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.

sudo pip install -U colomoto-docker   # only once; you may have to use pip3
colomoto-docker

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

By default, the script will fetch the most recent colomoto/colomoto-docker tag. A specific tag can be specified using the -V option; or use -V same to use the most recently fetched image. For example:

colomoto-docker -V 2018-05-29
colomoto-docker -V same         # use the most recently downloaded 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. To have access to the files of your current directory you should use the --bind option:

colomoto-docker --bind .

See

colomoto-docker --help

for other options.

Having issues? have a look at our Troubleshooting page, or open an issue.

Available software tools with Python API

Tutorials and use cases

Short tutorials for individual tools
Executable paper showing combination of GINsim, bioLQM, MaBoSS, and Pint (doi:10.3389/fphys.2018.00787)

From the above links, you can download the notebook .ipynb files to upload and re-execute them in your running CoLoMoTo Jupyter web interface.

Extending the CoLoMoTo Docker

You can easily extend the CoLoMoTo Docker image to integrate your own tool and distribute it as its own Docker image, using a Dockerfile skeleton like this:

FROM colomoto/colomoto-docker:next

USER root
RUN <insert installation instructions>

USER user

You may want to replace next with any other suitable colomoto/colomoto-docker tag. You should also consider using a persistent tagging policy.

The Dockerfile can be built using the command

docker build -t your-docker-image:your-tag .

The script colomoto-docker can then be used to run your own Docker image:

colomoto-docker --image your-docker-image -V your-tag

Contribute

Contributions are very welcome, being for adding new software or improving the user experience.

Consider opening an issue on GitHub and reading the CONTRIBUTING guidelines.

Citation

Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Frontiers in Physiology 9:680, 2018. | doi: 10.3389/fphys.2018.00680

Contact

Questions? Bugs? Requests? Open an issue on GitHub.

You can also reach us at colomoto.org.

The CoLoMoTo Consortium – Consortium for Logical Models and Tools