XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
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#Simulation of pituitary GH(3) cells, firing of action potentials with three slow variable #IK(erg) was incorporated. gkatp channels were regulated. # Wu SN and Chang HD, Diethyl pyrocarbonate, a histidine-modifying agent, # directly stimulate activity of ATP-sensitive potassium channels in pituitary GH(3) cells. # Biochem Pharmacol 2005 Dec 19; [Epub ahead of print]. #units: V=mV; t=ms; g=pS; I=fA #Reference: Bertram and Sherman. #Calcium-based model for pituitary GH3 cells # #Ica- calcium current #Ik- delayed rectifier K+ current #Ik(Ca)- Ca2+ dependent K+ current #Ik(ATP)- nucleotide-sensitive K+ current #Iir- erg-like K+ current #c - cytosolic free Ca2+ concentration #cer - ER Ca2+ concentration #initial conditions init v=-60.0, c=0.10, n=0.01, cer=100, a=0.46, nIR=0.008, rIR=0.282 #parameters par gca=1000, gkca=900, gk=1400, gir=5 par vca=50, vk=-75, vir=-75, cm=5300 par taun=16, alpha=4.5e-6 par fcyt=0.01, kpmca=0.2, kd=0.3 par vn=-16, vm=-20, sn=5, sm=12 par kserca=0.4, dact=0.35, dinact=0.4 par fer=0.01, pleak=0.0005, dip3=0.5, vcytver=5 par ip3=0, sa=0.1, r=0.14 taua=300000 par tstim=3e4 gkatp=if(t<tstim)then(500)else(530) # Iir parameters alphaIRn(v) = 0.09/(1+exp(0.11*(v+100))) betaIRn(v) = 0.00035*exp(0.07*(v+25)) nIRinf(v) = 1/(1+betaIRn(v)/alphaIRn(v)) tauIRn(v) = 1/(alphaIRn(v) + betaIRn(v)) alphaIRr(v) = 30/(1+exp(0.04*(v+230))) betaIRr(v) = 0.15/(1+exp(-0.05*(v+120))) rIRinf(v) = 1/(1+betaIRr(v)/alphaIRr(v)) tauIRr(v) = 1/(alphaIRr(v) + betaIRr(v)) #Iir activation and inactivation functions nIR' = (nIRinf(v) - nIR)/tauIRn(v) rIR' = (rIRinf(v) - rIR)/tauIRr(v) # ionic currents ica(v)=gca*minf(v)*(v-vca) ik(v)=gk*n*(v-vk) ikca(v)=gkca*w*(v-vk) ikatp(v)=gkatp*a*(v-vk) iir(v)=gir*nIR*rIR*(v-vir) #activation functions minf(v)=1.0/(1.0+exp((vm-v)/sm)) ninf(v)=1.0/(1.0+exp((vn-v)/sn)) ainf(c)=1.0/(1.0+exp((r-c)/sa)) #fraction of K(Ca) channels activated by cytosolic Ca2+ w=c^5/(c^5+kd^5) #flux of Ca2+ through the membrane jmem=-(alpha*Ica(v)+kpmca*c) #Ca2+ influx into the ER via SERCA jserca=kserca*c #efflux out of the ER has two components # 1. Ca2+ leak is proportional to gradient between Ca2+ and ER jleak=pleak*(cer-c) # 2. Ca2+ efflux through the IP3R jip3=oinf*(cer-c) #fraction of open channels oinf=(c/(dact+c))*(ip3/(dip3+ip3))*(dinact/(dinact+c)) #net Ca2+ efflux from the ER jer=jleak+jip3-jserca #differential equations v'=-(ica(v)+ik(v)+ikca(v)+ikatp(v)+iir(v))/cm n'=(ninf(v)-n)/taun c'=fcyt*(jmem+jer) cer'=-fer*(vcytver)*jer a'=(ainf(c)-a)/taua aux tsec=t/1000.0 @ meth=cvode, dtmax=1, dt=2, total=8e4, maxstor=80000 @ bounds=1000, xp=tsec, yp=v, toler=1.0e-7, atoler=1.0e-7 @ xlo=0, xhi=80, ylo=-80, yhi=5 done
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Copyright © 2017 Matthias Koenig
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Model :
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type | FunctionDefinitions [20] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | max
|
minimum | |||
FunctionDefinition | min
|
maximum | |||
FunctionDefinition | heav
|
heavyside | |||
FunctionDefinition | mod
|
modulo | |||
FunctionDefinition | alphairn
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FunctionDefinition | betairn
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FunctionDefinition | nirinf
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FunctionDefinition | tauirn
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FunctionDefinition | alphairr
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FunctionDefinition | betairr
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FunctionDefinition | ririnf
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FunctionDefinition | tauirr
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FunctionDefinition | ica
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FunctionDefinition | ik
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FunctionDefinition | ikca
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FunctionDefinition | ikatp
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FunctionDefinition | iir
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FunctionDefinition | minf
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FunctionDefinition | ninf
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FunctionDefinition | ainf
|
type | Parameters [46] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | v
|
v = -60.0 | F | -60.0 | None | |||
Parameter | c
|
c = 0.10 | F | 0.1 | None | |||
Parameter | n
|
n = 0.01 | F | 0.01 | None | |||
Parameter | cer
|
cer = 100 | F | 100.0 | None | |||
Parameter | a
|
a = 0.46 | F | 0.46 | None | |||
Parameter | nir
|
nir = 0.008 | F | 0.008 | None | |||
Parameter | rir
|
rir = 0.282 | F | 0.282 | None | |||
Parameter | gca
|
gca = 1000 | F | 1000.0 | None | |||
Parameter | gkca
|
gkca = 900 | F | 900.0 | None | |||
Parameter | gk
|
gk = 1400 | F | 1400.0 | None | |||
Parameter | gir
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gir = 5 | F | 5.0 | None | |||
Parameter | vca
|
vca = 50 | F | 50.0 | None | |||
Parameter | vk
|
vk = -75 | F | -75.0 | None | |||
Parameter | vir
|
vir = -75 | F | -75.0 | None | |||
Parameter | cm
|
cm = 5300 | F | 5300.0 | None | |||
Parameter | taun
|
taun = 16 | F | 16.0 | None | |||
Parameter | alpha
|
alpha = 4.5e-6 | F | 4.5e-06 | None | |||
Parameter | fcyt
|
fcyt = 0.01 | F | 0.01 | None | |||
Parameter | kpmca
|
kpmca = 0.2 | F | 0.2 | None | |||
Parameter | kd
|
kd = 0.3 | F | 0.3 | None | |||
Parameter | vn
|
vn = -16 | F | -16.0 | None | |||
Parameter | vm
|
vm = -20 | F | -20.0 | None | |||
Parameter | sn
|
sn = 5 | F | 5.0 | None | |||
Parameter | sm
|
sm = 12 | F | 12.0 | None | |||
Parameter | kserca
|
kserca = 0.4 | F | 0.4 | None | |||
Parameter | dact
|
dact = 0.35 | F | 0.35 | None | |||
Parameter | dinact
|
dinact = 0.4 | F | 0.4 | None | |||
Parameter | fer
|
fer = 0.01 | F | 0.01 | None | |||
Parameter | pleak
|
pleak = 0.0005 | F | 0.0005 | None | |||
Parameter | dip3
|
dip3 = 0.5 | F | 0.5 | None | |||
Parameter | vcytver
|
vcytver = 5 | F | 5.0 | None | |||
Parameter | ip3
|
ip3 = 0 | F | 0.0 | None | |||
Parameter | sa
|
sa = 0.1 | F | 0.1 | None | |||
Parameter | r
|
r = 0.14 | F | 0.14 | None | |||
Parameter | taua
|
taua = 300000 | F | 300000.0 | None | |||
Parameter | tstim
|
tstim = 3e4 | F | 30000.0 | None | |||
Parameter | gkatp
|
F | 0.0 | dimensionless | None | |||
Parameter | w
|
F | 0.0 | dimensionless | None | |||
Parameter | jmem
|
F | 0.0 | dimensionless | None | |||
Parameter | jserca
|
F | 0.0 | dimensionless | None | |||
Parameter | jleak
|
F | 0.0 | dimensionless | None | |||
Parameter | jip3
|
F | 0.0 | dimensionless | None | |||
Parameter | oinf
|
F | 0.0 | dimensionless | None | |||
Parameter | jer
|
F | 0.0 | dimensionless | None | |||
Parameter | tsec
|
F | 0.0 | dimensionless | None | |||
Parameter | t
|
model time | F | 0.0 | dimensionless | None |
type | Rules [17] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | d nir/dt
|
= | None | ||||
Rule | d rir/dt
|
= | None | ||||
Rule | d v/dt
|
= | None | ||||
Rule | d n/dt
|
= | None | ||||
Rule | d c/dt
|
= | None | ||||
Rule | d cer/dt
|
= | None | ||||
Rule | d a/dt
|
= | None | ||||
Rule | gkatp
|
= | None | ||||
Rule | w
|
= | None | ||||
Rule | jmem
|
= | None | ||||
Rule | jserca
|
= | None | ||||
Rule | jleak
|
= | None | ||||
Rule | jip3
|
= | None | ||||
Rule | oinf
|
= | None | ||||
Rule | jer
|
= | None | ||||
Rule | tsec
|
= | None | ||||
Rule | t
|
= | None |