Cytoscape is an open source platform for network analysis and visualization. It supports standard data formats and has flexible visualization capabilities through visual styles and layout algorithms. The Cytoscape ecosystem includes apps that expand its functionality and Cytoscape.js, a JavaScript library for graph visualization compatible with browsers.

1. Cytoscape
An Open Source Platform for Network Analysis and Visualization
Cytoscape is an open source platform for graph analysis and
visualization. It is the de-facto standard tool in life science field and
its core features are domain independent. Its ecosystem is open and
still expanding to support emerging technologies. It is free for both
academic and commercial use.
- Open Source (LGPL)
- Support for standard data file formats
- GraphML, SIF, XGMML, GML, CSV, etc.
- Flexible visualization with Visual Styles
- Large selection of graph layout algorithms
- Open for expansion: wide variety of Apps
Features The Cytoscape Consortium
www.cytoscape.org @cytoscape github.com/cytoscape

2. Cytoscape Ecosystem
Java desktop application for network
analysis and visualization. Can generate
web application friendly data files (JSON).
Expandable by Apps.
Cytoscape
JavaScript library for graph data visualization.
Compatible with browsers and node.js.
Cytoscape.js
Central repository of all applications build on top of
Cytoscape.
Cytoscape App Store
Funding for continued development and maintenance of Cytoscape is provided by the U.S. National Institute of General Medical Sciences (NIGMS) under
award number GM070743. Cytoscape user support, education and new initiatives are supported by the National Resource for Network Biology (NRNB)
under award numbers P41 RR031228 and GM103504.
Cytoscape App Store
Data Bus (Internet)
Raw Data Files
Annotations
Experimental Data
Networks
Internal Databases Web Applications using Cytoscape.js
Web Browsers
Public Data Services
NDEx
Other Web Services
PSICQUIC
Services
External Computing Resources
For Graph Layout / Statistical Analysis / Data Preprocessing
Interactive Analysis Shells
RStudio
NumPy
SciPy
NetworkXIPython Notebook
File Hosting Services
Cytoscape Desktop
RESTful API Module for
Cytoscape
Cytoscape Apps
For Data Sharing / Visualization