You may be interested in Cytoscape.js, a newer HTML5-based JavaScript library with an updated API and new features.

Background

Cytoscape Web was initially developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary Bader and Quaid Morris. Cytoscape Web development was originally funded by Genome Canada, through the Ontario Genomics Institute (2007-OGI-TD-05). It is now actively developed as part of the Cytoscape project which is funded by grants from the U.S. National Institutes of Health (NIH), under award number GM070743-01 (U.S. National Institute of General Medical Sciences (NIGMS)) and number RR031228 (NIH National Center for Research Resources (NCRR) Biomedical Technology Research Center (BTRC)).

The i-Vis Information Visualization Research Group of Bilkent University implemented the compound graph feature, including the Compound Spring Embedder layout algorithm.

Cytoscape Web was created as a result of the need for a visualization interface for the GeneMANIA project at the University of Toronto. The idea was to create a simple version of Cytoscape for the Web, not as a complete user application, but as an independent component that could be reused by other developers. Despite using different technologies (Flex and JavaScript) compared to Cytoscape, Cytoscape Web follows most of the Cytoscape concepts (e.g. node shapes, visual mappings, XGMML support). We chose Flex/Flash because were not able to find any other solutions to the problem of visualizing interactive networks on the web that fit our requirements.

Cytoscape Web is open-source software released under LGPL 2.1 license.

If you use Cytoscape Web, please link us back.

Client applications

Cytoscape Web is currently being used by a gene function prediction server, GeneMANIA. The data provided to Cytoscape Web in GeneMANIA is unique to every user query, and easily modified with each new query. The rendering speed of Cytoscape Web allows for dynamic user interaction.

iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.

Pathguide is a meta-database that provides an overview of more than 300 web-accessible biological pathway and network databases. It uses Cytoscape Web to display networks that illustrate the interactions among different resources.

Many more...

Linking back to Cytoscape Web

We appreciate people linking back to us, because that helps us keep Cytoscape Web development funded.

Feel free to link to us however you choose or use one of the examples below:

Cytoscape Web

<a href="http://cytoscapeweb.cytoscape.org/">
    <img src="http://cytoscapeweb.cytoscape.org/img/logos/cw_s.png" alt="Cytoscape Web"/>
</a>

Cytoscape Web

<a href="http://cytoscapeweb.cytoscape.org/">
    <img src="http://cytoscapeweb.cytoscape.org/img/logos/cw.png" alt="Cytoscape Web"/>
</a>

Publication

Cytoscape Web has been published in Bioinfomatics.

Developers

Cytoscape Web is maintained by Christian Lopes and Max Franz, from the Donnelly Centre for Cellular and Biomolecular Research.

Selcuk Onur Sumer and Ugur Dogrusoz, from the i-Vis Information Visualization Research Group of Bilkent University, were responsible for the compound graph support.

Credits

Cytoscape Web uses a number of libraries, and we would like to thank the creators and contributors of those projects for their contributions to open source software. Cytoscape Web uses: