XPP model

This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6.

# Modified Morris-Lecar model from Prescott (2008, 2008) + T-current from Rubin (2004)
# modified from ml_salka.ode

#stim used in experiments, mean=0, std=0.1
table Iext stim.tab
#Iext(t)=0

nd=normal(0,0.3)
par dc_noise=6.9511
aux noise=dc_noise+nd

dV/dt = (i_dc(t)+amp*Iext(t)+dc_noise+nd-gna*minf(V)*(V-Vna)-gk*y*(V-VK)-gl*(V-Vl)-itf(V,mtinf(V),h)-gadap*z*(V-VK))/c
dy/dt = phi_y*(yinf(V)-y)/tauy(V)
dh/dt = qht*(htinf(V)-h)/tauht(V)
dz/dt = alpha_z*(zinf(V)-z)
par c=2


i_dc(t)=idc
# idc is -20.89 voor -80, -2 voor -70, 16.27 voor -60, 31.43 voor -50
par idc=32
par amp=150
aux stim=i_dc(t)+amp*Iext(t)

init V=-50, y=0, h=0, z=0

# FAST INWARD CURRENT (INa or activation variable)
# This is assumed to activate instantaneously with changes in voltage
# voltage-dependent activation curve is described by m
minf(V)=.5*(1+tanh((V-beta_m)/gamma_m))
# maximal conductance and reversal potential
par beta_m=-1.2,gamma_m=18
par gna=20,vna=50

# DELAYED RECTIFIER CURRENT (IKdr or recovery variable)
# this current activates more slowly than INa
# In this code, activation of IKdr is controlled by y
yinf(V)=.5*(1+tanh((V-beta_y)/gamma_y))
tauy(V)=1/cosh((V-beta_y)/(2*gamma_y))
# in the 2D model, varying beta_w shifts the w activation curve (w=y here) and can convert the neuron between class 1, 2, and 3 
par beta_y=0, gamma_y=10
# maximal conductance and reversal potential
par gk=20, vk=-100, phi_y=0.15

# LEAK CURRENT (Il)
# just a passive leak conductance
par gl=2, vl=-70

# T CURRENT (IT)
itf(v,mt,ht)=gtbar*mt^2*ht*v
# fast (instantaneous) activation
mtinf(v)  = 1/(1+exp(-(v+60)/6.2)) 
# slow inactivation
htinf(v)  = 1/(1+exp((v+84)/4))
tauht(v)=(28+apt*exp((v+25)/(-10.5)))
par gtbar=20,qht=2.5,apt=1

# Adaptation current
zinf(v)=1/(1+exp((beta_z-v)/gamma_z))
# deze parameters zijn om hem op Destexhe 1993 K2 stroom te laten lijken
# par beta_z=-43, gamma_z=17, alpha_z=0.08, gadap=2
# Deze zijn voor de 'AHP-stroom'
par beta_z=0, gamma_z=5, alpha_z=0.005, gadap=40
# en deze voor de 'M-stroom'
#par beta_z=-35, gamma_z=5, alpha_z=0.005, gadap=2
# NB alpha_z lijk op 1/tau 

# following parameters control duration of simulation and axes of default plot
@ total=303000,xlo=0,xhi=6000,ylo=-100,yhi=50
#@ total=12000,xlo=0,xhi=6000,ylo=-100,yhi=50
@ meth=euler, dt=0.1, bounds=1000     
@ MAXSTOR=3030010
@ OUTPUT=prescott_rubin_adap.dat

done
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Terms of use

Copyright © 2017 Matthias Koenig

Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


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Access SBML model  L3V1

FunctionDefinitions [13] name math sbo cvterm
max minimum x y x x y y
min maximum x y x x y y
heav heavyside x 0 x 0 0.5 x 0 1 x 0 0
mod modulo x y x y x y x 0 y 0 x y x y
i_dc t idc idc
minf v beta_m gamma_m 0.5 1 v beta_m gamma_m
yinf v beta_y gamma_y 0.5 1 v beta_y gamma_y
tauy v beta_y gamma_y 1 v beta_y 2 gamma_y
itf v mt ht gtbar gtbar mt 2 ht v
mtinf v 1 1 v 60 6.2
htinf v 1 1 v 84 4
tauht v apt 28 apt v 25 10.5
zinf v beta_z gamma_z 1 1 beta_z v gamma_z

Parameters [30] name constant value unit derived unit sbo cvterm
dc_noise dc_noise = 6.9511 6.9511 None
c c = 2 2.0 None
idc idc = 32 32.0 None
amp amp = 150 150.0 None
v v = -50 -50.0 None
y y = 0 0.0 None
h h = 0 0.0 None
z z = 0 0.0 None
beta_m beta_m = -1.2 -1.2 None
gamma_m gamma_m = 18 18.0 None
gna gna = 20 20.0 None
vna vna = 50 50.0 None
beta_y beta_y = 0 0.0 None
gamma_y gamma_y = 10 10.0 None
gk gk = 20 20.0 None
vk vk = -100 -100.0 None
phi_y phi_y = 0.15 0.15 None
gl gl = 2 2.0 None
vl vl = -70 -70.0 None
gtbar gtbar = 20 20.0 None
qht qht = 2.5 2.5 None
apt apt = 1 1.0 None
beta_z beta_z = 0 0.0 None
gamma_z gamma_z = 5 5.0 None
alpha_z alpha_z = 0.005 0.005 None
gadap gadap = 40 40.0 None
nd 0.0 dimensionless None
noise 0.0 dimensionless None
stim 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [8]   assignment name derived units sbo cvterm
d v/dt = i_dc t idc amp iext t dc_noise nd gna minf v beta_m gamma_m v vna gk y v vk gl v vl itf v mtinf v h gtbar gadap z v vk c None
d y/dt = phi_y yinf v beta_y gamma_y y tauy v beta_y gamma_y None
d h/dt = qht htinf v h tauht v apt None
d z/dt = alpha_z zinf v beta_z gamma_z z None
nd = normal 0 0.3 None
noise = dc_noise nd None
stim = i_dc t idc amp iext t None
t = time None