XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
" ball and stick model w 2 comps " copied from model_I_long_range_better_offset.ode " Na params close enough to accept this as wildtype cocktail model. " Can change only 2 out of 3 passive parameters. The last one is dependent to preserve total input resistance. # # conductances in nS, resistances in GOhm # currents in pA # Voltages in mV # time in ms # capacitances in pF # Larger soma capacitance, but still low leak # 3-steps: 16, 36, 56 # Params: gaxon=1.8, NaP=0.1, NaT=350, gKs=1, gaKs=550, Cm=15, Ca=10, gL=0.1, gaL=3, eleak=-55, ealeak=-59 # principles: # - good for spike height => gaxon, Cm = (3, 20); (1.6, 15) # - gaKs > gNaT makes longer delay # - lowering gaL increases first spike voltage offset # - high gaKs makes spike asymmetric with slow depolarization # - lowering Cm increases spike height # - decreasing gaxon makes spikes shorter and more asymmetric, but requires more current to fire # - increasing zi increases offset slightly # firing rate rules: # - increasing gl decreases galeak and therefore increases f # - increasing gaxon increases f # - increasing zi increases f # - reducing Ca increases f! # Params: gaxon=1, NaP=0.14, NaT=350, gKs=1, gaKs=550, Cm=15, Ca=10, gL=0.1, gaL=dep(zi), zi=1.6, eleak=-60, ealeak=-60 # pros: nice spike height, goes up to >-10mV # cons: threshold @ -50mV, spikes a bit too short # Params: gaxon=1.6, NaP=0.05, NaT=450, gKs=1, gaKs=500, Cm=15, Ca=10, gL=0.1, gaL=dep(zi), zi=1.6, eleak=-60, ealeak=-60 # pros: nice spike height, goes up to >-10mV, threshold @ -40mV # cons: initial rate too high, spike shape not nice, too small # Params: gaxon=1.6, NaP=0.08, NaT=260, gKs=1, gaKs=1000, Cm=15, Ca=10, gL=0.1, gaL=dep(zi), zi=1.6, eleak=-60, ealeak=-60 # pros: nice spike height, asymmetric spike shape, initial rate low # cons: threshold @ -45mV, offset a bit too small # Params: NaP=0.08, NaT=300, gKs=1, gaKs=1000, Cm=15, Ca=10, gaxon=1.6, gL=0.1, gaL=dep(zi), zi=1.1, eleak=-60, ealeak=-60 # pros: nice spike height, asymmetric spike shape, initial rate low, threshold @ -40mV # cons: starts firing at 14 pA, must compare f-I curve to recordings # TODO: make mlab figure and attach to bif.lyx #dV/dt=-1/c*(gKs*mKs^4*(V-EK) + gKf*mKf^4*(fh*hKf+(1-fh)*hKf2)*(V-EK) + gNa*mNa^3*hNa*(V-ENa) + gleak*(V-Eleak)-I) # soma voltage dVm/dt=-1/Cm*(IksVm+IkfVm+gleak*(Vm-Eleak)-I+gaxon*(Vm-Va)) # axon compartment voltage dVa/dt=-1/Ca*(IksVa+IkfVa+Ina+Inap+galeak*(Va-Ealeak)+gaxon*(Va-Vm)) #slow K # orig = 5.1 par gKs=1 gaKs=700 minfKs(V) = 1/(1+exp((V+12.85)/(-19.91))) mtauKs(V) = 2.03 + 1.96 /(1+exp((V-29.83)/3.32)) dmKsVm/dt=(minfKs(Vm)-mKsVm)/mtauKs(Vm) dmKsVa/dt=(minfKs(Va)-mKsVa)/mtauKs(Va) IksVm=gKs*mKsVm^4*(Vm-EK) IksVa=gaKs*mKsVa^4*(Va-EK) aux IksVm=IksVm aux IksVa=IksVa #fast K with 2 inactivation time constants dmKfVm/dt=(minfKf(Vm)-mKfVm)/mtauKf(Vm) dhKfVm/dt=(hinfK(Vm)-hKfVm)/htauK(Vm) dhKf2Vm/dt=(hinfK2(Vm)-hKf2Vm)/116 IkfVm=gKf*mKfVm^4*(fh*hKfVm + (1-fh)*hKf2Vm)*(Vm-EK) dmKfVa/dt=(minfKf(Va)-mKfVa)/mtauKf(Va) dhKfVa/dt=(hinfK(Va)-hKfVa)/htauK(Va) dhKf2Va/dt=(hinfK2(Va)-hKf2Va)/116 IkfVa=gaKf*mKfVa^4*(fh*hKfVa + (1-fh)*hKf2Va)*(Va-EK) minfKf(V) = 1/(1+exp((V+17.55)/(-7.27))) mtauKf(V) = 1.94+2.66/(1+exp((V-8.12)/7.96)) hinfK(V) = 1/(1+exp((V+45)/6)) htauK(V) = 1.79+515.8/(1+exp((V+147.4)/(28.66))) # mistake; should be hinfK == hinfK2 hinfK2(V) = 1/(1+exp((V+44.2)/1.5)) aux IkfVm=IkfVm aux IkfVa=IkfVa #na # from O'Dowd and Aldrich (1988) dmNa/dt=(minfNa(Va)-mNa)/mtauNa(Va) dhNa/dt=(hinfNa(Va)-hNa)/htauNa(Va) Ina=gNa*mNa^3*hNa*(Va-ENa) # gNa reported as 500 pS/pF, multiply with C=20 pF par gNa=180 minfNa(V) = 1/(1+exp((V+29.13)/(-8.922))) mtauNa(V) = 0.1270 + 3.434/(1+exp((V+45.35)/(5.98))) hinfNa(V) = 1/(1+exp((V+47)/5)) htauNa(V) = 0.36 + exp(-(V+20.65)/(10.47)) aux Ina=Ina # NaP from DmNav10 of WHL oocyte #1 dmNaP/dt=(minfNaP(Va)-mNaP)/mtauNaP(Va) Inap=(gNaP+modgNaP)*mNaP*(Va-ENa) par gNaP=.01 minfNap(V) = 1/(1+exp((V+48.77)/(-3.68))) mtauNap(V) = 1 aux Inap=Inap global 1 t {I=Ihold} global 1 t-10 {I=Ipulse} global 1 t-510 {I=Ihold} # initial conditions for settled at I=-6.5 # easiest way is to get this is to save "info" from File menu # after running for a long while and then doing a "run last" init VM=-68.81670299025546 VA=-64.34801596094069 MKSVM=0.05673345401938218 MKSVA=0.07000969210752514 MKFVM=0.0008650853390965969 HKFVM=0.9814660312384692 HKF2VM=0.9839995279862832 MKFVA=0.001598416867905559 HKFVA=0.961752460873017 HKF2VA=0.9900602079074428 MNA=0.01894063272630685 HNA=0.9695223296922046 MNAP=0.01429909346846636 @ total=600,bounds=10000000000,meth=euler,dt=.001, nout=100, maxstor=10000000 # window ranges @ xlo=0, xhi=600, ylo=-65, yhi=0 # do a I range from -9 to +51 with 7 steps # do a I range from 5 to +45 with 2 steps par Cm=10 Ca=1.8 Ipulse=-6.5 # conserve total input resistance par zi=2.1 # connection strength par gaxon=1.3 gleak=0.05 # make some parameters dependent to preserve zi gad=1/zi-gleak galeak=1/(1/gad-1/gaxon) par eleak=-55 ealeak=-55 Ihold=-6.5 # unneeded pars at the end par gKf=1 gaKf=200 par ENa=45 EK=-80 I=0 fh=.95 modNaAct=0 modNaInact=0 modgNaP=0 done
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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
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minimum | |||
FunctionDefinition | min
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maximum | |||
FunctionDefinition | heav
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heavyside | |||
FunctionDefinition | mod
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modulo | |||
FunctionDefinition | minfks
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FunctionDefinition | mtauks
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FunctionDefinition | minfkf
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FunctionDefinition | mtaukf
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FunctionDefinition | hinfk
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FunctionDefinition | htauk
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FunctionDefinition | hinfk2
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FunctionDefinition | minfna
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FunctionDefinition | mtauna
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FunctionDefinition | hinfna
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FunctionDefinition | htauna
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FunctionDefinition | minfnap
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FunctionDefinition | mtaunap
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type | Parameters [44] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | gks
|
gks = 1 | F | 1.0 | None | |||
Parameter | gaks
|
gaks = 700 | F | 700.0 | None | |||
Parameter | gna
|
gna = 180 | F | 180.0 | None | |||
Parameter | gnap
|
gnap = .01 | F | 0.01 | None | |||
Parameter | vm
|
vm = -68.81670299025546 | F | -68.8167029902555 | None | |||
Parameter | va
|
va = -64.34801596094069 | F | -64.3480159609407 | None | |||
Parameter | mksvm
|
mksvm = 0.05673345401938218 | F | 0.0567334540193822 | None | |||
Parameter | mksva
|
mksva = 0.07000969210752514 | F | 0.0700096921075251 | None | |||
Parameter | mkfvm
|
mkfvm = 0.0008650853390965969 | F | 0.000865085339096597 | None | |||
Parameter | hkfvm
|
hkfvm = 0.9814660312384692 | F | 0.981466031238469 | None | |||
Parameter | hkf2vm
|
hkf2vm = 0.9839995279862832 | F | 0.983999527986283 | None | |||
Parameter | mkfva
|
mkfva = 0.001598416867905559 | F | 0.00159841686790556 | None | |||
Parameter | hkfva
|
hkfva = 0.961752460873017 | F | 0.961752460873017 | None | |||
Parameter | hkf2va
|
hkf2va = 0.9900602079074428 | F | 0.990060207907443 | None | |||
Parameter | mna
|
mna = 0.01894063272630685 | F | 0.0189406327263069 | None | |||
Parameter | hna
|
hna = 0.9695223296922046 | F | 0.969522329692205 | None | |||
Parameter | mnap
|
mnap = 0.01429909346846636 | F | 0.0142990934684664 | None | |||
Parameter | cm
|
cm = 10 | F | 10.0 | None | |||
Parameter | ca
|
ca = 1.8 | F | 1.8 | None | |||
Parameter | ipulse
|
ipulse = -6.5 | F | -6.5 | None | |||
Parameter | zi
|
zi = 2.1 | F | 2.1 | None | |||
Parameter | gaxon
|
gaxon = 1.3 | F | 1.3 | None | |||
Parameter | gleak
|
gleak = 0.05 | F | 0.05 | None | |||
Parameter | eleak
|
eleak = -55 | F | -55.0 | None | |||
Parameter | ealeak
|
ealeak = -55 | F | -55.0 | None | |||
Parameter | ihold
|
ihold = -6.5 | F | -6.5 | None | |||
Parameter | gkf
|
gkf = 1 | F | 1.0 | None | |||
Parameter | gakf
|
gakf = 200 | F | 200.0 | None | |||
Parameter | ena
|
ena = 45 | F | 45.0 | None | |||
Parameter | ek
|
ek = -80 | F | -80.0 | None | |||
Parameter | i
|
i = 0 | F | 0.0 | None | |||
Parameter | fh
|
fh = .95 | F | 0.95 | None | |||
Parameter | modnaact
|
modnaact = 0 | F | 0.0 | None | |||
Parameter | modnainact
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modnainact = 0 | F | 0.0 | None | |||
Parameter | modgnap
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modgnap = 0 | F | 0.0 | None | |||
Parameter | iksvm
|
F | 0.0 | dimensionless | None | |||
Parameter | iksva
|
F | 0.0 | dimensionless | None | |||
Parameter | ikfvm
|
F | 0.0 | dimensionless | None | |||
Parameter | ikfva
|
F | 0.0 | dimensionless | None | |||
Parameter | ina
|
F | 0.0 | dimensionless | None | |||
Parameter | inap
|
F | 0.0 | dimensionless | None | |||
Parameter | gad
|
F | 0.0 | dimensionless | None | |||
Parameter | galeak
|
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 vm/dt
|
= | None | ||||
Rule | d va/dt
|
= | None | ||||
Rule | d mksvm/dt
|
= | None | ||||
Rule | d mksva/dt
|
= | None | ||||
Rule | d mkfvm/dt
|
= | None | ||||
Rule | d hkfvm/dt
|
= | None | ||||
Rule | d hkf2vm/dt
|
= | None | ||||
Rule | d mkfva/dt
|
= | None | ||||
Rule | d hkfva/dt
|
= | None | ||||
Rule | d hkf2va/dt
|
= | None | ||||
Rule | d mna/dt
|
= | None | ||||
Rule | d hna/dt
|
= | None | ||||
Rule | d mnap/dt
|
= | None | ||||
Rule | iksvm
|
= | None | ||||
Rule | iksva
|
= | None | ||||
Rule | ikfvm
|
= | None | ||||
Rule | ikfva
|
= | None | ||||
Rule | ina
|
= | None | ||||
Rule | inap
|
= | None | ||||
Rule | gad
|
= | None | ||||
Rule | galeak
|
= | None | ||||
Rule | t
|
= | None |
type | Events [3] | name | trigger | priority | delay | assignments | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Event | e0
|
initialValue = False persistent = True |
i =
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Event | e1
|
initialValue = False persistent = True |
i =
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Event | e2
|
initialValue = False persistent = True |
i =
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