Tutorial

BioSimulators-COPASI 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-COPASI is available here.

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

Conventions for values of changes to algorithm parameters

This package follows SED-ML conventions for Boolean-, integer- and float-valued parameters.

New values of parameter KISAO_0000534 (list of deterministic reactions) of KISAO_0000563 (hybrid RK-45 method) should be JSON-encoded lists of the SBML ids of the reactions which should be deterministically simulated using the RK-45 portion of the method. For example, the following SED-ML indicates that the RK-45 partition should consist of the reactions that have the SBML ids reaction_1 and reaction_2.

<algorithm kisaoID="KISAO:0000563">
  <algorithmParameter kisaoID="KISAO:0000534" value="[\"reaction_1\", \"reaction_2\"]" />
</algorithm>

Command-line program for executing COMBINE/OMEX archives

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

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

BioSimulators-compliant command-line interface to the COPASI <http://copasi.org> 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-copasi -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/copasi:latest \
        -i /tmp/working-dir/modeling-study.omex \
        -o /tmp/working-dir

Command-line program for correcting COMBINE/OMEX archives created by COPASI

The fix-copasi-generated-combine-archive command-line program can be used to align COMBINE/OMEX archives created by COPASI with the specifications of the OMEX manifest and SED-ML formats.

usage: fix-copasi-generated-combine-archive [-h] [-d] [-q] -i IN_FILE -o OUT_FILE

Correct a COPASI-generated COMBINE/OMEX archive to be consistent with the specifications of the OMEX manifest and SED-ML formats

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i IN_FILE, --in-file IN_FILE
                        Path to COMBINE/OMEX file to correct
  -o OUT_FILE, --out-file OUT_FILE
                        Path to save the corrected archive

For example, the following command could be used to correct the example COPASI-generated archive in the tests/fixtures directory:

fix-copasi-generated-combine-archive \
    -i tests/fixtures/copasi-34-export.omex \
    -o tests/fixtures/copasi-34-export-fixed.omex