Cytoscape 2.x Plugins Release Note

Plugin Name: GeneMANIA

Version: 2.2

Release Note:

We are pleased to announce the release version 2.2 of the GeneMANIA Cytoscape plugin and command line tools. This release includes numerous bug fixes and a handful of new features. Read below for more details.

New Features:
* The plugin now provides access to three different types of data sets:
* "-core": Only contains the default selected networks.
* "-open_license": Only contains networks with a non-restrictive license.
* Data sets with no suffix are the same as before.
* It's now possible to distinguish between different networks in the command line tools by also providing their network type; e.g. "gi|BIOGRID" and "pi|BIOGRID".
* Node attributes now contain functional enrichment descriptions.
* Both JSON and text formats are now supported when importing search parameters.

Bug Fixes:

General:
* Fix a bug in user-created data sets where descriptions for a gene from a different organism are displayed instead of the proper description.

QueryRunner:
* "flat" and "xml" reports no longer scale gene scores by 100.
* "xml" report is no longer missing closing tags.

CrossValidator:
* CrossValidator no longer terminates early if it runs into as many errors as number of threads.
* Queries where some nodes are neither labeled positive or negative are now properly handled.

NetworkAssessor:
* NetworkAssessor no longer crashes for queries where the MANIA algorithm does not converge.

NetworkImporter:
* Imported networks are no longer marked as "default selected".

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 2.1.