begin name
abudukelimu1
end name

begin reactions
R10drugwashout {1.0}$drug + {1.0}washout = {1.0}washout
R11FLCdrugbinding {1.0}$drug + {1.0}FLC = {1.0}$FLCdrug
R12FLCdrugwashout {1.0}$FLCdrug + {1.0}washout = {1.0}washout
R13CRASecretionDyingFibr {1.0}DyingFibr = {1.0}CRA
R14CRAClipOffHealthyFibr {1.0}HealthyFibr + {1.0}MMP7 = {1.0}CRA + {1.0}MMP7 + {1.0}HealthyFibr
R15DyingFibroblastdeath {1.0}DyingFibr = {1.0}$EXTERNAL
R16HealthytoDyingfibroblast {1.0}HealthyFibr + {1.0}TNFalpha = {1.0}DyingFibr + {1.0}TNFalpha
R17HealthyBacteriaProduction {1.0}HealthyBacteria = {2.0}HealthyBacteria
R18HealthyFibProduction {1.0}HealthyFibr = {2.0}HealthyFibr
R19MMP7releaseHealthyFibr {1.0}HealthyFibr = {1.0}HealthyFibr + {1.0}MMP7
R1CRAdegradation {1.0}CRA + {1.0}MMP8 = {1.0}MMP8
R20MMP8releaseHealthyFibr {1.0}HealthyFibr = {1.0}HealthyFibr + {100.0}MMP8
R21HealthytoDyingBacteria {1.0}HealthyBacteria + {1.0}Protease = {1.0}DyingBacteria + {1.0}Protease
R22CRAbinding {1.0}MastCellsFLC + {1.0}CRA = {1.0}MastCellsFLCCRA
R23FLCbinding {1.0}FLC + {1.0}MastCells = {1.0}MastCellsFLC
R24TNFalphaproduction {1.0}MastCellsFLCCRA = {1.0}TNFalpha + {1.0}MastCellsFLCCRA
R25Proteaseproduction {1.0}MastCellsFLCCRA = {1.0}Protease + {1.0}MastCellsFLCCRA
R26DyingBacteriasecreteCRA {1.0}DyingBacteria = {1000.0}CRA
R27Dyingbacteriadie {1.0}DyingBacteria = {1.0}$EXTERNAL
R28Proteaseinflux {1.0}$EXTERNAL = {1.0}Protease
R2CRAwashout {1.0}CRA + {1.0}washout = {1.0}washout
R3CRAinflux {1.0}$EXTERNAL = {1.0}CRA
R4FLCwashout {1.0}FLC + {1.0}washout = {1.0}washout
R5MMP7washout {1.0}MMP7 + {1.0}washout = {1.0}washout
R6MMP8washout {1.0}MMP8 + {1.0}washout = {1.0}washout
R7Proteasewashout {1.0}Protease + {1.0}washout = {1.0}washout
R8TNFalphawashout {1.0}TNFalpha + {1.0}washout = {1.0}washout
R9FLCproduction {1.0}CRA + {1.0}$Bcells = {1.0}FLC + {1.0}CRA + {1.0}$Bcells
end reactions

begin rate equations
R10drugwashout = compartment*drug*R10drugwashoutk1*washout[t]
R11FLCdrugbinding = compartment*(-(FLCdrug*R11FLCdrugbindingk2) + drug*R11FLCdrugbindingk1*FLC[t])
R12FLCdrugwashout = compartment*FLCdrug*R12FLCdrugwashoutk1*washout[t]
R13CRASecretionDyingFibr = compartment*R13CRASecretionDyingFibrk1*DyingFibr[t]
R14CRAClipOffHealthyFibr = compartment*RateLawforBAFFclipoff[R14CRAClipOffHealthyFibrk1, HealthyFibr[t], MMP7[t]]
R15DyingFibroblastdeath = compartment*R15DyingFibroblastdeathk1*DyingFibr[t]
R16HealthytoDyingfibroblast = compartment*R16HealthytoDyingfibroblastk1*HealthyFibr[t]*TNFalpha[t]
R17HealthyBacteriaProduction = compartment*R17HealthyBacteriaProductionk1*HealthyBacteria[t]
R18HealthyFibProduction = compartment*freespace*R18HealthyFibProductionk1*HealthyFibr[t]
R19MMP7releaseHealthyFibr = compartment*R19MMP7releaseHealthyFibrk1*HealthyFibr[t]
R1CRAdegradation = compartment*R1CRAdegradationk1*CRA[t]*MMP8[t]
R20MMP8releaseHealthyFibr = compartment*R20MMP8releaseHealthyFibrk1*HealthyFibr[t]
R21HealthytoDyingBacteria = compartment*R21HealthytoDyingBacteriak1*HealthyBacteria[t]*Protease[t]
R22CRAbinding = compartment*(R22CRAbindingk1*CRA[t]*MastCellsFLC[t] - R22CRAbindingk2*MastCellsFLCCRA[t])
R23FLCbinding = compartment*(R23FLCbindingk1*FLC[t]*MastCells[t] - R23FLCbindingk2*MastCellsFLC[t])
R24TNFalphaproduction = compartment*R24TNFalphaproductionk1*MastCellsFLCCRA[t]
R25Proteaseproduction = compartment*R25Proteaseproductionk1*MastCellsFLCCRA[t]
R26DyingBacteriasecreteCRA = compartment*R26DyingBacteriasecreteCRAk1*DyingBacteria[t]
R27Dyingbacteriadie = compartment*R27Dyingbacteriadiek1*DyingBacteria[t]
R28Proteaseinflux = compartment*Constantfluxirreversible[kproteaseinflux]
R2CRAwashout = compartment*R2CRAwashoutk1*CRA[t]*washout[t]
R3CRAinflux = compartment*Constantfluxirreversible[kCRAinflux]
R4FLCwashout = compartment*R4FLCwashoutk1*FLC[t]*washout[t]
R5MMP7washout = compartment*R5MMP7washoutk1*MMP7[t]*washout[t]
R6MMP8washout = compartment*R6MMP8washoutk1*MMP8[t]*washout[t]
R7Proteasewashout = compartment*R7Proteasewashoutk1*Protease[t]*washout[t]
R8TNFalphawashout = compartment*R8TNFalphawashoutk1*TNFalpha[t]*washout[t]
R9FLCproduction = compartment*RateLawforBFLCproduction[R9FLCproductionk1, CRA[t], Bcells]
end rate equations

begin parameters
Metabolite18 = 1000.0
kCRAinflux = 0.0
kproteaseinflux = 0.0
Bcells = 1.0
FLCdrug = 0.0
drug = 0.0
R1CRAdegradationk1 = 0.0001
R2CRAwashoutk1 = 0.01
R4FLCwashoutk1 = 0.01
R5MMP7washoutk1 = 0.01
R6MMP8washoutk1 = 0.01
R7Proteasewashoutk1 = 0.01
R8TNFalphawashoutk1 = 0.01
R9FLCproductionk1 = 0.001
R10drugwashoutk1 = 0.0001
R11FLCdrugbindingk1 = "1e-05"
R11FLCdrugbindingk2 = "1e-05"
R12FLCdrugwashoutk1 = 0.0001
R13CRASecretionDyingFibrk1 = 0.001
R14CRAClipOffHealthyFibrk1 = "1e-08"
R15DyingFibroblastdeathk1 = 0.2
R16HealthytoDyingfibroblastk1 = "5e-07"
R17HealthyBacteriaProductionk1 = 0.01
R18HealthyFibProductionk1 = "4.85e-07"
R19MMP7releaseHealthyFibrk1 = 1.0
R20MMP8releaseHealthyFibrk1 = 0.1
R21HealthytoDyingBacteriak1 = 0.005
R22CRAbindingk1 = 0.1
R22CRAbindingk2 = 0.1
R23FLCbindingk1 = 0.1
R23FLCbindingk2 = 0.1
R24TNFalphaproductionk1 = 5000.0
R25Proteaseproductionk1 = 65.0
R26DyingBacteriasecreteCRAk1 = 10.0
R27Dyingbacteriadiek1 = 0.1
compartment = 1.0
end parameters

begin initial conditions
CRA[0] = CRAi
DyingBacteria[0] = DyingBacteriai
DyingFibr[0] = DyingFibri
FLC[0] = FLCi
HealthyBacteria[0] = HealthyBacteriai
HealthyFibr[0] = HealthyFibri
MMP7[0] = MMP7i
MMP8[0] = MMP8i
MastCells[0] = MastCellsi
MastCellsFLC[0] = MastCellsFLCi
MastCellsFLCCRA[0] = MastCellsFLCCRAi
Protease[0] = Proteasei
TNFalpha[0] = TNFalphai
washout[0] = washouti
end initial conditions

begin initial values
CRAi = 0.00999412
DyingBacteriai = 0.0
DyingFibri = 0.0
FLCi = 0.000999412
HealthyBacteriai = 1e-06
HealthyFibri = 999.509
MMP7i = 99951.0
MMP8i = 999509.0
MastCellsi = 0.0998992
MastCellsFLCi = 9.98404e-05
MastCellsFLCCRAi = 9.97816000000001e-07
Proteasei = 1.0
TNFalphai = 4.75162
washouti = 1.0
end initial values

begin assignment rules
freespace := Metabolite18 - DyingFibr[t] - HealthyFibr[t]
Totalspace := Metabolite18
end assignment rules

begin function definitions
RateLawforBAFFclipoff[k1_,s1_,s2_] := k1*s1*s2
RateLawforBFLCproduction[k1_,s1_,s2_] := k1*s1*s2
Constantfluxirreversible[v_] := v
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units