intel Core 2 Duo CPU Available memory (RAM) For 32-bit, 2 GB For 64-bit, minimum 8 GB Hard disk space Database Software Display Resolution Internet connectivity 100 GB free space minimum for MySQL 200 GB for common storage If MySQL is already installed, it must be version 5.1 Pro. If MySQL is not installed, it is installed when you install Agilent Genomic Workbench. MySQL configuration is done automatically as part of the Agilent Genomic Workbench installation. 1280 x768 minimum T1or T3 connection (1.5 Mbps) for use of earray 6 Agilent Genomic Workbench 6.5 Installation Guide

Table 2 System Requirements for user/client computers Operating system Processor Windows XP-SP2 32 bit (supported but not recommended), Windows XP-SP2 64-bit, Windows Vista Business 32-bit or 64-bit, Windows 7 32-bit (Professional), Windows 7 64-bit (Enterprise), Mac OS X v10.5.x 2 GHz or greater, Intel Core 2 Duo CPU (PC) 3 GHz Intel Core 2 Duo CPU or better (Mac) Available memory (RAM) For 32-bit, 2 GB For 64-bit, minimum 8 GB For Mac, minimum 4 GB Display Resolution Hard disk space Internet connectivity 1280 x768 minimum (all platforms) 40 GB free space minimum (all platforms) T1or T3 connection (1.5 Mbps) for use of earray (all platforms) b. Set up permissions for installer and users Make sure that the user account that is used to install the server software has administrator permissions on the database server computer. Make sure that the user account that is used to install the user/client software has administrator permissions on the user/client computer. Make sure that every user account who will run the user/client software has read/write permissions in the common storage folder (this is usually on the database server computer.) The way you set permissions varies between operating systems. Contact your Network Administrator for help in checking or changing user account permissions. If the correct user account permissions are not set correctly, the software may fail to install or run properly. Return to Flow chart for installation. Agilent Genomic Workbench 6.5 Installation Guide 7

c. Create a common storage folder Agilent Genomic Workbench database server and user client software require a common file storage folder set up with appropriate access so that it can store/access files created during various operations. NOTE The common storage folder is not where the database is located. For more information, on how the common storage folder is used, see the Product Overview Guide. 1 Create a folder to assign as your Common Storage Folder during installation of Agilent Genomic Workbench. Create the folder in a shared location on the network, with at least 200 GB of available space. (Usually, this is the database/server computer.) Create the folder without any spaces in the name. For example, name the folder AgilentCommon instead of Agilent Common. NOTE The folder can be located on a different computer than the one where Agilent Genomic Workbench server is being installed. It can even be a Network Access Storage (NAS-box) set up with appropriate configuration. 2 Share the folder and give read- write access to all users who are installing and using the Genomic Workbench user client software in your workgroup. a In Windows explorer, right- click the folder name and select Share. (This may read Share with or Sharing and Security, depending on your version of Windows.) b Give Read/Write, Contributor or Co- owner permissions to all users or groups that will use Agilent Genomic Workbench. (Permission name depends on the version of Windows you are using.) For Windows 7, in the File Sharing dialog box, select the user or group (or select everyone) from the list, and click Add. Then change the permission level to Read/Write, and click Share. 8 Agilent Genomic Workbench 6.5 Installation Guide

For Windows Vista, in the File Sharing dialog box, select the user or group (or select everyone) from the list, and click Add. Then change the permission level to Contributor, and click Share. For Windows XP, in Documents Properties > Sharing, mark Share this folder on the network and then mark Allow network users to change my files. Then click OK. For more information on how to share folders and set read- write permissions, see your System Administrator, or your operating system documentation. 3 Determine the UNC path name for the common storage folder. During installation, you are prompted to enter the Common Storage Folder path. For network installations (where database server and user/client software are installed on different computers) this path must be in UNC standard notation. This is the case even if you are installing Agilent Genomic Workbench on the computer where the common storage directory is located (see Example 2 below). Examples of UNC notation for path names: Example 1: Suppose you are installing Agilent Genomic Workbench user client software on a computer named 'machine1' while you configured a folder named 'CommonStorage' on another computer named 'machine2' with read- write access to it from 'machine1'. The UNC standard name for this folder is as follows: Correct: \\machine2\commonstorage Incorrect: E:\CommonStorage Example 2: If you are installing Agilent Genomic Workbench user client software on a computer named 'machine1' that has a shared folder on its local D:\ drive named 'CommonStorage', then you will enter the Common Storage Folder path during installation as: Correct: \\machine1\agilentcommon Incorrect: D:\CommonStorage Return to Flow chart for installation. Agilent Genomic Workbench 6.5 Installation Guide 9

d. Make sure you have a valid earray account Before you start the installation, make sure you have a valid earray login and that you are a registered user on earray Web site. You must provide your earray Web site login name and password during the installation of the software. To become a registered user, 1 Open your internet browser, and go to https://earray.chem.agilent.com 2 Click Request for Registration. For details, see the online help on the site. Return to Flow chart for installation. e. Create a folder for installation of MySQL Agilent Genomic Workbench uses a relational database management system called MySQL. You may already be using MySQL. If not, Agilent Genomic Workbench will install MySQL on your computer. Create a folder where you want to install MySQL. You must have full administrator permissions in this folder, and the name must not contain empty spaces. For example: Correct: C:\MySQL Incorrect: C:\My SQL NOTE Agilent Genomic Workbench requires MySQL version 5.1 or above. If you do not have version 5.1 or above installed on the computer, during installation, select to have Agilent Genomic Workbench install MySQL. Return to Flow chart for installation. 10 Agilent Genomic Workbench 6.5 Installation Guide

NOTE f. Disable user account settings for Windows Vista On Windows Vista (both 32 and 64 bit versions), you must disable User Account Control (UAC) before you install the Genomic Workbench user client. If User Access Control is enabled, some modules can fail to install or run. 1 Click the Start button in Windows Vista. 2 Select Control Panel. The Control Panel window opens. 3 Select User Accounts. The User Accounts window opens. 4 Select User Accounts again. 5 Select Turn User Account Control on or off. The User Account Control window opens. Click Continue to allow changes to be made to your computer. 6 Clear the box labeled Use User Account Control (UAC) to help protect your computer. 7 Click OK to continue. Return to Flow chart for installation. g. Change Windows 7 settings to Never Notify For installations on Windows 7 computers, change the User Account Control settings from the default setting to Never Notify. 1 Go to Control Panel. 2 Click User Accounts. 3 Click User Accounts. 4 Click Change User Account Control setting. 5 Change the setting to "Never Notify" and click OK. 6 Reboot the machine. Return to Flow chart for installation. If you do not set the User Account Control setting to Never Notify, then Agilent strongly recommends that you install Agilent Genomic Workbench on a drive where the operating system is not installed. Otherwise, you may have problems running workflows or importing design data. Agilent Genomic Workbench 6.5 Installation Guide 11

Step 2. Install the database server on a single computer The Agilent Genomic Workbench database server software is installed only once, on a single computer that has network access from all computers that will be running the Agilent Genomic Workbench user/client software. After installation, the database server software runs silently in the background and manages the shared database for all Agilent Genomic Workbench users. NOTE You You cannot install the database server software on a Mac. 1 Before beginning to install Agilent Genomic Workbench server, be sure you have completed all the pre- installation steps outlined in Step 1 of the Flow chart for installation on page 4. 2 Login to the Windows system where you want to install Agilent Genomic Workbench server. Use an account that has administrator privileges. 3 Double- click the Agilent_Genomic_Workbench_Server_6_5_0_xx.exe icon. The following message is displayed. Figure 2 InstallAnywhere dialog box - preparing to install 4 The installation wizard starts. Follow the instructions for each section and type requested information when required. When you complete the information in a section, click Next to display the next section. You can click Previous to review information in a previous section. Return to Flow chart for installation. 12 Agilent Genomic Workbench 6.5 Installation Guide

Step 3. Install the user/client software on one or more computers The Agilent Genomic Workbench user/client is the software you use to start and run the suite of Agilent Genomic Workbench programs. This includes Feature Extraction, the DNA Analytics modules, earray XD, Sample Manager, Workflow, and SureSelect Target Enrichment. You install the user/client software on one or more computers. If you want, you can also install the user/client software on the same computer where you installed the database server. 1 Double- click the Agilent_Genomic_Workbench_Standard_Edition_Installer_6_5_0_xx.exe icon. The following message is displayed. Figure 3 InstallAnywhere dialog box - preparing to install 2 The installation wizard starts. Follow the instructions for each section and type requested information when required. When you complete the information in a section, click Next to display the next section. You can click Previous to review information in a previous section. NOTE Note that some programs in the Agilent Genomic Workbench suite require that you purchase additional licenses from Agilent. Agilent Genomic Workbench 6.5 Installation Guide 13

The following data are downloaded to the server database by default. The time required to complete the download of default data varies depending on your internet connection speed, but the total time is approximately 30 minutes. You cannot use the Agilent Genomic Workbench user/client software to analyze data until this download is complete. Download workgroup admin data Download new control grids if required Design and probe group meta information for workgroup and catalog Installation notes for Mac computers You cannot install the server software on a Mac computer. The installation file you downloaded from the Agilent Web site is a.zip file. Extract the contents of the.zip file to a location on your hard drive. To start the installation of the software from the installer program, double- click the installer icon and follow the instructions in the installation wizard. Return to Flow chart for installation. Step 4. Start the Agilent Genomic Workbench user/client software After you install Agilent Genomic Workbench database server and user/client program as described in this manual, start the program as described below. 1 Double- click the Agilent Genomic Workbench Standard Edition 6.5 icon from your desktop or select Agilent Genomic Workbench Standard Edition 6.5 from the Windows Start menu. How you start the program depends on the choice you made for Shortcut Folder during installation of the Agilent Genomic Workbench user/client. 2 If this is the first time you have opened Agilent Genomic Workbench after installation, you are presented with a license agreement. Read the license and click I accept to proceed. 3 Type your earray User Name and Password, then click OK. 14 Agilent Genomic Workbench 6.5 Installation Guide

Figure 4 earray login when starting Agilent Genomic Workbench 4 If this is the first time you started Agilent Genomic Workbench after installing the server, you see the following message, if the database initial download is not complete: Figure 5 Database not yet initialized dialog box 5 If you click No, Agilent Genomic Workbench closes. You can open it later after the database initialization has completed. (This normally takes approximately 30 minutes.) If you click Yes, the following message is displayed. Agilent Genomic Workbench 6.5 Installation Guide 15

Figure 6 Database installation status message 6 Click OK to see the Job Queue Management Console that lists the progress of the initial download tasks. 7 If you don t see any jobs listed in the Job Queue Management Console, wait for a few minutes, and then click Search. A list of submitted jobs are shown. Jobs that are not yet complete show a Status of Processing. 8 When the download of initial data is complete, you see the download tasks with Complete Status in the Job Queue Management Console. 16 Agilent Genomic Workbench 6.5 Installation Guide

Figure 7 Job Queue Management Console when data download is complete 9 Click Close. 10 Start Agilent Genomic Workbench. 11 Select an application type (CGH, ChIP, CH3, Expression, microrna, or SureSelect Target Enrichment), then click OK. If you get an invalid license message, ignore it for now. You will get a chance to enter your license later (see Step 14). Agilent Genomic Workbench 6.5 Installation Guide 17

Figure 8 Select Application Type dialog box 12 When the Open Application window appears, in the upper right corner, click Product Overview. 13 Read the Product Overview Guide. 14 If your application requires a license, follow the instructions in the Product Overview Guide to enter its licence information. 15 Follow the instructions in the Product Overview Guide to open your application. NOTE Before you use Agilent Genomic Workbench, you must download Agilent Catalog and workgroup custom data. See the earray XD User Guide for information on how to download this data. 18 Agilent Genomic Workbench 6.5 Installation Guide

Starting Feature Extraction on PCs with Agilent Scanners Agilent Genomic Workbench software (including Feature Extraction) is pre- installed on PCs that are shipped with Agilent scanners. When you start the Feature Extraction or Agilent Genomic Workbench software for the first time on the PC that was shipped with your Agilent scanner, you will receive an error indicating that the software cannot find the database. Before you can use the software, you must set the database host name to the name of the scanner PC. Figure 9 Database connection error for Feature Extraction Figure 10 Database connection error for Agilent Genomic Workbench Use the following procedure to set the database host computer name. Agilent Genomic Workbench 6.5 Installation Guide 19

To set the database host name for Agilent Genomic Workbench and Feature Extraction 1 Start the Agilent Genomic Workbench software. 2 When the Database connection error message appears, click Yes. The Enter database parameters dialog box appears. Figure 11 Database parameters dialog box 3 In the box next to Host, type the name of your PC. You can find the name of the computer by opening the Windows Control Panel, and selecting System. 4 Leave the Port set to 3306. 5 Click OK to close the dialog box. 6 You can now log into Agilent Genomic Workbench, or close it and start the Feature Extraction software. 20 Agilent Genomic Workbench 6.5 Installation Guide

Upgrading Agilent Genomic Workbench to a New Version The flowchart below shows the steps required to upgrade Agilent Genomic Workbench to a new version of the database server and client software. Close all user/clients Uninstall user/client software on all user/client computers. See To uninstall Agilent Genomic Workbench user/client software on page 22. Uninstall the database server software, without removing the database. See To uninstall Agilent Genomic Workbench server without removing database on page 22. Install the new database server software. See To reinstall Agilent Genomic Workbench server with an existing database on page 23. Install the new user/client software on all client computers. See Step 3. Install the user/client software on one or more computers on page 13. Figure 12 Flow chart for upgrading Agilent Genomic Workbench software Agilent Genomic Workbench 6.5 Installation Guide 21

To uninstall Agilent Genomic Workbench user/client software You use the Uninstall program to remove the Agilent Genomic Workbench user/client software from each computer where it was originally installed. You can find the uninstaller program in the shortcut location you selected when you installed the software. 1 Log in to the computer where you installed the user/client software. Use an account that has administrator privileges. 2 Double- click the Uninstall Agilent Genomic Workbench Standard Edition <version> icon on your desktop. OR Start the Uninstall program from Start > All Programs > Agilent Genomic Workbench Standard Edition<version> > Uninstall Agilent Genomic Workbench Standard Edition <version>. NOTE You will only see the Uninstall program icon or shortcut location if you were the person who installed the software, or if the shortcut was created for all users. 3 Follow the instructions for each step of the uninstallation. Click Next to go to the next step, or click Previous to go back to the previous step. 4 When you reach the Uninstall Complete page, click Done to close the Uninstall program. To uninstall Agilent Genomic Workbench server without removing database This option lets you uninstall the Agilent Genomic Workbench server software without removing the database that it created during installation, and data that was added to it by users. This lets you install an updated version of the software while maintaining your workgroup data. 1 Log in to the computer where you installed the database server software. Use an account that has administrator privileges. 2 Run the Uninstall Agilent Genomic Workbench Server program, which is located in the Shortcut Folder you selected during the Agilent Genomic Workbench Server installation. A message is displayed while the Uninstall program starts up. 22 Agilent Genomic Workbench 6.5 Installation Guide

3 When the Uninstaller program wizard appears, follow the instructions for each step of the process. When prompted, select Uninstall Application, do not remove Database. 4 When the Uninstall Complete page appears, click Done. To uninstall Agilent Genomic Workbench server completely When you uninstall the Agilent Genomic Workbench database server using the Uninstall Database and all its contents option, the software, database, and all user data are removed from the computer. This option does not remove MySQL from the computer, but it does remove the Agilent Genomic Workbench database from MySQL. CAUTION If If you choose to uninstall the database and all its contents, you will lose all user data and content in your database. Do this only if you have backed up your database first, or you no longer want to have access to this data. 1 Log in to the Windows system where you installed the application. Use an account that has administrator privileges. 2 Run the Uninstall Agilent Genomic Workbench Server program, which is located in the Shortcut Folder you selected during the Agilent Genomic Workbench Server installation. A message is displayed while the Uninstall program starts up. 3 When the Uninstaller program wizard appears, follow the instructions for each step of the process. When prompted, select Uninstall Database and all its contents along with application. 4 When the Uninstall Complete pane appears, click Done. To reinstall Agilent Genomic Workbench server with an existing database This section explains how to reinstall the Agilent Genomic Workbench database server software without creating a new database.use this procedure to reinstall a new version of the database server after you removed the previous version without removing the database. See To uninstall Agilent Genomic Workbench server without removing database on page 22. Agilent Genomic Workbench 6.5 Installation Guide 23

CAUTION Before you reinstall the Agilent Genomic Workbench server, make sure that all user/clients are not using the software, and no workflows are running. Otherwise, they will be disconnected and may lose valuable experiments and data. 1 Login to the computer where you want to reinstall the Agilent Genomic Workbench database server software. Use an account that has administrator privileges. 2 Double- click the installer program to start the installation. This program is located in the folder you used when you downloaded it from the Agilent Web site. Make sure you use the correct installation program for your computer and operating system. For example, Agilent_Genomic_Workbench_Server_<version>_64_bit.exe. 3 When the installer starts, follow the prompts for each section. Click Next to display the next section, or click Previous to go back to a previous section. 4 When the database server software installation is complete, click Done to close the installer program. To install a new version of the user/client software on each client computer, see Step 3. Install the user/client software on one or more computers on page 13. 24 Agilent Genomic Workbench 6.5 Installation Guide

Contacting Agilent Technical Support Technical support is available by phone and/or e- mail. A variety of useful information is also available on the Agilent Technical Support Web site. Resource Agilent Technical Support Web site Contact Agilent Technical Support by telephone or e-mail (United States and Canada) Contact Agilent Technical Support by telephone or e-mail (for your country) To find technical support contact information 1 Go to http://chem.agilent.com. 2 Select a country or area. 3 Under Quick Links, select Technical Support. 4 Select from the available links to display support information. Telephone: (800-227-9770) E-mail: informatics_support@agilent.com 1 Go to http://chem.agilent.com. 2 Select Contact Us. 3 Under Worldwide Sales and Support Phone Assistance, click to select a country, and then click Go. Complete e-mail and telephone contact information for your country is displayed. To learn about Agilent products and services To display information about the Life Sciences and Chemical Analysis products and services that are available from Agilent, go to www.chem.agilent.com. Agilent Genomic Workbench 6.5 Installation Guide 25

www.agilent.com In this book This book tells you how to install Agilent Genomic Workbench 6.5 on your computer. Agilent Technologies, Inc. 2010 Revision A0, September 2010 *G3800-90031* G3800-90031 Agilent Technologies