GeneMapper Software v3.5

Transcription

1 GeneMapper Software v3.5 User Guide August 29, :32 am, GM v3.5 Title.fm

2 Copyright 2003, 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. GeneMapper Software has not undergone specific developmental validation for human identification applications. Human identification laboratories analyzing single-source or parentage samples which choose to use GeneMapper Software for data analysis should perform their own developmental validation studies. ABI PRISM, Applied Biosystems, and SNaPshot are registered trademarks, and the AB Design, Applera, GeneMapper, GeneScan, SNPlex, and ZipChute are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries. AppleScript and Macintosh are registered trademarks of Apple Computer, Inc. This product includes software developed by the Apache Software Foundation ( Copyright The Apache Software Foundation. All rights reserved. This product includes software developed by the ExoLab Project ( exolab.org/). Copyright 2000 Intalio Inc. All rights reserved. JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., Microsoft Windows NT and Microsoft Excel 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. 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. All other trademarks are the sole property of their respective owners. Part Number Rev. A3 09/2003 August 29, :32 am, GM v3.5 Title.fm

3 Contents Preface How to Use This Guide vii How to Obtain More Information viii Contacting Applied Biosystems viii Chapter 1 Getting Started New Features in v Before You Install v GeneMapper Software Flowchart Software Overview Logging Into and Out of the GeneMapper Software Window Elements Chapter 2 Auditing and Software Access Control Overview Access Control Administration Tool Creating a New User Creating a New Profile Security Settings on Multiple Computers Audit Audit Map Configuration Audit History Viewer GeneMapper Software v3.5 User Guide August 29, :07 pm, BTOC.fm iii

4 Chapter 3 Archiving Data Overview Starting the Archiver Application Exiting the Archiver Application Archiver Functions Archiving Data Archiving and Restoring Overview Creating and Submitting Archive Requests Restoring Data Searching for Objects to Archive Searching for Objects to Restore Viewing Archive Locations Chapter 4 Software Functions GeneMapper Software Genotyping Algorithms Peak Detection Optimizing Peak Detection Sensitivity Slope Thresholds for Peak Start and Peak End Parameters Slope Threshold Example Size/Match-Calling Algorithm Size Calling Methods for Classic and Advanced Modes Allele-Calling Algorithm Component-Based Quality Values (PQV) Process Quality Value Determination iv GeneMapper Software v3.5 User Guide August 29, :07 pm, BTOC.fm

5 Chapter 5 Example Workflows General Workflow Sizing Workflow Microsatellite Workflow (Sizing Only) Auto Panel Workflow OLA_Analysis Workflow SNPlex Kit Assays Workflow Glossary Index GeneMapper Software v3.5 User Guide August 29, :07 pm, BTOC.fm v

6 vi GeneMapper Software v3.5 User Guide August 29, :07 pm, BTOC.fm

7 Preface How to Use This Guide Purpose of This Guide Audience Text Conventions User Attention Words The Applied Biosystems GeneMapper Software v3.5 User Guide provides procedures for the using the software features. This guide is intended for trained laboratory personnel. Applied Biosystems is not liable for damage or injury that results from use of this guide by unauthorized or untrained parties. This guide uses the following conventions: Bold indicates user action. For example: Type 0, then press Enter for each of the remaining fields. Italic text indicates new or important words and is also used for emphasis. For example: Before analyzing, always prepare fresh matrix. A right arrow bracket (>) separates successive commands you select from a drop-down or shortcut menu. For example: Select File > Open > Spot Set. Right-click the sample row, then select View Filter > View All Runs. Two user attention words appear in Applied Biosystems user documentation. Each word implies a particular level of observation or action as described below: Note: Provides information that may be of interest or help but is not critical to the use of the product. IMPORTANT! Provides information that is necessary for proper instrument operation, accurate chemistry kit use, or safe use of a chemical. GeneMapper Software v3.5 User Guide August 28, :18 pm, GM v3.5_preface.fm vii

8 Preface How to Obtain More Information Related Documentation Online help is available within the software. Access the online help by pressing F1 on the keyboard or from the Help dropmenu on the tool bar. GeneMapper Software v3.5 Installation Guide PN Contacting Applied Biosystems How to Obtain Services and Support Send Us Your Comments To contact Applied Biosystems Technical Support from North America by telephone, call For the latest services and support information for all locations, go to then click the link for Support. At the Services and 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 Services and 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 viii GeneMapper Software v3.5 User Guide August 28, :18 pm, GM v3.5_preface.fm

9 Contacting Applied Biosystems 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: Software installed: Data Collection Software v Status of Data Collection Services GeneMapper Software v Other Applied Biosystems software: GeneMapper Software v3.5 User Guide August 28, :18 pm, GM v3.5_preface.fm ix

10 Preface Table 1 Check Troubleshooting Checklist (continued) Information for Technical Support 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 v 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 Exported panels Exported bins Exported size standard definition Exported analysis method Sample (.fsa) files GeneMapper_log.txt PanelImportLog.txt Printed results x GeneMapper Software v3.5 User Guide August 28, :18 pm, GM v3.5_preface.fm

11 Getting Started 1 1 This chapter covers: New Features in v Before You Install v GeneMapper Software Flowchart Software Overview Logging Into and Out of the GeneMapper Software Window Elements GeneMapper Software v3.5 User Guide 1-1 August 29, :06 pm, 1 Getting Started.fm

12 Chapter 1 Getting Started New Features in v3.5 Access control and auditing Automated analysis with ABI Prism 3100/3100-Avant Genetic Analyzers Remote analysis New features and functions for analysis using the SNPlex Genotyping System: Cluster plot analysis and display for SNP genotyping New assay-specific 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 plots performance speed Improved printing speeds and views Drag-and-drop marker management Database archiving Database management 1-2 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

13 Before You Install v3.5 Before You Install v3.5 Computer Requirements Important Notes Supported Instruments For optimal performance of the software, 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, 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 Analyzers 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. Note: The Oracle database version in GeneMapper Software v3.0 is an embedded license database. This license allows access to the database for 5 named users at any given time. To accommodate more than 5 named users, you should either purchase additional GeneMapper Software licenses or, purchase additional Oracle named user privileges and therby, honoring Applied Biosystems agreement with Oracle. 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 GeneMapper Software v3.5 User Guide 1-3 August 29, :06 pm, 1 Getting Started.fm

14 Chapter 1 Getting Started Data Collection Software Compatibility Functional compatibility between GeneMapper Software v3.5 and Data Collection Software v1.0 and v2.0: Data Collection Software Version Sample File Compatibility Co-installation and Autoanalysis 2.0 Yes Yes 1.0 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 Applied Biosystems 3730 DNA Analyzer, Applied Biosystems 3730xl 3730 DNA Analyzer, ABI PRISM 3100 Genetic Analyzer, and/or ABI PRISM 3100-Avant Genetic Analyzer 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 (new for v3.5) Custom microsatellites (G5 dye set only) Note: Analysis of non-str applications, including AFLP, SSCP, and polyploidy data, is not supported. 1-4 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

15 Before You Install v3.5 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 (new for v3.5) StockMarks Animal Parentage Typing Kits Custom microsatellites Certain oligo ligation assay (OLA)-based mutation analysis assays Note: Analysis of non-str applications, including AFLP, SSCP, and polyploidy data, is not supported. GeneMapper Software v3.5 User Guide 1-5 August 29, :06 pm, 1 Getting Started.fm

16 1-6 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm GeneMapper Software Flowchart Kits, panels, binsets Projects Analysis methods Size standards SNP sets Table settings Plot settings Import/export Import/ export Import/ export Set Up Fragment Analysis Panel Manager GeneMapper Manager Log Access Create, import, or edit Auditing Create, import, or edit GeneMapper Kits, panels, markers, bins Apply panels CD DNA analyzers.fsa Projects Table settings Plot settings Secondary database Sample Apply Analysis methods Size standards SNP sets Archive Database Analyze Projects Apply Delete Examine Results Size standards Raw data Samples table Genotypes table Cluster plot Samples plot Genotypes plot Export to *.ser, *.txt Print Chapter 1 Getting Started

17 Software Overview Software Overview Installation For installation procedures, refer to the GeneMapper Software v3.5 Installation Guide PN Logging In for the First Time The first time that you log into the software, use the default user name and change the password. To log in for the first time: 1. Enter: a. User Name: gm b. Password: password 2. Click OK to display the Password Change Required dialog box. Since the password is pre-expired you are required to it on first login. 3. Click OK to display the Change Password Dialog box. GeneMapper Software v3.5 User Guide 1-7 August 29, :06 pm, 1 Getting Started.fm

18 Chapter 1 Getting Started 4. Type a new password, retype the new password to confirm, and click OK. 5. Two license agreements display during the first login. Click Accept for each and an new, untitled Project window displays. 1-8 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

19 Logging Into and Out of the GeneMapper Software Logging Into and Out of the GeneMapper Software Logging into the Computer Installing the GeneMapper software v3.5 on the computer requires that you log into the computer: As the administrator Into the local domain IMPORTANT! Do not log on to the network. To log into the GeneMapper software: 1. When you start the GeneMapper software application, the following dialog box opens. a. Select your user name from the User Name drop-list or, if your name is not listed there, type it in. b. Enter your password c. Click OK. Note: If you do not have a User Name: Request a username and/or password from the Administrator. If you are the Administrator use: User Name: Administrator GeneMapper Software v3.5 User Guide 1-9 August 29, :06 pm, 1 Getting Started.fm

20 Chapter 1 Getting Started Password: Administrator You are prompted to create a password if, when you click OK, your password is pre-expired. Connecting to a New Host To connect to a new host: 1. Click New Host on the Login to GeneMapper dialog box. The New Host dialog box displays. This option allows you to connect to GeneMapper software v3.5 databases on other computers. 2. In the Host Name field, enter the machine name or IP address of the database host. The window displays the new database host and its user names list. If the GeneMapper software cannot connect to the database host you entered, the following error message opens: You have entered an invalid host. Click OK to exit and reenter the database host information. 3. Select the appropriate machine type from the drop-down list. 4. Click OK GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

21 Logging Into and Out of the GeneMapper Software Logging Out Close the GeneMapper software in one of three ways: Click File > Logout, or Click File > Exit, or Click the Close button. If you close GeneMapper software with a new or blank Project window (or no changes in your Project), the Save Project (logout) dialog box does not open. When you log out of the GeneMapper software, you have the option of saving or discarding the changes you made since the last time you updated the project. If you close the GeneMapper software using the Logout command, the login window reopens after you select either Yes or No. GeneMapper software closes completely if you use either the Exit command or the Close button. GeneMapper Software v3.5 User Guide 1-11 August 29, :06 pm, 1 Getting Started.fm

22 Chapter 1 Getting Started Window Elements Panel Manager The Panel Manager allows you to create, edit, import, export, and view kits, panels, bin sets, markers, bins, and reference data. To open the Panel Manager: Click (Panel Manager) in the Project window toolbar. Menu bar Navigation pane Toolbar Information Reference pane Panel Manager Toolbar The active buttons on the toolbar vary according to which items (kits, panels, bin sets, markers, bins, or reference data) are selected and viewed. New Folder Delete New Folder New Folder New Folder New Folder Panel Manager New Folder New Plot 1-12 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

23 Window Elements Cluster Plot Manager You can display the cluster plot from the samples table or the genotypes table. The table that you use to access the cluster plot affects which electropherogram plot is directly accessible from the Cluster Plot Manager. Click (Display Cluster Plots) to open the Cluster Plot Manager. SNP Table Scatter Plot Genotypes Table GeneMapper Software v3.5 User Guide 1-13 August 29, :06 pm, 1 Getting Started.fm

24 Chapter 1 Getting Started Procedures that Use the Cluster Plot Manager: Adjusting the Cluster Plot Manager panes Adjusting the cluster plot graph settings Zooming in and out of the cluster plot Displaying electropherogram plots Finding samples Filtering samples Clustering samples Omitting samples from clustering Changing calls Hiding samples Finding SNPs Printing Filtering SNPs Exporting data About the Cluster Plot Manager The cluster plot displays for each marker: Cluster Plot: Scatter plot of the homozygous, heterozygous, and undetermined genotype calls for selected samples and controls SNP Table: Information, results, and confidence values for each SNP Cluster Plot Genotypes Table: Information, results, and quality values for samples Cluster Plot The cluster plot is displayed on the right side of the Cluster Plot Manager. There are two different graph settings: Cartesian Cluster Plot Polar Cluster Plot Cartesian Cluster Plot In the cartesian cluster plot, samples are plotted according to the peak height: The peak height for Allele 1 is plotted along the x axis. The peak height for Allele 2 is plotted along the y axis GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

25 Window Elements The symbol indicates the genotype calls for the samples and genotypes cluster in different locations in the linear cluster plot: Symbol Genotype Plot Location Angle Allele 1 homozygote Along the x axis Close to 0 C Heterozygote Along the diagonal Close to 45 C Allele 2 homozygote Along the y axis Close to 90 C No Template Control (NTC) Close to the origin NA Polar Cluster Plot In the polar cluster plot, the (x, y) coordinate from the linear cluster plot is converted to (log r, θ), where r equals the distance of the coordinate from the origin and θ equals the angle from the x axis. Log10 (intensity) is plotted along the x axis. Angle in radians is plotted along the y axis. IThe symbol indicates the genotype calls for the samples and genotypes cluster in different locations in the polar cluster plot: Symbol Genotype Plot Location Angle Allele 1 homozygote Closest to x axis Close to 0 C Heterozygote Above Allele 1 Close to 45 C homozygotes Allele 2 homozygote Above heterozygotes Close to 90 C No Template Control (NTC) Close to origin NA SNP Table The SNP table is in the upper left side of the Cluster Plot Manager. The table shows information, results, and confidence values for each SNP. Column Header (Analysis Status) SNP Description Analyzed Requires reanalysis Not analyzed Name of the SNP tested in the SNPlex assay. Comes from the SNP set used to analyze the samples. GeneMapper Software v3.5 User Guide 1-15 August 29, :06 pm, 1 Getting Started.fm

26 Chapter 1 Getting Started Marker Run Name Panel Name Dye Allow Autocall SNPQ Column Header Description Name of the marker from the panel file used to analyze the samples. Name of the run from the.fsa file. Name of the panel file used to analyze the samples. Color of the dye on the ZipChute probe used to detect the SNP. Checkbox for displaying samples in the cluster plot: Select for the software to make calls based on the clustering algorithm. Deselect to make the calls manually. SNP Quality PQV, a statistical confidence value of the SNP. Some values used in the calculations of the SNP Quality: Number of clusters Sigma separation: how distinct the two clusters are Hardy-Weinberg equilibrium If only two clusters are present, the angle difference between clusters Call rate: Number of samples with low quality Genotype Quality (GQ) PQV Signal median value Model fit Column Header Cluster Plot Genotypes Table The cluster plot genotypes table is in the lower left side of the Cluster Plot Manager. After selecting a SNP in the SNP table, the table shows information, results, and quality values for the samples. Description (Analysis Status) Sample is analyzed Sample is omitted from analysis Sample file not found Sample File Sample Name A1 If A1: Sample contains at least one copy of Allele 1 If A2: Sample is Allele 2 homozygous A2 If A1: Sample is Allele 1 homozygous If A2: Sample contains at least one copy of Allele 2 Height 1 Peak height for Allele 1 Height 2 Peak height for Allele 2 CV Clustering CV 1-16 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

27 Window Elements Column Header GQ Omit Hide Run Name AE OS PHR LPH SPU AN BD XTLK Description Genotype Quality Select to omit a sample from clustering Select to hide a sample from the cluster plot view Allele Edit Offscale PQV Peak Height Ratio PQV Low Peak Height PQV Spectral Pull-Up PQV Allele Number PQV Broad Peak PQV Crosstalk PQV Adjusting the Cluster Plot Manager To adjust the size of the tables and plots using the sizing bars: Use the dark gray bar to the left of the cluster plot to adjust the size of the cluster plot. Use the light gray bar between the SNP table and genotypes table to adjust the size of tables. 1. Position the cursor over a sizing bar until the cursor changes to sizing arrows. 2. Click and drag the sizing arrows to adjust the size of the panes. 3. Click the sizing bar to restore the default view. To toggle the display of the cluster plot using the dark gray bar to the left of the cluster plot: Click the upper black triangle to display the cluster plot only. Click the lower black triangle to hide the cluster plot. Adjusting the Cluster Plot Graph Settings 1. Right-click within the plot to access the Settings menu. 2. Select the type of cluster plot that you want to view: Cartesian or Polar. GeneMapper Software v3.5 User Guide 1-17 August 29, :06 pm, 1 Getting Started.fm

28 Chapter 1 Getting Started 3. Set the scale for the x axis and the y axis. Select Auto Scale for the software to scale each plot to the maximum x and y values obtained for the marker. Deselect Auto Scale and enter Minimum and Maximum values to view for all plots. 4. Click OK to activate the cluster plot settings. Zooming In and Out of the Cluster Plot To zoom in: Select (Zoom In) in the toolbar, position the crosshatch over the plot, and draw a box around the samples to view more closely. To zoom out: Select (Zoom Out) in the toolbar and then click the plot until you obtain the desired view. Project Window Project Window Toolbar New project Display plots Panel Manager Export table Size Match editor Low quality to top My AB links to website Search Help Save Display cluster plot Begin analysis Add sample Analysis Method Editor Open folder GeneMapper manager Current table setting Print Table settings editor 1-18 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

29 Window Elements GeneMapper Manager Use the GeneMapper Manager to create, open, edit, import, export, and delete: Projects Analysis methods Table settings Plot settings Cluster plot settings Matrices Size standards SNP sets (for analyzing SNPlex kits only) GeneMapper Software v3.5 User Guide 1-19 August 29, :06 pm, 1 Getting Started.fm

30 Chapter 1 Getting Started 1-20 GeneMapper Software v3.5 User Guide August 29, :06 pm, 1 Getting Started.fm

31 Auditing and Software Access Control 2 2 This chapter covers: Overview Access Control Administration Tool Creating a New User Creating a New Profile Security Settings on Multiple Computers Audit Audit Map Configuration Audit History Viewer GeneMapper Software v3.5 User Guide 2-1 August 29, :06 pm, 2 Controlling Access to the Software.fm

32 Chapter 2 Auditing and Software Access Control Overview Administrator s Function The administrator sets up the security and audit features for all users of GeneMapper software: 1. Choose Tools > Security Manager to start the Access Control tool for: Creating, duplicating, and deleting users (see page 2-8) Editing user properties (see page 2-10) Setting password policies (see page 2-4) Creating, duplicating, and deleting user profiles (see page 2-11) 2. Choose Tools > Audit Manager > Settings to start the Audit Map Configuration tool: Selecting which events to audit in GeneMapper software (see page 2-22) Selecting the auditing mode (see page 2-23) 3. Choose Tools > Audit Manager > Report to start the Audit History Viewer for: Searching for and viewing audit events (see page 2-26) IMPORTANT! Do not misplace the administrator password! If the administrator password is lost, access control must be reset, causing the lose of all users and profiles. 2-2 GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

33 Access Control Access Control Overview Functional Access Control Access Control allows an administrator to restrict or grant access to features and functions of the software. Administrators can enable or disable application functionality for certain classes of users as well as disable certain applications entirely for one or more classes of users. A user s access to functionality is not controlled by membership in user groups. Instead, each function is enabled or disabled in an object called a User Profile. Each user is assigned a single profile. This enables administrators to control data and function access independently. GeneMapper Software v3.5 User Guide 2-3 August 29, :06 pm, 2 Controlling Access to the Software.fm

34 Chapter 2 Auditing and Software Access Control Administration Tool Description The Administration Tool allows an administrator to manage the creation and deletion of: Users Profiles Applications An administration user is always associated with the Administration User Group and cannot be deleted. And, only one administrator is allowed to modify Access Control data at one time. IMPORTANT! Do not misplace the administrator password! If the administrator password is lost, access control must be reset, causing the lose of all users and profiles. Type Selection In the left tree pane, Users or Applications are types. When you select a type, the List of Users pane displays a list of identifiers of the type selected. IMPORTANT! Do not remove any applications from the default list in the left tree pane. 2-4 GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

35 Administration Tool Name Selection When you highlight a name, properties of that name display in the User Properties pane. Note: If you select the EULA (End User License Agreement) check box, the license agreement displays the next time the user is authenticated. GeneMapper Software v3.5 User Guide 2-5 August 29, :06 pm, 2 Controlling Access to the Software.fm

36 Chapter 2 Auditing and Software Access Control Properties Panes List Panes Access control identifiers have an additional drop-list labeled, Control Security Group. This defines the security group for control of access to the corresponding access control data itself within the Administrative Tool. The identifiers under access control are: User Profile When a reserved (undeletable) identifier is selectable, a label in the Properties pane indicates this (see the specific Property panes below). Working with List Panes: In a List pane, clicking a column header sorts the rows in the table in ascending case-sensitive alphabetic order. Clicking the column header again sorts in reverse. Ascending order Click header Descending order The column width can be widened or shortened. When widening or shortening the column width, no sorting occurs. In security groups, each cell in the Security Group column is configured to be a drop-list. Commands Commonly used commands: Toolbar. Frequently used commands appear in the application toolbar. Tool tip help text appears when you place the cursor over a button in the toolbar. Save: Save commits changes in the Admin Tool to data store and is accessible from the menu bar, keyboard shortcut, or toolbar. 2-6 GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

37 Administration Tool Exit: Exit is invoked by the standard upper-right-corner control or by the Files/Exit menu selection. If you have updated memory but have not yet committed changes to data store, the application asks, Information has been modified, Save changes? The message box provides buttons for Yes, No, and Cancel. Duplicate: Duplicates the selected indentifier. Duplicate is accessible from the menu bar and toolbar. Find: locates the name specified in the text field in the navigator tree Print: prints all or some identifiers in various formats selected from the dialog shown below. Menu Bar. Each command has a corresponding menu item. Each menu item has a unique mnemonic. The mnemonics are an underlined letter or number when viewing menu items (for example, View, on the toolbar). View Status Bar: Toggles between displaying and hiding the status bar on the bottom of the application framework. View Tool Bar: View Tool Bar toggles between displaying and hiding the toolbar underneath the menu bar of the application framework. View Association Pane: Hides or displays View Association Pane. If, for example, you are interested in identifier properties only, this allows you to hide the View Association Pane. GeneMapper Software v3.5 User Guide 2-7 August 29, :06 pm, 2 Controlling Access to the Software.fm

38 Chapter 2 Auditing and Software Access Control Creating a New User To create a new user: 1. Click the New User icon The New User dialog displays. 2. Click Next. The Configure pane displays. 3. Click Next. The Summary pane displays the new user profile data. 2-8 GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

39 Creating a New User 4. Click Finish to complete the creation of a new user. 5. Click Save. GeneMapper Software v3.5 User Guide 2-9 August 29, :06 pm, 2 Controlling Access to the Software.fm

40 Chapter 2 Auditing and Software Access Control User Properties A user must be assigned to a: Profile: Allows the administrator to grant or deny a user the right to execute functions defined by applications When one user is selected in the left navigator tree, the user profile displays in the User Properties pane and the User Details pane. User Properties pane User Details pane Note: When a user is deleted, their name no longer displays although it is permanently stored in the database; it cannot be used again GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

41 Creating a New Profile Creating a New Profile To create a new rights profile: 1. Click the New Profile icon The New Profile dialog displays. 2. Click Next. The Configure pane displays. GeneMapper Software v3.5 User Guide 2-11 August 29, :06 pm, 2 Controlling Access to the Software.fm

42 Chapter 2 Auditing and Software Access Control 3. Complete: a. Profile properties b. Select OIR (override inherited rights) and/or Execute Execute: Select this to give access to the function to any user assigned to this Profile. OIR: Select this to override inherited rights. Any lower level in the hierarchy inherits the access rights of the node above it. To override the inherited defaults, check the OIR check box. This allow the administrator to grant or deny the groups ability to execute a specific function on a lower level of the hierarchy tree. For example: Suppose the administrator selects the Scientist group profile. Anyone in the Scientist group has, by default, full use of all the plate manager buttons. (inherited from the Plate Manager node) However, to prevent all users associated with this profile from importing plates, the administrator would check the OIR box for Import, and then deselect the execute check box. In this way, importing plates--an inherited function--is overridden GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

43 Creating a New Profile 4. Click Next. The Summary pane displays the properties and associations of the new profile name. 5. Click Finish to complete the creation of a new User Profile Name. GeneMapper Software v3.5 User Guide 2-13 August 29, :06 pm, 2 Controlling Access to the Software.fm

44 Chapter 2 Auditing and Software Access Control Security Settings on Multiple Computers To use the same (cloned) security settings on multiple computers: 1. Select Tools > Security Manager. 2. When the System Authentication dialog box displays, enter your login name and password and then click OK. The Access Control Administration window displays. 3. Select File > Export Database GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

45 Security Settings on Multiple Computers 4. Save as a <fn>.acc file. 5. From the computer that you want to import the file: a. Select File > Import Database. b. Double-click the <fn>.acc file. Note: The imported settings completely replace the current security settings on the importing computer. GeneMapper Software v3.5 User Guide 2-15 August 29, :06 pm, 2 Controlling Access to the Software.fm

46 Chapter 2 Auditing and Software Access Control Audit Purpose Description Data Changes that Generate Audits Audit trails maintain a history of data changes made by the user. Data changes fall into three basic categories: Project changes Analysis methods changes Panels changes An audit is generated when data are changed. The following table lists the three general categories and the events within them that generate an audit. Projects An audit record is generated when you... Create, delete, or rename a project Add or delete a run Add or delete a sample Overwrite a GQ value Add, delete, or modify an allele Analysis Methods An audit record is generated when you... Add an analysis method Change any analysis parameter values Delete an analysis method 2-16 GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

47 Audit Panels an audit record is generated when you... Add, delete, or rename a chemistry kit Note: deleting a kit is recorded as one audit record. When you delete a kit, all panels, markers, and bin sets associated with that kit are deleted as well, but they do not generate any individual audit records. Add, delete, or rename a panel Add, delete, modify a marker Add or delete a bin set Add, delete, or modify a bin Reason For Change When a change occurs and auditing is required, the Reasons For Change dialog displays and contains: The attribute that was changed, created, or deleted. The old and new values, if applicable. A Text box where you enter the reason for the change. When you click OK, changes to the attribute and the audit data are saved. Click Cancel (it is not always available) to cancel the action and generate no audit record. GeneMapper Software v3.5 User Guide 2-17 August 29, :06 pm, 2 Controlling Access to the Software.fm

48 Chapter 2 Auditing and Software Access Control Reading GeneMapper Software Audit Records Use the descriptions in the table below to interpret the audit records. Example 1: Modify bin Refer to the table directly below the graphic for descriptions of the text boxes in the Reason(s) for Change dialog box. Text Box Example (from the graphic above) What it Means Attribute PANEL.TestPanel.MARKER.TestMarker. BIN.235.modified BIN 235, in marker named TestMarker, in panel named TestPanel, is modified Old Value [Right Offset] [BINSET.TestBinSet] The attribute Right Offset was and the bin is in bin set TestBinSet New Value [Right Offset] 76.8 [BINSET.TestBinSet] The attribute Right Offset is now 76.8 and the bin is in bin set TestBinSet 2-18 GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

49 Audit Example 2: Rename an Allele To rename an allele you would: a. Open an analyzed project b. Open the Samples Plot c. Rename an allele Refer to the table directly below the graphic for descriptions of the text boxes in the Reason(s) for Change dialog box. Text Box Example (from the graphic above) What it Means Attribute Old Value New Value RUN.Microsatellite.SAMPLE.C006_E01 9_Run_C006_ _205_07.fsa.ALLELE.test.modified test [KIT.Microsatellite Tutorial PANEL.Tutorial Panel 9.MARKER.D6S264] newname [KIT.Microsatellite Tutorial PANEL.Tutorial Panel 9.MARKER.D6S264] Allele named test in sample named C006_E019_Run_C006_ _205_07.fsa, in run named MicroSatellite is modified Allele was named test, in marker D6S264, in panel Tutorial Panel 9, in kit named MicroSatellite Tutorial Allele is now named newname in marker D6S264, in panel Tutorial Panel 9, in kit MicroSatellite Tutorial GeneMapper Software v3.5 User Guide 2-19 August 29, :06 pm, 2 Controlling Access to the Software.fm

50 Chapter 2 Auditing and Software Access Control Audit Map Configuration Overview Accessing the Audit Map Configuration Tool The Audit Map Configuration Tool is used to manage Audit Maps. Audit Maps are used to control how auditing is done for a given data type. Some features of the Audit Map Configuration Tool: You can set the audit states of an audit map to On, Off, or Silent. There is no SAVE command. All changes to audit maps are saved automatically. The Audit Map Configuration tool checks to see if the application is known by the Security component. If Security does not know about this application, the application does not start. Note: Any changes you make to an audit map do not take effect until you restart GeneMapper Software. To access the Audit Map Configuration tool: 1. In the Project window, select Tools > Audit Manager > Setting GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

51 Audit Map Configuration The System Authentication dialog box displays. 2. Type your login name and password and click OK to display the Audit Map Configuration window. GeneMapper Software v3.5 User Guide 2-21 August 29, :06 pm, 2 Controlling Access to the Software.fm

52 Chapter 2 Auditing and Software Access Control Audit Map Configuration Functions The Audit Map Configuration Tool: Audit Map Configuration Functions: If You want to... Then... Enable or disable all the attributes in an audit map Change the audit state of an attribute Select or deselect a cell in the Enabled column in the Audit Map Objects pane. Select a different audit state in a cell under the State column in the Attributes pane. Audit states are: On, Off, or Silent. Sort a row Click on a column header. Note: Disabled Audit Maps (Enabled column) display their attribute list in italics GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

53 Audit Map Configuration Commands The following table lists the commands you can perform in the Audit Map Configuration Tool. Toolbar Menu Command Function File Visual Print Displays Print Dialog. Visual Print Preview Exit Displays Print Preview. Exits Audit Map Configuration application. Auditing On/Silent Select auditing to be turned on for the Audit Map Configuration. When a change is made to an Audit Map s enabled state or when a change is made to the state of an attribute, auditing occurs, and A Reason For Change (RFC) dialog displays. Note: When RFC Dialog Displays and You... Click OK Click Cancel Then... The map or attribute state changes and an Audit Record is created. The map or attribute state does not change. Silent Off When a change is made to an Audit Map s enabled state or when a change is made to the state of an attribute, auditing occurs. Although the RFC Dialog does not display, a silent Audit Record is created. All attributes of an Audit Map Objection are turned off. GeneMapper Software v3.5 User Guide 2-23 August 29, :06 pm, 2 Controlling Access to the Software.fm

54 Chapter 2 Auditing and Software Access Control Changing the State of An Audit Map Initially, the Audit Map Attributes are turned off. To turn them on, click the Audit Map Object and then turn on the attributes individually. An audit map may contain another audit map as its attribute. For example, in the illustration below, the Kit map contains a Panel attribute (Panel is of a type PanelT map). To change the state of the Panel audit map: 1. In the Audit Map Objects pane (left), click the Kit folder. 2. In the Access to Audit map pane (right), select Panel Attribute. 3. Click the panel State choose one: a. Off: No Attributes in Panel are audited. b. On/Silent: All attributes in the Panel are audited based on the Panel audit map. IMPORTANT! If the attribute type is not primitive, the ON state does not guarantee that the object is audited. You need to go to the Audit Map Object of the specified type and turn on all the relevant attributes. For example, in the graphic below, the Audit Map Object, Kit, has attributes BINSET and PANEL which are types of BinSetT and PanelT. To enable or disable auditing for BINSET and PANEL, you need to go to the BinSet and the Panel Audit Map Objects to change the state of their attributes. Audit Map Object is Kit Attributes for Kit Type of attribute Change the state of attributes here GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

55 Audit History Viewer Audit History Viewer Overview The Audit History Viewer is used to view historical audit data. This tool is used as a read-only viewer for audit records. The tool provides data filtering so that audit records can be viewed in different formats. Audit records that you can view with the Audit History Viewer are: Date and time the audit record was created. The user who triggered the audit event. The attribute that was changed. The old and the new values. The reason for the change. Note: The audit records are stored in a permanent data store. GeneMapper Software v3.5 User Guide 2-25 August 29, :06 pm, 2 Controlling Access to the Software.fm

56 Chapter 2 Auditing and Software Access Control Viewing an Audit History To view an audit history: 1. In the Audit Objects pane, expand the objects tree until the object of interest displays. 2. Highlight an object and then click (Detail Panel) to display audit record details. Note: Click the column headers to sort the read-only records columns GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

57 Audit History Viewer Filter Command The filter allows you to categorize audit history records. To use the Filter command: 1. Click (Filter). The Filter Audit Records pane displays. 2. Enter search criteria in the applicable text boxes. 3. Click Find Now. You can filter audit records by: Name Date (and, before or after a date or between two dates) User name Matching whole words Case GeneMapper Software v3.5 User Guide 2-27 August 29, :06 pm, 2 Controlling Access to the Software.fm

58 Chapter 2 Auditing and Software Access Control Commands Toolbar Menu Command Function File Reload Reloads the audit record display with the most recent data from the database Exit Visual Print Visual Print Preview Exits Audit History Viewer application. Displays Print Dialog. Displays Print Preview. View Filter Displays the filter pane on the top of the frame when selected. It allows the user to specify criteria that limits the amount of audit records in the Audit Record table. Details Panel Displays the details of the audit record. Settings Password Allows you to change your password GeneMapper Software v3.5 User Guide August 29, :06 pm, 2 Controlling Access to the Software.fm

59 Archiving Data 3 3 This chapter covers: Overview Starting the Archiver Application Exiting the Archiver Application Archiver Functions Archiving Data Archiving and Restoring Overview Creating and Submitting an Archive Request Restoring Data Searching for Objects to Archive Searching for Objects to Restore Viewing Archive Locations Viewing Archive Requests and Restore Requests GeneMapper Software v3.5 User Guide 3-1 September 5, :07 am, 3 Archiving the Data_DM.fm

60 Chapter 3 Archiving Data Overview The GeneMapper Software v3.5 Archiver allows you to remove data from a production database and move it to offline storage, such as a hard drive, a CD ROM, or other storage media. After data is archived, you can restore it to the original database. Specifically, you can use the archiver to: Search for the objects that you want to archive Archive projects and audit objects Restore data to original database. View the archive history of objects. 3-2 GeneMapper Software v3.5 User Guide September 5, :07 am, 3 Archiving the Data_DM.fm

61 Starting the Archiver Application Starting the Archiver Application To start the Archiver application, start in the Project window and select Tools > Archiver. The Archiver Client window displays. Exiting the Archiver Application On the Archiver Menu Bar, select File > Exit. This ends only the Archiver application. If you click close the GeneMapper software. you will GeneMapper Software v3.5 User Guide 3-3 September 5, :07 am, 3 Archiving the Data_DM.fm

62 Chapter 3 Archiving Data Archiver Functions Archiver functions are available from the menu bar or the toolbar, which remains the same no matter what the Archiver context. Shortcut menus are available from the various panes. The functions available in a shortcut menu vary depending on the pane, object, or item you pick. To display a shortcut menu, right-click on the pane, object, or item. Archiver Toolbar The toolbar consists of buttons representing functions that are also available from commands in the menu bar. These functions are based on standard Windows OS (operating system) conventions. Toolbar Button Description Save: updates the archiver database. Corresponding Command in Menu Bar File > Save Cut: deletes a field, and stores it in temporary memory. Edit > Cut or, Ctrl + X Copy: copies a field. Edit > Copy or, Ctrl + C Paste: pastes a field to the cursor location. Edit > Paste or, Ctrl + V Home: clears the working area. None View Archive Requests: lets you view in the working area all the archive requests that have ever been made. displays archive requests by request ID, the contents of the request and its status. View Archive Locations: lets you view in the working area all the locations to which objects have been archived. displays archive locations by location ID and the contents of the location. View > Archive Requests or, Alt + V, Alt + r View > Archive Locations or, Alt + V, Alt + L 3-4 GeneMapper Software v3.5 User Guide September 5, :07 am, 3 Archiving the Data_DM.fm

63 Archiver Functions Resizing Panes Navigator Pane Clearing the Navigator Pane You can change the amount of space a pane uses by dragging the divider between panes, for example, between the working area and search panes. When you exit Archiver, it saves the state and size of each pane, so that the next time you log on, the window appears as it did when you exited. The navigator pane is the starting point for most archiver activities. It may contain any of the objects that the application knows about. You can populate the navigator pane in two ways: Select an object from the shortcut menu or search for the object. In the following illustration, the navigator pane displays the object archiver as a node. A node is an object that has no parents. After you select objects from the shortcut menu in the navigator pane, the object archiver becomes a folder and the objects that you selected become roots. After you have performed a number of searches, the navigator pane may become congested. You can clear the results of these previous searches. To clear the navigator pane: 1. In the navigator pane, right-click the Object Archiver folder to display the shortcut menu. 2. Select Clear All. All objects are removed and the Object Archiver folder displays as a node. Displaying Objects in the Navigator Pane You can expand and contract all the folders in the navigator pane in one step. To expand all folders in the navigator pane: In the navigator, select the Object Archiver folder, then select Expand All from the shortcut menu. To contract all folders in the navigator pane: In the navigator, select the Object Archiver folder, then select Collapse All from the shortcut menu. GeneMapper Software v3.5 User Guide 3-5 September 5, :07 am, 3 Archiving the Data_DM.fm

64 Chapter 3 Archiving Data Rearranging Columns The Archiver application allows you to rearrange columns in the working area. Rearrangement of columns applies only to the current view. The default settings will appear when you next open the window. To rearrange columns: In the pane where you want to change the order of the columns, click and hold any column heading, then drag it left or right. The columns will change position. The following illustrations show the default View Archive Requests column layout and the column layout after a user has rearranged columns. Searching The Archiver search lets you find archivable objects. The Archiver has date range fields that allow you to search for objects based on dates and times. The search function is case sensitive. 3-6 GeneMapper Software v3.5 User Guide September 5, :07 am, 3 Archiving the Data_DM.fm