GenePattern Team Blog

Scheduled Maintenance Downtime - Saturday, June 25, 2016

Posted on Tuesday, June 21, 2016 at 01:33PM by Barbara Hill

The Broad Institute IT team has scheduled a maintenance window for the entire day of Saturday, June 25, 2016.

This will impact both GenePattern servers hosted at the Broad:

In preparation for this downtime, we will need to clear the job queue by Saturday morning. We therefore suggest that you plan for your jobs to complete by 5pm (EST) on Friday, June 24, 2016, at which point we will also cease accepting jobs in on both servers. 

The server should be back up on Sunday morning (June 26, 2016) and accepting jobs, however our team's monitoring of the servers will be light on Sunday, and will resume in full on Monday morning during normal business hours (EST).

Our server running at Indiana University will be up during this maintenance window (http://gp.indiana.edu) however, the registration can take a day or so to process, so if you plan to use that resource, we would recommend you...

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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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