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cyREST: a language-agnostic RESTful API for Cytoscape

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In One Sentence

An application to control Cytoscape from RStudio, IPython Notebook, Node.js or other programming languages.

More Details

This is a Cytoscape App to provide low-level API access to Cytoscape data objects, including networks, data tables, and Visual Styles, for programming languages such as R, Python, JavaScript, and MATLAB via RESTful API. You can write your own Cytoscape workflows with programming languages of your choice.

This app is still in beta status and we need your feedback!

System Requirements

To use cyREST 0.9.16 and newer, you need the following:

  • Java 8
    • Oracle JDK is recommended, but should be compatible with OpenJDK.
    • Does not work with Java 7 and older!!
  • Cytoscape 3.2.1+


All documents, including tutorials and full API list, are available from our Wiki.

Problems or Feature Requests?

The API Version 1 is not finalized yet. Please send your feature requests to our mailing list.

Please report the problems to our issue tracker:

And of course, pull requests are always welcome!


Cite cyREST


© 2014-2015 Cytoscape Consortium. Developed and maintained by Keiichiro Ono, UCSD Trey Ideker Lab.