biosimulators-pyneuroml 0.0.16

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

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