XPP model

This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6.

#D.P.Dougherty 2010
#Spiking model of mouse ORN
#This is a multi-scale extension of the model in Dougherty et al 2005. PNAS 102(30):10415-10420
#which includes cilium, dendrite, and soma compartments.
#
#The XPP file is configured to demonstrate the slow transduction current
#and fast action potential generation during a prolonged odorant presentation
#

#Alphabetically sorted listing of all model parameters (descriptions given below).

param cap=0.0035
param cc1lin=2.6
param cc2=40.231
param ck1lin=40
param ck2=2.412
param clmax=0.8294
param cnmax=3.6417
param ef=7.832
param gl=15.4267
param hmc1=1.5965
param hmc2=7.6415
param inf=1.4654
param inhmax=0.98
param k1=2.2748
param k2lin=42.0896
param kI=16.5304
param kinh=1.3875
param kinhcng=0.2242
param n1=5.6384
param n2=3.4161
param ninh=8.4067
param ninhcng=0.6306
param pd=7.3132
param r1=9.4574
param r2=12.5485
param smax=63.0987
param vcl=-7.3248
param vcng=0.4641
param vl=-69.6653

#Spiking aspect of the model -- dendrite and soma parameters.
param ge1=70.244          
param ge2=20.245          
param tau_soma=6100       
param epsilon=0.09        
param beta=0.092          
param beta_cap=0.95          
param cap_max=400.5      
param cap_off=-75.01         
param gamma=43.92         
param VSspike=-58.23     
param VSamp=14.36         
param vd=0.05   

#cap	  #Capacitance of ORN ciliary membrane# nF 										   
#cc1lin   #Rate at which Ca2+ associates with CaM to form CaCaM # s^-1							   
#cc2	  #Rate at which CaCaM dissociates to Ca2+ and CaM # s^-1 							   
#ck1lin   #Rate at which CaCaM activates CaMK	# s^-1								   
#ck2	  #Rate at which active CaMK deactivates # s^-1										   
#clmax    #Maximal conductance of ANO2 Cl(Ca) channels # nS								   
#cnmax    #Maximal conductance of CNG channels # nS							   
#ef	  #Maximum calcium efflux (assumed sodium & potassium independent) #s^-1				   
#gl	  #Maximum leak (generic) conductance # nS									   
#hmc1	  #Concentration of cAMP needed to achieve half-maximal activation (K1/2) of the CNG channel # uM						   
#hmc2	  #Concentration of Ca2+ needed to achieve half-maximal activation (K1/2) of the Cl(Ca) channel| # uM							   
#inf	  #Net calcium inward flux via CNG channel # uM*pC^-1								   
#inhmax   #Maximum inhibition of CNG by CaCAM # unitless								   
#k1	  #Receptor affinity for ligand # (um*s)^-1								   
#k2lin    #Rate of G-protein activation per bound receptor complex  # s^-1						   
#kinh	  #Concentration of aCaMK needed for half-maximal inhibition (IC50) of cAMP production # uM							   
#kinhcng  #Concentration of CaCaM needed for half-maximal inhibition of the CNG channel # uM							   
#n1	  #Hill coefficient of the CNG channel activation function #	unitless						   
#n2	  #Hill coefficient of the Cl(Ca) channel activation function	# unitless							   
#ninh	  #Steepness of the decreasing sigmoid representing aCaMK-mediated inhibition of cAMP synthesis	 # unitless					   
#ninhcng  #Steepness of the sigmoid inhcng representing inhibition of CNG channel by CaCaM # unitless				   
#pd	  #Rate at which a cAMP molecule is degraded by phosphodiesterase # s^-1									   
#r1	  #Rate of unbinding of odorant from receptor	 # s^-1								   
#r2	  #Rate at which a G-protein becomes deactivate rate # s^-1								   
#smax	  #Maximal (uninhibited) rate of cAMP production by adenylyl cyclase per active G-protein # uM*s^-1						   
#vcl	  #Reversal potential of Cl(Ca) channels  # mV							   
#vcng	  #Reversal potential of CNG channels # mV								   
#vl	  #Effective reversal potential for leak current # mV 							   
#ge1	  #Coupling strength between cilia and dendrite compartments	# s^-1				   
#ge2	  #Coupling strength between dendrite and soma compartments 	# mV^-1				   
#tau_soma #Relative time scale of soma to cilia dynamics #s^-1						   
#epsilon  #Relative time scale of Na and K channel dynamics to voltage dynamics in soma #Unitless		   
#beta	  #Sharpness of Na and K channel response to voltage	# mV					   
#beta_cap #Sharpness of soma capacitance dependence on voltage  # mV					   
#cap_max  #Maximum soma capacitance	# nF 							   
#cap_off  #Voltage at which soma capacitance is half maximal	#mV					   
#gamma    #Na and K channel activation rate (sets height of channel manifold)	#unitless			   
#VSspike  #Reference voltage for action potentials by soma # mV						   
#VSamp    #Sharpness of soma voltage response #mV								   
#vd	  #Diffusive dendritic voltage leak/loss. #s^-1					   


 
#Below here are non-physiological parameters related to the experimental design: 
 
#Micromolar concentration of odorant at full concentration
param ostim=100 
#Sharpness of odorant plume          
param SHARPNESS=0.0001    

%hv defines a "heaviside-like" pulse but with adjustable steepness parameter.  
%Use this to describe a smeared odorant plume reaching the neuron.

hv(x,s)=1/(1+exp(-x/s))
PULSE(t)=(hv(t-1,SHARPNESS) - hv(t-60,SHARPNESS))			   			   
OD(t) = ostim*PULSE(t)

#The vertebrate ORN model has 3 compartments i) Cilia, ii) Dendrite, and iii) Soma.


#### Cilia Compartment ####
dbLR/dt       = k1*OD(t)*(1-bLR)-r1*bLR
daG/dt        = k2lin*bLR*(1-aG) - r2*aG
dcAMP/dt      = (aG*smax)/(1 + ((CAMK/kinh)^ninh)) - pd*cAMP
dCa/dt        = inf*Icng(cAMP,Vcilia) - ef*Ca + (-cc1lin*Ca + cc2*CaCAM)
dCaCAM/dt     = cc1lin*Ca - cc2*CaCAM
dCAMK/dt      = ck1lin*CaCAM - ck2*CAMK
dVcilia/dt    = (1/cap)*(Icng(cAMP,Vcilia) + Icacl(Ca,Vcilia) + Il(Vcilia))

#### Dendrite Compartment ####
dVdend/dt     = ge1*(Vcilia-Vdend) - vd*Vdend

#### Soma Compartment ####
dVsoma/dt     = VOLTAGE(V(Vsoma),Vcilia,Vdend)
dNaKXsoma/dt  = tau_soma*(epsilon*(gamma*(1+tanh(V(Vsoma)/beta))-NaKXsoma))


Input(x,y)  = ge2*(x-y)
V(x)      = (x-VSspike)/(0.5*VSamp)
VOLTAGE(x,y,z) = tau_soma*(3*x - x^3 + 2 - NaKXsoma + Input(y,z))

inhcng(CaCAM) = 1+(inhmax-1)*((CaCAM^ninhcng)/(CaCAM^ninhcng + kinhcng^ninhcng))

#Current models:
Icng(cAMP,Vcilia) = ((cnmax*cAMP^n1)/(cAMP^n1 + (inhcng(CaCAM)*hmc1)^n1))*(vcng-Vcilia)
Icacl(Ca,Vcilia)  = ((clmax*Ca^n2)/(Ca^n2 + hmc2^n2))*(vcl-Vcilia)
Il(Vcilia)     = gl*(vl-Vcilia)
cap_soma(Vcilia) = cap_max*(1+tanh((cap_off-Vcilia)/beta_cap))
Isoma(x,y,z)  = cap_soma(Vcilia)*VOLTAGE(x,y,z)


#These auxilliary functions simply model what is actually measured by suction pipette recording
#from whole cell.

aux Icilia=-(Icng(cAMP,Vcilia) + Icacl(Ca,Vcilia))
aux WholeCell=Isoma(V(Vsoma),Vcilia,Vdend) -(Icng(cAMP,Vcilia) + Icacl(Ca,Vcilia))
aux Odorant=100*PULSE(t)
#The number 100 is used above simply to give the odorant pulses a nice magnitude when plotted in the 
#same axes as the currrents.  Unfortunately XPP does not have real double y-axis plots.
#Anyway, at least you can see the odorant pulses now!

#Initial conditions.  Note that we actually run the model to steady-state in the absence 
#of odorant for a second before simulation of the experiment. See T0 option below.

init bLR=1.e-8
init aG=1.e-8
init cAMP=1.e-8
init Ca=1.e-8
init CaCAM=1.e-8
init CAMK=1.e-8
init Vcilia=vl
init Vdend=vl
init Vsoma=vl
init NaKXsoma=3.e-8



@ BUT=RunModel:ig,BUT=FitAxes:wf,MAXSTOR=8000000
@ meth=cvode,TOL=1e-5,ATOL=1e-5,T0=-1,DT=0.00001,DTMIN=0.0001,DTMAX=0.001
@ TOTAL=60.0,BOUND=1000000,XLO=0,XHI=60,YLO=-300,YHI=150
@ NPLOT=2,YP=WholeCell,YP2=Odorant

done




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Copyright © 2017 Matthias Koenig

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This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


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Access SBML model  L3V1

FunctionDefinitions [16] name math sbo cvterm
max minimum x y x x y y
min maximum x y x x y y
heav heavyside x 0 x 0 0.5 x 0 1 x 0 0
mod modulo x y x y x y x 0 y 0 x y x y
hv x s 1 1 x s
pulse t sharpness hv t 1 sharpness hv t 60 sharpness
od t ostim sharpness ostim pulse t sharpness
input x y ge2 ge2 x y
v x vsamp vsspike x vsspike 0.5 vsamp
voltage x y z ge2 nakxsoma tau_soma tau_soma 3 x x 3 2 nakxsoma input y z ge2
inhcng cacam inhmax kinhcng ninhcng 1 inhmax 1 cacam ninhcng cacam ninhcng kinhcng ninhcng
icng camp vcilia cacam cnmax hmc1 inhmax kinhcng n1 ninhcng vcng cnmax camp n1 camp n1 inhcng cacam ninhcng inhmax kinhcng hmc1 n1 vcng vcilia
icacl ca vcilia clmax hmc2 n2 vcl clmax ca n2 ca n2 hmc2 n2 vcl vcilia
il vcilia gl vl gl vl vcilia
cap_soma vcilia beta_cap cap_max cap_off cap_max 1 cap_off vcilia beta_cap
isoma x y z beta_cap cap_max cap_off ge2 nakxsoma tau_soma vcilia cap_soma vcilia cap_max cap_off beta_cap voltage x y z ge2 nakxsoma tau_soma

Parameters [57] name constant value unit derived unit sbo cvterm
cap cap = 0.0035 0.0035 None
cc1lin cc1lin = 2.6 2.6 None
cc2 cc2 = 40.231 40.231 None
ck1lin ck1lin = 40 40.0 None
ck2 ck2 = 2.412 2.412 None
clmax clmax = 0.8294 0.8294 None
cnmax cnmax = 3.6417 3.6417 None
ef ef = 7.832 7.832 None
gl gl = 15.4267 15.4267 None
hmc1 hmc1 = 1.5965 1.5965 None
hmc2 hmc2 = 7.6415 7.6415 None
inf inf = 1.4654 1.4654 None
inhmax inhmax = 0.98 0.98 None
k1 k1 = 2.2748 2.2748 None
k2lin k2lin = 42.0896 42.0896 None
ki ki = 16.5304 16.5304 None
kinh kinh = 1.3875 1.3875 None
kinhcng kinhcng = 0.2242 0.2242 None
n1 n1 = 5.6384 5.6384 None
n2 n2 = 3.4161 3.4161 None
ninh ninh = 8.4067 8.4067 None
ninhcng ninhcng = 0.6306 0.6306 None
pd pd = 7.3132 7.3132 None
r1 r1 = 9.4574 9.4574 None
r2 r2 = 12.5485 12.5485 None
smax smax = 63.0987 63.0987 None
vcl vcl = -7.3248 -7.3248 None
vcng vcng = 0.4641 0.4641 None
vl vl = -69.6653 -69.6653 None
ge1 ge1 = 70.244 70.244 None
ge2 ge2 = 20.245 20.245 None
tau_soma tau_soma = 6100 6100.0 None
epsilon epsilon = 0.09 0.09 None
beta beta = 0.092 0.092 None
beta_cap beta_cap = 0.95 0.95 None
cap_max cap_max = 400.5 400.5 None
cap_off cap_off = -75.01 -75.01 None
gamma gamma = 43.92 43.92 None
vsspike vsspike = -58.23 -58.23 None
vsamp vsamp = 14.36 14.36 None
vd vd = 0.05 0.05 None
ostim ostim = 100 100.0 None
sharpness sharpness = 0.0001 0.0001 None
blr blr = 1.e-8 1e-08 None
ag ag = 1.e-8 1e-08 None
camp camp = 1.e-8 1e-08 None
ca ca = 1.e-8 1e-08 None
cacam cacam = 1.e-8 1e-08 None
camk camk = 1.e-8 1e-08 None
vcilia vcilia 0.0 None
vdend vdend 0.0 None
vsoma vsoma 0.0 None
nakxsoma nakxsoma = 3.e-8 3e-08 None
icilia 0.0 dimensionless None
wholecell 0.0 dimensionless None
odorant 0.0 dimensionless None
t model time 0.0 dimensionless None

InitialAssignments [3] name assignment derived units sbo cvterm
vcilia = vl None
vdend = vl None
vsoma = vl None

Rules [14]   assignment name derived units sbo cvterm
d blr/dt = k1 od t ostim sharpness 1 blr r1 blr None
d ag/dt = k2lin blr 1 ag r2 ag None
d camp/dt = ag smax 1 camk kinh ninh pd camp None
d ca/dt = inf icng camp vcilia cacam cnmax hmc1 inhmax kinhcng n1 ninhcng vcng ef ca cc1lin ca cc2 cacam None
d cacam/dt = cc1lin ca cc2 cacam None
d camk/dt = ck1lin cacam ck2 camk None
d vcilia/dt = 1 cap icng camp vcilia cacam cnmax hmc1 inhmax kinhcng n1 ninhcng vcng icacl ca vcilia clmax hmc2 n2 vcl il vcilia gl vl None
d vdend/dt = ge1 vcilia vdend vd vdend None
d vsoma/dt = voltage v vsoma vsamp vsspike vcilia vdend ge2 nakxsoma tau_soma None
d nakxsoma/dt = tau_soma epsilon gamma 1 v vsoma vsamp vsspike beta nakxsoma None
icilia = icng camp vcilia cacam cnmax hmc1 inhmax kinhcng n1 ninhcng vcng icacl ca vcilia clmax hmc2 n2 vcl None
wholecell = isoma v vsoma vsamp vsspike vcilia vdend beta_cap cap_max cap_off ge2 nakxsoma tau_soma vcilia icng camp vcilia cacam cnmax hmc1 inhmax kinhcng n1 ninhcng vcng icacl ca vcilia clmax hmc2 n2 vcl None
odorant = 100 pulse t sharpness None
t = time None