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cyREST: RESTful API for Cytoscape

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

Important

cyREST is a Cytoscape Core app. You don't have to install this app separately. However, when the new version is available, you can upgrade it anytime from Cytoscape App Store.

Updates

• 7/11/2016: New setup guide is available
• 5/20/2016: Tutorial added (Using server/cloud/clusters to control Cytoscape)
• 6/18/2015: User documentation updated
• 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.

News Archive

Quick Introduction and Examples

With cyREST, you can:

• Obtain, create, update, and delete Cytoscape data objects from Jupyter Notebook
• Directly visualize network data stored as igraph object in R session
• Script your workflows in your favorite programming languages

Samples

High-res version

High-res version

Network visualization using statistics calculated from network structure. The entire workflow is available as an R script.

High-res version

Complete cyREST API v1 Documentation

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Table of Contents

Introduction

• What is cyREST?

Before you start...

• Setup Guide

Quick Start Guide

Tutorials

Complete cyREST API v1 Documentation

Roadmap

Code Snippet Collection

(TBD)

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Please Cite cyREST for project sustainability

(TBD)

Questions?

Please send us your questions and comments to our mailing list or direct to me (kono at ucsd edu).

License

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