begin name
leber1
end name

begin reactions
CdiffDeath {1.0}Cdiff = {1.0}$EXTERNAL
CdiffGrowth {1.0}Cdiff = {2.0}Cdiff
CommensalDeath {1.0}CommensalDead = {1.0}$EXTERNAL
CommensalHarmfulDeath {1.0}CommensalHarmful = {1.0}$EXTERNAL
CommensalRegrowth {1.0}CommensalBeneficial = {1.0}CommensalDead
EDamage {1.0}E = {1.0}Ed
EHeal {1.0}Ed = {1.0}E
EInflame {1.0}E = {1.0}Ei
EiDamage {1.0}Ei = {1.0}Ed
EiNaturalDeath {1.0}Ei = {1.0}Ed
MActivation {1.0}$M0 = {1.0}MLP
MDeath {1.0}MLP = {1.0}$EXTERNAL
NActivationMigration {1.0}$NLP = {1.0}NLum
NDegradation {1.0}NLum = {1.0}$EXTERNAL
Th17Degradation {1.0}Th17LP = {1.0}$EXTERNAL
Th17Differentiation {1.0}eDCMLN = {1.0}Th17MLN
Th17Migration {1.0}Th17MLN = {1.0}Th17LP
Th17Plasticity {1.0}Th17LP = {1.0}iTregLP
Th1Degradation {1.0}Th1LP = {1.0}$EXTERNAL
Th1Differentiation {1.0}eDCMLN = {1.0}Th1MLN
Th1Migration {1.0}Th1MLN = {1.0}Th1LP
TregDegradation {1.0}iTregLP = {1.0}$EXTERNAL
TregDifferentiation {1.0}tDCMLN = {1.0}iTregMLN
TregMigration {1.0}iTregMLN = {1.0}iTregLP
eDCDegradation {1.0}eDCMLN = {1.0}$EXTERNAL
eDCMigration {1.0}eDCLP = {1.0}eDCMLN
eDCProduction {1.0}$iDCE + {1.0}Cdiff = {1.0}eDCLP
tDCDegradation {1.0}tDCMLN = {1.0}$EXTERNAL
tDCMigration {1.0}tDCLP = {1.0}tDCMLN
tDCProduction {1.0}$iDCE + {1.0}Cdiff = {1.0}tDCLP
end reactions

begin rate equations
CdiffDeath = Lumen*RateLawforCDLumendeath[CdiffDeathK, Cdiff[t], MLP[t], CdiffDeathm2, NLum[t], CdiffDeathm3, CommensalHarmful[t]]
CdiffGrowth = Lumen*KSA[CdiffGrowthK, Cdiff[t], CommensalHarmful[t]]
CommensalDeath = CommensalDeathk1*Lumen*CommensalDead[t]
CommensalHarmfulDeath = Lumen*RateLawforCommensalHarmfulDeath1[CommensalHarmfulDeathK, CommensalHarmful[t], NLP, CommensalHarmfulDeathA1, Ei[t], CommensalHarmfulDeathA2]
CommensalRegrowth = Lumen*RateLawforCommensalRegrowth[CommensalRegrowthk1, CommensalBeneficial[t], NLum[t], Ei[t], CommensalRegrowthk2, CommensalDead[t]]
EDamage = Epithelium*RateLawforEdamage[EDamagev, E[t], EDamagek1, NLum[t], EDamagek2, Th17LP[t], EDamagek3, MLP[t]]
EHeal = Epithelium*EHealk1*Ed[t]
EInflame = Epithelium*KSA[EInflameK, E[t], Cdiff[t]]
EiDamage = Epithelium*RateLawforEdamage[EiDamagev, Ei[t], EiDamagek1, NLum[t], EiDamagek2, Th17LP[t], EiDamagek3, MLP[t]]
EiNaturalDeath = Epithelium*EiNaturalDeathk1*Ei[t]
MActivation = RateLawforMActivation[MActivationK, M0, MActivatione1, Th17LP[t], Cdiff[t], MActivatione2, iTregLP[t]]
MDeath = Epithelium*MDeathk1*MLP[t]
NActivationMigration = RateLawforNActivationMigration[NActivationMigrationv, NLP, Cdiff[t], NActivationMigrationk1, Ed[t], NActivationMigrationk2, Th17LP[t], NActivationMigrationk3, iTregLP[t]]
NDegradation = Lumen*KSA[NDegradationK, NLum[t], CommensalBeneficial[t]]
Th17Degradation = LP*Th17Degradationk1*Th17LP[t]
Th17Differentiation = MLN*Th17Differentiationk1*eDCMLN[t]
Th17Migration = Th17Migrationk1*Th17MLN[t]
Th17Plasticity = LP*RateLawforTh17plas[Th17Plasticityk1, Th17LP[t], Th17Plasticityk2, Cdiff[t], iTregLP[t]]
Th1Degradation = LP*Th1Degradationk1*Th1LP[t]
Th1Differentiation = MLN*RateLawforeDC[Th1DifferentiationK, eDCMLN[t], CommensalDead[t], CommensalBeneficial[t], Th1Differentiationk2, E[t], Th1Differentiationk1]
Th1Migration = Th1Migrationk1*Th1MLN[t]
TregDegradation = LP*TregDegradationk1*iTregLP[t]
TregDifferentiation = TregDifferentiationk1*tDCMLN[t]
TregMigration = TregMigrationk1*iTregMLN[t]
eDCDegradation = eDCDegradationk1*MLN*eDCMLN[t]
eDCMigration = eDCMigrationk1*eDCLP[t]
eDCProduction = RateLawforEffectorDCProduction1[eDCProductionk, Cdiff[t]]
tDCDegradation = Lumen*RateLawforEffectorDCProduction1[tDCDegradationk, tDCMLN[t]]
tDCMigration = Lumen*tDCMigrationk1*tDCLP[t]
tDCProduction = RateLawfortDCProduction[tDCProductionK, Cdiff[t], tDCProductionk1, CommensalBeneficial[t], CommensalDead[t], tDCProductionk2, E[t], Ei[t]]
end rate equations

begin parameters
M0 = 1714285.71428571
NLP = 714285.714285714
iDCE = 500000.0
nT = 12000000.0
TregDegradationk1 = 0.5069887
eDCDegradationk1 = "1.72495199303666e-05"
Th17Degradationk1 = 2.39665140586358
Th1Degradationk1 = 0.99505694359
NDegradationK = "2.35932924820229e-07"
EDamagev = "1.59920673150176e-06"
EDamagek1 = "1.1e-05"
EDamagek2 = "2.3381277077344e-06"
EDamagek3 = 62.5911647602982
eDCMigrationk1 = 10.5
eDCProductionk = 0.55
CdiffDeathK = "6.27092296294148e-10"
CdiffDeathm2 = 594.896546415159
CdiffDeathm3 = 0.102702503781515
NActivationMigrationv = "5.29827880572231e-05"
NActivationMigrationk1 = 0.120935308788409
NActivationMigrationk2 = 0.171190728888258
NActivationMigrationk3 = 0.129717307334483
CdiffGrowthK = "5e-11"
TregMigrationk1 = 5.5
Th1Migrationk1 = 1.459
Th17Plasticityk1 = 1.27393226093773
Th17Plasticityk2 = 0.0020401460213434
Th17Migrationk1 = 2.50454427171444
EInflameK = 0.000171079818745428
EiDamagev = 0.065
EiDamagek1 = 0.006
EiDamagek2 = 0.0106698310809694
EiDamagek3 = "1.16013457036959e-06"
MActivationK = "4.5e-05"
MActivatione1 = 2.0
MActivatione2 = 0.092308585205372
MDeathk1 = 20.0
CommensalRegrowthk1 = "4.5e-10"
CommensalRegrowthk2 = 0.156287382551622
EHealk1 = 4000.0
tDCProductionK = 0.0002
tDCProductionk1 = 559.297141527983
tDCProductionk2 = 26.8747332769592
tDCMigrationk1 = 3.65
tDCDegradationk = 0.00095
Th17Differentiationk1 = 2255.80469507059
Th1DifferentiationK = 0.0430096
Th1Differentiationk2 = "9.65568121975566e-05"
Th1Differentiationk1 = 0.0648415756801505
TregDifferentiationk1 = 53.9130568911728
CommensalHarmfulDeathK = "2.33225e-05"
CommensalHarmfulDeathA1 = 0.00478
CommensalHarmfulDeathA2 = 0.18
CommensalDeathk1 = 0.0933277452272273
EiNaturalDeathk1 = 2.5
Epithelium = 4.0
LP = 0.07
Lumen = 1.0
MLN = 1.0
end parameters

begin initial conditions
Cdiff[0] = Cdiffi
CommensalBeneficial[0] = CommensalBeneficiali
CommensalDead[0] = CommensalDeadi
CommensalHarmful[0] = CommensalHarmfuli
E[0] = Ei
Ed[0] = Edi
Ei[0] = Eii
MLP[0] = MLPi
NLum[0] = NLumi
Th17LP[0] = Th17LPi
Th17MLN[0] = Th17MLNi
Th1LP[0] = Th1LPi
Th1MLN[0] = Th1MLNi
eDCLP[0] = eDCLPi
eDCMLN[0] = eDCMLNi
iTregLP[0] = iTregLPi
iTregMLN[0] = iTregMLNi
tDCLP[0] = tDCLPi
tDCMLN[0] = tDCMLNi
end initial conditions

begin initial values
Cdiffi = 484.0
CommensalBeneficiali = 1.0
CommensalDeadi = 50000000000.0
CommensalHarmfuli = 15000000000.0
Ei = 1052500.0
Edi = 0.0
Eii = 0.0
MLPi = 3250.0
NLumi = 0.0
Th17LPi = 0.0
Th17MLNi = 0.0
Th1LPi = 0.0
Th1MLNi = 0.0
eDCLPi = 0.0
eDCMLNi = 0.0
iTregLPi = 0.0
iTregMLNi = 0.0
tDCLPi = 0.0
tDCMLNi = 0.0
end initial values

begin assignment rules
end assignment rules

begin function definitions
RateLawforCommensalHarmfulDeath1[K_,S_,m1_,A1_,m2_,A2_] := K*(A1*m1 + A2*m2)*S
RateLawforCommensalRegrowth[k1_,S_,m1_,m2_,k2_,P_] := -(k2*P) + k1*m1*m2*S
RateLawforNActivationMigration[v_,S_,m_,k1_,A1_,k2_,A2_,k3_,I1_] := (-(I1*k3) + (A1*k1 + A2*k2)*m)*S*v
RateLawforMActivation[K_,S_,e1_,A1_,A2_,e2_,I1_] := (A2 + A1*e1 - e2*I1)*K*S
RateLawfortDCProduction[K_,S_,k1_,M1_,M2_,k2_,M3_,M4_] := K*((k1*M1)/M2 + (k2*M3)/(100 + M4))*S
RateLawforCDLumendeath[K_,S_,A1_,m2_,A2_,m3_,A3_] := K*(A1 + A2*m2 - A3*m3)*S
RateLawforeDC[K_,S_,M1_,M2_,k2_,M3_,k1_] := (K*M1*S)/(k1*M2 + k2*M3)
RateLawforEffectorDCProduction1[k_,S_] := k*S
RateLawforTh17plas[k1_,s_,k2_,m2_,p_] := -(k2*m2*p) + k1*s
RateLawforEdamage[v_,S_,k1_,a1_,k2_,a2_,k3_,a3_] := (a1*k1 + a2*k2 + a3*k3)*S*v
KSA[K_,S_,A_] := A*K*S
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
Cdiff http://identifiers.org/taxonomy/1496
end species annotations

begin units
end units