View source

61[http://www.broadinstitute.org/gsea/ GSEA Home] |
[http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | 
[http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | 
[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |
[http://www.broadinstitute.org/gsea/contact.jsp Contact]<br />

<br />
<h2> GSEA Desktop v4.0.0 (Aug 2019)</h2>

The GSEA v4.0.0 release includes a number of improvements and bug fixes, including:

* Updates for the '''MSigDB v7.0''' release.
* Updates for compatibility with Java 11 and the (free) OpenJDK version of Java.
* New options for downloading and launching the application: 
** Windows installer, Mac app, and Linux bundle, each with an '''embedded OpenJDK Java 11''', which means no separate Java installation is needed.  
** Command-line scripts for running batch analyses, which means users no longer need to enter Java commands directly. Note that a '''separate Java 11''' installation is required.
** Note: Launching the application using Java Web Start still requires a '''separate Java 8''' installation.
* Miscellaneous performance improvements and code simplifications. These add up to a roughly 40% improvement in our informal testing.
* Changed the Cytoscape integration to avoid issues with platform-specific launching issues, newer Cytoscape versions, multiple installations, custom installations, and so on.  The integration now prompts the user to launch Cytoscape manually before it attempts to connect.  Cytoscape 3.3+ is required.
* Fixed an indefinite wait cursor in the Leading Edge Tool.
* DAVID I WANT TO REMOVE THIS ONE. UNLESS THERE ARE ANY USER-FACING IMPLICATIONS OF THIS CHANGE? IN WHICH CASE CAN THEY BE DESCRIBED INSTEAD? Removed implicit dependence on out-of-date internal annotation CHIP file.  Removed other special CHIP handling code to avoid conflicting with the results of the new symbol conversion from MSigDB 7.0 and better support RNA-Seq workflows.  Annotations now come from the CHIP used to collapse, or else from the dataset itself (and are left untouched).