Tutorial

BioSimulators-AMICI 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-AMICI is available here.

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

Command-line program

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

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

BioSimulators-compliant command-line interface to the AMICI <https://github.com/AMICI-dev/AMICI> 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-amici -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/amici:latest \
        -i /tmp/working-dir/modeling-study.omex \
        -o /tmp/working-dir