XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
# RESPIRATORY RHYTHM MODEL # J. Rubin, N. Shevtsova, B. Ermentrout, J. Smith, I. Rybak # J. Neurophysiol. 101:2146-2165, 2009 # parameters/initial conditions set to give 3-phase rhythm # general parameters p C=20 p gL=2.8 p Eleak=-60 p gsynE=10 p EsynE=0 p gsynI=60 p EsynI=-75 p EK=-85 p ENa=50 # parameters of NaP and Kdr currents p V12n=-29,kn=-4,gKdr=5,V12mp=-40,kmp=-6 p V12hp=-48,khp=6,tauhp=6000,gNaP=5 # parameters of adaptive neurons p gAD=10,Tad2=2000,Tad3=1000,Tad4=2000 p Kad2=0.9,Kad3=1.3,Kad4=0.9 # parameters of output function p V12outpute=-30,Koutpute=-8 p V12outputi=-30,Koutputi=-4 foute(v)=1./(1+exp((v-V12outpute)/Koutpute)) fouti(v)=1./(1+exp((v-V12outputi)/Koutputi)) # between neurons p a12=0.4,b23=0.25,b24=0.35,b31=0.3,b32=0.05,b34=0.35 p b41=0.2,b42=0.35,b43=0.1 p Drive1=1,Drive2=1,Drive3=1 p c11=0.115,c12=0.3,c13=0.63,c14=0.33 p c21=0.07,c22=0.3,c24=0.4,c31=0.025 p nf=1 p sdum1=0,sdum2=0,sdum3=0,sdum4=0,edum=0 init v1=-60,v2=-60,v3=-60,v4=-60 init h=0.35,m2=0,m3=0,m4=0 # functions ninf(v)=1./(1+exp((v-V12n)/kn)) mpinf(v)=1./(1+exp((v-V12mp)/kmp)) hpinf(v)=1./(1+exp((v-V12hp)/khp)) tauinf(v)=tauhp/cosh((v-V12hp)/(2*khp)) # currents Inap(v,h)=gNaP*mpinf(v)*h*(v-ENa) Ikdr(v)=gKdr*ninf(v)^4*(v-EK) Iad(v,m)=gAD*m*(v-EK) Il(v)=gL*(v-Eleak) # ODEs v1'=(-Inap(v1,h)-Ikdr(v1)-Il(v1)-gsynI*(b31*fouti(v3)+b41*fouti(v4)+sdum1)*(v1-EsynI)-gsynE*(c11*Drive1+c21*Drive2+c31*Drive3)*(v1-EsynE))/C v2'=(-Iad(v2,m2)-Il(v2)-gsynI*(b32*fouti(v3)+b42*fouti(v4)+sdum2)*(v2-EsynI)-gsynE*(a12*foute(v1)+c22*Drive2+c12*Drive1+edum)*(v2-EsynE))/C v3'=(-Iad(v3,m3)-Il(v3)-gsynI*(b23*fouti(v2)+b43*fouti(v4)+sdum3)*(v3-EsynI)-gsynE*(c13*Drive1)*(v3-EsynE))/C v4'=(-Iad(v4,m4)-Il(v4)-gsynI*(b24*fouti(v2)+b34*fouti(v3)+sdum4)*(v4-EsynI)-gsynE*(c14*Drive1+c24*Drive2)*(v4-EsynE))/C h'=(hpinf(v1)-h)/tauinf(v1) m2'=(-m2+Kad2*fouti(v2))/Tad2 m3'=(-m3+Kad3*fouti(v3))/Tad3 m4'=(-m4+Kad4*fouti(v4))/Tad4 aux inh1=b31*fouti(v3)+b41*fouti(v4) aux inh2=b32*fouti(v3)+b42*fouti(v4) aux inh3=b23*fouti(v2)+b43*fouti(v4) aux inh4=b24*fouti(v2)+b34*fouti(v3) aux exc2=a12*foute(v1) @ dt=0.1,total=10000,meth=qualrk,xp=t,yp=v1,xlow=0,xhi=1000,ylo=-80,yhi=20.,bound=5000,maxstor=10000001 done
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Copyright © 2017 Matthias Koenig
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Model :
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type | FunctionDefinitions [14] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | max
|
minimum | |||
FunctionDefinition | min
|
maximum | |||
FunctionDefinition | heav
|
heavyside | |||
FunctionDefinition | mod
|
modulo | |||
FunctionDefinition | foute
|
||||
FunctionDefinition | fouti
|
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FunctionDefinition | ninf
|
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FunctionDefinition | mpinf
|
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FunctionDefinition | hpinf
|
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FunctionDefinition | tauinf
|
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FunctionDefinition | inap
|
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FunctionDefinition | ikdr
|
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FunctionDefinition | iad
|
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FunctionDefinition | il
|
type | Parameters [69] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | c
|
c = 20 | F | 20.0 | None | |||
Parameter | gl
|
gl = 2.8 | F | 2.8 | None | |||
Parameter | eleak
|
eleak = -60 | F | -60.0 | None | |||
Parameter | gsyne
|
gsyne = 10 | F | 10.0 | None | |||
Parameter | esyne
|
esyne = 0 | F | 0.0 | None | |||
Parameter | gsyni
|
gsyni = 60 | F | 60.0 | None | |||
Parameter | esyni
|
esyni = -75 | F | -75.0 | None | |||
Parameter | ek
|
ek = -85 | F | -85.0 | None | |||
Parameter | ena
|
ena = 50 | F | 50.0 | None | |||
Parameter | v12n
|
v12n = -29 | F | -29.0 | None | |||
Parameter | kn
|
kn = -4 | F | -4.0 | None | |||
Parameter | gkdr
|
gkdr = 5 | F | 5.0 | None | |||
Parameter | v12mp
|
v12mp = -40 | F | -40.0 | None | |||
Parameter | kmp
|
kmp = -6 | F | -6.0 | None | |||
Parameter | v12hp
|
v12hp = -48 | F | -48.0 | None | |||
Parameter | khp
|
khp = 6 | F | 6.0 | None | |||
Parameter | tauhp
|
tauhp = 6000 | F | 6000.0 | None | |||
Parameter | gnap
|
gnap = 5 | F | 5.0 | None | |||
Parameter | gad
|
gad = 10 | F | 10.0 | None | |||
Parameter | tad2
|
tad2 = 2000 | F | 2000.0 | None | |||
Parameter | tad3
|
tad3 = 1000 | F | 1000.0 | None | |||
Parameter | tad4
|
tad4 = 2000 | F | 2000.0 | None | |||
Parameter | kad2
|
kad2 = 0.9 | F | 0.9 | None | |||
Parameter | kad3
|
kad3 = 1.3 | F | 1.3 | None | |||
Parameter | kad4
|
kad4 = 0.9 | F | 0.9 | None | |||
Parameter | v12outpute
|
v12outpute = -30 | F | -30.0 | None | |||
Parameter | koutpute
|
koutpute = -8 | F | -8.0 | None | |||
Parameter | v12outputi
|
v12outputi = -30 | F | -30.0 | None | |||
Parameter | koutputi
|
koutputi = -4 | F | -4.0 | None | |||
Parameter | a12
|
a12 = 0.4 | F | 0.4 | None | |||
Parameter | b23
|
b23 = 0.25 | F | 0.25 | None | |||
Parameter | b24
|
b24 = 0.35 | F | 0.35 | None | |||
Parameter | b31
|
b31 = 0.3 | F | 0.3 | None | |||
Parameter | b32
|
b32 = 0.05 | F | 0.05 | None | |||
Parameter | b34
|
b34 = 0.35 | F | 0.35 | None | |||
Parameter | b41
|
b41 = 0.2 | F | 0.2 | None | |||
Parameter | b42
|
b42 = 0.35 | F | 0.35 | None | |||
Parameter | b43
|
b43 = 0.1 | F | 0.1 | None | |||
Parameter | drive1
|
drive1 = 1 | F | 1.0 | None | |||
Parameter | drive2
|
drive2 = 1 | F | 1.0 | None | |||
Parameter | drive3
|
drive3 = 1 | F | 1.0 | None | |||
Parameter | c11
|
c11 = 0.115 | F | 0.115 | None | |||
Parameter | c12
|
c12 = 0.3 | F | 0.3 | None | |||
Parameter | c13
|
c13 = 0.63 | F | 0.63 | None | |||
Parameter | c14
|
c14 = 0.33 | F | 0.33 | None | |||
Parameter | c21
|
c21 = 0.07 | F | 0.07 | None | |||
Parameter | c22
|
c22 = 0.3 | F | 0.3 | None | |||
Parameter | c24
|
c24 = 0.4 | F | 0.4 | None | |||
Parameter | c31
|
c31 = 0.025 | F | 0.025 | None | |||
Parameter | nf
|
nf = 1 | F | 1.0 | None | |||
Parameter | sdum1
|
sdum1 = 0 | F | 0.0 | None | |||
Parameter | sdum2
|
sdum2 = 0 | F | 0.0 | None | |||
Parameter | sdum3
|
sdum3 = 0 | F | 0.0 | None | |||
Parameter | sdum4
|
sdum4 = 0 | F | 0.0 | None | |||
Parameter | edum
|
edum = 0 | F | 0.0 | None | |||
Parameter | v1
|
v1 = -60 | F | -60.0 | None | |||
Parameter | v2
|
v2 = -60 | F | -60.0 | None | |||
Parameter | v3
|
v3 = -60 | F | -60.0 | None | |||
Parameter | v4
|
v4 = -60 | F | -60.0 | None | |||
Parameter | h
|
h = 0.35 | F | 0.35 | None | |||
Parameter | m2
|
m2 = 0 | F | 0.0 | None | |||
Parameter | m3
|
m3 = 0 | F | 0.0 | None | |||
Parameter | m4
|
m4 = 0 | F | 0.0 | None | |||
Parameter | inh1
|
F | 0.0 | dimensionless | None | |||
Parameter | inh2
|
F | 0.0 | dimensionless | None | |||
Parameter | inh3
|
F | 0.0 | dimensionless | None | |||
Parameter | inh4
|
F | 0.0 | dimensionless | None | |||
Parameter | exc2
|
F | 0.0 | dimensionless | None | |||
Parameter | t
|
model time | F | 0.0 | dimensionless | None |
type | Rules [14] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | d v1/dt
|
= | None | ||||
Rule | d v2/dt
|
= | None | ||||
Rule | d v3/dt
|
= | None | ||||
Rule | d v4/dt
|
= | None | ||||
Rule | d h/dt
|
= | None | ||||
Rule | d m2/dt
|
= | None | ||||
Rule | d m3/dt
|
= | None | ||||
Rule | d m4/dt
|
= | None | ||||
Rule | inh1
|
= | None | ||||
Rule | inh2
|
= | None | ||||
Rule | inh3
|
= | None | ||||
Rule | inh4
|
= | None | ||||
Rule | exc2
|
= | None | ||||
Rule | t
|
= | None |