Neural mass model of the sleeping thalamocortical system (Schellenberger Costa et al 2016)

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Accession:226474
This paper generates typical human EEG data of sleep stages N2/N3 as well as wakefulness and REM sleep.
References:
1 . Weigenand A, Schellenberger Costa M, Ngo HV, Claussen JC, Martinetz T (2014) Characterization of K-complexes and slow wave activity in a neural mass model. PLoS Comput Biol 10:e1003923 [PubMed]
2 . Schellenberger Costa M, Weigenand A, Ngo HV, Marshall L, Born J, Martinetz T, Claussen JC (2016) A Thalamocortical Neural Mass Model of the EEG during NREM Sleep and Its Response to Auditory Stimulation. PLoS Comput Biol 12:e1005022 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neural mass;
Brain Region(s)/Organism: Thalamus; Neocortex;
Cell Type(s): Neocortex L2/3 pyramidal GLU cell; Thalamus reticular nucleus GABA cell; Thalamus geniculate nucleus/lateral principal GLU cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; Neocortex layer 2-3 interneuron;
Channel(s): I Calcium; Na/K pump; I_K,Na;
Gap Junctions:
Receptor(s): AMPA; Gaba; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: Network; C or C++ program (web link to model); MATLAB (web link to model);
Model Concept(s): Calcium dynamics; Sleep; Activity Patterns; Oscillations; Bifurcation; Spindles; Audition;
Implementer(s): Schellenberger Costa, Michael [mschellenbergercosta at gmail.com];
Search NeuronDB for information about:  Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex L2/3 pyramidal GLU cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; AMPA; NMDA; Gaba; I Calcium; I_K,Na; Na/K pump;
/*
 *	Copyright (c) 2015 University of Lübeck
 *
 *	Permission is hereby granted, free of charge, to any person obtaining a copy
 *	of this software and associated documentation files (the "Software"), to deal
 *	in the Software without restriction, including without limitation the rights
 *	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 *	copies of the Software, and to permit persons to whom the Software is
 *	furnished to do so, subject to the following conditions:
 *
 *	The above copyright notice and this permission notice shall be included in
 *	all copies or substantial portions of the Software.
 *
 *	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 *	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 *	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 *	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 *	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 *	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 *	THE SOFTWARE.
 *
 *	AUTHORS:	Michael Schellenberger Costa: mschellenbergercosta@gmail.com
 *
 *	Based on:	A thalamocortical neural mass model of the EEG during NREM sleep and its response
 *				to auditory stimulation.
 *				M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
 *				JC Claussen.
 *				PLoS Computational Biology http://dx.doi.org/10.1371/journal.pcbi.1005022
 */

/******************************************************************************/
/*                  Main file for compilation and runtime tests				  */
/******************************************************************************/
#include <iostream>
#include <chrono>

#include "Cortical_Column.h"
#include "ODE.h"
#include "Thalamic_Column.h"

/******************************************************************************/
/*                          Fixed simulation settings						  */
/******************************************************************************/
typedef std::chrono::high_resolution_clock::time_point timer;
extern const int T      = 30;		/* Time until data is stored in  s		  */
extern const int res 	= 1E4;		/* Number of iteration steps per s		  */
extern const double dt 	= 1E3/res;	/* Duration of a time step in ms		  */
extern const double h	= sqrt(dt); /* Square root of dt for SRK iteration	  */

/******************************************************************************/
/*                              Main simulation routine						  */
/******************************************************************************/
int main(void) {
    /* Initializing the populations */
    std::vector<double> param = {6, 1.33, 1E-3};
    std::vector<double> con   = {2, 10};
    Cortical_Column Cortex(param.data(), con.data());

    param = {0.2, 0.06};
    con   = {2, 10};
    Thalamic_Column Thalamus (param.data(), con.data());

    /* Connect both modules */
    Cortex.get_Thalamus(Thalamus);
    Thalamus.get_Cortex(Cortex);

    /* Take the time of the simulation */
    time_t start,end;
    time (&start);
    /* Simulation */
    for (unsigned t=0; t< T*res; ++t) {
        ODE(Cortex, Thalamus);
    }

    time (&end);
    /* Time consumed by the simulation */
    double dif = difftime(end,start);
    std::cout << "simulation done!\n";
    std::cout << "took " << dif 	<< " seconds" << "\n";
    std::cout << "end\n";
}
/****************************************************************************************************/
/*										 		end													*/
/****************************************************************************************************/

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