jpahle / Biosimulations_COPASI

COPASI Simulator for BioSimulations

Biosimulations_COPASI

BioSimulations-compliant command-line interface to the COPASI simulation program.

Contents

• Installation
• Usage
• License
• Development team
• Questions and comments

Installation

Install Python package

pip install git+https://github.com/reproducible-biomedical-modeling/Biosimulations_COPASI

Install Docker image

docker pull crbm/biosimulations_copasi

Local usage

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

BioSimulations-compliant command-line interface to the COPASI simulation program <http://copasi.org>.

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

docker run \
  --tty \
  --rm \
  --mount type=bind,source="$(pwd)"/tests/fixtures,target=/root/in,readonly \
  --mount type=bind,source="$(pwd)"/tests/results,target=/root/out \
  crbm/biosimulations_copasi:latest \
    -i /root/in/BIOMD0000000297.omex \
    -o /root/out

License

This package is released under the MIT license.

Development team

This package was developed by the Center for Reproducible Biomedical Modeling.

Questions and comments

Please contact the Center for Reproducible Biomedical Modeling with any questions or comments.