You need Docker. We support GNU/Linux, macOS, and Windows.
You need Python.
The script can be installed and upgraded by executing the following command
(you may have to use pip3 instead of pip depending on your configuration):
pip install -U colomoto-docker
The CoLoMoTo notebook can then 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.
By default, the script will fetch the most recent colomoto/colomoto-docker tag. A specific tag can be specified using the -V option. For example:
colomoto-docker -V 2018-05-29
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.
First fetch the image with
docker pull colomoto/colomoto-docker:TAG
where TAG is the version of the image, among colomoto/colomoto-docker tags.
The image can be ran using
docker run -it --rm -p 8888:8888 colomoto/colomoto-docker:TAG
then, open your browser and go to http://localhost:8888 for the Jupyter notebook web interface
(note: when using Docker Toolbox, replace localhost with the result of
docker-machine ip default command).
Besides the Jupyter notebook, the docker image provides access to the following softwares:
| Software tool | Homepage | Description | Jupyter interface |
|---|---|---|---|
| bioLQM | http://colomoto.org/biolqm/ | Logical Qualitative Modelling toolkit | Python module biolqm |
| CellCollective | https://cellcollective.org | Model repository and knowledge base | Python module cellcollective |
| GINsim | http://ginsim.org | Boolean and multi-valued network modelling | Python module ginsim |
| MaBoSS | http://maboss.curie.fr | Markovian Boolean Stochastic Simulator | Python module maboss |
| NuSMV | http://nusmv.fbk.eu | Symbolic model-checker | Python module nusmv |
| Pint | https://loicpauleve.name/pint | Static analyzer for dynamics of Automata Networks | Python module pypint |
| R-BoolNet | https://cran.r-project.org/package=BoolNet | Analysis and reconstruction of Boolean networks dynamics | RPY2 python interface |
Docker images are timestamped with tags of the form YYYY-MM-DD after each tool addition or upgrade.
In order to guarantee the re-executability of your notebook, we recommend to use these tagged images instead of the non-persistent next tag.
See CONTRIBUTING.md.