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:


    • 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
docker pull
docker pull
docker pull