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Current Plugins


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.

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Upcoming Events

UCSF RBVI Cytoscape Plugins

The Resource for Biocomputing, Visualization, and Informatics ( RBVI has a specific focus on creating innovative computational and visualization-based data analysis methods and algorithms, implementing these as professional-quality easy-to-use software tools, and applying these tools for solving a wide range of genomic and molecular recognition problems within the complex sequence→structure→function triad Our historical emphasis has been on developing tools for the support of structural biology, such as the broadly used molecular modeling package, UCSF Chimera. Recognizing the importance of the biological context in understanding the sequence→structure→function triad, (see Visualization and Analysis of Biological Context), we have are now providing tools to assist in the analysis and visualization of biological context, with an emphasis on providing broader context for Chimera and the Structure-Function Linkage Database (SFLD). Our strategy for providing and visualizing biological context has been to utilize the network visualization tool, Cytoscape, which is a very widely used open-source tool. Cytoscape provides and excellent plugin mechanism that we have used to add functionality, and we also participate in the development of the Cytoscape core. This work is funded by the NIH National Center for Research Resources (grant P41-RR01081).

Plugin Highlights


Linking structural and network data

In this screenshot the PFAM family PTE (phosphotriesterase) has been opened in Cytoscape. Three of the available structures have been opened in UCSF Chimera and aligned using Chimera's structural alignment tools. The functional residues of one of the structures (pdb: 1EZ2) have also been selected (green highlights in Chimera).

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Clustering and Visualizing Expression Data

In this screenshot the expression data in the sampleData file galFiltered.cys has been clustered using the hierarchical clusterer and visualized using a heatmap with associated dendogram. The groups created by the cluster are shown on the network.

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