#maiwald

FIX: extVariable

#reactions
v_1:
 {0.5}ReceptorIFNAR1 + {0.5}TYK = {0.5}ReceptorTYKcomplex
  cytoplasm * (k1 * ReceptorIFNAR1 * TYK - k2 * ReceptorTYKcomplex)
v_10:
 {0.5}ISGF3c = {1.0}ISGF3n
  k19*ISGF3c-k29*ISGF3n
v_11:
 {0.5}STAT1cstarSTAT2cstar = {1.0}STAT1nstarSTAT2nstar
  PhosphoTransport*STAT1cstarSTAT2cstar-k210*STAT1nstarSTAT2nstar
v_12:
 {1.0}STAT1nstarSTAT2nstar + {1.0}IRF9n = {1.0}ISGF3n
  nucleus*(k111*STAT1nstarSTAT2nstar*IRF9n-k211*ISGF3n)
v_13:
 {1.0}OpenISGF3nbindingsites + {1.0}ISGF3n = {1.0}OccupiedISGF3nbindingsites
  nucleus*(k112*OpenISGF3nbindingsites*ISGF3n-k212*OccupiedISGF3nbindingsites)
v_14:
 {1.0}extVariable = {1.0}mRNAn
  nucleus * function4Transcription
v_15:
 {1.0}mRNAn = {0.5}mRNAc
  k114*mRNAn-k214*mRNAc
v_16:
 {1.0}extVariable = {0.5}IRF9c
  cytoplasm * function4
v_17:
 {1.0}extVariable = {0.5}SOCS1
  cytoplasm * function6
v_18:
 {0.5}ActivatedReceptorComplex = {0.5}ReceptorIFNAR1 + {0.5}species6 + {0.5}JAK + {0.5}TYK
  cytoplasm * function5
v_19:
 {0.5}ActivatedReceptorComplex = {0.5}IFNARdimer
  cytoplasm*k118*ActivatedReceptorComplex
v_2:
 {0.5}JAK + {0.5}species6 = {0.5}ReceptorJAKcomplex
  cytoplasm*(k11*JAK*species6-k21*ReceptorJAKcomplex)
v_20:
 {1.0}IRF9n = {1.0}extVariable
  nucleus*IRF9deg*IRF9n
v_21:
 {0.5}STAT2cIRF9 = {0.5}STAT2c
  cytoplasm*IRF9deg*STAT2cIRF9
v_22:
 {1.0}STAT2nIRF9 = {1.0}STAT2n
  nucleus*IRF9deg*STAT2nIRF9
v_23:
 {0.5}ISGF3c + {0.5}CP = {0.5}ISGF3cCP
  cytoplasm*(k122*ISGF3c*CP-k222*ISGF3cCP)
v_24:
 {0.5}ISGF3cCP = {0.5}STAT1c + {0.5}STAT2c + {0.5}CP + {0.5}IRF9c
  cytoplasm*k123*ISGF3cCP
v_25:
 {0.5}STAT1cstarSTAT2cstar + {0.5}CP = {0.5}STAT1cstarSTAT2cstarCP
  cytoplasm*(k124*STAT1cstarSTAT2cstar*CP-k224*STAT1cstarSTAT2cstarCP)
v_26:
 {0.5}STAT1cstarSTAT2cstarCP = {0.5}STAT1c + {0.5}STAT2c + {0.5}CP
  cytoplasm*k125*STAT1cstarSTAT2cstarCP
v_27:
 {1.0}NP + {1.0}STAT1nstarSTAT2nstar = {1.0}STAT1nstarSTAT2nstarNP
  nucleus*(NPfreebinding*NP*STAT1nstarSTAT2nstar-NPfreeunbinding*STAT1nstarSTAT2nstarNP)
v_28:
 {1.0}STAT1nstarSTAT2nstarNP = {1.0}STAT1n + {1.0}STAT2n + {1.0}NP
  nucleus*k127*STAT1nstarSTAT2nstarNP
v_29:
 {1.0}ISGF3n + {1.0}NP = {1.0}ISGF3nNP
  nucleus*(NPfreebinding*ISGF3n*NP-NPfreeunbinding*ISGF3nNP)
v_3:
 {0.5}ReceptorJAKcomplex + {0.5}ReceptorTYKcomplex + {0.5}IFN = {0.5}IFNARdimer
  cytoplasm*(k12*ReceptorJAKcomplex*ReceptorTYKcomplex*IFN-k22*IFNARdimer)
v_30:
 {1.0}ISGF3nNP = {1.0}STAT1n + {1.0}STAT2n + {1.0}NP + {1.0}IRF9n
  nucleus*k129*ISGF3nNP
v_31:
 {1.0}NP + {1.0}OccupiedISGF3nbindingsites = {1.0}OccupiedISGF3nbindingsitesNP
  nucleus*(k130*NP*OccupiedISGF3nbindingsites-k230*OccupiedISGF3nbindingsitesNP)
v_32:
 {1.0}OccupiedISGF3nbindingsitesNP = {1.0}STAT1n + {1.0}STAT2n + {1.0}IRF9n + {1.0}OpenISGF3nbindingsites + {1.0}NP
  nucleus*k131*OccupiedISGF3nbindingsitesNP
v_33:
 {1.0}PIAS + {1.0}ISGF3n = {1.0}PIASISGF3n
  nucleus*(k132*PIAS*ISGF3n-k232*PIASISGF3n)
v_34:
 {0.5}mRNAc = {1.0}extVariable
  cytoplasm*k133*mRNAc
v_35:
 {1.0}STAT1n = {0.5}STAT1c
  k134*STAT1n-k234*STAT1c
v_36:
 {1.0}STAT2n = {0.5}STAT2c
  k135*STAT2n-k235*STAT2c
v_37:
 {0.5}STAT2c + {0.5}IRF9c = {0.5}STAT2cIRF9
  cytoplasm*(k136*STAT2c*IRF9c-k236*STAT2cIRF9)
v_38:
 {1.0}STAT2n + {1.0}IRF9n = {1.0}STAT2nIRF9
  nucleus*(k137*STAT2n*IRF9n-k237*STAT2nIRF9)
v_39:
 {0.5}STAT2cIRF9 = {1.0}STAT2nIRF9
  k138*STAT2cIRF9-k238*STAT2nIRF9
v_4:
 {0.5}IFNARdimer = {0.5}ActivatedReceptorComplex
  cytoplasm*k13*IFNARdimer
v_40:
 {0.5}IRF9c = {1.0}IRF9n
  k139*IRF9c-k239*IRF9n
v_41:
 {0.5}preIFN = {0.5}IFN
  cytoplasm*k140*preIFN
v_5:
 {0.5}STAT2cIRF9 + {0.5}ActivatedReceptorComplex = {0.5}ActivatedReceptorComplexSTAT2c + {0.5}IRF9c
  cytoplasm*statrecbinding*STAT2cIRF9*ActivatedReceptorComplex
v_6:
 {0.5}STAT2c + {0.5}ActivatedReceptorComplex = {0.5}ActivatedReceptorComplexSTAT2c
  cytoplasm*(statrecbinding*STAT2c*ActivatedReceptorComplex-statrecunbinding*ActivatedReceptorComplexSTAT2c)
v_7:
 {0.5}STAT1c + {0.5}ActivatedReceptorComplexSTAT2c = {0.5}ActivatedReceptorComplexSTAT2cSTAT1c
  cytoplasm*(statrecbinding*STAT1c*ActivatedReceptorComplexSTAT2c-statrecunbinding*ActivatedReceptorComplexSTAT2cSTAT1c)
v_8:
 {0.5}ActivatedReceptorComplexSTAT2cSTAT1c = {0.5}ActivatedReceptorComplex + {0.5}STAT1cstarSTAT2cstar
  cytoplasm*k17*ActivatedReceptorComplexSTAT2cSTAT1c
v_9:
 {0.5}IRF9c + {0.5}STAT1cstarSTAT2cstar = {0.5}ISGF3c
  cytoplasm*(k18*IRF9c*STAT1cstarSTAT2cstar-k28*ISGF3c)


#parameters
IRF9deg = 0.0001
NPfreebinding = 0.01
NPfreeunbinding = 0.1
PhosphoTransport = 0.015
ReceptorSOCSdeg = 1.2e-05
Receptordegradation = 0.0003
SOCSbinding = 0.02
SOCSunbinding = 0.1
STAT1Start = 1500.0
STAT2Start = 250.0
StartingJak = 26.0
StartingReceptor = 1000.0
StartingTyk = 13.0
activatedsynth = 0.045
constdeg = 0.0005
cytoplasm = 2.0
k1 = 0.1
k11 = 0.1
k111 = 0.01
k112 = 0.1
k113 = 2.5e-05
k114 = 0.001
k118 = 0.01
k12 = 0.01
k122 = 0.001
k123 = 0.003
k124 = 0.001
k125 = 0.003
k127 = 0.1
k129 = 0.002
k13 = 0.005
k130 = 0.0001
k131 = 0.1
k132 = 0.1
k133 = 0.0005
k134 = 0.01
k135 = 0.0014
k136 = 0.01
k137 = 0.01
k138 = 0.00125
k139 = 0.02
k140 = 0.0009
k17 = 8.0
k18 = 0.1
k19 = 0.015
k2 = 0.05
k21 = 0.05
k210 = 0.0
k211 = 0.01
k212 = 0.1
k214 = 0.0
k22 = 0.01
k222 = 0.2
k224 = 0.2
k230 = 0.1
k232 = 0.1
k234 = 0.00125
k235 = 8.17e-05
k236 = 0.01
k237 = 0.01
k238 = 0.0014
k239 = 0.005
k28 = 0.1
k29 = 0.0
nucleus = 1.0
startkin = 13.0
statrecbinding = 0.002
statrecunbinding = 4.0
vactivated = 0.045
vconst = 0.005
extVariable = 0.0
default_compartment = 1.0


#initial values
ActivatedReceptorComplex = 0.0
ActivatedReceptorComplexSTAT2c = 0.0
ActivatedReceptorComplexSTAT2cSTAT1c = 0.0
CP = 20.0
IFN = 0.0
IFNARdimer = 0.0
IRF9c = 45.0
IRF9n = 0.0
ISGF3c = 0.0
ISGF3cCP = 0.0
ISGF3n = 0.0
ISGF3nNP = 0.0
JAK = 26.0
NP = 40.0
OccupiedISGF3nbindingsites = 0.0
OccupiedISGF3nbindingsitesNP = 0.0
OpenISGF3nbindingsites = 500.0
PIAS = 10.0
PIASISGF3n = 0.0
ReceptorIFNAR1 = 1000.0
ReceptorJAKcomplex = 0.0
ReceptorTYKcomplex = 0.0
SOCS1 = 0.0
STAT1c = 1500.0
STAT1cstarSTAT2cstar = 0.0
STAT1cstarSTAT2cstarCP = 0.0
STAT1n = 0.0
STAT1nstarSTAT2nstar = 0.0
STAT1nstarSTAT2nstarNP = 0.0
STAT2c = 250.0
STAT2cIRF9 = 0.0
STAT2n = 250.0
STAT2nIRF9 = 0.0
TYK = 13.0
mRNAc = 0.0
mRNAn = 0.0
preIFN = 6.5
species6 = 1000.0


#assignment rules
!F DNAbinding = OccupiedISGF3nbindingsites * 2
!F function6 = activatedsynth*mRNAc-constdeg*SOCS1
!F function4Transcription = k1*OccupiedISGF3nbindingsites
!F function5 = ActivatedReceptorComplex*Receptordegradation+ActivatedReceptorComplex*ReceptorSOCSdeg*SOCS1
!F function4 = vconst+mRNAc*vactivated-IRF9c*IRF9deg