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.(Previous news...)
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).
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...)