GenePattern 3.0.0 Release Notes

Released April 1, 2007

New in release 3.0

Pipelines & Modules

New features enhance pipeline construction and module execution:


  • Pipeline construction. You can now build pipelines that are more complex and easier to use:
    • You can build pipelines that include other pipelines.
    • When you build pipelines that that have "prompt when run" parameters, you can provide the names and descriptions for the parameters.
  • Module execution. You can define a command line prefix for all modules or for individual modules. This allows you, for example, to use clustering service software (SGE, LSF) to send different modules to different job queues.


Web Client

The Web Client has been redesigned for improved useability, including the addition of features previously availably only in the Java Desktop Client. For example:

  • Jobs can now be re-loaded and re-run.
  • Results files now have menus that list the modules that you might want to use next.


User Accounts

GenePattern users now have their own accounts, which improves security and customization:

  • Optional password protection is now available for user accounts.
  • Each user can define how many jobs to display in the "recent jobs" list and the email address that receives notification when jobs complete.
  • Each user can customize the Java flags used for jobs run on the client machine. This is particularly useful for specifying the amount of memory Java uses (-Xmx512M). Customizing memory usage helps to avoid memory issues on client machines with limited memory and improve memory utilization on client machines with increased memory.


Programming Environment Clients

The GenePattern libraries for the Java, MATLAB, and R programming environments have been updated for release 3.0. If you use the programming environments:

  • You need to download and install the programming libraries from the GenePattern 3.0 Web Client: start the Web Client and select Downloads>Programming Libraries.
  • If you are connecting to a GenePattern server that has enabled password protection, you need to specify your username and password in the programming environment. The following Java code fragment shows how to specify the username and password:
        AdminSoapBindingStub stub = 
            new AdminSoapBindingStub(new URL(endpoint), service);
            stub .setUsername(username);
            stub .setPassword(password); // additional call to set password 


Server Administration

New features simplify server administration:

  • A greater number of GenePattern server settings are customizable from the GenePattern 3.0 Web Client: start the Web Client and select Administration>Server Settings.
  • Problems you may have encountered using proxy settings to install modules from the Broad repository have been corrected. If your organization uses a web proxy, to define the proxy settings for the GenePattern server, modify the server's Proxy settings.
  • A GenePattern server can now access multiple module/suite repositories, allowing you to install modules/suites from alternate sites more easily. To select a module/suite repository, modify the server's Repositories settings.
  • An updated and more granular security model allows you to set up a GenePattern server that provides greater privacy between users. For more information, see "Securing the Server" in the Web Client Guide.


Current Technology Versions

Following are the technology versions used in GenePattern 3.0.
Updated technologies are shown in bold face.

  • Java 1.5
  • R 2.0.1
  • Perl 5.8.8
  • Tomcat 5.5.* series
  • HSQL 1.8.0