Cytoscape is an

open source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

software platform A computing platform, digital platform, or software platform is the infrastructure on which software is executed. While the individual components of a computing platform may be obfuscated under layers of abstraction, the ''summation of the requi ...

for visualizing molecular interaction networks and integrating with

gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...

profiles and other state data. Additional features are available as plugins. 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

Java Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...

software architecture by anyone and plugin community development is encouraged. Cytoscape also has a

JavaScript JavaScript (), often abbreviated as JS, is a programming language and core technology of the World Wide Web, alongside HTML and CSS. Ninety-nine percent of websites use JavaScript on the client side for webpage behavior. Web browsers have ...

-centric sister project name
Cytoscape.js
that can be used to analyse and visualise graphs in JavaScript environments, like a browser.

History

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 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.

Development

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.
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Usage

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 plugins for specialized features. Plugins are developed by core developers and the greater user community.

References

External links

* ** https://cytoscape.org/screenshots.html
Cytoscape wiki

Cytoscape omictools webpage
{{Graph Analysis Software Bioinformatics software Systems biology Mathematical and theoretical biology Graph drawing software Cross-platform software Java platform software

History

Development

Usage

See also

References

External links