User Bulletin GeneMapper Software Version 4.1 April 2009 SUBJECT: Autoanalysis In This User Bulletin This user bulletin covers: Autoanalysis Using GeneMapper Software v4.1.............. 2 Autoanalysis Setup and Workflow.......................... 5 Setting Up the GeneMapper Software...................... 7 Setting Up a Shared Folder (Remote Autoanalysis Only)........ 10 For the Windows XP Operating System................ 10 For the Windows Vista Operating System............... 13 Setting Up the Data Collection Software.................... 17 Creating Instrument Protocols......................... 18 Creating Results Groups............................. 22 Creating and Saving Plate Records......................... 31 Starting the Autoanalysis Manager......................... 34 Scheduling and Starting a Run............................ 35 What Happens During Autoanalysis........................ 35 Autoanalysis Manager Functions.......................... 38 Overview This user bulletin supplements the GeneMapper Software v4.1 Installation and Administration Guide (PN 4403614) and provides information about setting up the GeneMapper Software and the Data Collection Software for autoanalysis of data.
GeneMapper Software Version 4.1 Autoanalysis Using GeneMapper Software v4.1 Overview The GeneMapper Software Version 4.1 can perform automatic analysis (autoanalysis) of data generated on the following instruments: Applied Biosystems 3500/3500xL Genetic Analyzers Applied Biosystems 3500 Dx/3500xL Dx Genetic Analyzers Applied Biosystems 3130/3130xl Genetic Analyzers Applied Biosystems 3730/3730xl DNA Analyzers With these instruments, you can configure the Data Collection Software and the GeneMapper Software to perform data collection and then data analysis without requiring user interaction. The Data Collection Software and the GeneMapper Software can be installed on the same computer (local autoanalysis) or on separate computers (remote autoanalysis), as shown in Figure 1. Local Autoanalysis (The GeneMapper Software is installed in the Instrument configuration) Local computer Compatible Applied Biosystems electrophoresis instrument Data Collection Software GeneMapper Software Remote Autoanalysis (The GeneMapper Software is installed in the Remote Autoanalysis configuration) Local computer Remote analysis computer Compatible Applied Biosystems electrophoresis instrument Data Collection Software Shared folder GeneMapper Software Figure 1 Examples of autoanalysis configurations 2 User Bulletin
Autoanalysis Using GeneMapper Software v4.1 Software Components Autoanalysis requires the following software packages: Data Collection Software Runs the instrument and collects data from samples. Autoanalysis can be performed using Data Collection Software on the following instruments: Applied Biosystems 3500/3500xL Genetic Analyzers (Data Collection Software v1.0) Applied Biosystems 3500 Dx/3500xL Dx Genetic Analyzers (Data Collection Software v1.0) Applied Biosystems 3130/3130xl Genetic Analyzers (Data Collection Software v3.1) Applied Biosystems 3730/3730xl DNA Analyzers (Data Collection Software v3.1) Autoanalysis Manager Provides an interface between the Data Collection Software and the GeneMapper Software (Figure 2). It queues jobs and tracks the status of their processing. A job can contain a single run, or multiple runs as part of a result group. The Autoanalysis Manager is installed during installation of the GeneMapper Software. When installing the GeneMapper Software, you must select either the Instrument or Remote Autoanalysis configuration. Note: Autoanalysis is not available in the Stand-Alone configuration of the GeneMapper Software. GeneMapper Software v4.1 Analyzes data collected by the Data Collection Software. Autoanalysis 3
GeneMapper Software Version 4.1 Figure 2 shows the software component workflow between the Data Collection Software v3.1 and the GeneMapper Software v4.1 on the 3130 and 3730 series systems. Note: For software component workflow with the Data Collection Software v1.0 on the 3500 series genetic analyzers, refer to the user guide: Applied Biosystems 3500/3500xL Genetic Analyzer User Guide (PN 4401661) or Applied Biosystems 3500 Dx/3500xL Dx Genetic Analyzer User Guide (PN 4401688) Data Collection v3.1 Run complete Autoanalysis Manager Open Closes and reports status GeneMapper Software Message Service Analysis Methods Instrument Protocols Results Groups Plate Records Raw Data SNP Set Size Standard Panel/Bin Study Figure 2 Relationships between the software components 4 User Bulletin
Autoanalysis Setup and Workflow Autoanalysis Setup and Workflow Autoanalysis Setup Tasks To set up the Data Collection Software and the GeneMapper Software to automatically analyze data, perform the following tasks: Task 1. Set up the GeneMapper Software: a. Install and register the software and create user IDs. For instructions, see the GeneMapper Software v4.1 Installation and Administration Guide (PN 4403614). b. Create definitions for the analysis method, panel, size standard, SNP sets. For instructions, see the appropriate GeneMapper Software Getting Started Guide. 2. Synchronize the GeneMapper Software data with the Data Collection Software by restarting the GeneMapper Software while the Data Collection services running. 3. Remote autoanalysis only: Set up a shared folder on the remote analysis computer. 4. In the Data Collection Software, create an instrument protocol for autoanalysis. 5. In the Data Collection Software, create a results group for autoanalysis. See page 7 7 10 18 22 To see the typical workflow for performing autoanalysis, go to page 6. Autoanalysis 5
GeneMapper Software Version 4.1 Autoanalysis Workflow Diagram Figure 3 shows the typical workflow for performing autoanalysis. Make sure the GeneMapper Software and the Data Collection Software are already set up for autoanalysis (see page 5). Set up the instrument and prepare samples. (For instructions, see your instrument user guide) Are the necessary analysis parameters created? YES NO In the GeneMapper Software, create any necessary analysis parameters. (For instructions, see the appropriate GeneMapper Software Getting Started Guide) Synchronize the data with the Data Collection Software. (See page 7) Create and save the plate record. (See page 31) Close the GeneMapper Software. Start the Autoanalysis Manager. (See page 34) In the Data Collection Software, search for the plate record, then schedule a run. (For instructions, see your instrument user guide) After autoanalysis finshes, review the processed data in the GeneMapper Software. Figure 3 Autoanalysis workflow 6 User Bulletin
Setting Up the GeneMapper Software Setting Up the GeneMapper Software If the GeneMapper Software is installed and set up: Local autoanalysis Go to Setting Up the Data Collection Software on page 17. Remote autoanalysis Go to Setting Up a Shared Folder (Remote Autoanalysis Only) on page 10. Otherwise: Install the software according to the instructions for the Instrument or Remote Autoanalysis configuration (as appropriate) Register the GeneMapper Software Create user accounts Create analysis parameters (analysis method, size standard, SNP set, panel/bin) See the GeneMapper Software Version 4.1 Installation and Administration Guide for information about installing and registering the GeneMapper Software and creating user IDs. See the appropriate GeneMapper Software Getting Started Guide for information about creating analysis parameters (analysis method, panel, size standard, study). Synchronizing GeneMapper Software Data with the Data Collection Software IMPORTANT! If you create or change any of the analysis parameters in the GeneMapper Software, you need to synchronize the data with the Data Collection software. To synchronize data: 1. Close the GeneMapper Software. 2. Verify that the Data Collection services are running. 3. Start the GeneMapper Software. Autoanalysis 7
GeneMapper Software Version 4.1 GeneMapper Software Security Settings To autoanalyze data you need a GeneMapper Software user account to which the Scientist or higher security profile is assigned. Table 1 shows the minimum privilege requirements for a user account that allows autoanalysis: Table 1 Minimum privileges for autoanalysis Element All GeneMapper objects GeneMapper project GeneMapper study Minimum privileges READ READ and UPDATE READ and UPDATE Creating a New User Account for Autoanalysis (Optional) Use the following procedure if you want to create a separate user account specifically for performing autoanalysis, To create a user for performing autoanalysis: 1. Start the Access Control Administration Software. a. In the GeneMapper window, select Tools Security Manager. b. In the AdminToolAcc dialog box, type a user name and password for a user account with administrative privileges, then click OK. 2. Select File New User. 3. In the Create User wizard, click Next. 4. In the Configure the New User page, type a name and description for the new user. IMPORTANT! The user name cannot begin with a number (1, 2, 3, ) or contain symbols (&, $, #, ). IMPORTANT! You cannot create a user account with the same name as a user account that has been deleted. 5. Specify the user details for the autoanalysis account: a. For Full Name, type Autoanalysis. b. Deselect Show EULA. c. In the Status drop-down list, select Active. 8 User Bulletin
Setting Up the GeneMapper Software 6. Select the control properties for the new user: a. In the Profile drop-down list, select Scientist. b. Use the default selection for Default Security Group and Control Security Group. IMPORTANT! Do not set the Default Security Group to AdminSecurityGroup. IMPORTANT! Do not modify the Control Security Group setting. The Control Security Group drop-down list assigns the security group data object you are editing to an existing security group. If you assign the data object to an unassociated security group, the group you are editing will be unavailable. 7. Set the password for the new user: a. Click Set Password. b. In the Change Password dialog box, type a temporary password in the Type and Retype fields. c. Click OK. Note: Because the password is configured to Pre-Expire by default, the password that you set in this step is temporary. When the user logs in for the first time, the software prompts the user to enter a password of his or her choice. 8. When you finish assigning rights to the user, click Next. 9. (Optional) Select the appropriate check boxes in the Associate column to associate the user account with the appropriate user groups, then click Next. Note: The user account must be associated with at least one group that has write privileges to the security group assigned in step 6b. 10. Click Finish to complete the user setup. 11. Select File Save. Autoanalysis 9
GeneMapper Software Version 4.1 Setting Up a Shared Folder (Remote Autoanalysis Only) IMPORTANT! If the Data Collection Software and GeneMapper Software are installed on the same computer, go to Setting Up the Data Collection Software on page 17. For the Windows XP Operating System Creating a Shared Folder (Windows XP) Remote autoanalysis of data requires a shared folder on the remote analysis computer. 1. Select Start My Computer, then double-click the drive on which you want the shared folder. 2. Select File New Folder. 3. Name the folder (for example, Remote_Autoanalysis). 4. Right-click the new folder, then select Properties. 5. In the Sharing tab, select Share this folder. 6. (Optional) Type a comment for the folder. 7. Click OK. 5 6 7 10 User Bulletin
Setting Up a Shared Folder (Remote Autoanalysis Only) Setting Security Preferences for the Shared Folder (Windows XP) If you are using the Microsoft Windows XP operating system, modify the security preferences of the shared folder as follows: 1. Right-click the shared folder, then select Properties. 2. Select the Sharing tab, then click Permissions. 3. In the Permissions for <shared folder name> dialog box, select the check box for Full Control in the Allow column. 4. Click OK. 3 4 5. Select the Security tab, then click Add. 6. In the Select Users, Computers, or Groups dialog box, type Guest in the Enter the object names to select field. 7. Click OK. Autoanalysis 11
GeneMapper Software Version 4.1 6 7 8. In the Group or user names list box in the Security tab: a. Select Guest. b. Select the check box for Full Control in the Allow column. c. Click OK. 8a 8b 8c The shared folder is now configured for use. 12 User Bulletin
Setting Up a Shared Folder (Remote Autoanalysis Only) For the Windows Vista Operating System Creating a Shared Folder (Windows Vista ) 1. Select Start Computer, then double-click the drive on which you want the shared folder. 2. Select File New Folder. 3. Name the folder (for example, Remote_Autoanalysis). 4. Right-click the new folder, then select Properties. 5. In the Sharing tab, click Share. 5 6. In the File Sharing dialog box, click the drop down button and select Everyone (All users in this list). 6 7 8 7. Click Add. 8. Click Share. Autoanalysis 13
GeneMapper Software Version 4.1 9. Click Done. 9 10. Click OK. Setting Security Preferences for the Shared Folder (Windows Vista ) 1. Right-click the shared folder, then select Properties. 2. Select the Sharing tab, then click Advanced Sharing. 2 14 User Bulletin
Setting Up a Shared Folder (Remote Autoanalysis Only) 3. On Advanced sharing windows, click Permissions. 3 4. In the Permissions for the <shared folder name> dialog box, select the check box for Full Control in the Allow column. 4 5. Click OK twice. 6. Click CLOSE. Autoanalysis 15
GeneMapper Software Version 4.1 Turn Off the Password Protected Sharing (Windows Vista ) IMPORTANT! Before starting Remote Autoanalysis, you must make sure that the password protected sharing settings on the data collection computer are disabled. 1. On the data collection computer, select Start Control Panel Network and Sharing Center. 2. Click the expand button ( ) for Password protected sharing. 3. Select Turn off password protected sharing. 4. Click Apply. 3 4 16 User Bulletin
Setting Up the Data Collection Software Setting Up the Data Collection Software Note: For information on how to set up autoanalysis for the Data Collection Software v1.0 for the 3500 series genetic analyzers, refer to the user guide: Applied Biosystems 3500/3500xL Genetic Analyzer User Guide (PN 4401661) or Applied Biosystems 3500 Dx/3500xL Dx Genetic Analyzer User Guide (PN 4401688) For autoanalysis, the Data Collection Software must have a(n): Instrument protocol Contains all the settings needed to run the instrument, including the protocol name, type of run, run module, and dye set. Results group Defines the file type, file name, file save locations, user name and password, and specifies whether autoanalysis is performed on a run-by-run basis or after the Results Group is complete. The results group organizes samples and certain user settings under a single name. It is used to prepare samples for analysis and to name, sort, and deliver samples that result from a run If the instrument protocols and results groups have already been created, go to Creating a Plate Record on page 31. Autoanalysis 17
GeneMapper Software Version 4.1 Creating Instrument Protocols For more information about instrument protocols, see your instrument user guide. You can either create a new instrument protocol or import an existing one. Creating an Instrument Protocol for Autoanalysis 1. In the Navigation pane of the Data Collection Software, select GA Instruments <Instrument Name> Protocol Manager. Create instrument protocols here 18 User Bulletin
Setting Up the Data Collection Software 2. In the Instruments Protocols area, click New to open the Protocol Editor. 3. In the Protocol Editor: 3a 3b 3c 3d 3e a. Type a name for the protocol. b. (Optional) Type a description for the protocol. c. Select REGULAR in the Type drop-down list. Autoanalysis 19
GeneMapper Software Version 4.1 d. Select the appropriate run module in the Run Module drop-down list. Note: For the list of run modules for the 3500 series genetic analyzers, refer to the user guide: Applied Biosystems 3500/3500xL Genetic Analyzer User Guide (PN 4401661) or Applied Biosystems 3500 Dx/3500xL Dx Genetic Analyzer User Guide (PN 4401688) Instrument Run Module Capillary Length (cm) 3730/3730xl GeneMapper36_POP7 36 GeneMapper50_POP7 50 HTSNP36_POP7_V3 (SNPlex ) 36 HTSNP50_POP7 (SNPlex ) 50 3130/3130xl FragmentAnalysis22_POP4_1 22 FragmentAnalysis36_POP4_1 36 FragmentAnalysis36_POP7_1 36 FragmentAnalysis50_POP4_1 50 FragmentAnalysis50_POP6_1 50 FragmentAnalysis50_POP7_1 50 SNP22_POP4_1 22 ConformationAnalysis36_CAP_1 36 Available only with Data Collection Software v3.1. e. Select the appropriate dye set in the Dye Set drop-down list. f. Click OK. 20 User Bulletin
Setting Up the Data Collection Software Importing an Instrument Protocol 1. In the Navigation pane of the Data Collection Software, select GA Instruments <Instrument Name> Protocol Manager. 2. In the Protocol Manager, click Import in the Instrument Protocols area. 3. Navigate to the protocol you want to import. Note: The import file type is.xml (extensible markup language). 4. Double-click the protocol to import it. The imported files are displayed alphabetically in the Instrument Protocol area. Autoanalysis 21
GeneMapper Software Version 4.1 Creating Results Groups For more information about results groups, see your instrument user guide. IMPORTANT! You need to create new results groups after upgrading or reinstalling the GeneMapper Software. Note: The maximum number of samples that the Data Collection Software can assign to a results group using the GeneMapper-Generic or GeneMapper-<computer name> analysis type is 7000.fsa files. If you are analyzing more than 7000 sample files, create several results groups. Creating a Results Group for Autoanalysis 1. In the Navigation pane of the Data Collection Software, select GA Instruments Results Group. 2. Click New to open the Results Group Editor. 3. In the General tab: a. Type the Results Group Name, which can be the GeneMapper Software project name. It must be unique (see page 27 for a list of accepted characters). b. (Optional) Type the Results Group Owner, which can be used in naming and sorting sample files. c. (Optional) Type a Results Group Comment. 3a 3b 3c 22 User Bulletin
Setting Up the Data Collection Software 4. In the Analysis tab: a. Select GeneMapper-<computer name> for the Analysis Type. Note: You cannot perform autoanalysis if you select GeneMapper-Generic. b. Select Do Autoanalysis. c. (Optional) Select the Results Group Entry Complete if you want autoanalysis to begin after all samples using the same results group have been run. Note: If you want to manually begin analysis before all the samples from the results group are extracted, click the Analyze Now button. d. Type the GeneMapper Software Login ID and password. IMPORTANT! Autoanalysis requires the login ID and password of a user with a Scientist or higher security profile in the GeneMapper Software. 4a 4d 4b 4c Autoanalysis 23
GeneMapper Software Version 4.1 5. Complete the Destination tab if you want to change the destination for the analyzed data or if you are performing remote autoanalysis. a. Select Use Custom Location. b. Modify the destination: Local autoanalysis only Click Browse, then select a destination. Remote autoanalysis only Enter the destination, using the format: \\<remote analysis computer name>\<shared folder name> For example: \\MYPC\Remote_AutoAnalysis 5a 5c (For remote autoanalysis only) 5b 5c c. For remote autoanalysis only: Establish a connection with the remote analysis computer by selecting Start button Run, entering the destination path as shown step b, then clicking OK. d. Click Test to test the Location path name connection. If the test: Passes The message Path Name test successful, displays. Fails The message Could not make the connection. Please check that the Path Name is correct, displays. Click Browse, then select a different location. 24 User Bulletin
Setting Up the Data Collection Software 6. In the Naming tab, create unique sample file and run folder names. If you want to use a custom naming format, see Customizing the Sample File and Run Folder Names in the Results Group Editor on page 27. The default formats for names are: Sample files: <App Prefix>_<Capillary Number>_<Well Position>.<ext> For example: frag_008_a01.fsa Run folders: <Root Destination>\<instrument type>\<instrument name>\ <Run Name> For example: E:\AppliedBiosystems\udc\datacollection\Data\ga3730\ 3730xl-08\ Run_3730xl-08_2003-11-12_11-14_0012 Note: The Root Destination is specified in the Destination tab. Note: Sample name, run folder name, and path name, combined, can total no more than 250 characters. See page 27 for a list of characters that cannot be used in file and folder names. Sample file name format area Run folder name format area Autoanalysis 25
GeneMapper Software Version 4.1 7. In the Automated Processing tab (available only if you selected GeneMapper-<computer name> in step 4 on page 23), specify when you want your samples autoanalyzed: Only when the result group is complete If you want samples to be analyzed after all the samples that use the same results group have been processed. Note: In the Analysis tab, select both Do Autoanalysis and Results Group Entry Complete. When every run completes If you want samples to be analyzed after each run, regardless of the results group. Note: In the Analysis tab, select only Do Autoanalysis. Do not select Results Group Entry Complete. Select an autoanalysis option 8. Click OK to save the Results Group. 26 User Bulletin
Setting Up the Data Collection Software Customizing the Sample File and Run Folder Names in the Results Group Editor Unique Identifiers in the Sample File or Run Folder Name Samples from a single run are placed in the same run or results folder, therefore each sample from a single run must have a unique name. Because most of the format components do not differ between samples, take care to select at least one of the format components that makes the sample names unique within a run. If your custom format does not create unique sample file or run folder names, the Results Group Editor displays a warning message below the Example line (Figure 4). Figure 4 Invalid name warning message To remove the warning message and proceed within the Results Group Editor window, select a format component that distinguishes one file from another (for example, the capillary number is unique but the instrument name is not). If you do not correct the format, the software automatically appends numbers (incrementally) before the file extension. Characters Not Allowed in Sample File or Run Folder Names The following alphanumeric characters are not allowed in file or folder names: spaces \ / : *? " < > IMPORTANT! An error message is displayed if you use any of these characters. You must remove the invalid character to continue. Autoanalysis 27
GeneMapper Software Version 4.1 Customizing the Sample File Name As you select the components for the file name, they are reflected in the Example line (Figure 5), up to 72 characters. Example line Figure 5 Sample File Name Format area 1. (Optional) In the Prefix field, type a prefix for the file name. 2. (Optional) In the Name Delimiter drop-down list, select a symbol that will separate the Format elements in the file name. The default symbol is an underscore (_). Note: You can select only one delimiter symbol. 28 User Bulletin
Setting Up the Data Collection Software 3. Select a format component in the Format drop-down list. Each time you select a format component, another drop-down list of components is added to the Format area. As you add components to the sample file name format, the drop-down lists shrink until you can no longer read the component name. To view the component names, place the cursor on the edge of the drop-down list until it turns into a double-arrow, then drag horizontally to expand the list. Expand the list Autoanalysis 29
GeneMapper Software Version 4.1 4. (Optional) In the Suffix field, type a suffix for the file name. The File Extension field displays the appropriate file extension for the Analysis Type specified in the Analysis tab (page 23). For example, fragment analysis produces sample files with an.fsa extension. Customizing the Run Folder Name Follow the same steps described in Unique Identifiers in the Sample File or Run Folder Name on page 27 to change the name of the sub-folder that is in the run folder. Figure 6 Run Folder Name Format area 30 User Bulletin
Creating and Saving Plate Records Creating and Saving Plate Records Each run of samples must have an instrument protocol and a results group assigned within a plate record, which is created in the Data Collection software. Plate records are data tables in the instrument database that store information about the plates and the samples they contain, such as the instrument protocol, results group, analysis parameters, and study name (SNPlex only). For more information about plate records, see your instrument user guide. IMPORTANT! You need to create new plate records after upgrading or reinstalling the GeneMapper Software. Note: When you autoanalyze data, you cannot set a specific project type (for example, SNPlex or Microsatellite assay). The software automatically sets the project type to Generic. Creating a Plate Record 1. Click the Plate Manager icon in the Navigation pane of the Data Collection Software. 2. Click New to open the New Plate Dialog dialog box. 3. In the New Plate Dialog: a. For 3730/3730xl instruments only: Type an ID (bar code) for the plate. b. Type a name for the plate. c. (Optional) Type a description for the plate. d. Select GeneMapper-<computer name> in the Application drop-down list. e. Select 96-well or 384-well in the Plate Type drop-down list. f. For 3730/3730xl instruments only: Define a scheduling pattern for a 384-well plate. Select Heat Sealing or Septa in the Plate Sealing drop-down list. g. Type names for the owner and operator. h. Click OK. Autoanalysis 31
GeneMapper Software Version 4.1 3a (Unavailable on the 3130/3130xl instruments) 3b 3c 3d 3e 3f (Unavailable on the 3130/3130xl instruments) 3g 3h 4. In the Plate Editor: IMPORTANT! You must create the size standards, panels, analysis methods, and SNP sets in the GeneMapper Software before creating a new plate. Note: (Optional) For GeneMapper-Generic, manually enter the information for steps d through g in the text field. a. Type the name of the sample. b. (Optional) Type a comment about the sample. c. Identify the sample as Sample, Positive Control, Allelic Ladder, or Negative Control. d. Select a saved size standard from the drop-down list. e. Select a saved panel from the drop-down list. f. Select a saved analysis method from the drop-down list. g. Select a saved SNP set from the drop-down list. h. For SNPlex systems only Type the name of the study. The software adds the runs to the study with the name you enter. i. (Optional) Enter text in the user-defined text columns. You cannot perform autoanalysis if you select GeneMapper-Generic as the application. 32 User Bulletin
Creating and Saving Plate Records j. Select a results group from the drop-down list. The drop-down list also provides the following options: New Opens the Results Group Editor dialog box. See Creating Results Groups on page 22 for more information. Edit Opens the Results Group Editor dialog box for the results group listed in the cell Duplicate Note: You must have a results group selected for each sample entered in the Sample Name column. k. Select an instrument protocol from the drop-down list. The drop-down list also provides the following options: New Opens the Protocol Editor dialog box. See Creating Instrument Protocols on page 18 for more information. Edit Opens the Protocol Editor dialog box for the instrument protocol listed in the cell. None Sets the cell to have no selected protocol. Note: You must have an instrument protocol selected for each sample entered in the Sample Name column. 4a 4b 4c 4d 4e 4f 4g 4h 4i 4j 4k Autoanalysis 33
GeneMapper Software Version 4.1 Starting the Autoanalysis Manager Automatic analysis of data requires that: The Autoanalysis Manager and Data Collection Software are running The GeneMapper Software is closed No applications other than the Autoanalysis Manager and Data Collection Software are running No other remote clients are connected to the GeneMapper Software database if the GeneMapper Software is installed on the same computer as the Data Collection Software The 3730/3730xl, 3130/3130xl, or 3100/3100-Avant instrument is set up to run, and samples are prepared The files for a Data Collection Software plate record are available. To start the Autoanalysis Manager: 1. Confirm that the GeneMapper Software is closed. 2. Select Start Applied Biosystems Autoanalysis Manager Autoanalysis Manager 5.0 Figure 7 Autoanalysis Manager IMPORTANT! The Autoanalysis Manager starts and closes the GeneMapper Software automatically, as necessary. Never manually start the GeneMapper Software or open a project while the Autoanalysis Manager is analyzing active jobs. 34 User Bulletin
Scheduling and Starting a Run Scheduling and Starting a Run For instructions on scheduling and starting runs, see your instrument user guide. IMPORTANT! Start the Autoanalysis Manager before scheduling and starting runs. What Happens During Autoanalysis Autoanalysis occurs in the following sequence (Figure 8 on page 36): 1. When the Data Collection Software finishes a run, the data is stored in the destination specified by the results group 2. The Data Collection Message Service sends the message Run Completed to the Autoanalysis Manager. The Autoanalysis Manager receives the message, then adds the job to the job queue. 3. The Autoanalysis Manager polls for jobs every two minutes and opens the GeneMapper Software client to analyze the data stored by the Data Collection Software. 4. The GeneMapper Software client analyzes the data, then saves it to the default host. Note: The default host is the GeneMapper Software server that is specified by the GeneMapper Software client. For instructions on changing the default host, see Changing the Default Host on page 36. 5. At the end of analysis, the Autoanalysis Manager closes the GeneMapper Software client, then updates the status in the job queue. Note: To maintain sufficient storage space on your hard drive, move or archive the sample files created by the Data Collection Software that are no longer needed. Autoanalysis 35
GeneMapper Software Version 4.1 Compatible Applied Biosystems electrophoresis instrument Sample files Data Collection Software Run completed Autoanalysis Manager Opens Closes, then updates status GeneMapper Software analysis application (client) Specified by the results group Analyzed files Folder Specified by the results group GeneMapper Software software database (server) Specified by the GeneMapper Software client Figure 8 Flow of data during autoanalysis Changing the Default Host The default host is the GeneMapper Software server in which the analyzed data is stored. After installing the GeneMapper Software, the default host is: For full installations The computer on which the GeneMapper Software is installed. For client-server installations The computer specified during installation of the GeneMapper Software client. Full installation Client-server installation Computer GeneMapper Software Client computer GeneMapper Software Server computer GeneMapper Software Client (analysis application) Client (analysis application) Server (software database) Server (software database) Default host Default host Figure 9 Default host in full and client-server installations 36 User Bulletin
What Happens During Autoanalysis To change the default host: 1. Open the Login to GeneMapper dialog box by starting the GeneMapper Software or, if you are already logged in, by selecting File Log Out. 2. In the Database Host drop-down list, select the GeneMapper Software database you want to set as the default. If the host you want to use is not in the drop-down list: a. Click New Host to open the New Host dialog box. b. In the Host Name field, type the server name or IP address of the database host. c. Select the appropriate machine type. d. Click OK. 3. Click Default Host. Autoanalysis 37
GeneMapper Software Version 4.1 Autoanalysis Manager Functions Components General Tab The Autoanalysis Manager has the following tabs: General GeneMapper v4.1 SeqScape x.x (if SeqScape is installed) Note: The Autoanalysis Manager may show additional tabs, depending on the other software applications that are installed on the computer. Use the General tab to view the jobs that have been submitted and their statuses. The following commands are available in the General tab: Delete Job Deletes the selected job from the Autoanalysis Manager Delete Completed Jobs Deletes all the completed jobs from the Autoanalysis Manager. Move Job Up Moves a pending job higher in the queue Move Job Down Moves a pending job lower in the queue Figure 10 Autoanalysis Manager General tab 38 User Bulletin
Autoanalysis Manager Functions GeneMapper v4.1 Tab Use the GeneMapper v4.1 tab to view jobs, project, and status information. Commands The following commands are available in the GeneMapper v4.1 tab: Configure Schedule Sets the schedule for when autoanalysis can run. Also sets schedule for auto delete. Edit Properties Edits the user name and password (active only if analysis failed due to the wrong user name or password entered in the results group). Requeue If a job fails, resubmits for analysis. Delete Job Deletes the selected job from the Autoanalysis Manager Delete Completed Jobs Deletes all the completed jobs from the Autoanalysis Manager. Note: For optimal performance, delete the completed jobs from the Autoanalysis Manger every few weeks. Move Job Up Moves a pending job higher in the queue Move Job Down Moves a pending job lower in the queue Autoanalysis Manager GeneMapper v4.1 tab Autoanalysis 39
GeneMapper Software Version 4.1 GeneMapper Job Queue The GeneMapper Job Queue area of the GeneMapper v4.1 tab shows the statuses of the jobs that have been submitted for autoanalysis. In addition to the job order, job/project name, and name of the person who scheduled the run, the GeneMapper Job Queue shows the date the job arrived in the queue (Arrival Date), the date the run was completed (Completed Date), and the status of the analysis. If the status of the analysis is: Complete Analysis completed successfully, without errors. Failed Analysis is incomplete (for example, user name/password is incorrect), or analysis completed with errors. The Status Message column provides additional information about the status of the analysis. Figure 11 GeneMapper Job Queue 40 User Bulletin
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GeneMapper Software Version 4.1 42 User Bulletin
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For Research Use Only. Not for use in diagnostic procedures. Information in this document is subject to change without notice. APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. NOTICE TO PURCHASER: DISCLAIMER OF LICENSE 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 Applied Biosystems, either expressly, or by estoppel. TRADEMARKS: Applied Biosystems, AB (Design), ABI PRISM, and GeneMapper are registered trademarks, and SNPlex is a trademark of Applied Biosystems or its affiliates in the U.S. and/or certain other countries. All other trademarks are the sole property of their respective owners. Copyright 2009, Applied Biosystems. All rights reserved. Part Number 4403670 Rev. A 04/2009 Stock Number 133UB12-01 Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA Phone 650.638.5800 Toll Free 800.345.5224 www.appliedbiosystems.com Technical Resources and Support For the latest technical resources and support information for all locations, please refer to our Web site at www.appliedbiosystems.com/support