Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data.

[2][3] 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.

This represented a major change in the Cytoscape architecture; it is a more modularized, expandable and maintainable version of the software.

[4] While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage.

A vital aspect of the software architecture of Cytoscape is the use of plugins for specialized features.