Quick Start

The quickest way to see py4cytoscape in action is via the Overview of py4cytoscape Jupyter-based workflow.

You can avoid installing Python or py4cytoscape by clicking on the Open in Colab button, and running the Python workflow in the Google Cloud, though you will still have to install Cytoscape on your workstation.

You can follow the notes in the Jupyter Notebook as the workflow automates Cytoscape execution.

General Tutorials

A broad set of Cytoscape Automation Jupyter notebooks are available on the Cytoscape Automation for Python scripters.

We recommend you to try the Overview-of-py4cytoscape.ipynb first.

You have two options to try the notebooks.

  1. is (LOCAL Cytoscape + LOCAL Jupyter environment).

  2. is (LOCAL Cytoscape + REMOTE Jupyter environment [for example Google Colab]).

If you want to try the latter, click on the “Open in Colab” badge at the top of each notebook (ipynb file).