Cytoscape 2.x Plugins Release Note

Plugin Name: GeneMANIA

Version: 3.2

Release Note:

We are pleased to announce the release of version 3.2 of the GeneMANIA Cytoscape plugin and command line tools for really fast gene function prediction. Extend and analyze your gene lists using our database of over 292 million interactions spanning 1,400 networks. You can also perform predictions on your own data by importing networks and expression profiles.

This release fixes a critical bug with importing networks and adds a number of new features to the command line tools:

- QueryRunner now supports exporting the entire combined network for a query
- CrossValidator and NetworkAssessor now support attribute-based networks
- Command line tools now support a simplified launch syntax

Simplified Launch Syntax for Command Line Tools:

In older versions of the command line tools, you'd use the following syntax:

java -cp GeneMania.jar org.genemania.plugin.apps.AppName [options]

Now you can use the following:

java -jar GeneMania.jar AppName [options]

Cytoscape 2.X users can install the new version through the plugin manager. Cytoscape 3.0 users can use the app manager or the App Store website[1] to install GeneMANIA.

Documentation for the command line tools can be found here[2].


This release works with Cytoscape 2.6.3+, 2.7, 2.8+ and 3.0 beta. Sessions created by version 1.0 of the GeneMANIA plugin cannot be loaded fully by 3.0.