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Kdr.mod
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Kdr.mod
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COMMENT
**************************************************
File generated by: neuroConstruct v1.6.0
**************************************************
This file holds the implementation in NEURON of the Cell Mechanism:
Kdr (Type: Channel mechanism, Model: Template based ChannelML file)
with parameters:
/channelml/@units = Physiological Units
/channelml/notes = ChannelML file containing a single Channel from De Schutter and Bower 1998
/channelml/ion/@name = k
/channelml/ion/@charge = 1
/channelml/ion/@default_erev = -85
/channelml/channel_type/@name = Kdr
/channelml/channel_type/@density = yes
/channelml/channel_type/status/@value = stable
/channelml/channel_type/status/comment = Agreement of generated NEURON to original NEURON mod. Agreement on GENESIS when v1.7.1 XSL is used
/channelml/channel_type/status/contributor/name = Padraig Gleeson
/channelml/channel_type/notes = Delayed rectifier type K current. Based on Roth et al's reimplementation of original GENESIS model in NEURON
/channelml/channel_type/authorList/modelAuthor[1]/name = De Schutter, E.
/channelml/channel_type/authorList/modelAuthor[2]/name = Bower, J.
/channelml/channel_type/authorList/modelTranslator[1]/name = Padraig Gleeson
/channelml/channel_type/authorList/modelTranslator[1]/institution = UCL
/channelml/channel_type/authorList/modelTranslator[1]/email = p.gleeson - at - ucl.ac.uk
/channelml/channel_type/authorList/modelTranslator[2]/name = Jenny Davie
/channelml/channel_type/authorList/modelTranslator[2]/institution = UCL
/channelml/channel_type/authorList/modelTranslator[2]/comment = Conversion of GENESIS model to NEURON
/channelml/channel_type/authorList/modelTranslator[3]/name = Arnd Roth
/channelml/channel_type/authorList/modelTranslator[3]/institution = UCL
/channelml/channel_type/authorList/modelTranslator[3]/comment = Conversion of GENESIS model to NEURON
/channelml/channel_type/authorList/modelTranslator[4]/name = Volker Steuber
/channelml/channel_type/authorList/modelTranslator[4]/institution = UCL
/channelml/channel_type/authorList/modelTranslator[4]/comment = Conversion of GENESIS model to NEURON
/channelml/channel_type/authorList/modelTranslator[5]/name = Michael Hausser
/channelml/channel_type/authorList/modelTranslator[5]/institution = UCL
/channelml/channel_type/authorList/modelTranslator[5]/comment = Conversion of GENESIS model to NEURON
/channelml/channel_type/publication/fullTitle = De Schutter, E., and Bower, J. M. (1994). An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. J Neurop ...
/channelml/channel_type/publication/pubmedRef = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=7512629
/channelml/channel_type/neuronDBref/modelName = K channels
/channelml/channel_type/neuronDBref/uri = http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3
/channelml/channel_type/current_voltage_relation/ohmic/@ion = k
/channelml/channel_type/current_voltage_relation/ohmic/conductance/@default_gmax = 600
/channelml/channel_type/current_voltage_relation/ohmic/conductance/rate_adjustments/q10_settings/@q10_factor = 3
/channelml/channel_type/current_voltage_relation/ohmic/conductance/rate_adjustments/q10_settings/@experimental_temp = 37
/channelml/channel_type/current_voltage_relation/ohmic/conductance/gate[1]/@power = 2
/channelml/channel_type/current_voltage_relation/ohmic/conductance/gate[1]/state/@name = m
/channelml/channel_type/current_voltage_relation/ohmic/conductance/gate[1]/state/@fraction = 1
/channelml/channel_type/current_voltage_relation/ohmic/conductance/gate[2]/@power = 1
/channelml/channel_type/current_voltage_relation/ohmic/conductance/gate[2]/state/@name = h
/channelml/channel_type/current_voltage_relation/ohmic/conductance/gate[2]/state/@fraction = 1
/channelml/channel_type/hh_gate[1]/@state = m
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/@type = linoid
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/@expr = A*(k*(v-d))/(1 - exp(-(k*(v-d))))
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/parameter[1]/@name = A
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/parameter[1]/@value = 0.282
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/parameter[2]/@name = k
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/parameter[2]/@value = 0.08333333
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/parameter[3]/@name = d
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/alpha/parameterised_hh/parameter[3]/@value = 8
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/@type = exponential
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/@expr = A*exp(k*(v-d))
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/parameter[1]/@name = A
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/parameter[1]/@value = 5
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/parameter[2]/@name = k
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/parameter[2]/@value = -0.0333333
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/parameter[3]/@name = d
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/beta/parameterised_hh/parameter[3]/@value = -127
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/@type = linoid
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/@expr = A*(k*(v-d))/(1 - exp(-(k*(v-d))))
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/parameter[1]/@name = A
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/parameter[1]/@value = 0.282
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/parameter[2]/@name = k
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/parameter[2]/@value = 0.08333333
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/parameter[3]/@name = d
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/gamma/parameterised_hh/parameter[3]/@value = -12
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/@type = exponential
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/@expr = A*exp(k*(v-d))
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/parameter[1]/@name = A
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/parameter[1]/@value = 5
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/parameter[2]/@name = k
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/parameter[2]/@value = -0.0333333
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/parameter[3]/@name = d
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/zeta/parameterised_hh/parameter[3]/@value = -147
/channelml/channel_type/hh_gate[1]/transition/voltage_gate/tau/generic_equation_hh/@expr = 1/(gamma + zeta)
/channelml/channel_type/hh_gate[2]/@state = h
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/tau/generic_equation_hh/@expr = v < -25 ? 1200 : 10
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/@type = sigmoid
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/@expr = A/(1 + exp(k*(v-d)))
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/parameter[1]/@name = A
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/parameter[1]/@value = 1
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/parameter[2]/@name = k
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/parameter[2]/@value = 0.25
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/parameter[3]/@name = d
/channelml/channel_type/hh_gate[2]/transition/voltage_gate/inf/parameterised_hh/parameter[3]/@value = -25
/channelml/channel_type/impl_prefs/comment = Note, Using the NEURON mod file impl settings to get a closer match
/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 = 200
// File from which this was generated: /Users/hashmup/nC_projects/PurkinjeCell.ncx/cellMechanisms/Kdr/Kdr_Chan.xml
// XSL file with mapping to simulator: /Users/hashmup/nC_projects/PurkinjeCell.ncx/cellMechanisms/Kdr/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 from De Schutter and Bower 1998
ENDCOMMENT
TITLE Channel: Kdr
COMMENT
Delayed rectifier type K current. Based on Roth et al's reimplementation of original GENESIS model in NEURON
ENDCOMMENT
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(S) = (siemens)
(um) = (micrometer)
(molar) = (1/liter)
(mM) = (millimolar)
(l) = (liter)
}
NEURON {
SUFFIX Kdr
USEION k READ ek WRITE ik VALENCE 1 ? reversal potential of ion is read, outgoing current is written
RANGE gmax, gion
RANGE minf, mtau
RANGE hinf, htau
}
PARAMETER {
gmax = 0.6 (S/cm2) ? default value, should be overwritten when conductance placed on cell
}
ASSIGNED {
v (mV)
celsius (degC)
? Reversal potential of k
ek (mV)
? The outward flow of ion: k calculated by rate equations...
ik (mA/cm2)
gion (S/cm2)
minf
mtau (ms)
hinf
htau (ms)
}
BREAKPOINT {
SOLVE states METHOD cnexp
gion = gmax*((1*m)^2)*((1*h)^1)
ik = gion*(v - ek)
}
INITIAL {
ek = -85
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, k_alpha_m, d_alpha_m, A_beta_m, k_beta_m, d_beta_m, A_gamma_m, k_gamma_m, d_gamma_m, A_zeta_m, k_zeta_m, d_zeta_m, A_tau_m, k_tau_m, d_tau_m, temp_adj_h, A_tau_h, k_tau_h, d_tau_h, A_inf_h, k_inf_h, d_inf_h
TABLE minf, mtau,hinf, htau
DEPEND celsius
FROM -100 TO 100 WITH 200
UNITSOFF
? There is a Q10 factor which will alter the tau of the gates
temp_adj_m = 3^((celsius - 37)/10)
temp_adj_h = 3^((celsius - 37)/10)
? *** Adding rate equations for gate: m ***
? Found a parameterised form of rate equation for alpha, using expression: A*(k*(v-d)) / (1 - exp(-(k*(v-d))))
A_alpha_m = 0.282
k_alpha_m = 0.08333333
d_alpha_m = 8
alpha = A_alpha_m * vtrap((v - d_alpha_m), (1/k_alpha_m))
? Found a parameterised form of rate equation for beta, using expression: A*exp(k*(v-d))
A_beta_m = 5
k_beta_m = -0.0333333
d_beta_m = -127
beta = A_beta_m * exp((v - d_beta_m) * k_beta_m)
? Found a parameterised form of rate equation for gamma, using expression: A*(k*(v-d)) / (1 - exp(-(k*(v-d))))
A_gamma_m = 0.282
k_gamma_m = 0.08333333
d_gamma_m = -12
gamma = A_gamma_m * vtrap((v - d_gamma_m), (1/k_gamma_m))
? Found a parameterised form of rate equation for zeta, using expression: A*exp(k*(v-d))
A_zeta_m = 5
k_zeta_m = -0.0333333
d_zeta_m = -147
zeta = A_zeta_m * exp((v - d_zeta_m) * k_zeta_m)
? Found a generic form of the rate equation for tau, using expression: 1/(gamma + zeta)
tau = 1/(gamma + zeta)
mtau = tau/temp_adj_m
minf = alpha/(alpha + beta)
? *** Finished rate equations for gate: m ***
? *** Adding rate equations for gate: h ***
? Found a generic form of the rate equation for tau, using expression: v < -25 ? 1200 : 10
if (v < -25 ) {
tau = 1200
} else {
tau = 10
}
htau = tau/temp_adj_h
? Found a parameterised form of rate equation for inf, using expression: A / (1 + exp(k*(v-d)))
A_inf_h = 1
k_inf_h = 0.25
d_inf_h = -25
inf = A_inf_h / (exp((v - d_inf_h) * k_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