GenePattern Team Blog

Older Java Applet Visualizers No Longer Work in Chrome

Posted on Tuesday, December 01, 2015 at 11:58AM by Barbara Hill

In a previous blog post from April we provided a work around for the the Chrome NPAPI plugin deprecation, which prevented our Java applet based visualizers from working.

As of September 1, 2015, this work around is no longer valid and Java applet based visualizers simply do not work in Chrome.

To this end, the GenePattern team has been replacing our older Java applet based visualizers with new JavaScript based versions of the same name.


To date, the following have been updated:

  • CLSFileCreator
  • ComparativeMarkerSelectionViewer


Soon to be released:

  • HeatMapViewer
  • IGV


If you are experiencing any other issues with visualizers, not in Chrome, please review our FAQ.


Please contact us with any questions you may have, and follow us to get updates as we release these new JavaScript viewers.




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Upcoming Job Queue Downtime Wednesday Nov 4, 2015

Posted on Monday, November 02, 2015 at 12:47PM by Barbara Hill

On Wednesday, November 4, 2015 the GenePattern Broad-hosted servers will be down for scheduled system maintenance from 6am to 2pm EST (GMT -5).

The Broad-hosted GenePattern servers are:

  • (internal, requires Broad VPN access)

To facilitate a quick recovery from this downtime, we suggest that you refrain from submitting long-running jobs (4+ hours) after 5pm EST (GMT -5) today, Monday, November 2, 2015

After 5pm EST (GMT -5) tomorrow, Tuesday, November 3, 2015 job submission will be turned off. We have everything back up and running as close to 2pm EST (GMT -5) on Wednesday, November 4, as possible.


We will update this post, our Twitter feed, and the servers' system messages when the maintenance is complete. 


Nov 8 - Update: The system maintenance has completed successfully and the server has resumed normal function.

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GenePattern 3.9.5 is released!

Posted on Tuesday, October 13, 2015 at 03:52PM by The GenePattern Team

GenePattern 3.9.5 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, fixes and modules released since August 7, 2015. These details include:

  • It is now possible to submit a batch job, which batches over text, numeric or dropdown parameters
  • When reloading a job with advanced parameters, the relevant advanced parameter sections will now automatically expand to display their values
  • GenePattern will now, by default, display the latest non-development version of a module, basing this assessment on the Software Quality attribute in the module's manifest
  • The beta release of the JavaScript versions of ComparativeMarkerSelectionViewer and CLSFileCreator

Feel free to contact us with any questions or comments.


The GenePattern Team

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