GSEA v4.0.x Release Notes

GSEA Desktop v4.0.0 (Aug 2019)

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 over v3.0 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.
Updated the annotations and processing code used by the GSEA application to match the new symbol conversion procedure used to create MSigDB 7.0 (see the MSigDB release notes)

Miscellaneous bug fixes:

Fixed an issue with Collapse Dataset that was at-odds with the MSigDB recommendations for symbol remapping.
Fixed an issue with the Chip Chooser when FTP access is not available.
Fixed an issue with the Leading Edge Tool when launched from Java Web Start JNLPs.