jupyter-cytoscape

cytoscape.js in a Jupyter notebook widget

Quick start

If you're familiar with Docker, the following commands should work in most cases:

docker pull cytoscape/jupyter-cytoscape
docker run -d -p 8888:8888 cytoscape/jupyter-cytoscape start-notebook.sh --NotebookApp.token=''

and open a web browser to http://localhost:8888/notebooks/examples/smallNetwork/smallNetwork.ipynb.

Our Docker image is based on Base Jupyter Notebook Stack. See https://github.com/jupyter/docker-stacks/tree/master/base-notebook for more details on the Docker command options.

Installation

This is an early alpha release, best suited to developers. To install:

• install anaconda (or update if it is already installed: conda update anaconda)
• install npm and webpack
• cd to your local github repo root directory
• git clone https://github.com/cytoscape/jupyter-cytoscape.git
• cd jupyter-cytoscape
• make

A stand-alone version, useful for quick developer experiments, and not packaged up into a jupyter nbextension, is found in ./standalone/devel/