Installation

We advise you to implement the cerebellar-models package and the related simulators within a Conda or Python virtual environment.

The cerebellar-models package requires Python 3.10+.

Create a virtual environment in the current folder and activate it:

python3 -m venv cereb_env
# activate the environment
# this command can be added to your .bashrc, adapting the path
source cereb_venv/bin/activate
# if you need to leave the environment
deactivate

You can install the cerebellar-models package trough pip:

pip install cerebellar-models

To include simulation support for NEST and/or NEURON:

pip install cerebellar-models[nest]  # For NEST
pip install cerebellar-models[neuron]  # For NEURON

Alternatively, you can install it from sources:

git clone git@github.com:dbbs-lab/cerebellar-models
cd cerebellar-models
pip install -e .
# do not forget to add the optional simulator supports required.
pip install -e .[nest]  # for NEST

If you wish to contribute to the cerebellar-models repository, please also install the developers’ packages.

NEST simulator

Download and install the NEST simulator in the current folder within your virtual environment:

pip install cython
git clone https://github.com/nest/nest-simulator
cd nest-simulator
mkdir build/ && cd build
# The minimal cmake instruction is `cmake ..`, but if you wish to run simulation with MPI
cmake .. -Dwith-mpi=ON
# To speed up the process, you can set the number of process to compile NEST, here 4
make install -j4

What next:

If you want more information on the Biological context, head over to this section.

Otherwise, you can continue to the Contents section.