GSEA v4.0.x Release Notes

GSEA Desktop v4.0.0 (Aug 2019)

The algorithm in this version of GSEA is unchanged from the former code line and produces results equivalent to the previous version (v3.0).
GSEA Desktop v4.0.0 requires either Java 11 or Java 8. Java 11 is preferred; we provide bundles with an embedded OpenJDK 11 JVM for Mac, Windows (64-bit), and Linux.

Updated for the MSigDB v7.0 release.
Migrated code for Java 11 compatibility and corresponding better security.
Performance improvements: we are seeing a roughly 40% improvement in our informal testing.
Created dedicated Windows installer, Mac.app, and Linux bundle, each with an embedded OpenJDK 11 to avoid issues with the user needing to install Java. Created new command-line scripts for launching the GUI and running batch analyses so the user can avoid needing to deal directly with the more complex Java 11 command-line.
Removed implicit dependence on out-of-date internal annotation CHIP file.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).
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.
Switched from Ant to Gradle for builds.
Many code simplifications and removal of unnecessary code.
Fixed an indefinite wait cursor in the Leading Edge Tool.