The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g.
For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families. Clusters mean different things in different types of networks. MCODE is a Cytoscape plugin that finds clusters (highly interconnected regions) in a network. Released by: Ferro, Giugno, Pulvirenti group, University of Catania, Bader group, University of Toronto and Shasha group, New York University.Īvailable from the Bader Lab mirror of the NetMatch homepage Node and edge attributes of any type and paths of unknown length can be specified in the search. NetMatch is a Cytoscape plugin that finds user defined network motifs in any Cytoscape network.
#CYTOSCAPE PATHWAY SOFTWARE#
Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.Ĭytoscape was originally developed at the Institute of Systems Biology and is now a collaborative effort involving many different academic and commercial groups.įun link: Controlling Cytoscape using the Nintendo Wiimote Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. Additional features are available as plugins. cPath: Pathway Commons data integration and web servicesīiological Network Analysis and Visualization SoftwareĬytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.Biological Pathway and Network Database Software.Biological Network Analysis and Visualization Software.
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