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Current Plugins
News
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
Upcoming Events
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
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).
(More plugins...)
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.
(More plugins...)