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Language-agnostic RESTful API for Cytoscape

Build Status Coverage Status


We need your support to make this project sustainable. Please cite the following paper when you use cyREST in your projects:

Ono, Keiichiro, et al. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Research 4 (2015).


Important: Now cyREST is a Core App

From Cytoscape 3.3.0, cyREST is a Core App:

  • You don't have to install cyREST manually. It is a part of core distribution
  • Although it is part of core distribution, you will get updates after 3.3.0 release

What is cyREST?

An app to control Cytoscape from RStudio, Jupyter Notebook, Node.js or other programming languages.

System Requirements


  • CyREST API docs are available within Cytoscape main menu through the Help → Automation sub-menu.
  • cyREST Wiki

For Developers and Maintainers

Build instructions and notes are included in the Developers Guide

Problems or Feature Requests?

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!


© 2014-2016 Cytoscape Consortium.

Developed and maintained by Keiichiro Ono, UCSD Trey Ideker Lab.

Note to repository maintainers: Please *DO NOT* move this page ... the Cytoscape Automation paper refers directly to it.