Installation instructions¶
BioSimulators-pyNeuroML is available as four command-line programs and four command-line programs encapsulated into four Docker images.
Command-line program¶
First, install Python (>= 3.7), pip, and Java.
Second, install the following additional programs to use NetPyNe and NEURON:
NEURON
gcc
g++
make
NetPyNe
All of the above
libmpich-dev
mpi
mpi-default-bin
mpich
Third, set NEURON_HOME
to the parent directory of the nrniv
executable, up to but not including bin
(e.g., NEURON_HOME=$(which nrniv | rev | cut -d '/' -f 3- | rev)
).
Third, run the following command to install BioSimulators-pyNeuroML:
pip install biosimulators-pyneuroml
Add the brian2
option to install support for Brian 2.
pip install biosimulators-pyneuroml[brian2]
Add the netpyne
option to install support for NetPyNe.
pip install biosimulators-pyneuroml[netpyne]
Add the neuron
option to install support for NEURON.
pip install biosimulators-pyneuroml[neuron]
Docker images with command-line entrypoints¶
After installing Docker, run the following commands to install the Docker images for jNeuroML/pyNeuroML, NetPyNe, and NEURON:
docker pull ghcr.io/biosimulators/brian2
docker pull ghcr.io/biosimulators/netpyne
docker pull ghcr.io/biosimulators/neuron
docker pull ghcr.io/biosimulators/pyneuroml