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Cytoscape was originally created at the
Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002, and v1.0 was released in
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While
Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage. Cytoscape can visualize and analyze network graphs of any kind involving nodes and edges (e.g., social networks). A vital aspect of the software architecture of Cytoscape is the use of
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March 2003. Version 1.1.1 is the last stable release for the 1.0 series. Version 2.0 was initially released in 2004; Cytoscape 2.83, the final 2.xx version, was released in May 2012. Version 3.0 was released Feb 1, 2013, and the latest version, 3.4.0, was released in May 2016.
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The
Cytoscape core developer team continues to work on this project and released Cytoscape 3.0 in 2013. This represented a major change in the Cytoscape architecture; it is a more modularized, expandable and maintainable version of the software.
186:. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open
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Yeast
Protein–protein/Protein–DNA interaction network visualized by Cytoscape. Node degree is mapped to node size
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plugins for specialized features. Plugins are developed by core developers and the greater user community.
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software architecture by anyone and plugin community development is encouraged. Cytoscape also has a
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that can be used to analyse and visualise graphs in JavaScript environments, like a browser.
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profiles and other state data. Additional features are available as
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Bell GW, Lewitter F (2006). "Visualizing
Networks".
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365:. Meth. Enzymol. Vol. 411. pp. 408–21.
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73:3.8.2 / 29 October 2020
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288:"Cytoscape 3.8.2 is released!"
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194:-centric sister project named
176:molecular interaction networks
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786:National Institutes of Health
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37:Institute for Systems Biology
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866:Graph analysis software
733:Electrospray ionization
605:Human Epigenome Project
980:Java platform software
970:Graph drawing software
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690:Human proteome project
493:Computational genomics
243:Computational genomics
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753:Isotope affinity tags
707:Expression proteomics
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178:and integrating with
75:; 3 years ago
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498:Comparative genomics
253:JavaScript framework
723:2-D electrophoresis
697:Call-map proteomics
555:Structural genomics
542:Population genomics
503:Functional genomics
25:Cytoscape home page
677:Structural biology
488:Cognitive genomics
330:10.1101/gr.1239303
258:JavaScript library
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32:Original author(s)
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211:Development
173:visualizing
163:open source
949:Categories
685:Proteomics
622:Lipidomics
617:Immunomics
318:Genome Res
274:References
192:JavaScript
148:.cytoscape
93:Written in
80:2020-10-29
881:Cytoscape
612:Glycomics
159:Cytoscape
58:July 2002
906:NetworkX
886:Graphviz
824:Category
550:genomics
474:Genomics
389:16939803
348:14597658
297:11 March
237:See also
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202:History
184:plugins
141:Website
130:License
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188:Java
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
