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 at BioSimulators.

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