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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: Read this section first!

cyREST is a built-in feature and you don't have to install it separately. However, when the new version of cyREST is available, you can upgrade it anytime from Cytoscape App Store.

cyREST Paper

Please cite this paper for project sustainability:

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

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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

Highlights

Language-Agnostic

• cyREST provides programmer-friendly simple RESTful API. This means you can use virtually all kinds of programming languages to access Cytoscape basic functions, such as loading networks, visualizing them with custom Visual Styles, and generating PDF/SVG/PNG files from your network views.
• Wrappers for popular languages - Python and R are two most-widely used programing languages for network data analysis and visualizations. We provides wrappers for those languages for more natural APIs for R and Python programmers.
  • RCy3 - cyREST wrapper for R users. It is a part of Bioconductor distribution and it replaces RCytoscape.
  • py2cytoscape - Wrapper for Python

Perfect partner for your existing workflows written in Jupyter Notebooks

• Instead of using limited network visualization features in Python/R libraries, you can use powerful network visualization engine in Cytoscape - without touching your mouse!

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

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Table of Contents

Introduction

• What is cyREST?
• Samples and descriptions at Cytoscape App Store

Before you start...

• Setup Guide (Updated on 7/11/2016)

Basic User Guide

• Quick Start Guide
• Tutorials

Advanced User Guide

• Building reproducible workflows with cyREST, Jupyter Notebook and Docker
• cyREST and Clouds
• Calling cyREST from your services (TBD)

References

• cyREST paper: CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
• cyREST API v1 Reference Documentation

Roadmap

• Roadmap (as of July 2016)

Code Snippet Collection

(TBD)

• R
• Python
• JavaScript

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Questions?

Please send us your feature suggestions, 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