Network Data Integration, Analysis, and Visualization in a BoxCytoscape 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 network analysis, andsemantic web.Download CytoscapeWelcome LetterRelease NotesSample VisualizationsLearning CytoscapeIntroduction to CytoscapeTutorial for 3.xTutorial for 2.xDevelopers TutorialNRNB and CytoscapeIntroduction to the National Resource for Network BiologyHow to Cite CytoscapeCytoscape project needs your support!Please cite either of the following papers when you use Cytoscape in your publications, which is very importantto sustain our federal funding.Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T.A travel guide to Cytoscape pluginsNature Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6.[PubMed entry]Michael Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey IdekerCytoscape 2.8: new features for data integration and network visualizationBioinformatics. 2011 February 1; 27(3): 431–432.Published online 2010 December 12.[PubMedentry]Melissa S Cline, Michael Smoot, Ethan Cerami,Allan Kuchinsky, et al.Integration of biological networks and gene expression data using CytoscapeNature Protocols 2, 2366 - 2382 (2007) Published online: 27 September2007 | doi:10.1038/nprot.2007.324[PubMedentry]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 networks.Genome Research 2003 Nov; 13(11):2498-504[Abstract] [PDF] [PubMed entry]What Can You Do With Cytoscape?BiologyCytoscape supports many use cases in molecular and systems biology, genomics, and proteomics:Load molecular and genetic interaction data setsin many standards formatsProject and integrate global datasets and functional annotationsEstablish 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
Semantic Web
Cytoscape is also a tool of choice for the semantic web community, since the semantic web is encoded and
viewed as a network of knowledge and resources.
Load and visualize Resource Description Framework (RDF)
data as networks
Import data from Triplestore thro