is an open-source software Bioinformatics software platform for visualization (graphic) metabolic network modelling and integrating with gene expression profiles and other state data.
Here are some selected projects that are compatible with cytoscape: - Dagre layout engine - cola.js graph constraint engine - Vega agraph visualization grammar - Cytoscape.js
# Documentation
- Basic data visualisation slide show - cytoscape.org 
- Presentations - cytoscape.org
- Manual - cytoscape.org
- Documentation on cytoscape.org
- Animation Apps - cytoscape.org
- Cytoscape channel on youtube
# Plugins
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 (programming language) software architecture by anyone and plugin community development is encouraged. Cytoscape also has a JavaScript-centric sister project named Cytoscape.js that can be used to analyse and visualise graphs in JavaScript environments, like a browser - wikipedia
Cytoscape. open source software platform for visualizing molecular interaction networks and biological pathways
- wikimedia.org
# Usage
While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage. Cytoscape can be used to visualize and analyze network graphs of any kind involving nodes and edges (e.g., social networks). A key 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 - wikipedia
Yeast Protein–protein/Protein–DNA interaction network visualized by Cytoscape. Node degree is mapped to node size
- wikimedia.org
# Sections
# See also