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.shinstall_2.6.0_linux.shinstall_2.2.2_linux.shinstall_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