Guide for Python Users

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This page is here for legacy information. For more recent info on accessing Cytoscape through Python, please refer to the py2cytoscape library as well as the Sample Python Scripts in the Cytoscape Automation repository.

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Introduction

Python is one of the most popular programming languages, especially in scientific computing and data analysis community. By using Python with cyREST, you can access both of powerful Cytoscape visualization features and Python's wide variety of data analysis libraries, including pandas, numpy, and scipy.

py2cytoscape

New API wrapper for Python users is now available:

• py2cytoscape

Instead of calling raw cyREST API, you can use this wrapper to reduce huge amount of boilerplate code to work with cyREST. Unless you have good reason to use raw REST API, we recommend to use this wrapper if you are a Python user.

Python Examples as Jupyter Notebook

IPython Notebook, recently re-branded to Jupyter Notebook, is a great tool for data exploration. All of our Python examples are available as IPython Notebook files. They are available in this GitHub repository:

• https://github.com/idekerlab/cy-rest-python

Please visit the link above for the complete guide for Python users.