COMMENT
**************************************************
File generated by: neuroConstruct v1.7.1
**************************************************
This file holds the implementation in NEURON of the Cell Mechanism:
NaxSH10_ChannelML (Type: Channel mechanism, Model: ChannelML based process)
with parameters:
/channelml/@units = Physiological Units
/channelml/notes = ChannelML file containing a single Channel description
/channelml/channel_type/@name = NaxSH10_ChannelML
/channelml/channel_type/@density = yes
/channelml/channel_type/status/@value = stable
/channelml/channel_type/status/comment = Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and n traces on single comp with current pulse
/channelml/channel_type/status/contributor/name = Padraig Gleeson
/channelml/channel_type/notes = Na Channel
/channelml/channel_type/authorList/modelTranslator/name = Padraig Gleeson
/channelml/channel_type/authorList/modelTranslator/institution = UCL
/channelml/channel_type/authorList/modelTranslator/email = p.gleeson - at - ucl.ac.uk
/channelml/channel_type/current_voltage_relation/@cond_law = ohmic
/channelml/channel_type/current_voltage_relation/@ion = na
/channelml/channel_type/current_voltage_relation/@default_gmax = 40
/channelml/channel_type/current_voltage_relation/@default_erev = 67
/channelml/channel_type/current_voltage_relation/@charge = 1
/channelml/channel_type/current_voltage_relation/q10_settings/@q10_factor = 2
/channelml/channel_type/current_voltage_relation/q10_settings/@experimental_temp = 24
/channelml/channel_type/current_voltage_relation/gate[1]/@name = m
/channelml/channel_type/current_voltage_relation/gate[1]/@instances = 3
/channelml/channel_type/current_voltage_relation/gate[1]/closed_state/@id = m0
/channelml/channel_type/current_voltage_relation/gate[1]/open_state/@id = m
/channelml/channel_type/current_voltage_relation/gate[1]/open_state/@fraction = 1
/channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@name = alpha
/channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@from = m0
/channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@to = m
/channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@expr_form = exp_linear
/channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@rate = 2.880000018
/channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@scale = 7.2
/channelml/channel_type/current_voltage_relation/gate[1]/transition[1]/@midpoint = -20
/channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@name = beta
/channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@from = m
/channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@to = m0
/channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@expr_form = exp_linear
/channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@rate = 0.892800005
/channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@scale = -7.2
/channelml/channel_type/current_voltage_relation/gate[1]/transition[2]/@midpoint = -20
/channelml/channel_type/current_voltage_relation/gate[1]/time_course/@name = tau
/channelml/channel_type/current_voltage_relation/gate[1]/time_course/@from = m0
/channelml/channel_type/current_voltage_relation/gate[1]/time_course/@to = m
/channelml/channel_type/current_voltage_relation/gate[1]/time_course/@expr_form = generic
/channelml/channel_type/current_voltage_relation/gate[1]/time_course/@expr = 1/( (alpha + beta) * temp_adj_m ) < 0.02 ? (0.02 * temp_adj_m) : 1/(alpha + beta)
/channelml/channel_type/current_voltage_relation/gate[2]/@name = h
/channelml/channel_type/current_voltage_relation/gate[2]/@instances = 1
/channelml/channel_type/current_voltage_relation/gate[2]/closed_state/@id = h0
/channelml/channel_type/current_voltage_relation/gate[2]/open_state/@id = h
/channelml/channel_type/current_voltage_relation/gate[2]/open_state/@fraction = 1
/channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@name = alpha
/channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@from = h0
/channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@to = h
/channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@expr_form = exp_linear
/channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@rate = 0.045
/channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@scale = 1.5
/channelml/channel_type/current_voltage_relation/gate[2]/transition[1]/@midpoint = -35
/channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@name = beta
/channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@from = h
/channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@to = h0
/channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@expr_form = exp_linear
/channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@rate = 0.015
/channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@scale = -1.5
/channelml/channel_type/current_voltage_relation/gate[2]/transition[2]/@midpoint = -35
/channelml/channel_type/current_voltage_relation/gate[2]/time_course/@name = tau
/channelml/channel_type/current_voltage_relation/gate[2]/time_course/@from = h0
/channelml/channel_type/current_voltage_relation/gate[2]/time_course/@to = h
/channelml/channel_type/current_voltage_relation/gate[2]/time_course/@expr_form = generic
/channelml/channel_type/current_voltage_relation/gate[2]/time_course/@expr = 1/( (alpha + beta) * temp_adj_h ) < 0.5 ? (0.5 * temp_adj_h) : 1/(alpha + beta)
/channelml/channel_type/current_voltage_relation/gate[2]/steady_state/@name = inf
/channelml/channel_type/current_voltage_relation/gate[2]/steady_state/@from = h0
/channelml/channel_type/current_voltage_relation/gate[2]/steady_state/@to = h
/channelml/channel_type/current_voltage_relation/gate[2]/steady_state/@expr_form = sigmoid
/channelml/channel_type/current_voltage_relation/gate[2]/steady_state/@rate = 1
/channelml/channel_type/current_voltage_relation/gate[2]/steady_state/@scale = 4
/channelml/channel_type/current_voltage_relation/gate[2]/steady_state/@midpoint = -40
/channelml/channel_type/impl_prefs/table_settings/@max_v = 100
/channelml/channel_type/impl_prefs/table_settings/@min_v = -100
/channelml/channel_type/impl_prefs/table_settings/@table_divisions = 2000
// File from which this was generated: /home/Simon/NML2_Test/AOB_MC_neuroConstruct/cellMechanisms/NaxSH10_ChannelML/NaChannel.xml
// XSL file with mapping to simulator: /home/Simon/NML2_Test/AOB_MC_neuroConstruct/cellMechanisms/NaxSH10_ChannelML/ChannelML_v1.8.1_NEURONmod.xsl
ENDCOMMENT
? This is a NEURON mod file generated from a ChannelML file
? Unit system of original ChannelML file: Physiological Units
COMMENT
ChannelML file containing a single Channel description
ENDCOMMENT
TITLE Channel: NaxSH10_ChannelML
COMMENT
Na Channel
ENDCOMMENT
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(S) = (siemens)
(um) = (micrometer)
(molar) = (1/liter)
(mM) = (millimolar)
(l) = (liter)
}
NEURON {
SUFFIX NaxSH10_ChannelML
USEION na READ ena WRITE ina VALENCE 1 ? reversal potential of ion is read, outgoing current is written
RANGE gmax, gion
RANGE minf, mtau
RANGE hinf, htau
}
PARAMETER {
gmax = 0.04 (S/cm2) ? default value, should be overwritten when conductance placed on cell
}
ASSIGNED {
v (mV)
celsius (degC)
? Reversal potential of na
ena (mV)
? The outward flow of ion: na calculated by rate equations...
ina (mA/cm2)
gion (S/cm2)
minf
mtau (ms)
hinf
htau (ms)
}
BREAKPOINT {
SOLVE states METHOD cnexp
gion = gmax * ((1*m)
^3) * ((1*h)
^1)
ina = gion*(v - ena)
}
INITIAL {
ena = 67
rates(v)
m = minf
h = hinf
}
STATE {
m
h
}
DERIVATIVE states {
rates(v)
m' = (minf - m)/mtau
h' = (hinf - h)/htau
}
PROCEDURE rates(v(mV)) {
? Note: not all of these may be used, depending on the form of rate equations
LOCAL alpha, beta, tau, inf, gamma, zeta
, temp_adj_m,
A_alpha_m, B_alpha_m, Vhalf_alpha_m,
A_beta_m, B_beta_m, Vhalf_beta_m
, temp_adj_h,
A_alpha_h, B_alpha_h, Vhalf_alpha_h,
A_beta_h, B_beta_h, Vhalf_beta_h,
A_inf_h, B_inf_h, Vhalf_inf_h
TABLE minf, mtau,hinf, htau
DEPEND celsius FROM -100 TO 100 WITH 2000
UNITSOFF
? There is a Q10 factor which will alter the tau of the gates
temp_adj_m = 2^((celsius - 24)/10)
temp_adj_h = 2^((celsius - 24)/10)
? *** Adding rate equations for gate: m ***
? Found a parameterised form of rate equation for alpha, using expression: A*((v-Vhalf)/B) / (1 - exp(-((v-Vhalf)/B)))
A_alpha_m = 2.880000018
B_alpha_m = 7.2
Vhalf_alpha_m = -20
alpha = A_alpha_m * vtrap((v - Vhalf_alpha_m), B_alpha_m)
? Found a parameterised form of rate equation for beta, using expression: A*((v-Vhalf)/B) / (1 - exp(-((v-Vhalf)/B)))
A_beta_m = 0.892800005
B_beta_m = -7.2
Vhalf_beta_m = -20
beta = A_beta_m * vtrap((v - Vhalf_beta_m), B_beta_m)
? Found a generic form of the rate equation for tau, using expression: 1/( (alpha + beta) * temp_adj_m ) < 0.02 ? (0.02 * temp_adj_m) : 1/(alpha + beta)
if (1/( (alpha + beta) * temp_adj_m ) < 0.02 ) {
tau = (0.02 * temp_adj_m)
} else {
tau = 1/(alpha + beta)
}
mtau = tau/temp_adj_m
minf = alpha/(alpha + beta)
? *** Finished rate equations for gate: m ***
? *** Adding rate equations for gate: h ***
? Found a parameterised form of rate equation for alpha, using expression: A*((v-Vhalf)/B) / (1 - exp(-((v-Vhalf)/B)))
A_alpha_h = 0.045
B_alpha_h = 1.5
Vhalf_alpha_h = -35
alpha = A_alpha_h * vtrap((v - Vhalf_alpha_h), B_alpha_h)
? Found a parameterised form of rate equation for beta, using expression: A*((v-Vhalf)/B) / (1 - exp(-((v-Vhalf)/B)))
A_beta_h = 0.015
B_beta_h = -1.5
Vhalf_beta_h = -35
beta = A_beta_h * vtrap((v - Vhalf_beta_h), B_beta_h)
? Found a generic form of the rate equation for tau, using expression: 1/( (alpha + beta) * temp_adj_h ) < 0.5 ? (0.5 * temp_adj_h) : 1/(alpha + beta)
if (1/( (alpha + beta) * temp_adj_h ) < 0.5 ) {
tau = (0.5 * temp_adj_h)
} else {
tau = 1/(alpha + beta)
}
htau = tau/temp_adj_h
? Found a parameterised form of rate equation for inf, using expression: A / (1 + exp((v-Vhalf)/B))
A_inf_h = 1
B_inf_h = 4
Vhalf_inf_h = -40
inf = A_inf_h / (exp((v - Vhalf_inf_h) / B_inf_h) + 1)
hinf = inf
? *** Finished rate equations for gate: h ***
}
? Function to assist with parameterised expressions of type linoid/exp_linear
FUNCTION vtrap(VminV0, B) {
if (fabs(VminV0/B) < 1e-6) {
vtrap = (1 + VminV0/B/2)
}else{
vtrap = (VminV0 / B) /(1 - exp((-1 *VminV0)/B))
}
}
UNITSON
