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Fixed error in license and added option for noise free setting

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1 parent 45fda04 commit 03541c040ff885335d01deb2e23cd1af5d18c545 @miscco committed Mar 23, 2016
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Showing with 73 additions and 65 deletions.
  1. +2 −2 Data_Storage.h
  2. +2 −2 NM_Thalamus.pro
  3. +31 −25 Thalamic_Column.cpp
  4. +35 −32 Thalamic_Column.h
  5. +1 −1 Thalamus.cpp
  6. +2 −3 Thalamus_mex.cpp
View
4 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).
*/
/****************************************************************************************************/
@@ -44,4 +44,4 @@ void get_data(int counter, Thalamic_Column& Col, double* Vt, double* Vr, double*
}
/****************************************************************************************************/
/* end */
-/****************************************************************************************************/
+/****************************************************************************************************/
View
4 NM_Thalamus.pro
@@ -9,8 +9,8 @@ SOURCES += Thalamic_Column.cpp \
Thalamus.cpp \
Thalamus_mex.cpp
-HEADERS += ODE.h \
- Data_Storage.h \
+HEADERS += Data_Storage.h \
+ ODE.h \
Random_Stream.h \
Thalamic_Column.h
View
56 Thalamic_Column.cpp
@@ -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).
*/
/****************************************************************************************************/
@@ -45,8 +45,14 @@ void Thalamic_Column::set_RNG(void) {
/* Add the RNG for I_{l}*/
MTRands.push_back(random_stream_normal(0.0, dphi*dt));
- /* Add the RNG for I_{l,0} */
- MTRands.push_back(random_stream_normal(0.0, dt));
+ /* Add the RNG for I_{l,0}
+ * In the case of a noise free system (dphi=0) set I_{l,0}
+ * to zero.
+ */
+ if(dphi==0)
+ MTRands.push_back(random_stream_normal(0.0, 0));
+ else
+ MTRands.push_back(random_stream_normal(0.0, dt));
/* Get the random number for the first iteration */
Rand_vars.push_back(MTRands[2*i]());
@@ -82,24 +88,24 @@ 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 * s_tt[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_GABA * s_rt[N]* (Vt[N]- E_GABA);
+ double I = g_GABA * s_gt[N]* (Vt[N]- E_GABA);
return I;
}
/* Excitatory input to RE population */
double Thalamic_Column::I_er (int N) const{
- double I = g_AMPA * s_tr[N]* (Vr[N]- E_AMPA);
+ double I = g_AMPA * 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 * s_rr[N]* (Vr[N]- E_GABA);
+ double I = g_GABA * s_gr[N]* (Vr[N]- E_GABA);
return I;
}
/****************************************************************************************************/
@@ -251,21 +257,21 @@ double Thalamic_Column::noise_aRK(int M) const{
/****************************************************************************************************/
void Thalamic_Column::set_RK (int N) {
extern const double dt;
- 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)));
+ Vt [N+1] = Vt [0] + A[N]*dt*(-(I_L_t(N) + I_et(N) + I_gt(N))/tau_t - C_m * (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 - C_m * (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);
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);
m_h [N+1] = m_h [0] + A[N]*dt*((m_inf_h(N) * (1 - m_h2[N]) - m_h[N])/tau_m_h(N) - k3 * P_h(N) * m_h[N] + k4 * m_h2[N]);
m_h2 [N+1] = m_h2 [0] + A[N]*dt*(k3 * P_h(N) * m_h[N] - k4 * m_h2[N]);
- s_tt [N+1] = s_tt [0] + A[N]*dt*(x_tt[N]);
- s_tr [N+1] = s_tr [0] + A[N]*dt*(x_tr[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]);
- x_tt [N+1] = x_tt [0] + A[N]*dt*(pow(gamma_e, 2) * ( - s_tt[N]) - 2 * gamma_e * x_tt[N]);
- x_tr [N+1] = x_tr [0] + A[N]*dt*(pow(gamma_e, 2) * (N_tr * get_Qt(N) - s_tr[N]) - 2 * gamma_e * x_tr[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]);
+ 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_gt [N+1] = s_gt [0] + A[N]*dt*(x_gt[N]);
+ s_gr [N+1] = s_gr [0] + A[N]*dt*(x_gr[N]);
+ x_et [N+1] = x_et [0] + A[N]*dt*(pow(gamma_e, 2) * ( - 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) - s_er[N]) - 2 * gamma_e * x_er[N]);
+ x_gt [N+1] = x_gt [0] + A[N]*dt*(pow(gamma_g, 2) * (N_rt * get_Qr(N) - s_gt[N]) - 2 * gamma_g * x_gt[N]);
+ x_gr [N+1] = x_gr [0] + A[N]*dt*(pow(gamma_g, 2) * (N_rr * get_Qr(N) - s_gr[N]) - 2 * gamma_g * x_gr[N]);
}
/****************************************************************************************************/
/* end */
@@ -279,14 +285,14 @@ 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;
- s_tt [0] =(-3*s_tt [0] + 2*s_tt [1] + 4*s_tt [2] + 2* s_tt [3] + s_tt [4])/6;
- s_tr [0] =(-3*s_tr [0] + 2*s_tr [1] + 4*s_tr [2] + 2* s_tr [3] + s_tr [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;
- x_tt [0] =(-3*x_tt [0] + 2*x_tt [1] + 4*x_tt [2] + 2* x_tt [3] + x_tt [4])/6;
- x_tr [0] =(-3*x_tr [0] + 2*x_tr [1] + 4*x_tr [2] + 2* x_tr [3] + x_tr [4])/6;
- x_rt [0] =(-3*x_rt [0] + 2*x_rt [1] + 4*x_rt [2] + 2* x_rt [3] + x_rt [4])/6;
- x_rr [0] =(-3*x_rr [0] + 2*x_rr [1] + 4*x_rr [2] + 2* x_rr [3] + x_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_gt [0] =(-3*s_gt [0] + 2*s_gt [1] + 4*s_gt [2] + 2* s_gt [3] + s_gt [4])/6;
+ s_gr [0] =(-3*s_gr [0] + 2*s_gr [1] + 4*s_gr [2] + 2* s_gr [3] + s_gr [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;
+ x_gt [0] =(-3*x_gt [0] + 2*x_gt [1] + 4*x_gt [2] + 2* x_gt [3] + x_gt [4])/6;
+ x_gr [0] =(-3*x_gr [0] + 2*x_gr [1] + 4*x_gr [2] + 2* x_gr [3] + x_gr [4])/6;
h_T_t [0] =(-3*h_T_t[0] + 2*h_T_t[1] + 4*h_T_t[2] + 2* h_T_t [3] + h_T_t [4])/6;
h_T_r [0] =(-3*h_T_r[0] + 2*h_T_r[1] + 4*h_T_r[2] + 2* h_T_r [3] + h_T_r [4])/6;
m_h [0] =(-3*m_h [0] + 2*m_h [1] + 4*m_h [2] + 2* m_h [3] + m_h [4])/6;
View
67 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).
*/
/************************************************************************************************/
@@ -59,7 +59,7 @@ class Thalamic_Column {
/* Constructor for simulation */
Thalamic_Column(double* Par)
- : g_LK (Par[1]), g_h (Par[0])
+ : g_LK (Par[0]), g_h (Par[1])
{set_RNG();}
/* Iterate one time step through SRK4 */
@@ -116,20 +116,20 @@ class Thalamic_Column {
/* Declaration and Initialization of parameters */
/* Membrane time in ms */
- const double tau_t = 20;
- const double tau_r = 20;
+ const double tau_t = 20.;
+ const double tau_r = 20.;
/* Maximum firing rate in ms^-1 */
const double Qt_max = 400.E-3;
const double Qr_max = 400.E-3;
/* Sigmoid threshold in mV */
- const double theta_t = -58.6;
- const double theta_r = -58.6;
+ const double theta_t = -58.5;
+ const double theta_r = -58.5;
/* Sigmoid gain in mV */
- const double sigma_t = 6;
- const double sigma_r = 6;
+ const double sigma_t = 6.;
+ const double sigma_r = 6.;
/* Scaling parameter for sigmoidal mapping (dimensionless) */
const double C1 = (M_PI/sqrt(3));
@@ -138,7 +138,10 @@ class Thalamic_Column {
const double gamma_e = 70E-3;
const double gamma_g = 100E-3;
- /* Conductivities */
+ /* Membrane capacitance in muF/cm^2 */
+ const double C_m = 1.;
+
+ /* Weights/ conductivities */
/* Leak in aU */
const double g_L = 1.;
@@ -147,55 +150,55 @@ class Thalamic_Column {
const double g_GABA = 1.;
/* Potassium leak current in mS/m^2 */
- const double g_LK = 0.02;
+ double g_LK = 0.033;
/* T current in mS/m^2 */
const double g_T_t = 3;
const double g_T_r = 2.3;
/* h current in mS/m^2 */
- const double g_h = 0.051;
+ double g_h = 0.02;
/* Reversal potentials in mV */
/* Synaptic */
- const double E_AMPA = 0;
- const double E_GABA = -70;
+ const double E_AMPA = 0.;
+ const double E_GABA = -70.;
/* Leak */
- const double E_L_t = -70;
- const double E_L_r = -70;
+ const double E_L_t = -70.;
+ const double E_L_r = -70.;
/* Potassium */
- const double E_K = -100;
+ const double E_K = -100.;
/* I_T current */
- const double E_Ca = 120;
+ const double E_Ca = 120.;
/* I_h current */
- const double E_h = -40;
+ const double E_h = -40.;
/* Calcium parameters */
const double alpha_Ca = -51.8E-6; /* influx per spike in nmol */
- const double tau_Ca = 10; /* calcium time constant in ms */
+ const double tau_Ca = 10.; /* calcium time constant in ms */
const double Ca_0 = 2.4E-4; /* resting concentration */
/* I_h activation parameters */
const double k1 = 2.5E7;
const double k2 = 4E-4;
const double k3 = 1E-1;
const double k4 = 1E-3;
- const double n_P = 4;
- const double g_inc = 2;
+ const double n_P = 4.;
+ const double g_inc = 2.;
/* Noise parameters in ms^-1 */
const double mphi = 0E-3;
const double dphi = 0E-3;
double input = 0.0;
/* Connectivities (dimensionless) */
- const double N_tr = 3;
- const double N_rt = 5;
- const double N_rr = 30;
+ const double N_tr = 3.;
+ const double N_rt = 5.;
+ const double N_rr = 25.;
/* Parameters for SRK4 iteration */
const vector<double> A = {0.5, 0.5, 1.0, 1.0};
@@ -211,14 +214,14 @@ 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 */
- s_tt = _INIT(0.0), /* PostSP from TC population to TC population */
- s_tr = _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 */
- x_tt = _INIT(0.0), /* derivative of s_tt */
- x_tr = _INIT(0.0), /* derivative of s_tr */
- x_rt = _INIT(0.0), /* derivative of s_rt */
- x_rr = _INIT(0.0), /* derivative of s_rr */
+ 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_gt = _INIT(0.0), /* PostSP from RE population to TC population */
+ s_gr = _INIT(0.0), /* PostSP from RE population to RE population */
+ x_et = _INIT(0.0), /* derivative of s_et */
+ x_er = _INIT(0.0), /* derivative of s_er */
+ x_gt = _INIT(0.0), /* derivative of s_gt */
+ x_gr = _INIT(0.0), /* derivative of s_gr */
h_T_t = _INIT(0.0), /* inactivation of T channel */
h_T_r = _INIT(0.0), /* inactivation of T channel */
m_h = _INIT(0.0), /* activation of h channel */
View
2 Thalamus.cpp
@@ -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
5 Thalamus_mex.cpp
@@ -25,14 +25,13 @@
* 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).
*/
/****************************************************************************************************/
/* Implementation of the simulation as MATLAB routine (mex compiler) */
/* mex command is given by: */
-/* mex CXXFLAGS="\$CXXFLAGS -std=c++11" Thalamus_mex.cpp Thalamic_Column.cpp */
-/* The Simulation requires the following boost libraries: Random */
+/* mex CXXFLAGS="\$CXXFLAGS -std=c++11 -O3" Thalamus_mex.cpp Thalamic_Column.cpp */
/****************************************************************************************************/
#include "mex.h"
#include "matrix.h"

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