GenePattern Team Blog

End of support for GeneCruiser

Posted on Tuesday, March 15, 2016 at 05:23PM by Barbara Hill

Due to the ongoing effort required in maintaining and updating gene annotation databases, we have had to end support for the GeneCruiser module. This means GeneCruiser will no longer be installed on any of our servers and will no longer be available from any of our repositories.

We are looking into alternatives for microarray annotation and will be sure to keep you posted as a new option becomes available.

Please note that this also means that the GeneCruiser functionality in the Java Applet versions of ComparativeMarkerSelectionViewer, FeatureSummaryViewer, GeneListSignificanceViewer, HeatMapViewer, HierarchicalClusteringViewer, and Multiplot* is also no longer operational. 

If you need to convert Affymetrix probes to their corresponding genes, we recommend CollapseDataset. This module will combine all of the probe sets for a single gene into one representative value, "collapsing" Affymetrix probe sents into their corresponding HUGO gene annotations....

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Older Java Applet Visualizers Blocked by Default in Updated Firefox

Posted on Monday, March 07, 2016 at 04:32PM by Barbara Hill Meyers

UPDATE MARCH 17, 2017 : Java applet visualizers no longer work in any browser. Please click here to read the blog post.

Recent updates to Firefox may result in older GenePattern Java applet visualizer failing to launch.

A work around, posted on Java.com, can be found below. (additional work arounds are also available on this page)

(Note that while the webpage indicates Firefox 42 & Windows 8, this resolved my issue in Firefox 38 on Windows 7)

 

Option 1 (Simplest method)
Add property name dom.ipc.plugins.java.enabled in Firefox preferences
  1. Launch Firefox
  2. Type about:config in the address bar
  3. You will be presented with a Firefox warning about the configuration settings. After acknowledging the Firefox alert, you should see a listing of the configuration preferences.
  4. Right-click anywhere inside the displayed list of preferences. Select New then select Boolean.
  5. Add property name as dom.ipc.plugins.java.enabled 
    Add Preference...

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Upcoming Downtime Saturday March, 5, 2016

Posted on Friday, March 04, 2016 at 01:04PM by Barbara Hill Meyers

UPDATE: March 7, 2016 - The maintenance is complete. The job queue is back online and accepting new jobs. For best results you should cancel any jobs which you had started before today at 5:00 pm. We can not make any guarantees about results obtained for jobs that had not yet completed before the start of the maintanenace window.

 

On Saturday, March 5, 2016 Broad hosted GenePattern servers will be unavailable all day for scheduled system maintenance.

The Broad-hosted GenePattern servers are:

  • genepattern.broadinstitute.org
  • gpbroad.broadinstitute.org (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, Friday, March 4, 2016. 

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

 

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