README.md

Biosimulators_mpbn

BioSimulators-compliant command-line interface to the mpbn Most Permissive Boolean networks analysis program.

Installation

Install Python package

pip install <repository>

Install Docker image

docker pull <registry>/<organization>/<repository>

Usage

Local usage

usage: biosimulators-mpbn [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the <mpbn> program <https://mpbn.readthedocs.io>.

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i ARCHIVE, --archive ARCHIVE
                        Path to OMEX file which contains one or more SED-ML-
                        encoded simulation experiments
  -o OUT_DIR, --out-dir OUT_DIR
                        Directory to save outputs
  -v, --version         show program's version number and exit

Usage through Docker container

The entrypoint to the Docker image supports the same command-line interface described above.

For example, the following command could be used to use the Docker image to execute the COMBINE/OMEX archive ./modeling-study.omex and save its outputs to ./.

docker run \
  --tty \
  --rm \
  --mount type=bind,source="$(pwd)",target=/root/in,readonly \
  --mount type=bind,source="$(pwd)",target=/root/out \
  <registry>/<organization>/<repository>:latest \
    -i /root/in/modeling-study.omex \
    -o /root/out

Documentation

Documentation is available at .

License

This package is released under the MIT license.

Development team

This package was developed by Loïc Paulevé with assistance from the contributors listed here.

Contributing to Biosimulators_mpbn

We enthusiastically welcome contributions to Biosimulators_mpbn! Please see the guide to contributing and the developer's code of conduct.

Questions and comments

Please open an issue or contact Loïc Paulevé with any questions or comments.