#277 Added unit test for double mechanism reloading

Author: filippomc

tests/backend/cells/PTcell.hoc

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+from neuron import h
+h.load_file('PTcell.hoc')
+PTcell = h.PTcell 

tests/backend/cells/PTcell.py

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+: $Id: HCN1.mod,v 1.4 2013/01/02 15:01:55 samn Exp $ 
+
+TITLE HCN1 
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+ 
+NEURON {
+  SUFFIX HCN1
+  NONSPECIFIC_CURRENT ih
+  RANGE gbar, g, e, v50, htau, hinf
+  RANGE gfactor, htaufactor
+}
+ 
+PARAMETER {
+  celsius	(degC)
+  gbar = 0.0001	(mho/cm2)
+  e= -30	(mV)
+  v50= -73	(mV)
+  gfactor = 1
+  htaufactor = 1.0 : 4.78
+}
+ 
+STATE {
+  h
+}
+ 
+ASSIGNED {
+  ih	  (mA/cm2) 
+  hinf
+  htau    (ms)
+  v	  (mV)
+  g       (mho/cm2)
+}
+
+PROCEDURE giassign () { 
+  : ih=g*h*(v-e)*gfactor 
+  g = gbar*h*gfactor
+  ih = g*(v-e)
+}
+ 
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  giassign()
+}
+ 
+DERIVATIVE states { 
+  rates(v)
+  h'= (hinf- h)/ htau
+}
+
+INITIAL { 
+  rates(v)
+  h = hinf
+  giassign()
+}
+
+PROCEDURE rates(v (mV)) {
+  UNITSOFF
+  : HCN1
+  hinf = 1/(1+exp(0.151*(v-v50)))
+  htau = htaufactor*exp((0.033*(v+75)))/(0.011*(1+exp(0.083*(v+75))))
+  UNITSON
+}
+

tests/backend/mod/HCN1.mod

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+TITLE Ca-dependent potassium current
+:
+:   Ca++ dependent K+ current IC responsible for 
+:   action potentials AHP's
+:   Differential equations
+:
+:   Model of Yamada, Koch & Adams, in: Methods in Neuronal Modeling,
+:   Ed. by Koch & Segev, MIT press, 1989.
+:
+:   This current models the "fast" IK[Ca]:
+:      - potassium current
+:      - activated by intracellular calcium
+:      - VOLTAGE DEPENDENT
+:
+:   Written by Alain Destexhe, Salk Institute, Sept 18, 1992
+:
+: should be considered 'BK' - fast, big conductance
+
+NEURON {
+	SUFFIX ikc
+	USEION k READ ek WRITE ik
+	USEION ca READ cai
+        RANGE gkbar, ik
+	RANGE m_inf, tau_m
+        RANGE taumin
+        GLOBAL ascale,bscale,vfctr
+}
+
+UNITS {
+	(mA) = (milliamp)
+	(mV) = (millivolt)
+	(molar) = (1/liter)
+	(mM) = (millimolar)
+}
+
+PARAMETER {
+	v		(mV)
+        celsius         (degC)
+	ek		(mV)
+        cai             (mM)
+	gkbar	= .003	(mho/cm2)	: taken from 
+        taumin = 0.1
+        ascale = 250.0
+        bscale = 0.1
+        vfctr = 24.0
+}
+
+STATE {
+	m
+}
+
+INITIAL {
+	evaluate_fct(v,cai)
+	m = m_inf
+}
+
+ASSIGNED {
+	ik	(mA/cm2)
+	m_inf
+	tau_m	(ms)
+}
+
+BREAKPOINT { 
+	SOLVE states METHOD cnexp
+	ik = gkbar * m * (v - ek)
+}
+
+DERIVATIVE states { 
+	evaluate_fct(v,cai)
+	m' = (m_inf - m) / tau_m
+}
+
+UNITSOFF
+PROCEDURE evaluate_fct(v(mV),cai(mM)) {  LOCAL a,b,tadj
+:
+:  activation kinetics of Yamada et al were at 22 deg. C
+:  transformation to 36 deg assuming Q10=3
+:
+	tadj = 3 ^ ((celsius-22.0)/10)
+
+	a = ascale * cai * exp(v/vfctr)
+	b = bscale * exp(-v/vfctr)
+
+	tau_m = 1.0 / (a + b) / tadj
+        if(tau_m < taumin){ tau_m = taumin }
+	m_inf = a / (a + b)
+}
+UNITSON

tests/backend/mod/IC.mod

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+: Slowly inactivating K+ channel
+
+NEURON {
+	SUFFIX IKsin
+	USEION k READ ki, ko WRITE ik
+	RANGE gKsbar, ik, gk
+	
+}
+
+UNITS {
+	(mA) = (milliamp)
+	(mV) = (millivolt)
+        (mM) = (milli/liter)
+	
+}
+INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}
+PARAMETER {
+	v (mV)
+	dt (ms)
+	gKsbar= 0.00014 (mho/cm2) <0,1e9>
+	
+}
+
+
+STATE {
+	a b
+}
+
+
+ASSIGNED {
+	ik (mA/cm2)
+	ainf binf
+	atau (ms)
+	btau (ms)
+	gk (mho/cm2)
+	ek  (mV)
+	ki (mM)
+	ko  (mM)
+}
+
+
+
+INITIAL {
+	rate(v)
+	a = ainf
+	b = binf
+}
+
+BREAKPOINT {
+	SOLVE states METHOD cnexp
+		
+	gk = gKsbar * a * b
+	ek = 25 * log(ko/ki)
+	ik = gk*(v-ek)
+	
+}
+
+DERIVATIVE states {
+	rate(v)
+	
+	a' = (ainf-a)/atau
+	b' = (binf-b)/btau
+}
+UNITSOFF
+
+PROCEDURE rate(v (mV)) {LOCAL va, vb, vc, vd
+	
+	
+	va = v + 34
+	vb = v + 65
+	vd = v + 63.6
+	
+
+if (fabs(va)<1e-04){ va = va+0.00001 }
+	   ainf = 1/(1 + exp(-va/6.5))
+	   atau = 10
+	  :atau=6
+	
+
+if (fabs(vb)<1e-04){ vb = vb+0.00001 }
+	   binf = 1/(1 + exp(vb/6.6))
+
+ 
+if (fabs(vd)<1e-04){ vd = vd+0.00001 }
+	   btau = 200 + 3200 / (1 + exp(-vd/4))
+	:btau = 200 + 3200 / (1 + exp(-vd/4))
+}
+
+	
+UNITSON
+
+
+
+
+
+
+

tests/backend/mod/IKsin.mod

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+TITLE Anomalous rectifier current for RD Traub, J Neurophysiol 89:909-921, 2003
+
+COMMENT
+    Implemented by Maciej Lazarewicz 2003 (mlazarew@seas.upenn.edu)
+ENDCOMMENT
+
+INDEPENDENT { t FROM 0 TO 1 WITH 1 (ms) }
+
+UNITS {
+    (mV) = (millivolt)
+    (mA) = (milliamp)
+}
+
+NEURON {
+    SUFFIX ar_hnn
+    NONSPECIFIC_CURRENT i
+    RANGE gbar, i
+}
+
+PARAMETER {
+    gbar = 0.0  (mho/cm2)
+    v           (mV)
+    erev = -35  (mV)
+}
+
+ASSIGNED {
+    i           (mA/cm2)
+    minf        (1)
+    mtau        (ms)
+}
+
+STATE {
+    m
+}
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    i = gbar * m * ( v - erev )
+}
+
+INITIAL {
+    settables(v)
+    m = minf
+    m = 0.25
+}
+
+DERIVATIVE states {
+    settables(v)
+    m' = ( minf - m ) / mtau
+}
+
+UNITSOFF
+PROCEDURE settables(v) {
+    TABLE minf, mtau FROM -120 TO 40 WITH 641
+    minf  = 1 / ( 1 + exp( ( v + 75 ) / 5.5 ) )
+    mtau = 1 / ( exp( -14.6 - 0.086 * v ) + exp( -1.87 + 0.07 * v ) )
+}
+UNITSON

tests/backend/mod/ar.mod

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+TITLE Anomalous rectifier current for RD Traub, J Neurophysiol 89:909-921, 2003
+
+COMMENT
+
+	Implemented by Maciej Lazarewicz 2003 (mlazarew@seas.upenn.edu)
+
+ENDCOMMENT
+
+INDEPENDENT { t FROM 0 TO 1 WITH 1 (ms) }
+
+UNITS { 
+	(mV) = (millivolt) 
+	(mA) = (milliamp) 
+} 
+NEURON { 
+	SUFFIX ar
+	NONSPECIFIC_CURRENT i
+	RANGE gbar, i
+}
+PARAMETER { 
+	gbar = 0.0 	(mho/cm2)
+	v		(mV) 
+	erev = -35	(mV)  
+} 
+ASSIGNED { 
+	i 		(mA/cm2) 
+	minf 		(1)
+	mtau 		(ms) 
+} 
+STATE {
+	m
+}
+BREAKPOINT { 
+	SOLVE states METHOD cnexp
+	i = gbar * m * ( v - erev ) 
+} 
+INITIAL { 
+	minf  = 1 / ( 1 + exp( ( v + 75 ) / 5.5 ) )
+	mtau = 1 / ( exp( -14.6 - 0.086 * v ) + exp( -1.87 + 0.07 * v ) )
+	m = minf
+	: m = 0.25 : ??
+} 
+DERIVATIVE states { 
+	minf  = 1 / ( 1 + exp( ( v + 75 ) / 5.5 ) )
+	mtau = 1 / ( exp( -14.6 - 0.086 * v ) + exp( -1.87 + 0.07 * v ) )
+	m' = ( minf - m ) / mtau 
+}