XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
# Soma is Hodgkin Huxley p Ek=-77,Ena=50, El=-54.4 p gl=.3,gkdr=36,gna=120 p i=11 p C=1. p amphi=.1,amhalf=-40,amwidth=10 p bmphi=4,bmhalf=-65,bmwidth=18 p ahphi=0.07,ahhalf=-65,ahwidth=20 p bhphi=1,bhhalf=-35,bhwidth=10 p anphi=.01,anhalf=-55,anwidth=10 p bnphi=.125,bnhalf=-65,bnwidth=80 # functions am(v)=amphi*(v-amhalf)/(1-exp(-(v-amhalf)/amwidth)) bm(v)=bmphi*exp(-(v-bmhalf)/bmwidth) ah(v)=ahphi*exp(-(v-ahhalf)/ahwidth) bh(v)=bhphi/(1+exp(-(v-bhhalf)/bhwidth)) an(v)=anphi*(v-anhalf)/(1-exp(-(v-anhalf)/anwidth)) bn(v)=bnphi*exp(-(v-bnhalf)/bnwidth) #currents ina(v,m,h)=gna*m^3*h*(v-Ena) ikdr(v,n)=gkdr*n^4*(v-Ek) il(v)=gl*(v-El) Isyn(v,y)=gsyn*y*(v-Esyn) #diff. equ. v1'=(i-(ina(v1,m1,ha)+ikdr(v1,n1)+il(v1)+p0*Isyn(v1,y2))+eps*(ua1-v1)/dx)/C v2'=(i-(ina(v2,m2,hb)+ikdr(v2,n2)+il(v2)+p0*Isyn(v2,y1))+eps*(ub1-v2)/dx)/C m1'=am(v1)*(1-m1)-bm(v1)*m1 m2'=am(v2)*(1-m2)-bm(v2)*m2 n1'=an(v1)*(1-n1)-bn(v1)*n1 n2'=an(v2)*(1-n2)-bn(v2)*n2 ha'=ah(v1)*(1-ha)-bh(v1)*ha hb'=ah(v2)*(1-hb)-bh(v2)*hb ## synapse parameter taur=1,taud=3,thresh=-30 x1'=(-x1+.5*(1+tanh((v1-thresh)/3.0)))/taur x2'=(-x2+.5*(1+tanh((v2-thresh)/3.0)))/taur y1'=(-y1+x1)/taud y2'=(-y2+x2)/taud init x1=.001, y1=.001,x2=.001, y2=.001 p gsyn=.1, Esyn=0 p Vp=-50, Vsp=9, gnad=0.02, gld=.1, taupna=10 # !!!! the cable is passive if gnad=0 !!!! pinfd(V)=1/(1+exp(-(V-Vp)/Vsp)) Ih(V,y)=gnad*y*(V-Ena)/gld Ild(V)=V-El ha[1..50]'=(pinfd(ua[j])-ha[j])/taupna hb[1..50]'=(pinfd(ub[j])-hb[j])/taupna # NOT TO CONFUSE WITH h GATE IN SOMA!! # cable equation ua1'=((lambda/dx)^2*(ua2-2*ua1+v1)-Ild(ua1)-Ih(ua1,ha1)-p1*Isyn(ua1,y2)/gld)/tau ua[2..50]'= ((lambda/dx)^2*(ua[j+1]-2*ua[j]+ua[j-1])-Ild(ua[j])-Ih(ua[j],ha[j]) -p[j]*Isyn(ua[j],y2)/gld )/tau ua51=(c1+b1*ua50/dx)/(a1+b1/dx) ub1'=((lambda/dx)^2*(ub2-2*ub1+v2)-Ild(ub1)-Ih(ub1,hb1)-p1*Isyn(ub1,y1)/gld)/tau ub[2..50]'= ((lambda/dx)^2*(ub[j+1]-2*ub[j]+ub[j-1])-Ild(ub[j])-Ih(ub[j],hb[j])-p[j]*Isyn(ub[j],y1)/gld )/tau ub51=(c1+b1*ub50/dx)/(a1+b1/dx) par lambda=1,tau=10,dx=.1,c1=0,a1=0,b1=1,c0=0,a0=0,b0=1,eps=.025 #pulse(t)=heav(t)*heav(sigma-t) par sigma=.05 par t0=14.45 aux prc=t0-t p p[0..50]=0 @ total=300,xlo=0,xhi=300,ylo=-100,yhi=60,dt=0.05,bounds=10000000 d
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Copyright © 2017 Matthias Koenig
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Model :
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type | FunctionDefinitions [17] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | max
|
minimum | |||
FunctionDefinition | min
|
maximum | |||
FunctionDefinition | heav
|
heavyside | |||
FunctionDefinition | mod
|
modulo | |||
FunctionDefinition | am
|
||||
FunctionDefinition | bm
|
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FunctionDefinition | ah
|
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FunctionDefinition | bh
|
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FunctionDefinition | an
|
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FunctionDefinition | bn
|
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FunctionDefinition | ina
|
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FunctionDefinition | ikdr
|
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FunctionDefinition | il
|
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FunctionDefinition | isyn
|
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FunctionDefinition | pinfd
|
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FunctionDefinition | ih
|
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FunctionDefinition | ild
|
type | Parameters [71] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | ek
|
ek = -77 | F | -77.0 | None | |||
Parameter | ena
|
ena = 50 | F | 50.0 | None | |||
Parameter | el
|
el = -54.4 | F | -54.4 | None | |||
Parameter | gl
|
gl = .3 | F | 0.3 | None | |||
Parameter | gkdr
|
gkdr = 36 | F | 36.0 | None | |||
Parameter | gna
|
gna = 120 | F | 120.0 | None | |||
Parameter | i
|
i = 11 | F | 11.0 | None | |||
Parameter | c
|
c = 1. | F | 1.0 | None | |||
Parameter | amphi
|
amphi = .1 | F | 0.1 | None | |||
Parameter | amhalf
|
amhalf = -40 | F | -40.0 | None | |||
Parameter | amwidth
|
amwidth = 10 | F | 10.0 | None | |||
Parameter | bmphi
|
bmphi = 4 | F | 4.0 | None | |||
Parameter | bmhalf
|
bmhalf = -65 | F | -65.0 | None | |||
Parameter | bmwidth
|
bmwidth = 18 | F | 18.0 | None | |||
Parameter | ahphi
|
ahphi = 0.07 | F | 0.07 | None | |||
Parameter | ahhalf
|
ahhalf = -65 | F | -65.0 | None | |||
Parameter | ahwidth
|
ahwidth = 20 | F | 20.0 | None | |||
Parameter | bhphi
|
bhphi = 1 | F | 1.0 | None | |||
Parameter | bhhalf
|
bhhalf = -35 | F | -35.0 | None | |||
Parameter | bhwidth
|
bhwidth = 10 | F | 10.0 | None | |||
Parameter | anphi
|
anphi = .01 | F | 0.01 | None | |||
Parameter | anhalf
|
anhalf = -55 | F | -55.0 | None | |||
Parameter | anwidth
|
anwidth = 10 | F | 10.0 | None | |||
Parameter | bnphi
|
bnphi = .125 | F | 0.125 | None | |||
Parameter | bnhalf
|
bnhalf = -65 | F | -65.0 | None | |||
Parameter | bnwidth
|
bnwidth = 80 | F | 80.0 | None | |||
Parameter | taur
|
taur = 1 | F | 1.0 | None | |||
Parameter | taud
|
taud = 3 | F | 3.0 | None | |||
Parameter | thresh
|
thresh = -30 | F | -30.0 | None | |||
Parameter | x1
|
x1 = .001 | F | 0.001 | None | |||
Parameter | y1
|
y1 = .001 | F | 0.001 | None | |||
Parameter | x2
|
x2 = .001 | F | 0.001 | None | |||
Parameter | y2
|
y2 = .001 | F | 0.001 | None | |||
Parameter | gsyn
|
gsyn = .1 | F | 0.1 | None | |||
Parameter | esyn
|
esyn = 0 | F | 0.0 | None | |||
Parameter | vp
|
vp = -50 | F | -50.0 | None | |||
Parameter | vsp
|
vsp = 9 | F | 9.0 | None | |||
Parameter | gnad
|
gnad = 0.02 | F | 0.02 | None | |||
Parameter | gld
|
gld = .1 | F | 0.1 | None | |||
Parameter | taupna
|
taupna = 10 | F | 10.0 | None | |||
Parameter | lambda
|
lambda = 1 | F | 1.0 | None | |||
Parameter | tau
|
tau = 10 | F | 10.0 | None | |||
Parameter | dx
|
dx = .1 | F | 0.1 | None | |||
Parameter | c1
|
c1 = 0 | F | 0.0 | None | |||
Parameter | a1
|
a1 = 0 | F | 0.0 | None | |||
Parameter | b1
|
b1 = 1 | F | 1.0 | None | |||
Parameter | c0
|
c0 = 0 | F | 0.0 | None | |||
Parameter | a0
|
a0 = 0 | F | 0.0 | None | |||
Parameter | b0
|
b0 = 1 | F | 1.0 | None | |||
Parameter | eps
|
eps = .025 | F | 0.025 | None | |||
Parameter | sigma
|
sigma = .05 | F | 0.05 | None | |||
Parameter | t0
|
t0 = 14.45 | F | 14.45 | None | |||
Parameter | p[0..50] = 0 | F | 0.0 | None | ||||
Parameter | v1
|
F | 0.0 | dimensionless | None | |||
Parameter | v2
|
F | 0.0 | dimensionless | None | |||
Parameter | m1
|
F | 0.0 | dimensionless | None | |||
Parameter | m2
|
F | 0.0 | dimensionless | None | |||
Parameter | n1
|
F | 0.0 | dimensionless | None | |||
Parameter | n2
|
F | 0.0 | dimensionless | None | |||
Parameter | ha
|
F | 0.0 | dimensionless | None | |||
Parameter | hb
|
F | 0.0 | dimensionless | None | |||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | ua1
|
F | 0.0 | dimensionless | None | |||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | ub1
|
F | 0.0 | dimensionless | None | |||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | ua51
|
F | 0.0 | dimensionless | None | |||
Parameter | ub51
|
F | 0.0 | dimensionless | None | |||
Parameter | prc
|
F | 0.0 | dimensionless | None | |||
Parameter | t
|
model time | F | 0.0 | dimensionless | None |
type | Rules [22] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | d v1/dt
|
= | None | ||||
Rule | d v2/dt
|
= | None | ||||
Rule | d m1/dt
|
= | None | ||||
Rule | d m2/dt
|
= | None | ||||
Rule | d n1/dt
|
= | None | ||||
Rule | d n2/dt
|
= | None | ||||
Rule | d ha/dt
|
= | None | ||||
Rule | d hb/dt
|
= | None | ||||
Rule | d x1/dt
|
= | None | ||||
Rule | d x2/dt
|
= | None | ||||
Rule | d y1/dt
|
= | None | ||||
Rule | d y2/dt
|
= | None | ||||
Rule | = | None | |||||
Rule | = | None | |||||
Rule | d ua1/dt
|
= | None | ||||
Rule | = | None | |||||
Rule | d ub1/dt
|
= | None | ||||
Rule | = | None | |||||
Rule | ua51
|
= | None | ||||
Rule | ub51
|
= | None | ||||
Rule | prc
|
= | None | ||||
Rule | t
|
= | None |