The CoLoMoTo Docker and Notebook

The CoLoMoTo Docker and Notebook#

PyPI version Binder DOI:10.3389/fphys.2018.00680 DOI:10.5281/zenodo.17035228

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
colomto-docker --doi 10.5281/zenodo.17035229   # fetches image from Zenodo record

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.

Docker images are persistently archived on Zenodo at https://doi.org/10.5281/zenodo.17035228.

Contribute#

See how to add your tool.

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