XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
# The model consists of one DA neuron and one GABA neuron # for a reduced model set spike-producing currents (fast sodium and delayed rectifier potassium currents) to 0 # Injected currents to DA and GABA neurons par I=0, Iapp=0 # ===============DA neuron===================== # Synaptic conductances par gbarnmda=0, ggaba=0,gampa=0 # Reversal potentials par ECa=50., EK=-90., ENa=55., ENMDA=0., EAMPA=0., Egaba=-90.,Eh=-20. # Leak current par gL=0.18, EL=-35 IL=gL*(EL-v) # H-current par vhh=-95, slh=8, th0=625, vtauh=-112, gbarh=2 hinf(v)=1/(1+exp((v-vhh)/slh)) tauh(v)=th0*exp(0.075*(v-vtauh))/(1+exp(0.083*(v-vtauh))) Ih=gbarh*q*(Eh-v) # subthreshold Na current par gSNa=0.13, vhna=-50, slna=5 na(v)=1/(1+exp(-(v-vhna)/slna)) Isna=gSNa*na(v)*(Ena-v) # SK current par gbarKCa=7.8, k=160 gKCa(x)=gbarKCa*(x**4)/((x**4) + (k**4)) IKCa=gKCa(u)*(EK-v) # Instantaneous K+ current par gbarK=1., vHk=-10, vSk=7 gK(x)=gbarK/(1. + exp(-(x-vHk)/vSk)) IK=gK(v)*(EK-v) # Ca2+ balance parameters & constants par caLeak=0.1, caNMDA=0, buf=0.00023, r=0.2, tc=0.52, zF=.019298 # Ca2+ current par gbarCa=2.5, Vcah=-52, Sca=3., CaConst=0.016 alphac(V)=if (abs(V-Vcah)>0.00001) then (-0.0032*(V-Vcah)/(exp(-(V-Vcah)/Sca) - 1.)) else (-0.0032*0.00001/(exp(-0.00001/Sca)-1.)) betac(V)=0.05*exp(-(V-Vcah+5.)/40.) csinf(V)=alphac(V)/(alphac(V)+betac(V)) gCa(V)=gbarCa*(csinf(V)**4) Ica=gCa(v)*(ECa-v) # Na+ current par th=0.05, gbarNa=50; alpham(V)=-0.32*(V+31.)/(exp(-(V+31.)/4.) - 1.) betam(V)=0.28*(V+4.)/(exp((V+4.)/5.) - 1.) minf(v)=alpham(v)/(alpham(v)+betam(v)) alphah(V)=0.2*th*exp(-((V+47.)/18.)) betah(V)=25.*th/(1.+(exp(-(V+24.)/5.))) gNa(v,h)=gbarNa*(minf(v)**3)*h Ina=gNa(v,h)*(ENa-v) # Delayed rectifier K+ current par Vdrh=-5, tk=1, gbarDR=2 alphan(V)=-0.0032*tk*(V+5.)/(exp(-(V-Vdrh)/10.) - 1.) betan(V)=0.05*tk*exp(-((V-Vdrh+5.)/16.)) Idr=gbarDR*(n**4)*(EK-v) # NMDA current par Mg=0.5, me=0.062 gnmda(v)=gbarnmda/(1+0.28*Mg*exp(-me*v)) aux nmda=gnmda(v) #nmdasig=1/(1+exp(-(-nmdathresh)/nmdasl)); Inmda=gnmda(v)*(ENMDA-v) # AMPA current Iampa=gampa*(EAMPA-v) #ampasig=1/(1+exp(-(y[2]*y[6]-ampathresh)/ampasl)); v'=Ica + IKCa + IK + IsNa + IL + Ih + Idr + Ina + Inmda +Iampa + ggaba*gaba*(Egaba-v) + I u'= 2.*buf*((gCa(v)+gL*caLeak+gnmda(v)*caNMDA)*(ECa - v)/zF - u/tc)/r h'= alphah(v)*(1.-h)-betah(v)*h n'= alphan(v)*(1.-n)-betan(v)*n q'= (hinf(v)-q)/tauh(v) # =================GABA neuron========================================== par glg=0.05, gbarnag=22, gbardrg=7, tng=1, thg=5, tbn=0.7, as=12, bs=0.1, vgnz=0, dg=0 par gampag=0, gnmdabarg=0; # N+ on GABA neuron amg(vgaba)=0.1*(vgaba+30.0)/(1.0-exp(-(vgaba+30.0)/10.0)) bmg(vgaba)=4.0*exp(-(vgaba+55.0)/18.0) minfgg(vgaba)=amg(vgaba)/(amg(vgaba)+bmg(vgaba)) ahg(vgaba)=0.07*exp(-(vgaba+53.0)/20.0) bhg(vgaba)=1.0/(1.0+exp(-(vgaba+23.0)/10.0)) gnag(vgaba,hg)=gbarnag*(minfgg(vgaba)**3)*hg Inag = gnag(vgaba,hg)*(55-vgaba) # K+ on GABA neuron ang(vgaba)=0.01*(vgaba+29.0)/(1.0-exp(-(vgaba+29.0)/10.0)) bng(vgaba)=tbn*0.125*exp(-(vgaba+39.0)/80.0) gdrg(vgaba,ng)=gbardrg*(ng**4) gnmdagg(vgaba)=gnmdabarg/(1+0.28*Mg*exp(-me*vgaba)) gspikeg(vgaba)=1/(1+exp(-vgaba/2)) Idrg = gdrg(vgaba,ng)*(-90-vgaba) # Leak current on GABA neuron ILg=glg*(-51-vgaba) vgaba' = ILg + Inag + Idrg + gnmdagg(vgaba)*(eNMDA-vgaba) + gampag*(eAMPA-vgaba) + Iapp ng'=tng*(ang(vgaba)*(1-ng))-bng(vgaba)*ng hg'=thg*(ahg(vgaba)*(1-hg))-bhg(vgaba)*hg gaba'=as*gspikeg(vgaba)*(1-gaba)-bs*(1-gspikeg(vgaba))*gaba init v=-60, u=50, vgaba=-40, ng=0, hg=0, gaba=0 @ MAXSTOR=40000,TOTAL=1000,bell=0,XP=v,YP=u @ BOUND=10000,DT=0.05,METH=stiff,YLO=40,YHI=130,XLO=-80,XHI=0 done
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Copyright © 2017 Matthias Koenig
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Model :
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type | FunctionDefinitions [33] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | max
|
minimum | |||
FunctionDefinition | min
|
maximum | |||
FunctionDefinition | heav
|
heavyside | |||
FunctionDefinition | mod
|
modulo | |||
FunctionDefinition | hinf
|
||||
FunctionDefinition | tauh
|
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FunctionDefinition | na
|
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FunctionDefinition | gkca
|
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FunctionDefinition | gk
|
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FunctionDefinition | alphac
|
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FunctionDefinition | betac
|
||||
FunctionDefinition | csinf
|
||||
FunctionDefinition | gca
|
||||
FunctionDefinition | alpham
|
||||
FunctionDefinition | betam
|
||||
FunctionDefinition | minf
|
||||
FunctionDefinition | alphah
|
||||
FunctionDefinition | betah
|
||||
FunctionDefinition | gna
|
||||
FunctionDefinition | alphan
|
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FunctionDefinition | betan
|
||||
FunctionDefinition | gnmda
|
||||
FunctionDefinition | amg
|
||||
FunctionDefinition | bmg
|
||||
FunctionDefinition | minfgg
|
||||
FunctionDefinition | ahg
|
||||
FunctionDefinition | bhg
|
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FunctionDefinition | gnag
|
||||
FunctionDefinition | ang
|
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FunctionDefinition | bng
|
||||
FunctionDefinition | gdrg
|
||||
FunctionDefinition | gnmdagg
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||||
FunctionDefinition | gspikeg
|
type | Parameters [80] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | i
|
i = 0 | F | 0.0 | None | |||
Parameter | iapp
|
iapp = 0 | F | 0.0 | None | |||
Parameter | gbarnmda
|
gbarnmda = 0 | F | 0.0 | None | |||
Parameter | ggaba
|
ggaba = 0 | F | 0.0 | None | |||
Parameter | gampa
|
gampa = 0 | F | 0.0 | None | |||
Parameter | eca
|
eca = 50. | F | 50.0 | None | |||
Parameter | ek
|
ek = -90. | F | -90.0 | None | |||
Parameter | ena
|
ena = 55. | F | 55.0 | None | |||
Parameter | enmda
|
enmda = 0. | F | 0.0 | None | |||
Parameter | eampa
|
eampa = 0. | F | 0.0 | None | |||
Parameter | egaba
|
egaba = -90. | F | -90.0 | None | |||
Parameter | eh
|
eh = -20. | F | -20.0 | None | |||
Parameter | gl
|
gl = 0.18 | F | 0.18 | None | |||
Parameter | el
|
el = -35 | F | -35.0 | None | |||
Parameter | vhh
|
vhh = -95 | F | -95.0 | None | |||
Parameter | slh
|
slh = 8 | F | 8.0 | None | |||
Parameter | th0
|
th0 = 625 | F | 625.0 | None | |||
Parameter | vtauh
|
vtauh = -112 | F | -112.0 | None | |||
Parameter | gbarh
|
gbarh = 2 | F | 2.0 | None | |||
Parameter | gsna
|
gsna = 0.13 | F | 0.13 | None | |||
Parameter | vhna
|
vhna = -50 | F | -50.0 | None | |||
Parameter | slna
|
slna = 5 | F | 5.0 | None | |||
Parameter | gbarkca
|
gbarkca = 7.8 | F | 7.8 | None | |||
Parameter | k
|
k = 160 | F | 160.0 | None | |||
Parameter | gbark
|
gbark = 1. | F | 1.0 | None | |||
Parameter | vhk
|
vhk = -10 | F | -10.0 | None | |||
Parameter | vsk
|
vsk = 7 | F | 7.0 | None | |||
Parameter | caleak
|
caleak = 0.1 | F | 0.1 | None | |||
Parameter | canmda
|
canmda = 0 | F | 0.0 | None | |||
Parameter | buf
|
buf = 0.00023 | F | 0.00023 | None | |||
Parameter | r
|
r = 0.2 | F | 0.2 | None | |||
Parameter | tc
|
tc = 0.52 | F | 0.52 | None | |||
Parameter | zf
|
zf = .019298 | F | 0.019298 | None | |||
Parameter | gbarca
|
gbarca = 2.5 | F | 2.5 | None | |||
Parameter | vcah
|
vcah = -52 | F | -52.0 | None | |||
Parameter | sca
|
sca = 3. | F | 3.0 | None | |||
Parameter | caconst
|
caconst = 0.016 | F | 0.016 | None | |||
Parameter | th
|
th = 0.05 | F | 0.05 | None | |||
Parameter | gbarna
|
gbarna = 50 | F | 50.0 | None | |||
Parameter | vdrh
|
vdrh = -5 | F | -5.0 | None | |||
Parameter | tk
|
tk = 1 | F | 1.0 | None | |||
Parameter | gbardr
|
gbardr = 2 | F | 2.0 | None | |||
Parameter | mg
|
mg = 0.5 | F | 0.5 | None | |||
Parameter | me
|
me = 0.062 | F | 0.062 | None | |||
Parameter | glg
|
glg = 0.05 | F | 0.05 | None | |||
Parameter | gbarnag
|
gbarnag = 22 | F | 22.0 | None | |||
Parameter | gbardrg
|
gbardrg = 7 | F | 7.0 | None | |||
Parameter | tng
|
tng = 1 | F | 1.0 | None | |||
Parameter | thg
|
thg = 5 | F | 5.0 | None | |||
Parameter | tbn
|
tbn = 0.7 | F | 0.7 | None | |||
Parameter | as
|
as = 12 | F | 12.0 | None | |||
Parameter | bs
|
bs = 0.1 | F | 0.1 | None | |||
Parameter | vgnz
|
vgnz = 0 | F | 0.0 | None | |||
Parameter | dg
|
dg = 0 | F | 0.0 | None | |||
Parameter | gampag
|
gampag = 0 | F | 0.0 | None | |||
Parameter | gnmdabarg
|
gnmdabarg = 0 | F | 0.0 | None | |||
Parameter | v
|
v = -60 | F | -60.0 | None | |||
Parameter | u
|
u = 50 | F | 50.0 | None | |||
Parameter | vgaba
|
vgaba = -40 | F | -40.0 | None | |||
Parameter | ng
|
ng = 0 | F | 0.0 | None | |||
Parameter | hg
|
hg = 0 | F | 0.0 | None | |||
Parameter | gaba
|
gaba = 0 | F | 0.0 | None | |||
Parameter | h
|
F | 0.0 | dimensionless | None | |||
Parameter | n
|
F | 0.0 | dimensionless | None | |||
Parameter | q
|
F | 0.0 | dimensionless | None | |||
Parameter | il
|
F | 0.0 | dimensionless | None | |||
Parameter | ih
|
F | 0.0 | dimensionless | None | |||
Parameter | isna
|
F | 0.0 | dimensionless | None | |||
Parameter | ikca
|
F | 0.0 | dimensionless | None | |||
Parameter | ik
|
F | 0.0 | dimensionless | None | |||
Parameter | ica
|
F | 0.0 | dimensionless | None | |||
Parameter | ina
|
F | 0.0 | dimensionless | None | |||
Parameter | idr
|
F | 0.0 | dimensionless | None | |||
Parameter | nmda
|
F | 0.0 | dimensionless | None | |||
Parameter | inmda
|
F | 0.0 | dimensionless | None | |||
Parameter | iampa
|
F | 0.0 | dimensionless | None | |||
Parameter | inag
|
F | 0.0 | dimensionless | None | |||
Parameter | idrg
|
F | 0.0 | dimensionless | None | |||
Parameter | ilg
|
F | 0.0 | dimensionless | None | |||
Parameter | t
|
model time | F | 0.0 | dimensionless | None |
type | Rules [24] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | d v/dt
|
= | None | ||||
Rule | d u/dt
|
= | None | ||||
Rule | d h/dt
|
= | None | ||||
Rule | d n/dt
|
= | None | ||||
Rule | d q/dt
|
= | None | ||||
Rule | d vgaba/dt
|
= | None | ||||
Rule | d ng/dt
|
= | None | ||||
Rule | d hg/dt
|
= | None | ||||
Rule | d gaba/dt
|
= | None | ||||
Rule | il
|
= | None | ||||
Rule | ih
|
= | None | ||||
Rule | isna
|
= | None | ||||
Rule | ikca
|
= | None | ||||
Rule | ik
|
= | None | ||||
Rule | ica
|
= | None | ||||
Rule | ina
|
= | None | ||||
Rule | idr
|
= | None | ||||
Rule | nmda
|
= | None | ||||
Rule | inmda
|
= | None | ||||
Rule | iampa
|
= | None | ||||
Rule | inag
|
= | None | ||||
Rule | idrg
|
= | None | ||||
Rule | ilg
|
= | None | ||||
Rule | t
|
= | None |