Cytoscape 2.x Plugins Release Note

Plugin Name: GeneMANIA

Version: 2.3

Release Note:

We are pleased to announce the release of version 2.3 of the GeneMANIA
Cytoscape plugin and command line tools for really fast gene function predictions. Extend and analyze your gene lists using our database of over 400 million interactions spanning 1,300 networks. You can also perform predictions on your own data by importing networks and expression profiles.

This release includes numerous bug fixes and a handful of new features. We are also using a better linear system solver in the GeneMANIA algorithm so results may differ slightly compared to previous releases. You can install this new release through Cytoscape's plugin manager. Read below for
more details.

New Features - Cytoscape:
* Support for importing custom organisms into a GeneMANIA data set.
* Ability to create groups when importing networks.

New Features - Command Line:
* ValidationSetMaker: No longer requires a data set.
* IdImporter: No longer requires a data set. It will create one automatically as necessary.
* CrossValidator: Added option to write classifier label vector to disk.

Bug Fixes:
* Fixed an issue where CrossValidator and NetworkAssessor would intermittently hang when run with multiple threads.
* Fixed session loading issues involving genes/organisms with non-ASCII characters in their name.
* Fixed autocompletion entry issues in Ubuntu 11.10

Documentation for the command line tools can be found here:

http://pages.genemania.org/tools/

Compatibility:

This release works with Cytoscape 2.6.3+, 2.7, and 2.8. Sessions
created by version 1.0 of the GeneMANIA plugin cannot be loaded fully
by 2.3.