GenePattern Team Blog

Java Certificate Expiration causes "Application Blocked by Security Settings" error - FIXED

Posted on Monday, June 22, 2015 at 03:16PM by Barbara Hill Meyers

June 23, 2015 1:00PM UPDATE: This issue has now been resolved. Please let us know if you continue to encounter issues with launching visualizers.


Our Java certificate recently expired, and we are now in the process of renewing it. During this time, visualizers will fail to launch, returning the following error:


If you encounter this error, you'll need to add the URL for the GenePattern server to your Java exceptions, as detailed on the Java site. The URL for the server can be found in the URL bar in the top of your browser. The URL you add to the exceptions list should look something like:

Once you have added the exception, you may need to refresh your window. You will then see a message like this when you attempt to launch a visualizer:

Click the Check Box next to "I accept the risk and want to run this application" (and optionally, via Show Options, choose to do this always for this provider). Then,...

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GenePattern Downtime this Weekend (6/14/15)

Posted on Friday, June 12, 2015 at 01:11PM by Barbara Hill Meyers

Please note that the following Broad-hosted GenePattern servers will be unavailable from 12pm Sunday, Ju (ne 14 - 12am Monday, June 15, 2015 for scheduled system maintenance: (available to internal Broad users only)

We will update this post when the maintenance is complete.

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GenePattern v3.9.3 released

Posted on Thursday, June 11, 2015 at 05:24PM by The GenePattern Team

GenePattern 3.9.3 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 and fixes. These include:

  • The ability to expand the main panel 
  • The ability to download multiple jobs at once
  • The addition of a Python programming library
  • The deprecation of the Windows installer (see below for more information).

Deprecation of the Windows installer

Because of the number of new bioinformatics analysis tools that run only on Unix-based platforms (Linux and Mac), and the additional effort required to support Windows architecture, we have discontinued providing Windows-based installers for v3.9.3 and for future versions of GenePattern. The Windows installer for GenePattern v3.9.2 will continue to be available on the downloads page. Future versions of GenePattern may run on Windows but will not be tested. If you are concerned about...

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