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Corrected typo in the reference

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1 parent 60a768b commit bd16ba8cdc963dabc303fd894b937973cebf4fe2 @miscco committed Mar 21, 2016
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Showing with 56 additions and 52 deletions.
  1. +7 −3 Cortical_Column.cpp
  2. +9 −5 Cortical_Column.h
  3. +1 −1 Data_Storage.h
  4. +1 −1 ODE.h
  5. +2 −2 Stimulation.h
  6. +2 −5 TC.cpp
  7. +1 −2 TC_mex.cpp
  8. +18 −18 Thalamic_Column.cpp
  9. +15 −15 Thalamic_Column.h
View
10 Cortical_Column.cpp
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2015 UniVprsity of Lübeck
+ * 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
@@ -21,11 +21,15 @@
*
* AUTHORS: Michael Schellenberger Costa: mschellenbergercosta@gmail.com
*
- * Based on: A thalamocortical neural mass model of the EEG during NREM sleep and its response
+ * Based on: Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model
+ * A Weigenand, M Schellenberger Costa, H-VV Ngo, JC Claussen, T Martinetz
+ * PLoS Computational Biology. 2014;10:e1003923
+ *
+ * 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 In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/****************************************************************************************************/
View
14 Cortical_Column.h
@@ -21,11 +21,15 @@
*
* AUTHORS: Michael Schellenberger Costa: mschellenbergercosta@gmail.com
*
- * Based on: A thalamocortical neural mass model of the EEG during NREM sleep and its response
+ * Based on: Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model
+ * A Weigenand, M Schellenberger Costa, H-VV Ngo, JC Claussen, T Martinetz
+ * PLoS Computational Biology. 2014;10:e1003923
+ *
+ * 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 In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/************************************************************************************************/
@@ -137,14 +141,14 @@ class Cortical_Column {
/* Axonal flux time constant */
const double nu = 120E-3;
- /* Conductivities */
- /* Leak in aU*/
+ /* Leak weight in aU*/
const double g_L = 1.;
- /* Synaptic conductivities in ms */
+ /* Synaptic weight in ms */
const double g_AMPA = 1.;
const double g_GABA = 1.;
+ /* Conductivity */
/* KNa in mS/cm^2 */
const double g_KNa = 1.33;
View
2 Data_Storage.h
@@ -25,7 +25,7 @@
* to auditory stimulation.
* M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
* JC Claussen.
- * PLoS Computational Biology In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/****************************************************************************************************/
View
2 ODE.h
@@ -25,7 +25,7 @@
* to auditory stimulation.
* M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
* JC Claussen.
- * PLoS Computational Biology In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/****************************************************************************************************/
View
4 Stimulation.h
@@ -25,7 +25,7 @@
* to auditory stimulation.
* M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
* JC Claussen.
- * PLoS Computational Biology In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/****************************************************************************************************/
@@ -145,7 +145,7 @@ class Stim {
std::vector<int> marker_stimulation;
/* Random number generator in case of semi-periodic stimulation */
- random_stream_uniform_int Uniform_Distribution;
+ random_stream_uniform_int Uniform_Distribution;
};
/****************************************************************************************************/
/* end */
View
7 TC.cpp
@@ -25,17 +25,14 @@
* to auditory stimulation.
* M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
* JC Claussen.
- * PLoS Computational Biology In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/****************************************************************************************************/
-/* Main file for compilation tests */
-/* The Simulation requires the following boost libraries: Random */
+/* Main file for compilation tests */
/****************************************************************************************************/
#include <iostream>
#include <ctime>
-#include "Cortical_Column.h"
-#include "Thalamic_Column.h"
#include "ODE.h"
View
3 TC_mex.cpp
@@ -32,7 +32,6 @@
/* Implementation of the simulation as MATLAB routine (mex compiler) */
/* mex command is given by: */
/* mex CXXFLAGS="\$CXXFLAGS -std=c++11" TC_mex.cpp Cortical_Column.cpp Thalamic_Column.cpp */
-/* The Simulation requires the following boost libraries: Random */
/****************************************************************************************************/
#include <ctime>
#include "mex.h"
@@ -124,7 +123,7 @@ mxArray* GetMexArray(int N, int M) {
mxArray* Array = mxCreateDoubleMatrix(0, 0, mxREAL);
mxSetM(Array, N);
mxSetN(Array, M);
- #pragma omp critical
+#pragma omp critical
{mxSetData(Array, mxMalloc(sizeof(double)*M*N));}
return Array;
}
View
36 Thalamic_Column.cpp
@@ -25,11 +25,11 @@
* to auditory stimulation.
* M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
* JC Claussen.
- * PLoS Computational Biology In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/****************************************************************************************************/
-/* Functions of the cortical module */
+/* Functions of the thalamic module */
/****************************************************************************************************/
#include "Thalamic_Column.h"
@@ -83,24 +83,24 @@ double Thalamic_Column::get_Qr (int N) const{
/****************************************************************************************************/
/* Excitatory input to TC population */
double Thalamic_Column::I_et (int N) const{
- double I = g_AMPA * y_et[N]* (Vt[N]- E_AMPA);
+ double I = g_AMPA * s_et[N]* (Vt[N]- E_AMPA);
return I;
}
/* Inhibitory input to TC population */
double Thalamic_Column::I_gt (int N) const{
- double I = g_AMPA * y_rt[N]* (Vt[N]- E_GABA);
+ double I = g_AMPA * s_rt[N]* (Vt[N]- E_GABA);
return I;
}
/* Excitatory input to RE population */
double Thalamic_Column::I_er (int N) const{
- double I = g_GABA * y_er[N]* (Vr[N]- E_AMPA);
+ double I = g_GABA * s_er[N]* (Vr[N]- E_AMPA);
return I;
}
/* Inhibitory input to RE population */
double Thalamic_Column::I_gr (int N) const{
- double I = g_GABA * y_rr[N]* (Vr[N]- E_GABA);
+ double I = g_GABA * s_rr[N]* (Vr[N]- E_GABA);
return I;
}
/****************************************************************************************************/
@@ -255,15 +255,15 @@ void Thalamic_Column::set_RK (int N) {
Vt [N+1] = Vt [0] + A[N]*dt*(-(I_L_t(N) + I_et(N) + I_gt(N))/tau_t - (I_LK_t(N) + I_T_t(N) + I_h(N)));
Vr [N+1] = Vr [0] + A[N]*dt*(-(I_L_r(N) + I_er(N) + I_gr(N))/tau_r - (I_LK_r(N) + I_T_r(N)));
Ca [N+1] = Ca [0] + A[N]*dt*(alpha_Ca * I_T_t(N) - (Ca[N] - Ca_0)/tau_Ca);
- y_et [N+1] = y_et [0] + A[N]*dt*(x_et[N]);
- y_er [N+1] = y_er [0] + A[N]*dt*(x_er[N]);
- y_rt [N+1] = y_rt [0] + A[N]*dt*(x_rt[N]);
- y_rr [N+1] = y_rr [0] + A[N]*dt*(x_rr[N]);
+ s_et [N+1] = s_et [0] + A[N]*dt*(x_et[N]);
+ s_er [N+1] = s_er [0] + A[N]*dt*(x_er[N]);
+ s_rt [N+1] = s_rt [0] + A[N]*dt*(x_rt[N]);
+ s_rr [N+1] = s_rr [0] + A[N]*dt*(x_rr[N]);
y [N+1] = y [0] + A[N]*dt*(x [N]);
- x_et [N+1] = x_et [0] + A[N]*dt*(pow(gamma_e, 2) * ( + N_pt * Cortex->y[N] - y_et[N]) - 2 * gamma_e * x_et[N]) + noise_xRK(N,0);
- x_er [N+1] = x_er [0] + A[N]*dt*(pow(gamma_e, 2) * (N_tr * get_Qt(N) + N_pr * Cortex->y[N] - y_er[N]) - 2 * gamma_e * x_er[N]);
- x_rt [N+1] = x_rt [0] + A[N]*dt*(pow(gamma_g, 2) * (N_rt * get_Qr(N) - y_rt[N]) - 2 * gamma_g * x_rt[N]);
- x_rr [N+1] = x_rr [0] + A[N]*dt*(pow(gamma_g, 2) * (N_rr * get_Qr(N) - y_rr[N]) - 2 * gamma_g * x_rr[N]);
+ x_et [N+1] = x_et [0] + A[N]*dt*(pow(gamma_e, 2) * ( + N_pt * Cortex->y[N] - s_et[N]) - 2 * gamma_e * x_et[N]) + noise_xRK(N,0);
+ x_er [N+1] = x_er [0] + A[N]*dt*(pow(gamma_e, 2) * (N_tr * get_Qt(N) + N_pr * Cortex->y[N] - s_er[N]) - 2 * gamma_e * x_er[N]);
+ x_rt [N+1] = x_rt [0] + A[N]*dt*(pow(gamma_g, 2) * (N_rt * get_Qr(N) - s_rt[N]) - 2 * gamma_g * x_rt[N]);
+ x_rr [N+1] = x_rr [0] + A[N]*dt*(pow(gamma_g, 2) * (N_rr * get_Qr(N) - s_rr[N]) - 2 * gamma_g * x_rr[N]);
x [N+1] = x [0] + A[N]*dt*(pow(nu, 2) * ( get_Qt(N) - y [N]) - 2 * nu * x [N]);
h_T_t [N+1] = h_T_t[0] + A[N]*dt*(h_inf_T_t(N) - h_T_t[N])/tau_h_T_t(N);
h_T_r [N+1] = h_T_r[0] + A[N]*dt*(h_inf_T_r(N) - h_T_r[N])/tau_h_T_r(N);
@@ -282,10 +282,10 @@ void Thalamic_Column::add_RK(void) {
Vt [0] =(-3*Vt [0] + 2*Vt [1] + 4*Vt [2] + 2* Vt [3] + Vt [4])/6;
Vr [0] =(-3*Vr [0] + 2*Vr [1] + 4*Vr [2] + 2* Vr [3] + Vr [4])/6;
Ca [0] =(-3*Ca [0] + 2*Ca [1] + 4*Ca [2] + 2* Ca [3] + Ca [4])/6;
- y_et [0] =(-3*y_et [0] + 2*y_et [1] + 4*y_et [2] + 2* y_et [3] + y_et [4])/6;
- y_er [0] =(-3*y_er [0] + 2*y_er [1] + 4*y_er [2] + 2* y_er [3] + y_er [4])/6;
- y_rt [0] =(-3*y_rt [0] + 2*y_rt [1] + 4*y_rt [2] + 2* y_rt [3] + y_rt [4])/6;
- y_rr [0] =(-3*y_rr [0] + 2*y_rr [1] + 4*y_rr [2] + 2* y_rr [3] + y_rr [4])/6;
+ s_et [0] =(-3*s_et [0] + 2*s_et [1] + 4*s_et [2] + 2* s_et [3] + s_et [4])/6;
+ s_er [0] =(-3*s_er [0] + 2*s_er [1] + 4*s_er [2] + 2* s_er [3] + s_er [4])/6;
+ s_rt [0] =(-3*s_rt [0] + 2*s_rt [1] + 4*s_rt [2] + 2* s_rt [3] + s_rt [4])/6;
+ s_rr [0] =(-3*s_rr [0] + 2*s_rr [1] + 4*s_rr [2] + 2* s_rr [3] + s_rr [4])/6;
y [0] =(-3*y [0] + 2*y [1] + 4*y [2] + 2* y [3] + y [4])/6;
x_et [0] =(-3*x_et [0] + 2*x_et [1] + 4*x_et [2] + 2* x_et [3] + x_et [4])/6 + noise_aRK(0);
x_er [0] =(-3*x_er [0] + 2*x_er [1] + 4*x_er [2] + 2* x_er [3] + x_er [4])/6;
View
30 Thalamic_Column.h
@@ -25,7 +25,7 @@
* to auditory stimulation.
* M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
* JC Claussen.
- * PLoS Computational Biology In Review (in review).
+ * PLoS Computational Biology (in review).
*/
/************************************************************************************************/
@@ -76,7 +76,7 @@ class Thalamic_Column {
friend void get_data (int, Cortical_Column&, Thalamic_Column&, vector<double*>);
friend class Cortical_Column;
- /* Set strength of input */
+ /* Set strength of external input */
void set_input (double I) {input = I;}
private:
@@ -149,17 +149,17 @@ class Thalamic_Column {
const double gamma_e = 70E-3;
const double gamma_g = 100E-3;
- /* axonal flux time constant */
+ /* Axonal flux time constant in ms^-1*/
const double nu = 120E-3;
- /* Conductivities */
- /* Leak in aU */
+ /* Leak weight in aU */
const double g_L = 1.;
- /* Synaptic conductivity in ms */
+ /* Synaptic weights in ms */
const double g_AMPA = 1.;
const double g_GABA = 1.;
+ /* Conductivities */
/* Potassium leak current in mS/m^2 */
const double g_LK = 0.02;
@@ -168,7 +168,7 @@ class Thalamic_Column {
const double g_T_r = 2.3;
/* h current in mS/m^2 */
- const double g_h = 0.051;
+ const double g_h = 0.06;
/* Reversal potentials in mV */
/* Synaptic */
@@ -232,15 +232,15 @@ class Thalamic_Column {
vector<double> Vt = _INIT(E_L_t), /* TC membrane voltage */
Vr = _INIT(E_L_r), /* RE membrane voltage */
Ca = _INIT(Ca_0), /* Calcium concentration of TC population */
- y_et = _INIT(0.0), /* PostSP from TC population to TC population */
- y_er = _INIT(0.0), /* PostSP from TC population to RE population */
- y_rt = _INIT(0.0), /* PostSP from RE population to TC population */
- y_rr = _INIT(0.0), /* PostSP from RE population to RE population */
+ s_et = _INIT(0.0), /* PostSP from TC population to TC population */
+ s_er = _INIT(0.0), /* PostSP from TC population to RE population */
+ s_rt = _INIT(0.0), /* PostSP from RE population to TC population */
+ s_rr = _INIT(0.0), /* PostSP from RE population to RE population */
y = _INIT(0.0), /* axonal flux */
- x_et = _INIT(0.0), /* derivative of y_et */
- x_er = _INIT(0.0), /* derivative of y_er */
- x_rt = _INIT(0.0), /* derivative of y_rt */
- x_rr = _INIT(0.0), /* derivative of y_rr */
+ x_et = _INIT(0.0), /* derivative of s_et */
+ x_er = _INIT(0.0), /* derivative of s_er */
+ x_rt = _INIT(0.0), /* derivative of s_rt */
+ x_rr = _INIT(0.0), /* derivative of s_rr */
x = _INIT(0.0), /* derivative of y */
h_T_t = _INIT(0.0), /* inactivation of T channel */
h_T_r = _INIT(0.0), /* inactivation of T channel */

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