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RELEASE NOTES GeneMapper® Software 5 Fragment analysis sizing and genotyping software Copyright 2012, Life Technologies Corporation and/or its affiliate(s). All rights reserved. June 2012 CONTENTS: Software Overview Supported Data Files Changes in GeneMapper® v5.0 as Compared to GeneMapper® v.4.1 Compatible Operating Systems and PC Requirements Installing GeneMapper® v.5.0 General Tips and Recommendations Known Issues and Limitations SOFTWARE OVERVIEW GeneMapper® Software 5 is an updated and improved version of a popular fragment analysis software designed for ease of use, flexibility and quality allele calls when performing various types of genotyping experiments. GeneMapper® Software 5 is designed to run on Microsoft Windows® 7 Professional (32-bit) SP1 operating system. GeneMapper® Software 5 is offering flexible and user-friendly solutions for sizing, peak analysis, and allele calls based on the input from the fragment analysis performed on Capillary Electrophoresis (CE) instruments from Life Technologies. It includes major fragment analysis genotyping workflows such as AFLP®, LOH, Microsatellite and SNapShot analysis. SUPPORTED DATA FILES GeneMapper® Software 5 is designed to import and analyze fragment analysis sample files (.fsa) from all currently supported genetic analyzers including 3500 series. GeneMapper® Software 5 fully supports data generated from the following Applied Biosystems instruments: - Applied Biosystems 3500 Genetic Analyzer - Applied Biosystems 3500xl Genetic Analyzer - Applied Biosystems 3130 Genetic Analyzer - Applied Biosystems 3130xl Genetic Analyzer - Applied Biosystems 3730 DNA Analyzer - Applied Biosystems 3730xl DNA Analyzer - 310 Genetic Analyzer GeneMapper® Software 5 offers limited support for data generated on 3100 and 3700 instruments. CHANGES IN GENEMAPPER® v.5.0 AS COMPARED TO GENEMAPPER® v.4.1 GeneMapper® Software 5 supports Microsoft Windows® 7 Professional (32-bit) SP1 operating system. GeneMapper® Software 5 relies on Oracle 11g R2 database to store all project-related data. In addition to serving as a common data repository, the database provides user authentication, robust and scalable data management, and flexible archiving capabilities through the utilities provided with GeneMapper® software. GeneMapper® Software 5 incorporates Oracle Password 180-days expiration patch. The user no longer needs to apply a separate patch, to ensure that Oracle database password is set for a period longer than 180 days. GeneMapper® Software 5 incorporates Hotfix 2 patch. The user no longer needs to ensure that computer has MAC (Media Access Control) address starting with the “00” hexcode. There is no longer a need to apply a special patch if the MAC address starts with hexcode other than “00”. GeneMapper® Installation and Administration Guide was substantially revised and updated for GeneMapper® Software 5. GeneMapper® Software 5 no longer supports Auto-analysis functionality. GeneMapper® Software 5 no longer has a separate Server configuration. Use the Full version instead. COMPATIBLE OPERATING SYSTEMS AND PC REQUIREMENTS 1. Recommended configuration The software can be installed, launched and run on a computer with the following specification: The software shall be supported on Dell OptiPlex XE Windows® 7 SP1 professional 32-bit operating system. CPU: Core 2 Duo E8400/3.0GHz Memory: 4GB Disk: Free space: 500MB on the boot drive, 7 GB on the drive on which the GeneMapper® Software 5 is installed 2. Minimum configuration The software can be installed, launched and run as a standalone on a computer with the following specification: Windows® 7 Professional SP1, 32-bit CPU: 2GHz or faster Intel processor Memory: 2GB Disk: Free space: 500MB on the boot drive, 7 GB on the drive on which the full version of GeneMapper® Software 5 is installed (if only GeneMapper Client Software 5 is installed, 1 GB of free space on that drive is sufficient). 3. Display Requirements User can view all UI elements of the application on the screen without having to scroll vertically if the software is run on a monitor with minimum 1280x1024 pixel resolution for full screen display. User should use Windows® 7 default theme NOTE: This software has been extensively tested on Windows® 7 SP1 (32-bit) version. While there are some indications that software will run normally on the 64-bit version of Windows® 7 SP1 operating system, the 64-bit configuration is not officially supported. It is strongly recommended that this software is run on Windows® 7 SP1 (32-bit). INSTALLING GENEMAPPER® v.5.0 1. The TCP/IP protocol must be installed and configured on the computer prior to installation of GeneMapper® Software 5. 2. The user must have administrator privileges to install this application. a) Insert the installation CD or access installation directory from Windows Explorer. Follow the install wizard steps during the installation. If the launcher does not start automatically, manually click setup.exe from Windows Explorer. b) Once installation is completed, go to the Start menu. From the Start menu, go to All Programs > Applied Biosystems > GeneMapper 5 folder and click on the GeneMapper 5 shortcut to start GeneMapper® Software 5. 3. The Oracle® database version in GeneMapper® Software 5 is an embedded license database. This license allows for 5 "named users" to access the database at any time. To accommodate for more than 5 "named users", customers should either purchase additional GeneMapper® software licenses or purchase additional Oracle "named user" privileges. 4. For uninstalling GeneMapper® Software 5, the user must have administrator privileges. 5. If co-installing GeneMapper® Software 5 with 3x30 Data Collection (UDC) or 3500 Data Collection (MDC), make sure that Data Collecton version is compatible with Windows® 7 (32-bit) SP1. Specifically, GeneMapper® Software 5 can be co-installed only with the following versions of Data Collection software: 3130xl UDC v4.0 3730/3730xl UDC v4.0 3500 MDC v.2.0 GENERAL TIPS & RECOMMENDATIONS 1. For a typical multi-user client-server environment, the GeneMapper® Software 5 has been tested with 5 concurrent users only. 2. For optimal performance, copy sample files stored on a network drive to the local drive before using them in the software. 3. It is strongly recommended that the installation of GeneMapper® Software occur on drive with a sufficient free disk space. 4. When entering text into text boxes or tables in GeneMapper software, avoid using non-standard ASCII characters including the following characters: / \ : * ? " ' < > | & # 5. When naming a sample file in Data Collection or another application, avoid using non-standard ASCII characters and accents including the following characters: / \ : * ? " ' < > | & # KNOWN ISSUES AND LIMITATIONS 1. Make sure a printer is turned on and is available (i.e. it is set to Online) before using the print command. 2. Using the Ctrl+C keyboard command to copy Cluster Plot Tables and SNP Tables may result in inconsistent copy results. Use the Copy menu command instead. 3. For the SNPlexTM analysis method SNPlex_Model_373O some of the default settings are not optimal and will allow low quality SNPs to pass. The setting for SNP Quality Pass range (GeneMapper Manager, open SNPlex_Model__3730, select the Quality Flags tab) should be set to 0.95. SNP Quality Low Quality Pass range should be set to 0.80. 4. When importing settings created in previous GeneMapper® software versions, please check that all values are set as expected. 5. When auto-panelizing SNaPshot® Kit samples, the affected project(s) will not be marked as ready for analysis. Use Analyze All from the Analysis menu to reanalyze samples. 6. If the memory is insufficient, user may encounter the “Could not create the Java virtual machine" error message when they try to launch GeneMapper® via command line. The same might happen at the end of the installation. See above Recommended specifications for computer running GeneMapper®. 7. On rare occasions, the GeneMapper® server-side module can be disconnected when the Oracle server is down. When this occurs, if user tries to perform any task on the client application it will cause a series of "failed to save to database" messages. 8. Upon installation and first launch of GeneMapper® software, the EULA will appear twice. 9. In some cases, firewall settings on the computer where GeneMapper® database is installed might prevent GeneMapper® software client applications from connecting to the database. Check with your IT department regarding creating access to that computer for GeneMapper® clients. 10. In the scenario of migrating data, in Software Extras > GeneMapper® Utility Wizard, the window that indicates a completion of the data export, incorrectly displays version 4.1 instead of version 5. 11. Security/Access Control, Auditing & Electronic Signature: To apply changes made in the Security Manager, it is recommended that all clients log off from the database first. lf a Study is renamed and assigned to a different security group, projects associated with that Study remain assigned to their previous security group. The Electronic Signature challenge may not be presented if a Study is modified but not saved before opening another Study. Be sure to save the modified Study first. Concurrent users may be able to modify the Audit Map settings in the Audit Manager at the same time. If a GeneMapper® software client terminates unexpectedly (e. g. due to network or power failure) the client’s lock will not be released from the GeneMapper® Server Database. In this situation, the server and all clients should be immediately rebooted, otherwise client/server functionality could potentially be compromised. 12. Plot View It is recommended that the plot window be closed before making changes to the universal marker in Panel Manager. In the Plot View, it is recommended to use integer values when specifying Zoom to Marker Ranges. ln the Samples plot, if user zooms into a specific location in the electropherogram, zooms out to full view, then selects Show/Hide Dye icon, it will cause the electropherogram to zoom back in. In the Cluster Plot, if file name already exists, user will not be prompted to Save As JPEG, the existing file will be automatically overwritten. In the Cluster Plot, SNP selection will always return to the 1st row when user tries to enable the overlay function in Cluster Plots Manager. 13. Panel Manager When markers are copied or moved from one panel to another, the associated reference alleles are also carried along with the markers. It is recommended that these reference alleles be deleted. While editing data in the kit tables, users may have to press the tab key more than once to move to the next field. 14. Study Manager An Internal error message may be displayed when viewing cluster plots by selecting individual samples in the Replicate Test Details view. It is recommended that users select 4 the SNP instead to view the cluster plot. Make sure all open windows are closed when installing or uninstalling the QC plugins in the Study Manager. If re-extraction from 3x30 Data Collection (also known as Unified Data Collection or UDC) to a study is needed, it is recommended that previous samples be removed from the Study first. If a project is opened from within the Study Manager, study menus will be locked until the project is closed. In some circumstances an internal error will be generated when viewing cluster plots from replicates. It is recommended that viewing be done on an individual level. If a sample is rejected (WQ fails), then HW in secondary QC will fail as well. Number of samples in a study is updated only when the study is opened. 15. Database Dashboard Utility: The software will not identify any 3x30 Data Collection (UDC) connections to the database. Client connection information can be accessed from the Dashboard tab – client connections section. Only GeneMapper® connections to the database will be identified. In order to successfully import the database, the target computer must have the same folder structure as the computer from which the database was exported. The folder structure refers to the location of .DBF files, for which the default is <DRIVE>:\OracleGM\oradata\IFA and also <DRIVE>:\AppliedBiosystems\Database\IFA (if extra allocation was carried out during the install). The software will check the folder structure on the target computer before importing and will report any errors in the log. The import button will only be enabled if there are no errors. Database Dashboard v2.0 will display an SQL error if the user tries to allocate more space than is physically available on the drive. Once this error is dismissed users can then try to allocate space again. lf the user tries to connect to a computer that does not exist on the network, the application will display a SQL error and not launch. Before restarting the application, the user will have to use Windows Task Manager to stop the application. Database Dashboard v2.0 will not allow the user to export the database if there are any Data Collection software connections to the GeneMapper® software database. The utility will display a message asking all client connections to log off. However, the software will not identify any of the Data Collection connections to the database in the client connections section. For Project Data, the software will not allow the user to allocate less than 2.5GB (2560 MB) of space. If a lesser value is specified, the software will still allocate 2560 MB which is the default value shown in the message dialog. Database Dashboard v2.0 does not display a progress bar when allocating additionalspace in the custom allocation tab. While maintenance activities, such as space allocation, import/export, etc. are being performed on the database using Database Dashboard v2.0, GeneMapper® software client applications should be disconnected from the database. GeneMapper® software clients do not have the ability to detect if maintenance activities are being performed. The GeneMapper® application will show a warning message once the disk space allocation for Oracle® database is 70% full. When this happens the GeneMapper® software will report that the disk space allocation for Oracle database is 70% full even if some of the projects are deleted. This is an Oracle Database issue. Deleting project would not release disk space at all. User need execute the batch script ifa_shrink_tablespace.bat to release disk space. The ifa_shrink_tablespace.bat is located at <DRlVE>:\AppliedBiosystems\GeneMapper\Database\Admin folder. Import operation from Dashboard when GeneMapper® Software 5 is co-installed with 3130xl UDC v4.0 or 3730/3730xl UDC v4.0 might fail, with the import log file displaying message "enter login ID and Password" and not able to proceed further. It is recommended that for GeneMapper® co-installed with UDC v.4.0, Export/Import of data was performed via manual exporting and importing groups of objects (Projects, Libraries, etc). For more detail, see GeneMapper® Installation and Administration Guide. LEGAL DISCLAIMER AND TERMS AND CONDITIONS OF CUSTOMER INSTALLATIONS OR USE LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) MAKE NO REPRESENTATIONS REGARDING GENEMAPPER® SOFTWARE 5 USE OR PERFORMANCE AND ACCEPTS NO LIABILITY AS A RESULT OF THE INSTALLATION OR USE OF GENEMAPPER® SOFTWARE 5. GENEMAPPER® SOFTWARE 5 IS PROVIDED "AS IS" AND "WITH ALL FAULTS". LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES RELATING TO GENEMAPPER® SOFTWARE 5, EXPRESS OR IMPLIED, INCLUDING THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT. IN NO EVENT SHALL LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, GENEMAPPER® SOFTWARE 5 RELEASE OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES ARISING FROM OR RELATED TO LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S)’ AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF GENEMAPPER® SOFTWARE 5 RELEASE, SHALL NOT EXCEED IN THE AGGREGATE THE PURCHASE PRICE OF THE PRODUCT. SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. For Research Use Only. Not intended for animal or human therapeutic or diagnostic use. Information in this document is subject to change without notice. Life Technologies Corporation and/or its affiliate(s) assumes no responsibility for any errors that may appear in 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 Life Technologies Corporation and/or its affiliate(s), either expressly, or by estoppel. The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.