Welcome to cyREST Examples for Python Users!

What is Cytoscape?

Cytoscape is an open source software platform for visualizing complex networks and integrating them with any type of attributes. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

Introduction to cyREST

cyREST is a Cytoscape App providing access to Cytoscape core data objects including networks, tables, and Styles via RESTful API, which is totally platform/language independent. This means you can write your own workflows using Cytoscape in programming language of your choice.

Target Audience

  • Computational Biologists
  • Data Scientists
  • And all people who use graph data!

We assume you have basic knowlege of Cytoscape and Python. Some of the examples require third party libraries, and you need to know how to setup your own Python environment to satisfy the dependencies.

Docker Containers for Python Examples

We have a Docker container with standard libraries for network analysis:

And of course, you can use your own environment if you want.

Table of Contents

Warning: you need Cytoscape 3.2.1 and cyREST 0.9.17 and newer to run these examples


New! Examples Using py2cytoscape

Although cyREST provides a set of language-agnostic API, it requires some boilarplate code to access raw REST API. To avoid lots of duplicate code, we've released py2cytoscape, a Python wrapper for cyREST. If you use cyREST with py2cytoscape, you can signisicantly reduce lines of code in your workflow. Please visit the link below to see how natural the API is for Python users.


Examples Using Raw cyREST API


Note: You need to run IPython Notebook server to view the actual results. GitHub may not render notebooks linked from the following list.


Basic Exercises

cyREST Cookbook

Advanced Exercises

More Information

Workshop Materials

For R Users

R example scripts are available here.


Be sure to follow us on Twitter @cytoscape! When you tweet about your Cytoscape workflows, please use #cytoscape tag.

Contact

For questions, please join the cytoscape-discuss mailing list

Or directly to me (kono at ucsd dot edu)