GenePattern 3.1.0 Release Notes

Released February 1, 2008

In the GenePattern 3.1 Release Notes:
New in release 3.1
Fixed in release 3.1
Hardware requirements and software compatibility
Known issues 

New in release 3.1

GenePattern 3.1 includes several new features:

  • GenePattern server hosted by the Broad Institute: The Broad Institute now hosts a public GenePattern 3.1 server at:

    GenePattern 3.1 is also available for download from the GenePattern web site at:

    The hosted server uses an Oracle database implementation rather than the default HSQL implementation. If you are a GenePattern administrator interested in using the Oracle database implementation, see Changing the GenePattern Database (HSQL to Oracle) in the GenePattern Web Client Guide.

  • Analysis protocols: GenePattern 3.1 includes step-by-step instructions for performing four common analyses in GenePattern:


    • Differential expression analysis
    • Clustering
    • Prediction
    • SNP copy number and loss of heterozygosity (LOH) determination

    The protocols are displayed on the start page of the GenePattern Web Client.

  • R2.5 integration: GenePattern 3.1 installs and uses R2.5 (GenePattern 3.0 uses R2.0.1). New versions of the following R-based modules have been released for use with GenePattern 3.1 and R2.5:


    • AreaChange
    • CART
    • CARTXValidation
    • CompareSpectra
    • ComparativeMarkerSelection
    • ConsensusClustering
    • ExpressionFileCreator
    • GEOImporter
    • GLAD
    • ImputeMissingValues.KNN
    • LocatePeaks
    • Multiplot
    • MultiplotExtractor
    • MultiplotPreprocess
    • NMFConsensus
    • PeakMatch
    • Peaks
    • PlotPeaks
    • ProteomicsAnalysis
    • SVM

    GenePattern 3.1 supports modules written for either R2.0.1 or R2.5. Each module definition includes a command line that runs the analysis program. For an R module, the module developer specifies which version of R to use by including the appropriate substitution variable in the command line. The <R> variable translates to the full path of the R2.0.1 programming environment and the <R2.5> variable translates to the full path of the R2.5 programming environment.

    Installating GenePattern 3.1 installs R2.5 and sets the R 2.5 Home server configuration parameter, which defines the <R2.5> variable. This allows GenePattern 3.1 to run modules written for R2.5.


    • If you are upgrading from GenePattern 3.0, install GenePattern 3.1 into the same directory as GenePattern 3.0. Your existing R2.0.1 installation and <R> variable are preserved. This allows GenePattern 3.1 to run modules written for R2.0.1 or R2.5.
    • If you are not upgrading from GenePattern 3.0, you can add R2.0.1 to your GenePattern 3.1 installation as follows:
      1. Install R2.0.1.
      2. In the Web Client, click Administration>Server Settings and go to the Programming Languages page.
      3. Set the R 2.0.1 Home parameter to the full path of the R2.0.1 installation. This defines the <R> variable.
      4. Click Save to update the GenePattern server configuration.
      5. Exit from the Web Client.
      6. Stop and restart the server.
        GenePattern 3.1 can now run modules written for R2.0.1 or R2.5.



Fixed in release 3.1

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GenePattern 3.1 corrects the following known issues:

  • The execution log created by a pipeline is now listed with the analysis results files. In previous releases, it was not.


  • In the Web Client:
    • You can now install any released version of a module or pipeline. In previous releases, to install an earlier version of a module or pipeline you had to first delete the current version.
    • To display information about a job, click the icon next to the job name and select Info. The links to the input files now work as expected.
    • To use an analysis results files as input for your next analysis, click the icon next to the file name and select your next analysis module. Module names are no longer duplicated when multiple versions of the module are installed.
    • Mac users can now use Safari to modify the Access page of the server configuration settings (Administration>Server Settings).


  • In the Desktop Client:
    • You can now create both private and public pipelines. In previous releases, the Desktop Client created only public pipelines.



Hardware requirements and software compatibility

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  • 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
    Mac OS X 10.4 (Tiger), OS X 10.5 (Leopard)
    Linux Ubuntu 7.10, SuSE

    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.
    Updated technologies are shown in bold face.


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




Known issues

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The following are known issues in GenePattern 3.1:

  • Installation: In the Web Client, if the drop-down menus do not work immediately after installation, click the web browser Refresh button.


  • Suites: Private suites are visible to all users.


  • 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.



  • Ubuntu: On Ubuntu, use the GenePattern Web Client. The GenePattern Desktop Client is not supported on this platform.