June 2006, Number 5http://www.broad.mit.edu/genepattern/

 1. Announcements

GenePattern 2.0.2 Release

GenePattern 2.0.2 is now available. This release for the GenePattern server contains the following minor additions and fixes:
  • Redirect input and output when creating modules. Users can now define modules with command lines that explicitly specify the names of input and output files, for example:
    my_module.pl \< input_file \> output_file
    See Creating A Task in the GenePattern Web Client Guide for more information.
  • Fix for importing pipelines on the Macintosh platform. A bug in previous releases prevented Macintosh users from importing pipelines that contained modules. This has been fixed.
The GenePattern 2.0.2 installer is available at http://www.genepattern.org/download/. When updating GenePattern 2.0 to 2.0.2, you only need to install the server; you do not need reinstall the graphical client.

 2. Updated Modules

Two updated modules are available in the GenePattern module repository:
  • ExpressionFileCreator. Version 2 adds the dChip and gcRMA algorithms, and updates the package connecting to Bioconductor, which generates a "Error in getCdfInfo(object):Could not obtain CDF environment" message in previous versions.

  • KNNXValidation. Version 3 corrects a bug in the previous version that causes Windows users to be unable to view or edit tasks in the Web client.

To install the updated modules, open the GenePattern Web Client and click install/update tasks under the Tasks and Pipelines heading in the right column, as described in Installing and Updating Tasks in the GenePattern Web Client Guide. For comprehensive documentation on the modules in the repository, see our module page.

 3. New GSEA Module

A new module, GSEA, is available in the GenePattern module repository. GSEA runs the Gene Set Enrichment Analysis; a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two phenotypes (Subramanian & Tamayo, 2005). The GSEA module runs the same implementation that can be found in the standalone GSEA package (http://www.broad.mit.edu/gsea/).

 3. Talk to Us

Please let us know how you're using GenePattern!

User Survey

We'd like to know how GenePattern is working for you. Our user survey is a brief online form that lets you give us feedback about the software, documentation, and other aspects of using GenePattern. Your responses are greatly appreciated - they help us to understand how GenePattern is being used and how to make it a more valuable tool.


If you've published a paper that makes use of GenePattern, we'd love to hear about it: email the GenePattern team. Even if you are just using GenePattern in a novel way, let us know!

For future papers, please note that we've updated the GenePattern citation:
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500.

Early Adopters

If you'd like early access to new GenePattern releases to help us test new GenePattern features, please let us know.
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