GenePattern 3.2.0 Release Notes

Released July 1, 2009


New in Release 3.2

GenePattern 3.2 includes the following new features and improvements:

  • New job status page: The job status page, which is displayed when you run an analysis, now displays complete information about the analysis job, including current status, parameter values, analysis results, and any visualizers run. The new job status page can be displayed at any time for easy access to analysis results and the visualizers used to view them. more...
  • Shared analysis result files: GenePattern users can now share analysis result files. From the job status page, click the share icon to give other users access to your analysis job, including its input files, parameter values, and result files. You can share analysis result files with all GenePattern users or a group of GenePattern users. All jobs are still private by default. Unless you choose to share it, only you (and GenePattern administrators) can view or delete the job. more...
  • New results summary page: The results summary page, which lists your jobs and their result files, has been reorganized and simplified. Use this page to view all jobs that you have run or can access (for example, jobs that have been shared with groups to which you belong). more...
  • Groups: Members of a group can now share analysis result files. As in previous releases, a GenePattern administrator defines groups by editing the GenePatternServer/resources/userGroups.xml configuration file. To define a group on the GenePattern public server, send a request to gp-help (at) Specify a name for the group and the list of GenePattern users to be added to the group. Only users already registered on the public server can be added to a group. more...
  • Flexible authentication and authorization: GenePattern 3.2 can be configured through two new Java interfaces. System administrators configuring GenePattern to work within an existing infrastructure can modify GenePattern authentication by implementing the new IAuthenticationPlugin interface or by modifying the authentication filter. If the infrastructure defines user groups, system administrators can configure GenePattern to recognize those groups by implementing the IGroupMembershipPlugin interface. more...

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Desktop Client Retired

In previous releases, GenePattern offered a Java-based application interface called the Desktop Client. The features of the Desktop Client have been migrated to the web interface. The GenePattern install no longer includes the Desktop Client. GenePattern 3.2 and future releases will use the web interface.

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Hardware requirements and software compatibility

  • GenePattern components: The latest versions of the GenePattern components are:


      Component Version Build
      client 3.2 8501
      server 3.2 8501
  • Hardware requirements: GenePattern's hardware requirements are found on almost all currently available machines:


    • 256 MB RAM
    • 500 MHz Pentium 3 or equivalent
    • Hard drive space:
      • Server: 252 MB
      • Client: 84 MB

    As of June 2009, installing all GenePattern modules from the Broad repository requires approximately 1 GB of hard drive space. The SNPFileCreator module may require additional RAM depending on the chip type and number of CEL files being processed.


  • Supported operating systems: GenePattern installers are available for Windows, Mac OS X, and Linux. GenePattern should work with any operating system that has a Java 1.5 virtual machine installed. We have tested it on the following OS platforms:


    Windows XP, Vista On Vista:
    • The StartGenePatternServer and StopGenePatternServer applications must be run as administrator. To start or stop the GenePattern server, right-click the desktop icon and select the Run as administrator option.
    • Operating system timestamps are incorrectly written to the log files. Timestamps recorded in both the webserver and GenePattern logs are likely a few hours ahead or behind the system time.
    Mac OS X 10.4, OS X 10.5  
    Linux Ubuntu 8.04, 8.10, 9.04

    Users are also running GenePattern on the Red Hat, Debian, Gentoo, Mandrake and Fedora distributions of Linux.


  • Supported browsers: The GenePattern Web Client has been tested on the following browsers:


    Windows Firefox 3.0, MS Internet Explorer 7.0 and 8.0
    Mac Firefox 3.0, Safari
    Linux Firefox 3.0

    Safari: By default, Safari sets an open "safe" files after downloading preference. This setting prevents GenePattern from correctly exporting and importing zip files. To clear this preference: open Safari, select Safari>Preferences, select General preferences, and clear the Open "safe" files after downloading check box.


  • Current technology versions: Following are the technology versions used in GenePattern 3.2.


    • Java 1.5
    • R 2.5.0
    • Perl 5.8.8
    • Tomcat 5.5.* series
    • HSQL 1.8.0

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