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BioSimulators-pyNeuroML

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.

Installation

Install Python package

  1. Install Java
  2. Install this package 
    pip install biosimulators-pyneuroml
  3. To install support for NetPyNe, install NEURON and install this package with the netpyne option: 
    pip install biosimulators-pyneuroml
  4. To install support for NEURON, install NEURON and install this package with the neuron option: 
    pip install biosimulators-pyneuroml

Install Docker image

This package provides three Docker images:

docker pull ghcr.io/biosimulators/netpyne
docker pull ghcr.io/biosimulators/neuron
docker pull ghcr.io/biosimulators/pyneuroml

Usage

Local usage

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

Usage through Docker containers

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

Documentation is available at https://docs.biosimulators.org/Biosimulators_pyNeuroML/.

License

This package is released under the MIT.

Development team

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.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.