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Current Apps (3.x)

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.

App Highlights

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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clusterMaker

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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