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colomoto / colomoto-docker

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
https://colomoto.github.io/colomoto-docker/
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biological-networks docker jupyter-notebook model-analysis systems-biology

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The CoLoMoTo Docker and Notebook

PyPI version Binder Gitter DOI:10.3389/fphys.2018.00680

The CoLoMoTo Interactive Notebook relies on Docker and Jupyter technologies to provide a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks.

Quick usage guide

You need Docker and Python. We support GNU/Linux, macOS, and Windows.

Install the helper script in a terminal:

pip install -U colomoto-docker    # or python3 -m pip install ..

The CoLoMoTo notebook can be started by executing in a terminal (if using Docker Toolbox, in a Docker Terminal):

colomoto-docker

The container can be stopped by pressing Ctrl+C keys.

A specific tag can be specified using the -V option. For example:

colomoto-docker -V latest       # fetches the latest published image
colomoto-docker -V 2024-04-01   # fetches a specific image

Warning: by default, the files within the Docker container are isolated from the running host computer, therefore files are deleted after stopping the container, except the files within the persistent directory.

To have access to the files of your current directory you can use the --bind option:

colomoto-docker --bind .

See usage guide for further options and alternative methods.

Contribute

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