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Keiichiro Ono edited this page Jun 18, 2015 · 84 revisions

cyREST: a RESTful API Module for Cytoscape

Build your own Cytoscape workflows with R, Python, and all other popular tools

Updates

6/14/2015: 0.9.17 released. Layout attributes and local table columns are supported.
6/9/2015: 0.9.16 released. Now Layout parameters are accessible through API.
6/5/2015: Python wrapper (py2cytoscape) released.
12/11/2014: 0.9.7 released. cyREST opens access from external tools, i.e., accepts connection other than localhost.
11/9/2014: 0.9.6 released. TSV support for table GET method.
10/14/2014: 0.9.3 released. This version has new Session API.

Quick Introduction

With cyREST, you can:

Access Cytoscape data objects from IPython/Jupyter Notebook
Directly visualize network data stored as igraph object in R session
Script your workflow in your favorite programming languages

R+Cytoscape High-res version

High-res version

Table of Contents

Introduction: What is cyREST?

Installation

Quick Start Guide

User Guide for Popular Programming Languages

Python
R
JavaScript (Node.js)
(More coming soon...)

Complete REST API Documentation V1

Roadmap

Questions?

Please send us your questions and comments to our mailing list.

License

Source Code: The MIT license
Documentation: CC BY-SA 4.0

© 2014-2015 The Cytoscape Consortium

Developed and Maintained by Keiichiro Ono (UC, San Diego Trey Ideker Lab)