Tutorial¶

BioSimulators-COBRApy is available as a command-line program and as a command-line program encapsulated into a Docker image.

Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML¶

Information about how to create COMBINE/OMEX archives which can be executed by BioSimulators-COBRApy is available here.

A list of the algorithms and algorithm parameters supported by COBRApy is available at BioSimulators.

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.

Command-line program¶

The command-line program can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.

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

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

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

For example, the following command could be used to execute the simulations described in ./modeling-study.omex and save their results to ./:

biosimulators-cobrapy -i ./modeling-study.omex -o ./

Docker image with a command-line entrypoint¶

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 same simulations described in ./modeling-study.omex and save their results to ./:

docker run \
    --tty \
    --rm \
    --mount type=bind,source="$(pwd),target=/tmp/working-dir \
    ghcr.io/biosimulators/cobrapy:latest \
        -i /tmp/working-dir/modeling-study.omex \
        -o /tmp/working-dir