GenePattern Team Blog

GenePattern Downtime this Weekend (6/14/15)

Posted on Friday, June 12, 2015 at 01:11PM by Barbara Hill Meyers

Please note that the following Broad-hosted GenePattern servers will be unavailable from 12pm Sunday, Ju (ne 14 - 12am Monday, June 15, 2015 for scheduled system maintenance: (available to internal Broad users only)

We will update this post when the maintenance is complete.

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GenePattern v3.9.3 released

Posted on Thursday, June 11, 2015 at 05:24PM by The GenePattern Team

GenePattern 3.9.3 is available for use on our Public GenePattern Server, via download, and as an Amazon Machine Image (AMI). The Release Notes give details on new features and fixes. These include:

  • The ability to expand the main panel 
  • The ability to download multiple jobs at once
  • The addition of a Python programming library
  • The deprecation of the Windows installer (see below for more information).

Deprecation of the Windows installer

Because of the number of new bioinformatics analysis tools that run only on Unix-based platforms (Linux and Mac), and the additional effort required to support Windows architecture, we have discontinued providing Windows-based installers for v3.9.3 and for future versions of GenePattern. The Windows installer for GenePattern v3.9.2 will continue to be available on the downloads page. Future versions of GenePattern may run on Windows but will not be tested. If you are concerned about...

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How to enable GenePattern Visualizers in Chrome version 42+

Posted on Friday, April 24, 2015 at 01:15PM by Barbara Hill Meyers

UPDATE: As of September 1, 2015 Chrome no longer supports the NPAPI plugin - this work around is, therefore, no longer valid.

A new blog post has been added here:


In April of 2015, Google changed the way that Chrome version 42 supports plugins, which means that GenePattern visualizers may have recently stopped working for you, if you are using Chrome.


The symptoms in GenePattern are as follows:

  1. Run a visualizer module
  2. On job status page, nothing happens
    • Java console does not come up (if it was configured to do so)
    • No errors in the URL bar indicating that you need to enable a plugin (ie you did not see something like this)

To fix this you must configure your browse to enable the required plugin architecture. Details and instructions can be found on and we've included them here for quick reference.


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