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

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

NDExOther Web Services

PSICQUIC Services

External Computing Resources

For Graph Layout / Statistical Analysis / Data Preprocessing

Interactive Analysis Shells

RStudio

NumPySciPy

NetworkXIPython Notebook

File Hosting Services

Cytoscape Desktop

RESTful API Module for Cytoscape

Cytoscape Apps

For Data Sharing / Visualization