bsf_model_run.m

%% Neocortical slice model from Tomsett et al. 2014

bsf_tissue;
bsf_neurons;
bsf_connectivity;
bsf_recording;
bsf_simulation;

% Change this directory to where you would like to save the results of the
% simulation
RS.saveDir = '~/VERTEX_bsf_results/';

% Change these settings if you need to use fewer cores or a different
% parallel profile, or if you want to run in serial mode (this will take a
% long time)
SS.parallelSim = true;
SS.poolSize = 12;
SS.profileName = 'local';

% Initialise the network
[params, connections, electrodes] = initNetwork(TP, NP, CP, RS, SS);

% Run the simulation
runSimulation(params, connections, electrodes);

% Load the simulation results
Results = loadResults(RS.saveDir);
%%
% If you have experienced any problems when trying to run this code, please
% email Richard Tomsett: r _at_ autap _dot_ se

%% Reference
% Tomsett RJ, Ainsworth M, Thiele A, Sanayei M, Chen X et al. (2014)
% Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX):
% comparing multi-electrode recordings from simulated and biological
% mammalian cortical tissue, Brain Structure and Function.
% doi:10.1007/s00429-014-0793-x