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UCSF RBVI Cytoscape Apps

News

August 25, 2011

Cytoscape 2.8.2 has been released! This release provides a number of bug fixes, usability improvements, and a significantly improved memory detection and allocation process. Check it out at http://www.cytoscape.org.

April 10, 2011

clusterMaker 1.9 has been released! This release includes several new algorithms: AutoSOME, Affinity Propagation, Connected Components, Community Clustering (GLay), MCODE, Spectral Clustering of Protein Sequences (SCPS), and Transitivity Clustering. In addition, clusterMaker now provides a full CyCommand interface, and the clusterMaker version of MCL has been parallelized to take advantage of multi-core machines.

February 18, 2011

Cytoscape 2.8.1 is released! This release provides several new features and bug fixes, including the ability to load plugins from a file, improved usability of the data panel, and a significant rewrite of the group handling mechanism in Cytoscape to allow groups to be network-specific.

December 20, 2010

Version 0.91 of the commandTool plugin, which provides a command-line interface to Cytoscape has been released. This version is compatible with Cytoscape 2.8. For more information, see the commandTool documentation

December 20, 2010

The nodeCharts plugin has been released. This plugin provides programmers with the ability to paint charts on nodes in Cytoscape from their plugins. nodeCharts has no user interface, but exports a number of CyCommands that can be called from other plugins. Details of the commands supported by nodeCharts are available in the nodeCharts documentation.

December 20, 2010

The bioCyc plugin has been released. This plugin provides an interface to pathway resources running version 14.5 or better of Pathway Tools. Documentation is available at the bioCycPlugin documentation page.

December 12, 2010

Cytoscape 2.8 has been released! Check it out at http://www.cytoscape.org.

March 18, 2010

Cytoscape 2.7 has been released! Check it out at http://www.cytoscape.org.

March 2, 2009

Cytoscape 2.6.2 has been released. This release primarily consists of bug fixes and should be fully compatible with all 2.6.x plugins. See the Release Notes for details.

You can get the release here

February 25, 2009

UCSF clusterMaker 1.6 has been released. This new version includes a significantly faster MCL implementation and several visualization enhancements.

You can see more detailed documentation of clusterMaker at http://www.cgl.ucsf.edu/cytoscape/cluster/clusterMaker.html

September 23, 2008

UCSF clusterMaker, a Cytoscape plugin for creating and visualizing clusters within Cytoscape networks has been released!

You can see more detailed documentation of clusterMaker at http://www.cgl.ucsf.edu/cytoscape/cluster/clusterMaker.html

September 19, 2008

Cytoscape 2.6.1 has been released. This release primarily consists of bug fixes and should be fully compatible with all 2.6.0 plugins.. There are no API changes, however we have added a new centralized logging facility. See *Help->Error Console* to see Cytoscape's startup messages and any warnings or errors that occur during operation.

You can get the release here


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