BioSimulators-compliant command-line interfaces and Docker images for the jNeuroML/pyNeuroML, NEURON, NetPyNe, and simulation programs.
These command-line interfaces and Docker images enable users to use jNeuroML/pyNeuroML, NEURON, and NetPyNe to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in NeuroML/LEMS format).
A list of the algorithms and algorithm parameters supported by jNeuroML/pyNeuroML, NEURON, and NetPyNe is available at BioSimulators.
A simple web application and web service for using jNeuroML/pyNeuroML, NEURON, and NetPyNe to execute COMBINE/OMEX archives is also available at runBioSimulations.
- Install Java
- Install this package
pip install biosimulators-pyneuroml
- To install support for NetPyNe, install NEURON and install this package with the
netpyne
option:pip install biosimulators-pyneuroml
- To install support for NEURON, install NEURON and install this package with the
neuron
option:pip install biosimulators-pyneuroml
This package provides three Docker images:
docker pull ghcr.io/biosimulators/netpyne
docker pull ghcr.io/biosimulators/neuron
docker pull ghcr.io/biosimulators/pyneuroml
This package provides three command-line applications, each with the interface illustrated below.
biosimulators-neuron
biosimulators-netpyne
biosimulators-pyneuroml
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
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 Docker image to execute the COMBINE/OMEX archive ./modeling-study.omex
and save its outputs to ./
.
docker run \
--tty \
--rm \
--mount type=bind,source="$(pwd)",target=/root/in,readonly \
--mount type=bind,source="$(pwd)",target=/root/out \
ghcr.io/biosimulators/pyneuroml:latest \
-i /root/in/modeling-study.omex \
-o /root/out
Documentation is available at https://docs.biosimulators.org/Biosimulators_pyNeuroML/.
This package is released under the MIT.
This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai and the Center for Reproducible Biomedical Modeling with assistance from the contributors listed here.
Please contact the BioSimulators Team with any questions or comments.