Tutorial#
BioSimulators-MASSpy 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-MASSpy is available here.
A list of the algorithms and algorithm parameters supported by MASSpy is available at BioSimulators.
Models (MASSpy)#
BioSimulators-MASSpy can execute models encoded in MASSpy format.
Simulation experiments (SED-ML, KISAO)#
BioSimulators-MASSpy can execute simulation experiments encoded in SED-ML, using KiSAO to indicate specific algorithms and their parameters. Information about the algorithms (KiSAO terms), algorithm parameters (KiSAO terms), and outputs (XML XPaths for variables) supported by BioSimulators-MASSpy is available from the BioSimulators registry.
Example COMBINE/OMEX archives#
Examples of COMBINE/OMEX archives for simulations which BioSimulators-MASSpy can execute are available in the BioSimulators test suite.
Command-line program#
The command-line program can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.
usage: biosimulators-masspy [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the MASSpy <https://masspy.readthedocs.io/> 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-masspy -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/masspy:latest \
-i /tmp/working-dir/modeling-study.omex \
-o /tmp/working-dir