GenePattern Team Blog

GenePattern 3.8.1

Posted on Thursday, April 17, 2014 at 05:29PM by GenePattern Team

GenePattern 3.8.1 has been released! 3.8.1 (build 13243)  is available for use on our Public GenePattern Server,  via download and as an Amazon Machine Image (AMI)

New features include:

  • A new file uploader, replacing the Java-Applet-based file uploader with a new html5/JavaScript file uploader
  • New Jobs and Files tabs, which introduce new slide-out menus for all jobs and job output files
  • The ability to group parameters; for instance into "Advanced" and "Basic"
  • Website tours which walk users through new and basic features of GenePattern

We also made some user requested fixes and enhancements:

  • The new file uploader eliminates file upload failures occasionally encountered when uploading large files using the retired applet-based uploader.
  • Previously there existed a bug which prevented the termination of pending jobs. This has been resolved.

Full details about 3.8.1, including hardware/software requirements and known issues...

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GenePattern 3.8.0

Posted on Wednesday, February 12, 2014 at 04:42PM by GenePattern Team

GenePattern 3.8.0 has been released! 

3.8.0 (build 12839)  is available for use on our Public GenePattern Server,  via download and as an Amazon Machine Image (AMI)

New features include:

  • An updated User Interface
  • New and improved Modules & Pipelines Pane
  • Pinning favorite modules
  • Running a batch job over multiple dragged in files
  • Parallel execution of jobs in a pipeline
  • Pipeline designer improvements allowing the use of regular expressions to specify output files to be used as downstream input.
  • Multiple categories for individual modules and pipelines
  • Directories in dynamic drop downs
  • Setting of file purge intervals based on user or group

We also made some user requested fixes and enhancements:

  • A bug in GenePattern's SGE integration prevented job cancelation. This has been resolved.
  • Previously the pipeline designer did not allow non-admin users with createPublicPipeline permission to create public pipelines. This has been...

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Java 7 update 51 blocks GenePattern visualizers

Posted on Tuesday, January 21, 2014 at 04:37PM by David Eby

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

A new Java update (7u51) was released by Oracle a week ago and - as has been the pattern with other recent updates - once again tightens security on applets run from web browsers.  This affects all GenePattern visualizers as well as certain other components, most prominently the File Uploader.  The GenePattern team is currently evaluating the best way to modify these components to avoid these issues in the future.

This update introduces a new security exception list which will allow you to register an exception for GenePattern so that you can use visualizers in the interim.  The instructions are stratightforward (based on this page from Oracle):

  1. Open the Java Control Panel.  On a Mac this is accessed through System Preferences.  See these instructions to find it on Windows.
  2. Switch to the Security tab.
  3. In the section titled...

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