README.md

A Biologically Constrained Basal Ganglia model

This code implements a mean-field model of the whole basal ganglia, whose parameterization was optimized to respect best a collection of numerous anatomical and electrophysiological data.

This model was used for the paper "A biologically constrained model of the whole basal ganglia addressing the paradoxes of connections and selection." available at J Comput Neurosci (preprint in this repo: here).

Compiling

The code depends on the Boost libraries (1.37 or newer).

To compile, type:

$ make

This creates an executable file called single_run.

Reproduce the main results of the 2014 paper

Launch the script to run different parameterizations of the basal ganglia model and store the results in model_output:

$ bash tst_solutions.sh > model_output

The figures of the paper can be generated in R with the script output_figures.R:

R> setwd('your-working-directory')
R> source('output_figures.R')

(don't forget to replace your-working-directory with the actual one)