This is a basal ganglia model currently including striatum, globus pallidus, substantia nigra reticulata and subthalamus. The model includes dopamine modulated neurons and synapses, synapses with short-term plasticity and hybrid neuron models from Izhikevich and Brette.

This basal ganglia model (tag 1.0.0 and nest-2.2.2) were used in the paper "Untangling basal ganglia network dynamics and function – role of dopamine depletion and inhibition investigated in a spiking network model". It build using pyNEST that under the hood utilize the NEST simulator. The model have been run Nest 2.6 see nest download. Script used for the paper are located in python/scripts_inhibition.

Make sure you have installed all dependencies

clone the repository

git clone https://github.com/mickelindahl/bgmodel.git

Got to dist director within model

cd {path to model}/dist

These install scripts are available in nest/. Choose one for your system and run it.

• install_2.12.0_linux.sh
• install_2.6.0_linux.sh
• install_2.2.2_linux.sh
• install_2.12.0_mac.sh

Then copy sample.env to .env

cp sample.env .env

Open .env and set data result path

Done!

• python: numpy, scipy, mpi4py, NeuroTools (0.2.0), psycopg2 others: openmpi, libncurses-dev, libreadline-dev, libopenmpi-dev, libgsl, gsl (gnu scitific library, solver, neccesary for module)

Dependencies module

• autoconf, automake

Dependences python

• cython

suod apt-get install cython
sudo pip install python-dotenv
sudo pip install NeuroTools
sudo pip install mpi4py
sudo pip install psycopg2