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Python implementation of the graph visualization tool Cytoscape.

Project description


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Python implementation of the graph visualization tool Cytoscape.

Try it out using binder: Binder

cytoscape screencast


  • Conversion from NetworkX see example
  • Conversion from Pandas DataFrame see example


With conda: (recommended)

conda install -c conda-forge ipycytoscape

With pip:

pip install ipycytoscape

For jupyterlab users:

There is an aditional step if you're using JupyterLab:

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-cytoscape

If you are using Jupyter Notebook 5.2 or earlier, you may also need to enable the nbextension:

jupyter nbextension enable --py [--sys-prefix|--user|--system] ipycytoscape

For a development installation:

(requires npm)

git clone
cd ipycytoscape

It's recommended to create a conda environment:

conda create -n ipycytoscape -c conda-forge jupyterlab nodejs
conda activate ipycytoscape

Install and enable extension for jupyter notebook and jupyter lab:

python -m pip install -e .
npm install && npm run build
jupyter nbextension install --py --symlink --sys-prefix ipycytoscape
jupyter nbextension enable ipycytoscape --py --sys-prefix
jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-cytoscape
jupyter labextension install js


We use a shared copyright model that enables all contributors to maintain the copyright on their contributions.

This software is licensed under the BSD-3-Clause license. See the LICENSE file for details.

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