cytoscape.org
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CytoscapeNetwork Data Integration, Analysis, and Visualization in a BoxIntroductionDownloadCytoscape is an open source software platformfor visualizing complex networks and integrating these with any type ofattribute data. A lot of Appsare available for various kinds of problem domains, including bioinformatics, social networkanalysis, and semantic web. Learn more...Welcome LetterRelease NotesSample Visualizations3.x TutorialDevelopers TutorialNRNB and CytoscapeIntroduction to the National Resource for Network BiologyHow to Cite CytoscapeCytoscape project needs your support!Please cite the original Cytoscape paper when you use Cytoscape. This is critical to sustaining our federal funding.Shannon P, Markiel A, Ozier O, Baliga NS, WangJT, Ramage D, Amin N, Schwikowski B, Ideker T.Cytoscape: a software environment for integrated models ofbiomolecular interaction networksGenome Research 2003 Nov; 13(11):2498-504[Abstract] [PDF] [PubMed entry]Other articles and papers about Cytoscape are available here.Tweets by@cytoscape What Can You Do With Cytoscape? Biology Cytoscape supports many use cases in molecular and systems biology, genomics, and proteomics: Load molecular and genetic interaction data sets in many standards formats Project and integrate global datasets and functional annotations Establish powerful visual mappings across these data Perform advanced analysis and modeling using Cytoscape Apps Visualize and analyze human-curated pathway datasets such as WikiPathways, Reactome, and KEGG. Social Science Cytoscape is used by social scientists to: Visualize and analyze large social networks of interpersonal relationships Assemble social networks from tables and forms Gather social interactions from the web by variety of web service APIs with scripting languages and save it in standard data file formats. Cytoscape supports most of the standard file formats . Calculate network statistics using Apps Use with other tools, such as R with sna/ igraph package or NetworkX, for more advanced analysis General Complex Network Analysis Cytoscape is domain-independent and therefore is a powerful tool for complex network analysis in general. Calculate statistics for networks by Apps such as NetworkAnalyzer or CentiScaPe Find shortest path Find clusters by various kinds of algorithms Use with other tools for more advanced analysis Perform advanced network analysis in popular tools, including igraph, Pajek, or GraphViz and import it to Cytoscape as standard file formats like GraphML App Development Cytoscape is expandable and extensible. Cytoscape has a vibrant App developer community and over a hundred Apps developed by third parties. Source code is available on GitHub Running on OSGi framework Develop simple and complex Apps in Java Clean, Rich Cytoscape Application Programming Interface (API) Active developer community Write simple functions with scripting languages, including Ruby, Python, Groovy, and JavaScript Featured Publications Let us know if you've pub
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