Install Python package

pip install biosimulators-cobrapy

Install Docker image

docker pull ghcr.io/biosimulators/cobrapy

SED-ML targets for simulation predictions

BioSimulators-COBRApy recognizes the following targets for simulation predictions:

• FBA (KISAO_0000437), parsimonious FBA (KISAO_0000528), geometric FBA (KISAO_0000527):

  • Objective: fbc:objective/@value

  • Reaction flux: sbml:reaction/@flux

  • Reaction reduced cost: sbml:reaction/@reducedCost

  • Species shadow price: sbml:species/@shadowPrice

• FVA (KISAO_0000526):

  • Minimum reaction flux: sbml:reaction/@minFlux

  • Maximum reaction flux: sbml:reaction/@maxFlux

Please see https://docs.biosimulations.org for more information.

Local usage

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

BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.

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 \
  ghcr.io/biosimulators/cobrapy:latest \
    -i /root/in/modeling-study.omex \
    -o /root/out