GenePattern Team Blog

Java 7 update 51 blocks GenePattern visualizers

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

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 Exception Site List, click the Edit Site List button.
  4. In the dialog that appears, add the base URL for your GenePattern...

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GenePattern server coverage December 23 - January 2

Posted on Thursday, December 19, 2013 at 12:41PM by GenePattern Team

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:

  • GenePattern staff will not be reachable by phone or responding to email. This includes our help system, Twitter, and Facebook.
  • Emails (including help tickets) and phone calls will be responded to as quickly as possible, once we return to the office on Jan 2, 2014.

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


Happy Holidays from the GenePattern team! 



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Using GenePattern with Mac OS X 10.9 Mavericks

Posted on Monday, December 02, 2013 at 10:49AM by Barbara Hill Meyers

Since the release of Mac OS X 10.9 (Mavericks) on Oct 22, 2013,  many of you may have already upgraded or are considering doing so, given the ease of access to this upgrade. Some of you have reported problems with GenePattern on this new OS and we have observed some in our own testing and exploring. This post aims to go over what we know and any work arounds or fixes we have so far . We will continue to provide updates for any incomplete or (unknowingly) inaccurate information.

There are 3 basic ways in which one may use GenePattern:

  1. GenePattern Public Server - (note that for the sake of this blog the information about this method will be assumed to pertain to any remote GenePattern server - ie not installed on your computer)
  2. A previously installed* version of GenePattern on your computer. (* previous to upgrading to Mac OS X 10.9 Mavericks on the Mac where the server is installed)
  3. A new installation of GenePattern , installed after upgrading to...

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