GenePattern Team Blog

GenePattern 3.9.7 is released!

Posted on Tuesday, April 12, 2016 at 10:59AM by Barbara Hill Meyers

GenePattern 3.9.7 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 January 22, 2016. These details include:

  • The beta release of the JavaScript version of HeatMapViewer
  • Updated releases of GSEA, GSEAPreranked and ssGSEAProjection, to provide access to MSigDB v5.1
  • Better retry handling in queueing system integration. Fixes "error getting status for job" failure.
  • GenomeSpace username and token can now be used to authenticate when using the REST API.

Feel free to contact us with any questions or comments.

Sincerely, 

The GenePattern Team

 

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End of support for GeneCruiser

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

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

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 name as dom.ipc.plugins.java.enabled.
  6. A window will be displayed, select false. Then select OK.

As always,...

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