dendrotweaks 0.3.1__py3-none-any.whl

dendrotweaks/membrane/default_mod/AMPA_NMDA.mod

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+TITLE NMDA synapse
+
+COMMENT
+Custom NMDA synapse model developed for DendroTweaks
+ENDCOMMENT
+
+NEURON {
+    POINT_PROCESS AMPA_NMDA
+    NONSPECIFIC_CURRENT i
+    RANGE gmax_AMPA, gmax_NMDA, mg, mgblock
+    RANGE tau_rise_AMPA, tau_decay_AMPA, tau_rise_NMDA, tau_decay_NMDA
+    RANGE mu, gamma
+    RANGE i, i_AMPA, i_NMDA, g, g_AMPA, g_NMDA, e
+}
+
+UNITS {
+    (nA) = (nanoamp)
+    (mV) = (millivolt)
+    (uS) = (microsiemens)
+    (mM) = (millimole)
+}
+
+PARAMETER {
+    gmax_AMPA = 0        (uS)
+    gmax_NMDA = 0        (uS)
+    e = 0                (mV)
+    tau_rise_AMPA = 0.1  (ms)
+    tau_decay_AMPA = 2.5 (ms)
+    tau_rise_NMDA = 2    (ms)
+    tau_decay_NMDA = 30  (ms)
+    mg = 1               (mM) 
+    mu = 0.28            (/mM)
+    gamma = 0.062        (/mV)
+}
+
+ASSIGNED {
+    v           (mV)
+    i           (nA)
+    i_AMPA      (nA)
+    i_NMDA      (nA)
+    g           (uS)
+    g_AMPA      (uS)
+    g_NMDA      (uS)
+    factor_AMPA (1)
+    factor_NMDA (1)
+    mgblock     (1)
+}
+
+STATE {
+    A_AMPA (1)
+    B_AMPA (1)
+    A_NMDA (1)
+    B_NMDA (1)
+}
+
+BREAKPOINT {
+    SOLVE state METHOD cnexp
+    g_AMPA = gmax_AMPA * (B_AMPA - A_AMPA)
+    i_AMPA = g_AMPA * (v - e)
+
+    mgblock = 1 / (1 + (mu * mg) * exp(-gamma * v))
+    g_NMDA = mgblock * gmax_NMDA * (B_NMDA - A_NMDA)
+    i_NMDA = g_NMDA * (v - e)
+    
+    g = g_AMPA + g_NMDA
+    i = i_AMPA + i_NMDA
+}
+
+DERIVATIVE state {
+    A_AMPA' = -A_AMPA / tau_rise_AMPA
+    B_AMPA' = -B_AMPA / tau_decay_AMPA
+    A_NMDA' = -A_NMDA / tau_rise_NMDA
+    B_NMDA' = -B_NMDA / tau_decay_NMDA
+}
+
+INITIAL {
+    LOCAL tp_AMPA, tp_NMDA
+
+    A_AMPA = 0
+    B_AMPA = 0
+
+    tp_AMPA = (tau_rise_AMPA * tau_decay_AMPA) / (tau_decay_AMPA - tau_rise_AMPA) * log(tau_decay_AMPA / tau_rise_AMPA)
+    factor_AMPA = -exp(-tp_AMPA / tau_rise_AMPA) + exp(-tp_AMPA / tau_decay_AMPA)
+    factor_AMPA = 1 / factor_AMPA
+
+    A_NMDA = 0
+    B_NMDA = 0
+
+    tp_NMDA = (tau_rise_NMDA * tau_decay_NMDA) / (tau_decay_NMDA - tau_rise_NMDA) * log(tau_decay_NMDA / tau_rise_NMDA)
+    factor_NMDA = -exp(-tp_NMDA / tau_rise_NMDA) + exp(-tp_NMDA / tau_decay_NMDA)
+    factor_NMDA = 1 / factor_NMDA
+
+}
+
+NET_RECEIVE(weight (1)) {
+    A_AMPA = A_AMPA + weight * factor_AMPA
+    B_AMPA = B_AMPA + weight * factor_AMPA
+    A_NMDA = A_NMDA + weight * factor_NMDA
+    B_NMDA = B_NMDA + weight * factor_NMDA
+}

dendrotweaks/membrane/default_mod/CaDyn.mod

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+TITLE Decay of internal calcium concentration
+
+NEURON {
+    SUFFIX CaDyn
+    USEION ca READ ica, cai WRITE cai
+    RANGE depth, taur, cainf, gamma, kt, kd
+}
+
+UNITS {
+    (molar) = (1/liter)          : moles do not appear in units
+    (mM)    = (millimolar)
+    (um)    = (micron)
+    (mA)    = (milliamp)
+    (msM)   = (ms mM)
+    FARADAY = (faraday) (coulomb)
+}
+
+PARAMETER {
+    depth = 0.1    (um)    : Depth of calcium shell
+    taur = 700     (ms)    : Time constant for calcium removal
+    cainf = 1e-8   (mM)    : Steady-state calcium concentration
+    gamma = 1              : Fraction of free calcium (not buffered)
+    kt = 1         (mM/ms) : Michaelis-Menten rate (not used by default)
+    kd = 5e-4      (mM)    : Michaelis-Menten dissociation constant (not used by default)
+}
+
+STATE { cai (mM) }
+
+ASSIGNED {
+    ica           (mA/cm2)
+    drive_channel (mM/ms)
+    drive_pump    (mM/ms)
+}
+
+INITIAL {
+    cai = cainf
+}
+
+BREAKPOINT {
+    SOLVE state METHOD cnexp
+}
+
+DERIVATIVE state { 
+    drive_channel = - (10000) * (ica * gamma) / (2 * FARADAY * depth)
+
+    if (drive_channel <= 0.) { 
+        drive_channel = 0. 
+    }   : Prevent inward pumping
+
+    drive_pump = - kt * cai / (cai + kd) : Michaelis-Menten removal
+
+    cai' = drive_channel + drive_pump + (cainf - cai) / taur
+    
+}

dendrotweaks/membrane/default_mod/GABAa.mod

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+TITLE GABAa synapse
+
+COMMENT
+Custom GABAa synapse model developed for DendroTweaks
+ENDCOMMENT
+
+NEURON {
+    POINT_PROCESS GABAa
+    NONSPECIFIC_CURRENT i
+    RANGE gmax
+    RANGE tau_rise, tau_decay
+    RANGE i, g, e
+}
+
+UNITS {
+    (nA) = (nanoamp)
+    (mV) = (millivolt)
+    (uS) = (microsiemens)
+}
+
+PARAMETER {
+    gmax = 0        (uS)
+    e = -70         (mV)
+    tau_rise = 0.2  (ms)
+    tau_decay = 1.4 (ms)
+}
+
+ASSIGNED {
+    v       (mV)
+    i       (nA)
+    g       (uS)
+    factor  (1)
+}
+
+STATE {
+    A (1)
+    B (1)
+}
+
+BREAKPOINT {
+    SOLVE state METHOD cnexp
+    g = gmax * (B - A)
+    i = g * (v - e)
+}
+
+DERIVATIVE state {
+    A' = -A / tau_rise
+    B' = -B / tau_decay
+}
+
+INITIAL {
+    LOCAL tp
+    A = 0
+    B = 0
+
+    tp = (tau_rise * tau_decay) / (tau_decay - tau_rise) * log(tau_decay / tau_rise)
+    factor = -exp(-tp / tau_rise) + exp(-tp / tau_decay)
+    factor = 1 / factor
+
+}
+
+NET_RECEIVE(weight (1)) {
+    A = A + weight * factor
+    B = B + weight * factor
+}

dendrotweaks/membrane/default_mod/Leak.mod

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+TITLE Leak channel
+
+COMMENT
+NEURON Book Listing 9.1, 
+Replaced g with gbar for consistency with other channels
+Overridden the default values of gbar to 0.0 and e to -70 mV
+ENDCOMMENT
+
+NEURON {
+	SUFFIX Leak
+	NONSPECIFIC_CURRENT i
+	RANGE i, e, gbar
+}
+
+PARAMETER {
+	gbar = 0.0   (siemens/cm2)     
+	e = -70   (millivolt)   
+} 
+
+ASSIGNED {
+	v       (millivolt)
+	i 	    (milliamp/cm2)
+}
+
+BREAKPOINT {
+    i = gbar * (v - e)
+}

dendrotweaks/membrane/default_mod/NMDA.mod

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+TITLE NMDA synapse
+
+COMMENT
+Custom NMDA synapse model developed for DendroTweaks
+ENDCOMMENT
+
+NEURON {
+    POINT_PROCESS NMDA
+    NONSPECIFIC_CURRENT i
+    RANGE gmax, mg, mgblock
+    RANGE tau_rise, tau_decay
+    RANGE mu, gamma
+    RANGE i, g, e
+}
+
+UNITS {
+    (nA) = (nanoamp)
+    (mV) = (millivolt)
+    (uS) = (microsiemens)
+    (mM) = (millimole)
+}
+
+PARAMETER {
+    gmax = 0       (uS)
+    e = 0          (mV)
+    tau_rise = 2   (ms)
+    tau_decay = 30 (ms)
+    mg = 1         (mM) 
+    mu = 0.28      (/mM)
+    gamma = 0.062  (/mV)
+}
+
+ASSIGNED {
+    v       (mV)
+    i       (nA)
+    g       (uS)
+    factor  (1)
+    mgblock (1)
+}
+
+STATE {
+    A (1)
+    B (1)
+}
+
+BREAKPOINT {
+    SOLVE state METHOD cnexp
+    mgblock = 1 / (1 + (mu * mg) * exp(-gamma * v))
+    g = mgblock * gmax * (B - A)
+    i = g * (v - e)
+}
+
+DERIVATIVE state {
+    A' = -A / tau_rise
+    B' = -B / tau_decay
+}
+
+INITIAL {
+    LOCAL tp
+    A = 0
+    B = 0
+
+    tp = (tau_rise * tau_decay) / (tau_decay - tau_rise) * log(tau_decay / tau_rise)
+    factor = -exp(-tp / tau_rise) + exp(-tp / tau_decay)
+    factor = 1 / factor
+
+}
+
+NET_RECEIVE(weight (1)) {
+    A = A + weight * factor
+    B = B + weight * factor
+}

dendrotweaks/membrane/default_mod/vecstim.mod

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+:  Vector stream of events
+
+NEURON {
+	ARTIFICIAL_CELL VecStim
+	RANGE delay
+}
+
+ASSIGNED {
+	index
+	etime (ms)
+	space
+	delay
+}
+
+PARAMETER { 
+	:delay = 0.0
+} 
+
+INITIAL {
+	index = 0
+	:delay = 0
+	element()
+	if (index > 0) {
+		net_send(delay + etime - t, 1)
+	}
+}
+
+NET_RECEIVE (w) {
+	if (flag == 1) {
+		net_event(t)
+		element()
+		if (index > 0) {
+			net_send(delay + etime -t, 1)
+		} 
+	}
+}
+
+VERBATIM
+extern double* vector_vec();
+extern int vector_capacity();
+extern void* vector_arg();
+ENDVERBATIM
+
+PROCEDURE element() {
+VERBATIM	
+  { void* vv; int i, size; double* px;
+	i = (int)index;
+	if (i >= 0) {
+		vv = *((void**)(&space));
+		if (vv) {
+			size = vector_capacity(vv);
+			px = vector_vec(vv);
+			if (i < size) {
+				etime = px[i];
+				index += 1.;
+			}else{
+				index = -1.;
+			}
+		}else{
+			index = -1.;
+		}
+	}
+  }
+ENDVERBATIM
+}
+
+PROCEDURE play() {
+VERBATIM
+	void** vv;
+	vv = (void**)(&space);
+	*vv = (void*)0;
+	if (ifarg(1)) {
+		*vv = vector_arg(1);
+	}
+ENDVERBATIM
+}