Tutorial¶
BioSimulators-pyNeuroML is available as three command-line programs and as a command-line programs encapsulated into three Docker images.
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-pyNeuroML is available here.
A list of the algorithms and algorithm parameters supported by jNeuroML/pyNeuroML, NetPyNe, and NEURON is available at BioSimulators.
Command-line program¶
The command-line programs can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.
usage: biosimulators-pyneuroml [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the pyNeuroML <https://github.com/NeuroML/pyNeuroML> 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 commands could be used to execute the simulations described in ./modeling-study.omex and save their results to ./:
biosimulators-netpyne -i ./modeling-study.omex -o ./
biosimulators-neuron -i ./modeling-study.omex -o ./
biosimulators-pyneuroml -i ./modeling-study.omex -o ./
Docker images with command-line entrypoints¶
The entrypoints to the Docker images support the same command-line interface described above.
For example, the following command could be used to use the jNeuroML/pyNeuroML 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/pyneuroml:latest \
-i /tmp/working-dir/modeling-study.omex \
-o /tmp/working-dir