GenePattern 3.1.1 Release Notes

Released July 1, 2008

New in Release 3.1.1

GenePattern 3.1.1 includes the following new features and improvements:

  • Broadcast messages to online users: A GenePattern user logged in as an Administrator can now broadcast a message to all users logged into the GenePattern server. Click Administration>Server Settings and select the System Message page to enter a message. The instructions on the System Message page fully describe this feature.
  • Job Results page displays faster: When you click Job Results>Results Summary, the page now displays job results within a few seconds regardless of the number of jobs run on your server. This enhancement makes it significantly easier to view jobs on high-traffic servers such as the GenePattern public server.
  • Support for larger data files: When you run an analysis, you select one or more data files for processing. In GenePattern 3.1.1, the maximum input file size has been increased to 10GB.

Fixed in Release 3.1.1

GenePattern 3.1.1 corrects the following known issues:

  • File menu: The File menu now includes a scroll bar to ensure that all menu items are accessible. In previous releases, the File menu was occasionally too long for the window.
  • Suites: Private suites are now private. In GenePattern 3.1, private suites were visible to all users.

Hardware requirements and software compatibility

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


      Component Version Build
      client 3.1.1 7777
      server 3.1.1 7777
  • 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 December 2007, 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 (Tiger), OS X 10.5 (Leopard)  
    Linux Ubuntu 7.10, SuSE On Ubuntu:
    • Use the GenePattern Web Client. The GenePattern Desktop Client is not supported on this platform.
    • A GenePattern patch is required to run modules implemented in R. Contact gp-help (at) for details.

    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 2.0, MS Internet Explorer 6.0 and 7.0
    Mac Firefox 2.0, Safari 2.0
    Linux Firefox 2.0

    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 3.1.1.


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