September 2006, Number 6http://www.broad.mit.edu/genepattern/

 1. Announcements

How are you using GenePattern?

Are you using GenePattern for scientific research? Does your organization use GenePattern as part of your production process? If so, we'd like to hear from you: email the GenePattern team. Help us understand how you use GenePattern so that we can make it a more valuable tool. Send us success stories for use in testimonials and grant proposals, which help to support GenePattern development.

GenePattern in the News

GenePattern 2.0 and its analysis modules have been in the news:
  • Drug Discovery News interviews GenePattern Principal Investigator Jill P Mesirov and Project Leader Michael Reich in an article published 30 June 2006: http://drugdiscoverynews.com/index.php?newsarticle=872.

  • Nature Genetics published an article by Michael Reich, et al. describing GenePattern 2.0:

    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 (http://www.nature.com/ng/journal/v38/n5/full/ng0506-500.html).

    To cite GenePattern, please reference this article.

  • Bioinformatics published an article by Joshua Gould, et al. describing the comparative marker selection modules available in GenePattern:

    Gould J, Getz G, Monti S, Reich M and Mesirov JP (2006), Comparative gene marker selection suite, Bioinformatics 2006 22(15):1924-1925; doi:10.1093/bioinformatics/btl196 (http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/15/1924?etoc).



 2. New and Updated Modules

Two new modules have been added to the GenePattern module repository:
  • HierarchicalClusteringViewer displays the results of HierarchicalClustering (or any files in Eisenís TreeView format) as a heat map image annotated using dendograms. From the viewer, you can create new datasets based on selected features and samples, display annotations using GeneCruiser, and use color to highlight features named in a feature list file.

  • UniquifyLabels makes row and column labels unique. For example, if the row label foo occurs three times in the input file, these row labels are changed to foo, foo-1, and foo-2 in the output file.

The following GenePattern modules have been updated:

  • HeatMapViewer includes feature descriptions, as well as feature names on the heat map; uses menus rather than an options panel to control the display, which provides more room for the heat map image; and correctly displays gene and microarray feature annotations using GeneCruiser.

  • MAGEMLImportViewer accepts the following input file formats: .tar, .tgz, .tar.gz, .zip, or .gz.

  • caArrayImportViewer contains updated module documentation.

  • ComparativeMarkerSelectionViewer
    FeatureSummaryViewer
    GeneCruiser
    GeneListSignificanceViewer correctly display gene and microarray feature annotations using GeneCruiser.

To install new and 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. Training and Events

GenePattern Training Workshops

Our next GenePattern workshop will be held on September 9 at the Meeting of the Microarray Gene Expression Data Society in Seattle, Washington.

This popular workshop teaches participants the features of GenePattern, including:
  • an intuitive graphical user interface for users at all levels of computational sophistication
  • comprehensive repository of clustering, prediction, preprocessing, and visualization modules for analysis of microarray data
  • a pipeline environment that allows users to chain tasks together to create and share methodologies
  • a task integration environment that allows rapid, code-free integration of new tools
  • a programming environment that allows users to access GenePattern modules from the Java, MATLAB, and R programming languages

Watch our web site for updates on future workshops, or sign up to be notified immediately.


 4. Talk to Us

Please let us know how you're using GenePattern!

User Survey

Tell us about your experiences with GenePattern. 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 you use GenePattern and how we can make it a more valuable tool.

Publications

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!

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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