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Source : http://www.cytoscape.org
Activity:
4 comments
311 views
last activity : 07 06 2010 20:18:04 +0000
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Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration and visualization. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. Plugins may be developed by anyone using the Cytoscape open API based on Java™ technology and plugin community development is encouraged. Most of the plugins are freely available.
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Mr. Rajendra a very nice article on Cytoscape. let me add on something to what you said: FEATURES * Load and save previously-constructed interaction networks in GML format (Graph Modelling Language). * Load and save networks and node/edge attributes in an XML document format called XGMML (eXtensible Graph Markup and Modeling Language). * Input mRNA expression profiles from tab- or space-delimited text files. * Load and save arbitrary attributes on nodes and edges. For example, input a set of custom annotation terms for your proteins, create a set of confidence values for your protein-protein interactions. * Import gene functional annotations from the Gene Ontology (GO) and KEGG databases. * Directly import GO Terms and annotations from OBO and Gene Association files. * Load and save state of the Cytoscape session in a Cytoscape Session (.cys) file. * Customize network data display using powerful visual styles. * View a superposition of gene expression ratios and p-values on the network. * Layout networks in two dimensions. A variety of layout algorithms are available, including cyclic and spring-embedded layouts. * Zoom in/out and pan for browsing the network.