January 2006, Number 4http://www.broad.mit.edu/genepattern/

 1. Announcements

Release of GenePattern 2.0

GenePattern 2.0 is now available! New features in this release include:
  • Integrated Pipeline and Graphical Environment: You can now create, view and edit pipelines in the easy-to-use Java Client.

  • Automatic Pipeline Creation: In addition to building a pipeline step by step, you can now select a result file and automatically create the analysis pipeline that produced that file.

  • Module Suites: Suites are groups of modules that can be installed, edited, exported, and viewed as a unit. For example, the Clustering suite contains all GenePattern modules that perform clustering, and the Proteomics suite contains all proteomic-related modules. In installing or exporting a suite, you install or export all of the modules in that suite. The Java and Web clients provide a filter-by-suite capability, allowing you to view only those modules in the suites you are interested in. You can create your own suites, or install suites from the GenePattern module repository.

  • Web Client Redesign: The layout of the Web Client has been redesigned to improve access to frequently used operations, previous analyses and result files.
GenePattern 2.0 is available at http://www.genepattern.org/download/. We welcome your feedback and encourage you to send questions and comments to gp-help@broad.mit.edu.

 2. Training and Events

GenePattern Training Workshops

GenePattern will be the subject of two events during MIT's Independent Activities Period (IAP):

  • January 12, 1-2PM, Bringing Research Tools to the Classroom. This workshop, presented by Ivica Ceraj and Violeta Ivanova, will feature a live demonstration of GenePattern as a front end for High Performance Computing (HPC) Beowulf Cluster and discussion of the potential for using computational tools in undergraduate teaching.
    No advance sign up required.

  • January 20, 10AM-1PM, GenePattern Workshop. This workshop, presented by Ted Liefeld and Michael Reich, will teach participants how to do microarray analysis using the features of GenePattern.
    Enrollment is limited; visit the registration page to register.
Watch our web site for updates on future workshops, or sign up to be notified immediately.

 3. Talk to Us

Please let us know how you're using GenePattern!

User Survey

If you use GenePattern, we would like to know how your experience has been. Our user survey is a brief online form that lets you give us feedback about the software and other aspects of using GenePattern. Your responses are greatly appreciated - they will help us to understand how GenePattern is being used and how to make it as valuable a tool as possible.


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

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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