XPP model

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

#Kim et al. PLoS Comp Biol 2010
####Models of Second Messenger Pathways in CA1 pyramidal cell.
#
## ALL Units in nM for concentration and second for time.
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#
# CaMCa4 binding Partner's affinities: (1) PP2B(28 pM); (2) PDE1B(10 nM); 
#                                      (3) CaMKII(80 nM); (4) AC1(150 nM)
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#
#
#### This version based on rebased with Cab=70 nM, CaMtot=15 uM, CK_tot=20 uM, Ca_max=10 uM

param t_rise=0.01
#300 sec inter-train interval:
#param Ca_max=10000, t_dur=0.009,tau=0.01,train_len=1, t1=100, t2=400, t3=700, t4=1000, Cab=70
#3 sec inter-tr
param Ca_max=10000, t_dur=0.009,tau=0.01,train_len=1, t1=100, t2=103, t3=106, t4=109, Cab=70

tm=mod(t, tau)
t_pulse=t_dur-tm

param t_tau=0.01

Ca_pre =Cab+(Ca_max-Cab)*heav(t-t1)*heav(t1+train_len-t)*heav(t_pulse)+(Ca_max-Cab)*heav(t-t2)*heav(t2+train_len-t)*heav(t_pulse)+(Ca_max-Cab)*heav(t-t3)*heav(t3+train_len-t)*heav(t_pulse)+(Ca_max-Cab)*heav(t-t4)*heav(t4+train_len-t)*heav(t_pulse)

dCa/dt=(Ca_pre-Ca)/t_tau
#aux Ca=Ca

#cam_rate - approximates additional calmodulin diffusing into spine or dissociating from neurogranin as calmodulin decreases
#make cam_rate = 0 to see how CaMKII activation changes consequent to depletion of calmodulin (figure S4A).
Par cam_rate=0.1
cam_a=cam_rate*(7924-cam)
aux cam_a=cam_a

##L##
param Lb=10, L_max=1000, tauL=2


L=Lb+(L_max-Lb)*heav(t-t1)*heav(t1+train_len-t)+(L_max-Lb)*heav(t-t2)*heav(t2+train_len-t)+(L_max-Lb)*heav(t-t3)*heav(t3+train_len-t)+(L_max-Lb)*heav(t-t4)*heav(t4+train_len-t)
#aux L=L

#param Cab=70, Lb=10

#Ca=Cab
#L=Lb

####G_protein part####################################
#
#L + R <--> LR (k1, k_1), Kd=9000
#LR + G <--> LRG (k2, k_2), Kd=1.666667
#G + R <--> GR (k1a, k_1a), Kd=5
#GR + L <--> LRG (k2a, k_2a), Kd=3000
#LRG -->LR + GaGTP + Gbg (k3)
# or maybe: LRG -->L + R + GaGTP + Gbg (k3)
#GaGTP -->GaGDP (k4)
#GaGDP + Gbg --> G (k5)
#
######################################################

par k2a=0.00333333 k_2a=10
par k1a=0.00006 k_1a=0.0003
par k_1=10 k1=0.0011111
par k2=0.0006 k_2=0.001
parameters k3=20
parameters k4=10
parameters k5=100

dLR/dt=k1*R*L-k_1*LR-k2*LR*G+k_2*LRG+k3*LRG
init LR=0.9886277

dLRG/dt=k2*LR*G-k_2*LRG-k3*LRG+k2a*GR*L-k_2a*LRG
init  LRG=0.5300418

dGaGTP/dt=k3*LRG-k4*GaGTP+E*k_6-GaGTP*AC1*k6
init  GaGTP=1.060084

dGaGDP/dt=k4*GaGTP-k5*GaGDP*Gbg
init  GaGDP=143.092094

dGR/dt=k1a*G*R-k_1a*GR-k2a*GR*L+k_2a*LRG
init  GR=434.160416

dGbg/dt=k3*LRG-k5*GaGDP*Gbg
init  Gbg=0.000739


G=Gtot-(LRG+GaGTP+GaGDP+E+ECam+ECamATP+GR)
#Aux G=G


par Gtot=3000
Galfa=GaGTP+GaGDP
#Aux Galfa=Galfa
R=Rtot-LR-LRG-GR
par Rtot=500
#aux R=R

##### AC part: AC1 & AC8 activation thr Ca4CaM ###########################
#
#GaGTP + AC1 <--> E (K6, K_6) : Kd=260 nM from Dessaur paper(AC5?)
#E+ CaMCa4 <---> ECam(k7, k_7): Kd=100 nM
#ECam + ATP <---> ECamATP(k8,k_8)--->ECam + cAMP(v8): Km=162 uM
#
# Synergic effect: v8 increase X10 or X100(see JNeuroscience2003_Wang et al., 23(30)9710_9718)
#
#AC1 + CaMCa4 <---> AC1Cam (k9,k_9): Kd=150 nM
#AC1Cam + ATP <--->AC1CamATP(k10,k_10)--->AC1Cam + cAMP(v10):Km=162 uM
#
#AC8 + CaMCa4 <--->AC8Cam(k11,k_11):Kd=800 nM
#AC8Cam + ATP <--->AC8CamATP(k12, k_12)--->AC8Cam + cAMP(v12):Km=162 uM
#
#k10=0.01------> cAMP_basal=56 nM
#
##########################################################################

par k6=0.0385,k_6=10
par k7=0.009,k_7=0.9


par k8=0.01, k_8=2273, v8=28.42
par k9=0.006,k_9=0.9
 

par k10=0.01, k_10=2273, v10=2.842
par k11=0.00125,k_11=1
par k12=0.01,k_12=2273,v12=2.842

par AC1tot=2500, AC8tot=2500

dE/dt=k6*GaGTP*AC1-K_6*E+k_7*ECam-k7*E*CaMCa4
dECam/dt=k7*E*CaMCa4-K_7*ECam+(k_8+v8)*ECamATP-k8*ECam*ATP
dECamATP/dt=k8*ECam*ATP-(k_8+v8)*ECamATP

dAC1Cam/dt=k9*AC1*CaMCa4-k_9*AC1Cam-k10*AC1Cam*ATP+(k_10+v10)*AC1CamATP
dAC1CamATP/dt=k10*AC1Cam*ATP-(k_10+v10)*AC1CamATP

dAC8Cam/dt=k11*AC8*CaMCa4-k_11*AC8Cam+(k_12+v12)*AC8CamATP-k12*AC8Cam*ATP
dAC8CamATP/dt=k12*AC8Cam*ATP-(k_12+v12)*AC8CamATP
  
dCAMP/dt=ECamATP*v8+AC1CamATP*v10+AC8CamATP*v12\
-KfPde1*PDE1cam*cAMP+KbPde1*PDE1cAMP-KfPde4*PDE4*cAMP+KbPde4*PDE4cAMP\
-2*kfhigh*camp*pka+2*kbhigh*PKAcamp1-2*kflow*camp*pkacamp1+2*kblow*pkacamp2


par ATPtot=2e6
par katp=10


ATP=ATPtot-cAMP-ECamATP-AC1CamATP-AC8CamATP-AMP-PDE1cAMP-PDE4cAMP\
-2*PKAcamp1-4*PKAcamp2-4*PKAr


ACCam=ECam + AC1Cam+AC8Cam+AC1CamATP+AC8CamATP
aux ACCam=ACCam

init  CAMP=135.9675
init  E=8.714253
init  ECam=0.221507627
init  ECamATP=1.923882
init  AC1Cam=36.38592
init  AC1CamATP=319.7911
init  AC8Cam=7.760417
init  AC8CamATP=68.15126


AC1=AC1tot-(E+ECam+ECamATP+AC1CamATP+AC1Cam)
AC8=AC8tot-(AC8Cam+AC8CamATP)

#Aux AC1=AC1
#Aux AC8=AC8
#Aux ATP=ATP

### PDE part ###########################################################################
#
# PDE1 + CaMca4 <=> PDECam (KbpdeCam, KfpdeCam :Kd=10 nM)
# PDE1cam + cAMP<=>PDE1-cAMP -> PDE1 + AMP : Km (K_PDE1) Vmax=V_PDE1 (KfPde1, KbPde1)
# PDE4 + cAMP<=>PDE4-cAMP -> PDE4 + AMP : Km (K_PDE4) Vmax=V_PDE4 (KfPde4, KbPde4)
#
########################################################################################

par K_Pde4=4000 V_Pde4=18 KfPde4=0.02 KbPde4=72
par K_Pde1=12000 V_Pde1=11 KfPde1=0.0046 KbPde1=44

par Pde1Tot=4000, Pde4Tot=2000

par speedpde=0.1
KbpdeCam=10*speedpde
KfpdeCam=1*speedpde


init  PDE1cAMP=9.2542541
init  PDE4cAMP=58.653095
init  AMP=115.76139

PDE1=Pde1Tot-PDE1cAMP-PDE1Cam
PDE4=Pde4Tot-PDE4cAMP
aux PDE1=PDE1
aux PDE4=PDE4


dPDE1cAMP/dt = KfPde1*PDE1Cam*cAMP - KbPde1*PDE1cAMP - V_Pde1*PDE1cAMP
dPDE4cAMP/dt = KfPde4*PDE4*cAMP - KbPde4*PDE4cAMP - V_Pde4*PDE4cAMP
dAMP/dt = V_Pde1*PDE1cAMP + V_Pde4*PDE4cAMP - katp*amp

dPDE1Cam/dt=KfpdeCam*PDE1*CaMCa4-KbpdeCam*PDE1Cam-KfPde1*PDE1Cam*cAMP+(KbPde1+V_Pde1)*PDE1cAMP
init  PDE1CaM=813.6621

### CaM,CaMCa4 & PP2B Binding ##############################################################
#
#CaM+2Ca <-> CaMCa2_C  (KfC, KbC; Kd=1.5 uM )
#CaMCa2_C + 2Ca <-> Ca4CaM (KfN, KbN; Kd=10 uM)
#CaM + PP2(2B) <-> PP2CaM (K33a, K_33a)
#CaMCa2 + PP2(2B) <-> PP2CaMCa2 (K33c, K_33c)
#CamCa4 + PP2(2B) <-> PP2B (K32, K_32) :: New rate constants from waxham 2006 paper!!!
#PP2CaM + 2Ca <-> PP2CaMCa2 (KfC, KbCP - old 34a; KbCP is ~10x slower than KbC)
#PP2CaMCa2 + 2 Ca <-> PP2B(= PP2CaMCa4) (KfN, KbNP - old 34c; KbNP is ~10x slower than KbN)
#
############################################################################################

Par KfN=0.1 KbN=1000 KbNP=10
Par KfC=6e-3 KbC=9.1 KbCP=0.91

par k33c=1 k_33c=0.3
par k33a=1 k_33a=3
par k32=0.046 k_32=0.0012

init  CaMCa2=365.7787
init  CaMCa4=2.561034
init  PP2B=720.91025
init  PP2cam=2236.603
init  PP2camc2=1029.996

#Par CaMtot=15000
Par PP2Btot=4000

#CaMtot=15000+cam_a
dCaMtot/dt=cam_a
init CaMtot=15000

dCaMCa2/dt=kfC*Ca*CaM-kbC*CaMCa2+kbN*CaMCa4-kfN*Ca*CaMCa2\
+k_33c*PP2camc2-k33c*CaMCa2*2B


#3rd line has been added into CaMCa4 & CaM eqns..
dCaMCa4/dt=kfN*Ca*CaMCa2-kbN*CaMCa4-k32*CaMCa4*2B+k_32*PP2B\
-k51*CaMCa4*CK+k_51*CKCam-KfpdeCam*PDE1*CaMCa4+KbpdeCam*PDE1Cam\
-k7*E*CaMCa4+k_7*ECam-k9*AC1*CaMCa4+k_9*AC1Cam-k11*AC8*CaMCa4+k_11*AC8Cam




CaM=CaMtot-(CaMca2+CaMca4+AC1Cam+AC8Cam+PP2cam+PP2camc2+PP2B+Ip35p1p2+Ip35pp2b\
+CKCam+CKpCam+PDE1cam+PDE1camp\
+ECam+ECamATP+AC1Cam+AC1CamATP+AC8Cam+AC8CamATP)
aux CaM=CaM


camc4bnd=PP2B+Ip35PP2B+Ip35p1p2+CKCam+CKpCam+pde1cam+pde1camp\
+ECam+ECamATP+AC1Cam+AC1CamATP+AC8Cam+AC8CamATP
aux camc4bnd=camc4bnd

totCaM=caM+caMca2+caMca4+PP2cam+PP2camc2+camc4bnd


dPP2B/dt=k32*CaMCa4*2B-k_32*PP2B+kfN*PP2camc2*Ca-KbNP*PP2B\
-k22*Ip35*PP2B+(k_22+v22)*Ip35pp2b-k23*Ip35pp1*PP2B+(k_23+v23)*Ip35p1p2


dPP2cam/dt=k33a*CaM*2B-k_33a*PP2cam-kfC*PP2cam*Ca+kbCP*PP2camc2


dPP2camc2/dt=k33c*CaMCa2*2B-k_33c*PP2camc2-kfN*PP2camc2*Ca+kbNP*PP2B\
+kfC*PP2Cam*Ca-kbCP*PP2camc2



2B=PP2Btot-(PP2B+PP2camc2+PP2cam+Ip35pp2B+Ip35p1p2)


#2B=2Btot-PP2B-PP2camc2-PP2cam-Ip35pp2B-Ip35p1p2
#PAR 2Btot=4000
aux 2B=2B

PP2Bact=PP2B+Ip35pp2B+Ip35p1p2

####CaMKII Part:modified from Dupont's Model:#######################################
#
#  Dec.2006: convert to qantitative model from Dupont's code
#  April,2007: eliminate CKpC form --> combined CKpCam & CKpC
#  June_2007 : simplified Va form to match De Koninck's Exp. data
#
## Chemical Reactions: CaMCa4 + CK <-> CKCam (k51, k_51): bounded form(kd=80 nM)
#                      CKCam --> CKpCam (Va : Autophoshorylation)
#                      CKpCam <--> CKp + CaMCa4 ( k52, k_52):trapped form(kd=10e-12)
#                                  K_52: 1/3 of K_51(0.26667)suggested by Meyer et al.(1992)
#                      Ckp + PP1 <-->CKpPP1 --> PP1 + CK :Dephoshop(k54,k_54,k54cat)
#                           ; Km=5.1 uM  from foulkes et. al.,  et al., Eur. JBiochem.1983 132(309-313))
#                           ; Vmax=5.7 umol/min --> kcat=3.5 sec-1 & kb=14 sec-1
#                           ; Simonelli 1984(Grad Thesis,CUNY) showed that other substrate are about 1/10
#                           ; rate of phosphorylase a so, reduce kf,kb,kcat by 10
#                           ; Schulman's Exp. data taken
########################################################################################


param CK_ini=20000


CK=CK_ini-CKCam-CkpCam-CKp-CKpPP1 
aux CK=CK

dCKCam/dt = k51*CaMCa4*CK - K_51*CKCam-Va*CK_ini
init CKCam=594.4366


dCKpCam/dt = Va*CK_ini + k_52*CKp*CaMCa4-k52*CKpCam
init CKpCam=812.7395


dCKp/dt =k52*CKpCam - k_52*CKp*CaMCa4 + k_54*CKpPP1-k54*CKp*PP1
init CKp=10.63496


dCKpPP1/dt =k54*CKp*PP1-(k_54+k54cat)*CKpPP1
init CKpPP1=3.341977

Va=Ka1*((qb*CKCam)^3/(CK_ini^3)+((qb*CKCam)^2*qp*CKpCam)/(CK_ini^3))

param k51=0.01,k_51=0.8,k52=0.0008,k_52=0.0133,Kd=1000,Ka1=0.46
param k54=0.000039,k_54=0.34,k54cat=0.086
param qb=0.75, qp=1, qt=0.8, qa=0.8, qpt=1.0

par pp1tot=3500
PP1= PP1tot-CKpPP1-Ip35PP1-Ip35P1P2
aux pp1=pp1



QActi=qpt*CKpCam+qa*CKp
Acti=QActi/CK_ini

aux QActi=QActi
#aux Acti=Acti


### PKA part:#############################
#
#PKA+2cAMP<->PKAcAMP1; Kdhigh, slow
#PKAcAMP1+2cAMP<->PKAcAMP2; Kdlow
#PKAcAMP2<->PKAr+2PKAc; Kd_diss, slow
#
##########################################

par speedpka=10.0
kbhigh=0.002*speedpka
kfhigh=4.3478e-06*speedpka*2
kblow=0.02*speedpka
kflow=5.7703e-6*speedpka*2
kasrc=0.00017*speedpka
kdisrc=0.0016*speedpka

par PKAtot=1200

dPKAcAMP1/dt=kfhigh*cAMP*PKA-kbhigh*PKAcAMP1-kflow*cAMP*PKAcAMP1+kblow*PKAcAMP2
dPKAcAMP2/dt=kflow*cAMP*PKAcAMP1-kblow*PKAcAMP2-kdisrc*PKAcAMP2+kasrc*PKAc*PKAr
dPKAc/dt=2*kdisrc*PKAcamp2-2*kasrc*PKAc*PKAr-k20*I1*PKAc+k_20*I1PKAc+v20*I1PKAc



Pka=PKAtot-PKAcAMP1-PKAcAMP2-0.5*(PKAc+I1PKAc)
PKAr=0.5*(PKAc+I1PKAc)





init  PKAcAMP1=428.0043
init  PKAcAMP2=33.5732
init  PKAc=22.17636

PKAact=PKAc+I1PKAc


totPKA=PKA+PKAcAMP1+PKAcAMP2+0.5*(PKAc+I1PKAc)




####Inhibitor 1 Phospho & Dephosphorylation ################
##
##  I1+PKAc <--> I1PKAc --> Ip35 + PKAc (20)
##  Ip35 + PP1 <--> Ip35pp1 (21)
##  Ip35 + PP2B <--> Ip35pp2b --> I1 + PP2B (22)
##  Ip35pp1 + PP2B <--> Ip35p1p2 --> I1 + PP1 + PP2B (23)
##
############################################################

par I1tot=1500

I1=I1tot-I1PKAc-Ip35-Ip35pp1-Ip35pp2b-Ip35p1p2
aux I1=I1

par k20=0.0014 k_20=5.6 v20=1.4
dI1PKAc/dt=k20*I1*PKAc-k_20*I1PKAc-v20*I1PKAc

init  I1PKAc=6.32017


dIp35/dt=v20*I1PKAc+k_22*Ip35pp2b-k22*Ip35*PP2B-k21*Ip35*PP1+k_21*Ip35pp1

init  Ip35=2.169742

#### Ip35 + PP1 <--> Ip35pp1 (21) #####

par  k21=0.001 k_21=0.0011
dIp35pp1/dt=k21*Ip35*PP1-k_21*Ip35pp1-k23*Ip35pp1*pp2b+k_23*Ip35p1p2

init  Ip35pp1=51.23495
#### Ip35 + PP2B <--> Ip35pp2b --> I1 + PP2B (22) #############

par  k22=0.00467 k_22=11.2 v22=2.8
dIp35pp2b/dt=k22*Ip35*PP2B-k_22*Ip35pp2b-v22*Ip35pp2b

init  Ip35pp2b=0.5217763

#### Ip35pp1 + PP2B <--> Ip35p1p2 --> I1 + PP1 + PP2B (23) #####

par k23_a=1.0
k23=0.001*k23_a
k_23=2*k23_a
v23=0.5*k23_a

dIp35p1p2/dt=k23*Ip35pp1*PP2B-k_23*Ip35p1p2-v23*Ip35p1p2

init  Ip35p1p2=14.77453

###########################################################


dPKAauc/dt=PKAc
init PKAauc=0


@ Total=1400 dt=0.1 method=stiff xlo=0 xhi=3000 ylo=0 yhi=1 maxstor=6000000 \
  bounds=10000000000 BACK=black nOutput=10000
d




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Copyright © 2017 Matthias Koenig

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Access SBML model  L3V1

FunctionDefinitions [4] 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

Parameters [181] name constant value unit derived unit sbo cvterm
t_rise t_rise = 0.01 0.01 None
ca_max ca_max = 10000 10000.0 None
t_dur t_dur = 0.009 0.009 None
tau tau = 0.01 0.01 None
train_len train_len = 1 1.0 None
t1 t1 = 100 100.0 None
t2 t2 = 103 103.0 None
t3 t3 = 106 106.0 None
t4 t4 = 109 109.0 None
cab cab = 70 70.0 None
t_tau t_tau = 0.01 0.01 None
cam_rate cam_rate = 0.1 0.1 None
lb lb = 10 10.0 None
l_max l_max = 1000 1000.0 None
taul taul = 2 2.0 None
k2a k2a = 0.00333333 0.00333333 None
k_2a k_2a = 10 10.0 None
k1a k1a = 0.00006 6e-05 None
k_1a k_1a = 0.0003 0.0003 None
k_1 k_1 = 10 10.0 None
k1 k1 = 0.0011111 0.0011111 None
k2 k2 = 0.0006 0.0006 None
k_2 k_2 = 0.001 0.001 None
k3 k3 = 20 20.0 None
k4 k4 = 10 10.0 None
k5 k5 = 100 100.0 None
lr lr = 0.9886277 0.9886277 None
lrg lrg = 0.5300418 0.5300418 None
gagtp gagtp = 1.060084 1.060084 None
gagdp gagdp = 143.092094 143.092094 None
gr gr = 434.160416 434.160416 None
gbg gbg = 0.000739 0.000739 None
gtot gtot = 3000 3000.0 None
rtot rtot = 500 500.0 None
k6 k6 = 0.0385 0.0385 None
k_6 k_6 = 10 10.0 None
k7 k7 = 0.009 0.009 None
k_7 k_7 = 0.9 0.9 None
k8 k8 = 0.01 0.01 None
k_8 k_8 = 2273 2273.0 None
v8 v8 = 28.42 28.42 None
k9 k9 = 0.006 0.006 None
k_9 k_9 = 0.9 0.9 None
k10 k10 = 0.01 0.01 None
k_10 k_10 = 2273 2273.0 None
v10 v10 = 2.842 2.842 None
k11 k11 = 0.00125 0.00125 None
k_11 k_11 = 1 1.0 None
k12 k12 = 0.01 0.01 None
k_12 k_12 = 2273 2273.0 None
v12 v12 = 2.842 2.842 None
ac1tot ac1tot = 2500 2500.0 None
ac8tot ac8tot = 2500 2500.0 None
atptot atptot = 2e6 2000000.0 None
katp katp = 10 10.0 None
camp camp = 135.9675 135.9675 None
e e = 8.714253 8.714253 None
ecam ecam = 0.221507627 0.221507627 None
ecamatp ecamatp = 1.923882 1.923882 None
ac1cam ac1cam = 36.38592 36.38592 None
ac1camatp ac1camatp = 319.7911 319.7911 None
ac8cam ac8cam = 7.760417 7.760417 None
ac8camatp ac8camatp = 68.15126 68.15126 None
k_pde4 k_pde4 = 4000 4000.0 None
v_pde4 v_pde4 = 18 18.0 None
kfpde4 kfpde4 = 0.02 0.02 None
kbpde4 kbpde4 = 72 72.0 None
k_pde1 k_pde1 = 12000 12000.0 None
v_pde1 v_pde1 = 11 11.0 None
kfpde1 kfpde1 = 0.0046 0.0046 None
kbpde1 kbpde1 = 44 44.0 None
pde1tot pde1tot = 4000 4000.0 None
pde4tot pde4tot = 2000 2000.0 None
speedpde speedpde = 0.1 0.1 None
pde1camp pde1camp = 9.2542541 9.2542541 None
pde4camp pde4camp = 58.653095 58.653095 None
amp amp = 115.76139 115.76139 None
pde1cam pde1cam = 813.6621 813.6621 None
kfn kfn = 0.1 0.1 None
kbn kbn = 1000 1000.0 None
kbnp kbnp = 10 10.0 None
kfc kfc = 6e-3 0.006 None
kbc kbc = 9.1 9.1 None
kbcp kbcp = 0.91 0.91 None
k33c k33c = 1 1.0 None
k_33c k_33c = 0.3 0.3 None
k33a k33a = 1 1.0 None
k_33a k_33a = 3 3.0 None
k32 k32 = 0.046 0.046 None
k_32 k_32 = 0.0012 0.0012 None
camca2 camca2 = 365.7787 365.7787 None
camca4 camca4 = 2.561034 2.561034 None
pp2b pp2b = 720.91025 720.91025 None
pp2cam pp2cam = 2236.603 2236.603 None
pp2camc2 pp2camc2 = 1029.996 1029.996 None
pp2btot pp2btot = 4000 4000.0 None
camtot camtot = 15000 15000.0 None
ck_ini ck_ini = 20000 20000.0 None
ckcam ckcam = 594.4366 594.4366 None
ckpcam ckpcam = 812.7395 812.7395 None
ckp ckp = 10.63496 10.63496 None
ckppp1 ckppp1 = 3.341977 3.341977 None
k51 k51 = 0.01 0.01 None
k_51 k_51 = 0.8 0.8 None
k52 k52 = 0.0008 0.0008 None
k_52 k_52 = 0.0133 0.0133 None
kd kd = 1000 1000.0 None
ka1 ka1 = 0.46 0.46 None
k54 k54 = 0.000039 3.9e-05 None
k_54 k_54 = 0.34 0.34 None
k54cat k54cat = 0.086 0.086 None
qb qb = 0.75 0.75 None
qp qp = 1 1.0 None
qt qt = 0.8 0.8 None
qa qa = 0.8 0.8 None
qpt qpt = 1.0 1.0 None
pp1tot pp1tot = 3500 3500.0 None
speedpka speedpka = 10.0 10.0 None
pkatot pkatot = 1200 1200.0 None
pkacamp1 pkacamp1 = 428.0043 428.0043 None
pkacamp2 pkacamp2 = 33.5732 33.5732 None
pkac pkac = 22.17636 22.17636 None
i1tot i1tot = 1500 1500.0 None
k20 k20 = 0.0014 0.0014 None
k_20 k_20 = 5.6 5.6 None
v20 v20 = 1.4 1.4 None
i1pkac i1pkac = 6.32017 6.32017 None
ip35 ip35 = 2.169742 2.169742 None
k21 k21 = 0.001 0.001 None
k_21 k_21 = 0.0011 0.0011 None
ip35pp1 ip35pp1 = 51.23495 51.23495 None
k22 k22 = 0.00467 0.00467 None
k_22 k_22 = 11.2 11.2 None
v22 v22 = 2.8 2.8 None
ip35pp2b ip35pp2b = 0.5217763 0.5217763 None
k23_a k23_a = 1.0 1.0 None
ip35p1p2 ip35p1p2 = 14.77453 14.77453 None
pkaauc pkaauc = 0 0.0 None
ca 0.0 dimensionless None
tm 0.0 dimensionless None
t_pulse 0.0 dimensionless None
ca_pre 0.0 dimensionless None
cam_a 0.0 dimensionless None
l 0.0 dimensionless None
g 0.0 dimensionless None
galfa 0.0 dimensionless None
r 0.0 dimensionless None
atp 0.0 dimensionless None
accam 0.0 dimensionless None
ac1 0.0 dimensionless None
ac8 0.0 dimensionless None
kbpdecam 0.0 dimensionless None
kfpdecam 0.0 dimensionless None
pde1 0.0 dimensionless None
pde4 0.0 dimensionless None
cam 0.0 dimensionless None
camc4bnd 0.0 dimensionless None
totcam 0.0 dimensionless None
0.0 dimensionless None
pp2bact 0.0 dimensionless None
ck 0.0 dimensionless None
va 0.0 dimensionless None
pp1 0.0 dimensionless None
qacti 0.0 dimensionless None
acti 0.0 dimensionless None
kbhigh 0.0 dimensionless None
kfhigh 0.0 dimensionless None
kblow 0.0 dimensionless None
kflow 0.0 dimensionless None
kasrc 0.0 dimensionless None
kdisrc 0.0 dimensionless None
pka 0.0 dimensionless None
pkar 0.0 dimensionless None
pkaact 0.0 dimensionless None
totpka 0.0 dimensionless None
i1 0.0 dimensionless None
k23 0.0 dimensionless None
k_23 0.0 dimensionless None
v23 0.0 dimensionless None
bounds 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [80]   assignment name derived units sbo cvterm
d ca/dt = ca_pre ca t_tau None
d lr/dt = k1 r l k_1 lr k2 lr g k_2 lrg k3 lrg None
d lrg/dt = k2 lr g k_2 lrg k3 lrg k2a gr l k_2a lrg None
d gagtp/dt = k3 lrg k4 gagtp e k_6 gagtp ac1 k6 None
d gagdp/dt = k4 gagtp k5 gagdp gbg None
d gr/dt = k1a g r k_1a gr k2a gr l k_2a lrg None
d gbg/dt = k3 lrg k5 gagdp gbg None
d e/dt = k6 gagtp ac1 k_6 e k_7 ecam k7 e camca4 None
d ecam/dt = k7 e camca4 k_7 ecam k_8 v8 ecamatp k8 ecam atp None
d ecamatp/dt = k8 ecam atp k_8 v8 ecamatp None
d ac1cam/dt = k9 ac1 camca4 k_9 ac1cam k10 ac1cam atp k_10 v10 ac1camatp None
d ac1camatp/dt = k10 ac1cam atp k_10 v10 ac1camatp None
d ac8cam/dt = k11 ac8 camca4 k_11 ac8cam k_12 v12 ac8camatp k12 ac8cam atp None
d ac8camatp/dt = k12 ac8cam atp k_12 v12 ac8camatp None
d camp/dt = ecamatp v8 ac1camatp v10 ac8camatp v12 kfpde1 pde1cam camp kbpde1 pde1camp kfpde4 pde4 camp kbpde4 pde4camp 2 kfhigh camp pka 2 kbhigh pkacamp1 2 kflow camp pkacamp1 2 kblow pkacamp2 None
d pde1camp/dt = kfpde1 pde1cam camp kbpde1 pde1camp v_pde1 pde1camp None
d pde4camp/dt = kfpde4 pde4 camp kbpde4 pde4camp v_pde4 pde4camp None
d amp/dt = v_pde1 pde1camp v_pde4 pde4camp katp amp None
d pde1cam/dt = kfpdecam pde1 camca4 kbpdecam pde1cam kfpde1 pde1cam camp kbpde1 v_pde1 pde1camp None
d camtot/dt = cam_a None
d camca2/dt = kfc ca cam kbc camca2 kbn camca4 kfn ca camca2 k_33c pp2camc2 k33c camca2 2 None
d camca4/dt = kfn ca camca2 kbn camca4 k32 camca4 2 k_32 pp2b k51 camca4 ck k_51 ckcam kfpdecam pde1 camca4 kbpdecam pde1cam k7 e camca4 k_7 ecam k9 ac1 camca4 k_9 ac1cam k11 ac8 camca4 k_11 ac8cam None
d pp2b/dt = k32 camca4 2 k_32 pp2b kfn pp2camc2 ca kbnp pp2b k22 ip35 pp2b k_22 v22 ip35pp2b k23 ip35pp1 pp2b k_23 v23 ip35p1p2 None
d pp2cam/dt = k33a cam 2 k_33a pp2cam kfc pp2cam ca kbcp pp2camc2 None
d pp2camc2/dt = k33c camca2 2 k_33c pp2camc2 kfn pp2camc2 ca kbnp pp2b kfc pp2cam ca kbcp pp2camc2 None
d ckcam/dt = k51 camca4 ck k_51 ckcam va ck_ini None
d ckpcam/dt = va ck_ini k_52 ckp camca4 k52 ckpcam None
d ckp/dt = k52 ckpcam k_52 ckp camca4 k_54 ckppp1 k54 ckp pp1 None
d ckppp1/dt = k54 ckp pp1 k_54 k54cat ckppp1 None
d pkacamp1/dt = kfhigh camp pka kbhigh pkacamp1 kflow camp pkacamp1 kblow pkacamp2 None
d pkacamp2/dt = kflow camp pkacamp1 kblow pkacamp2 kdisrc pkacamp2 kasrc pkac pkar None
d pkac/dt = 2 kdisrc pkacamp2 2 kasrc pkac pkar k20 i1 pkac k_20 i1pkac v20 i1pkac None
d i1pkac/dt = k20 i1 pkac k_20 i1pkac v20 i1pkac None
d ip35/dt = v20 i1pkac k_22 ip35pp2b k22 ip35 pp2b k21 ip35 pp1 k_21 ip35pp1 None
d ip35pp1/dt = k21 ip35 pp1 k_21 ip35pp1 k23 ip35pp1 pp2b k_23 ip35p1p2 None
d ip35pp2b/dt = k22 ip35 pp2b k_22 ip35pp2b v22 ip35pp2b None
d ip35p1p2/dt = k23 ip35pp1 pp2b k_23 ip35p1p2 v23 ip35p1p2 None
d pkaauc/dt = pkac None
tm = mod t tau None
t_pulse = t_dur tm None
ca_pre = cab ca_max cab heav t t1 heav t1 train_len t heav t_pulse ca_max cab heav t t2 heav t2 train_len t heav t_pulse ca_max cab heav t t3 heav t3 train_len t heav t_pulse ca_max cab heav t t4 heav t4 train_len t heav t_pulse None
cam_a = cam_rate 7924 cam None
l = lb l_max lb heav t t1 heav t1 train_len t l_max lb heav t t2 heav t2 train_len t l_max lb heav t t3 heav t3 train_len t l_max lb heav t t4 heav t4 train_len t None
g = gtot lrg gagtp gagdp e ecam ecamatp gr None
galfa = gagtp gagdp None
r = rtot lr lrg gr None
atp = atptot camp ecamatp ac1camatp ac8camatp amp pde1camp pde4camp 2 pkacamp1 4 pkacamp2 4 pkar None
accam = ecam ac1cam ac8cam ac1camatp ac8camatp None
ac1 = ac1tot e ecam ecamatp ac1camatp ac1cam None
ac8 = ac8tot ac8cam ac8camatp None
kbpdecam = 10 speedpde None
kfpdecam = 1 speedpde None
pde1 = pde1tot pde1camp pde1cam None
pde4 = pde4tot pde4camp None
cam = camtot camca2 camca4 ac1cam ac8cam pp2cam pp2camc2 pp2b ip35p1p2 ip35pp2b ckcam ckpcam pde1cam pde1camp ecam ecamatp ac1cam ac1camatp ac8cam ac8camatp None
camc4bnd = pp2b ip35pp2b ip35p1p2 ckcam ckpcam pde1cam pde1camp ecam ecamatp ac1cam ac1camatp ac8cam ac8camatp None
totcam = cam camca2 camca4 pp2cam pp2camc2 camc4bnd None
= pp2btot pp2b pp2camc2 pp2cam ip35pp2b ip35p1p2 None
pp2bact = pp2b ip35pp2b ip35p1p2 None
ck = ck_ini ckcam ckpcam ckp ckppp1 None
va = ka1 qb ckcam 3 ck_ini 3 qb ckcam 2 qp ckpcam ck_ini 3 None
pp1 = pp1tot ckppp1 ip35pp1 ip35p1p2 None
qacti = qpt ckpcam qa ckp None
acti = qacti ck_ini None
kbhigh = 0.002 speedpka None
kfhigh = 4.3478 -6 speedpka 2 None
kblow = 0.02 speedpka None
kflow = 5.7703 -6 speedpka 2 None
kasrc = 0.00017 speedpka None
kdisrc = 0.0016 speedpka None
pka = pkatot pkacamp1 pkacamp2 0.5 pkac i1pkac None
pkar = 0.5 pkac i1pkac None
pkaact = pkac i1pkac None
totpka = pka pkacamp1 pkacamp2 0.5 pkac i1pkac None
i1 = i1tot i1pkac ip35 ip35pp1 ip35pp2b ip35p1p2 None
k23 = 0.001 k23_a None
k_23 = 2 k23_a None
v23 = 0.5 k23_a None
bounds = 10000000000 None
t = time None