XPP model

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

#CA3_cell_fastslow_q.ode
#Atherton et al., 2016

#
#
#Declare parameters
param q=0.0001
param Is=0.3, Id=0.0, gCa_h=10.0, gKCa_h=15
param p=0.5, C_h=3, gL=0.1
param VL=-60, gNa_h=30, VNa_h=60
param gK_h=15, VK_h=-75
param VCa_h=80, gKAHP_h=0.8, gsd=2.1
param tau_AMPA=2
param gAMPA_PP_h=1e-0.6, VAMPA=0, tau_GABA_IP=7
param gGABA_IP_h=1e-06, VGABA=-75

#
# Define some functions
alpham=0.32*(-46.9-Vs)/(exp((-46.9-Vs)/4)-1)
betam=0.28*(Vs+19.9)/(exp((Vs+19.9)/5)-1)
m_inf=alpham/(alpham + betam)
alphah=0.128*exp((-43-Vs)/18)
betah=4./(1+exp((-20-Vs)/5))
alphan=0.016*(-24.9-Vs)/(exp((-24.9-Vs)/5)-1)
betan=0.25*exp(-1-0.025*Vs)
alphas=1.6 / (exp(-0.072*(Vd-5))+1)
betas=0.02*(Vd+8.9)/(exp((Vd+8.9)/5)-1)
qinf=(0.7894*exp(0.0002726*Ca))-(0.7292*exp(-0.01672*Ca))
tauq=(657.9*exp(-0.02023*Ca))+(301.8*exp(-0.002381*Ca))
cinf=(1.0/(1.0+exp((-10.1-Vd)/0.1016)))^0.00925
tauc=3.627*exp(0.03704*Vd)

#
# Define the fixed variables
I_Ls=gL*(Vs-VL)
I_Na=gNa_h*(m_inf^2)*h*(Vs-VNa_h)
I_K=gK_h*n*(Vs-VK_h)
I_sd=gsd*(Vs-Vd)
I_Ld=gL*(Vd-VL)
I_Ca=gCa_h*(s^2)*(Vd-VCa_h)
I_KAHP=gKAHP_h*q*(Vd-VK_h)
I_KCa=gKCa_h*c*(1.073*sin(0.003453*Ca+0.08095) + 0.08408*sin(0.01634*Ca-2.34) + 0.01811*sin(0.0348*Ca-0.9918))*(Vd-VK_h)


# Define the right-hand sides
Vs'=(-(I_Ls + I_Na + I_K) - I_sd/p + Is/p)/C_h
Vd'=(-( I_Ld + I_Ca + I_KAHP + I_KCa ) + I_sd/(1-p) + Id/(1-p))/C_h
Ca'=(-0.13*I_Ca - 0.075*Ca)
h'=(alphah - h*(alphah + betah))
n'=(alphan - n*(alphan + betan))
s'=(alphas - s*(alphas + betas))
#q'=(qinf-q)/tauq
c'=(cinf-c)/tauc


# Initial conditions
init Vs= -62.89223689
init Vd= -62.98248752
init Ca=0.21664282
init h=0.99806345
init n=0.00068604
init s=0.01086703
#init q=0.0811213
init c=0.00809387

#init sAMPA_PP=0
#init sGABA_IP=0

#
@ meth=cvode, toler=1.0e-10, atoler=1.0e-10, dt=0.05, total=10000
@ maxstore=10000000, bounds=10000000, noutput=10
@ xp=t, yp=vs, xlo=0, xhi=10000, ylo=-120, yhi=40

@ ntst=100.,nmax=2000000.,npr=2000000.,dsmin=0.00001,dsmax=0.5,ds=0.1,parmin=-500,parmax=500.
@ epsl=1e-08, epsu=1e-08, epss=1e-06, normmax=1000000
@ autoxmin=-100.,autoxmax=100,autoymin=-120.,autoymax=40.

done
This file has been produced by sbmlutils.

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.


Model :

id
name
time
substance
extent
volume
area
length
Access SBML model  L3V1

FunctionDefinitions [4] 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

Parameters [51] name constant value unit derived unit sbo cvterm
q q = 0.0001 0.0001 None
is is = 0.3 0.3 None
id id = 0.0 0.0 None
gca_h gca_h = 10.0 10.0 None
gkca_h gkca_h = 15 15.0 None
p p = 0.5 0.5 None
c_h c_h = 3 3.0 None
gl gl = 0.1 0.1 None
vl vl = -60 -60.0 None
gna_h gna_h = 30 30.0 None
vna_h vna_h = 60 60.0 None
gk_h gk_h = 15 15.0 None
vk_h vk_h = -75 -75.0 None
vca_h vca_h = 80 80.0 None
gkahp_h gkahp_h = 0.8 0.8 None
gsd gsd = 2.1 2.1 None
tau_ampa tau_ampa = 2 2.0 None
gampa_pp_h gampa_pp_h 0.0 None
vampa vampa = 0 0.0 None
tau_gaba_ip tau_gaba_ip = 7 7.0 None
ggaba_ip_h ggaba_ip_h = 1e-06 1e-06 None
vgaba vgaba = -75 -75.0 None
vs vs = -62.89223689 -62.89223689 None
vd vd = -62.98248752 -62.98248752 None
ca ca = 0.21664282 0.21664282 None
h h = 0.99806345 0.99806345 None
n n = 0.00068604 0.00068604 None
s s = 0.01086703 0.01086703 None
c c = 0.00809387 0.00809387 None
alpham 0.0 dimensionless None
betam 0.0 dimensionless None
m_inf 0.0 dimensionless None
alphah 0.0 dimensionless None
betah 0.0 dimensionless None
alphan 0.0 dimensionless None
betan 0.0 dimensionless None
alphas 0.0 dimensionless None
betas 0.0 dimensionless None
qinf 0.0 dimensionless None
tauq 0.0 dimensionless None
cinf 0.0 dimensionless None
tauc 0.0 dimensionless None
i_ls 0.0 dimensionless None
i_na 0.0 dimensionless None
i_k 0.0 dimensionless None
i_sd 0.0 dimensionless None
i_ld 0.0 dimensionless None
i_ca 0.0 dimensionless None
i_kahp 0.0 dimensionless None
i_kca 0.0 dimensionless None
t model time 0.0 dimensionless None

InitialAssignments [1] name assignment derived units sbo cvterm
gampa_pp_h = None None

Rules [29]   assignment name derived units sbo cvterm
d vs/dt = i_ls i_na i_k i_sd p is p c_h None
d vd/dt = i_ld i_ca i_kahp i_kca i_sd 1 p id 1 p c_h None
d ca/dt = 0.13 i_ca 0.075 ca None
d h/dt = alphah h alphah betah None
d n/dt = alphan n alphan betan None
d s/dt = alphas s alphas betas None
d c/dt = cinf c tauc None
alpham = 0.32 46.9 vs 46.9 vs 4 1 None
betam = 0.28 vs 19.9 vs 19.9 5 1 None
m_inf = alpham alpham betam None
alphah = 0.128 43 vs 18 None
betah = 4 1 20 vs 5 None
alphan = 0.016 24.9 vs 24.9 vs 5 1 None
betan = 0.25 1 0.025 vs None
alphas = 1.6 0.072 vd 5 1 None
betas = 0.02 vd 8.9 vd 8.9 5 1 None
qinf = 0.7894 0.0002726 ca 0.7292 0.01672 ca None
tauq = 657.9 0.02023 ca 301.8 0.002381 ca None
cinf = 1 1 10.1 vd 0.1016 0.00925 None
tauc = 3.627 0.03704 vd None
i_ls = gl vs vl None
i_na = gna_h m_inf 2 h vs vna_h None
i_k = gk_h n vs vk_h None
i_sd = gsd vs vd None
i_ld = gl vd vl None
i_ca = gca_h s 2 vd vca_h None
i_kahp = gkahp_h q vd vk_h None
i_kca = gkca_h c 1.073 0.003453 ca 0.08095 0.08408 0.01634 ca 2.34 0.01811 0.0348 ca 0.9918 vd vk_h None
t = time None