We are excited to announce a major new release of ErmineJ. There are a number of new features, and overall the software is improved and easier to use. Some highlights:

• Introduction of diagnostics and corrections for “gene multifunctionality”. See the documentation for details.
• Introduction of a new gene set scoring method based on precision-recall. See the documentation for details.
• Numerous user interface improvements have been made including filtering of displays and better error handling.
• Support is much improved for non-GO gene annotation schemes such as MolSigDB or KEGG, and the use of ‘hit lists’ as input is simplified.
• Improved Mac OSX support.
• Much of the code has been rewritten and many minor and major bugs have been fixed. Note that while the existing core algorithms of ErmineJ have not been changed, changes to the way gene annotations are handled may cause differences in results.

We believe this upgrade will increase the future maintainability of the software and sets the stage for the introduction of new features. We look forward to your feedback.

For a more complete change list see the version history