GenePattern and the latest Java 7 update (45)

Since the release of Java 7 update 45 (Oct 15, 2013) there have been some reports of difficulties with Java and GenePattern visualizers.

Release notes from Oracle can be found here.

The most prominent change in this latest release (as pertains to most GenePattern users) is a warning message that will appear when you try to run any Java app which is from an "unknown" publisher and does not have a, now required, permissions attribute. 

The GenePattern team is looking into how we can address this warning such that our software will not be blocked in a future release of Java. In the mean time. you can simply check the box next to "I accept the risk..." and then click run. This should allow you to use any visualizers as before. If you have any other issues after allowing the acception, please refer to this previous blog post about Java 7 and visualizer issues. (Note that Java 7 is still not compatible with the Chrome on Mac , as Java 7 is 64-bit and Chrome for Mac is still 32-bit)


Using Dropbox in GenePattern via GenomeSpace

The folks here on the GenePattern and GenomeSpace teams thought it might be nice to point out a little "pro tip" for you Dropbox users out there.

Back in July GenomeSpace announced the ability to connect to your Dropbox files via GenomeSpace. Which means, you can also use your Dropbox files in GenePattern.

So, how do you go about setting this up.

Step 1: Create or log in to your GenomeSpace account

Step 2: Follow the direction in this GenomeSpace blog to set up our Dropbox/GenomeSpace connection

Step 3: Either log into GenePattern using GenomeSpace 

or, if you are already logged into GenePattern, associate an existing GenePattern account with your GenomeSpace account:
Step 4: Use your GenomeSpace connected Dropbox files from the GenomeSpace tab, as you would any other file in GenePattern.



The Outage: October 17-20, 2013

The Outage is a scheduled, major four-day disruption to most Broad IT services. In preparation for our move into a new building the Broad IT Services group will move all central IT hardware to a new facility. During the move, which will take place from 12:01 am* Thursday, October 17 to 11:59pm Sunday, October 20, almost all of Broad's IT services will be unavailable.

*Please note the change in start time

Broad employees and associates may access more details on our intranet.

External users may read more information on the Broad website.

Users of any Broad Institute hosted GenePattern server should expect:

Prior to The Outage please contact us with any questions you may have. 
You may follow us on Twitter, Facebook or G+ for updates as they are available, or check our website where our Twitter Feed is displayed.
The Broad will also providing updates via Twitter 
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