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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.

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UCSF RBVI Cytoscape Apps

The Resource for Biocomputing, Visualization, and Informatics (RBVI) focuses on creating innovative computational and visualization-based data analysis methods and algorithms, implementing them as professional-quality, easy-to-use software tools, and applying these tools to solve a wide range of biomedical research problems. Our historical emphasis has been on developing tools for structural biology, such as the broadly used molecular modeling package, UCSF Chimera.

Recognizing the importance of biological context in understanding the sequence→structure→function triad, we are also developing tools for the analysis and visualization of networks with Cytoscape, a widely used open-source tool. Cytoscape provides an excellent “app” mechanism that we have used to add functionality, and we also participate in the development of the Cytoscape core.

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clusterMaker

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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