GenePattern 3.8.0

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:

We also made some user requested fixes and enhancements:

A video overview covering some of these new features can be found here.

Full details about 3.8.0, including hardware/software requirements and known issues can be found in our release notes.

We are working on updating the rest of our documentation to reflect this new version of GenePattern. We thank you for your patience as we make progress on this. Do let us know if you find anything to be out of date. We'll be happy to provide you with up-to-date information right away and update the page as soon as possible.

Please let us know what you think!

Java 7 update 51 blocks GenePattern visualizers

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 startightforward (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 Exception Site List, click the Edit Site List button.
  4. In the dialog that appears, add the base URL for your GenePattern server.  For our public server this will be  Accept the warning that follows, then click OK to save the changes.
  5. The GenePattern visualizers will still be blocked in your browser, but now you will be prompted to permit them to run just as with the previous Java update (7u45).  See our prior blog post on the subject for instructions.

Depending on how Java was updated, it is also possible that you will need to restart your browser and/or your computer as well.

Our apologies for the added steps.  We are in the process of figuring out how best to respond to these changes.

GenePattern server coverage December 23 - January 2

From December 21 to January 1, the GenePattern team will be unavailable due to the year-end closing of the Broad Institute.  During this time, the GenePattern servers and repositories (including GParc) will remain up and fully functional. We will be monitoring this daily and, should anything happen to disrupt service, we will work to resolve any issues within 24 hrs. However, due to the holiday closing, please be aware that:

If you have any questions, please feel free to contact us.


Happy Holidays from the GenePattern team! 



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