#leber1

FIX: M0 N_LP iDC_E nT

#reactions
Cdiff_Death:
 {1.0}Cdiff = $pool
  Lumen * Rate_Law_for_CD_Lumen_death(K, Cdiff, M_LP, m2, N_Lum, m3, Commensal_Harmful)
Cdiff_Growth:
 {1.0}Cdiff = {2.0}Cdiff
  Lumen * KSA(K, Cdiff, Commensal_Harmful)
Commensal_Death:
 {1.0}Commensal_Dead = $pool
  Lumen * k1 * Commensal_Dead
Commensal_Harmful_Death:
 {1.0}Commensal_Harmful = $pool
  Lumen * Rate_Law_for_Commensal_Harmful_Death_1(K, Commensal_Harmful, N_LP, A1, E_i, A2)
Commensal_Regrowth:
 {1.0}Commensal_Beneficial = {1.0}Commensal_Dead
  Lumen * Rate_Law_for_Commensal_Regrowth(k1, Commensal_Beneficial, N_Lum, E_i, k2, Commensal_Dead)
E_Damage:
 {1.0}E = {1.0}E_d
  Epithelium * Rate_Law_for_E_damage(v, E, k1, N_Lum, k2, Th17_LP, k3, M_LP)
E_Heal:
 {1.0}E_d = {1.0}E
  Epithelium * k1 * E_d
E_Inflame:
 {1.0}E = {1.0}E_i
  Epithelium * KSA(K, E, Cdiff)
E_i_Damage:
 {1.0}E_i = {1.0}E_d
  Epithelium * Rate_Law_for_E_damage(v, E_i, k1, N_Lum, k2, Th17_LP, k3, M_LP)
E_i_Natural_Death:
 {1.0}E_i = {1.0}E_d
  Epithelium * k1 * E_i
M_Activation:
 {1.0}M0 = {1.0}M_LP
  Rate_Law_for_M_Activation(K, M0, e1, Th17_LP, Cdiff, e2, iTreg_LP)
M_Death:
 {1.0}M_LP = $pool
  Epithelium * k1 * M_LP
N_Activation_Migration:
 {1.0}N_LP = {1.0}N_Lum
  Rate_Law_for_N_Activation_Migration(v, N_LP, Cdiff, k1, E_d, k2, Th17_LP, k3, iTreg_LP)
N_Degradation:
 {1.0}N_Lum = $pool
  Lumen * KSA(K, N_Lum, Commensal_Beneficial)
Th17_Degradation:
 {1.0}Th17_LP = $pool
  LP * k1 * Th17_LP
Th17_Differentiation:
 {1.0}eDC_MLN = {1.0}Th17_MLN
  MLN * k1 * eDC_MLN
Th17_Migration:
 {1.0}Th17_MLN = {1.0}Th17_LP
  k1 * Th17_MLN
Th17_Plasticity:
 {1.0}Th17_LP = {1.0}iTreg_LP
  LP * Rate_Law_for_Th17plas(k1, Th17_LP, k2, Cdiff, iTreg_LP)
Th1_Degradation:
 {1.0}Th1_LP = $pool
  LP * k1 * Th1_LP
Th1_Differentiation:
 {1.0}eDC_MLN = {1.0}Th1_MLN
  MLN * Rate_Law_for_eDC(K, eDC_MLN, Commensal_Dead, Commensal_Beneficial, k2, E, k1)
Th1_Migration:
 {1.0}Th1_MLN = {1.0}Th1_LP
  k1 * Th1_MLN
Treg_Degradation:
 {1.0}iTreg_LP = $pool
  LP * k1 * iTreg_LP
Treg_Differentiation:
 {1.0}tDC_MLN = {1.0}iTreg_MLN
  k1 * tDC_MLN
Treg_Migration:
 {1.0}iTreg_MLN = {1.0}iTreg_LP
  k1 * iTreg_MLN
eDC_Degradation:
 {1.0}eDC_MLN = $pool
  MLN * k1 * eDC_MLN
eDC_Migration:
 {1.0}eDC_LP = {1.0}eDC_MLN
  k1 * eDC_LP
eDC_Production:
 {1.0}iDC_E + {1.0}Cdiff = {1.0}eDC_LP
  Rate_Law_for_Effector_DC_Production_1(k, Cdiff)
tDC_Degradation:
 {1.0}tDC_MLN = $pool
  Lumen * Rate_Law_for_Effector_DC_Production_1(k, tDC_MLN)
tDC_Migration:
 {1.0}tDC_LP = {1.0}tDC_MLN
  Lumen * k1 * tDC_LP
tDC_Production:
 {1.0}iDC_E + {1.0}Cdiff = {1.0}tDC_LP
  Rate_Law_for_tDC_Production(K, Cdiff, k1, Commensal_Beneficial, Commensal_Dead, k2, E, E_i)


#parameters
M0 = 1714285.71428571
N_LP = 714285.714285714
iDC_E = 500000.0
nT = 12000000.0
Treg_Degradation_k1 = 0.5069887
eDC_Degradation_k1 = 1.72495199303666e-05
Th17_Degradation_k1 = 2.39665140586358
Th1_Degradation_k1 = 0.99505694359
N_Degradation_K = 2.35932924820229e-07
E_Damage_v = 1.59920673150176e-06
E_Damage_k1 = 1.1e-05
E_Damage_k2 = 2.3381277077344e-06
E_Damage_k3 = 62.5911647602982
eDC_Migration_k1 = 10.5
eDC_Production_k = 0.55
Cdiff_Death_K = 6.27092296294148e-10
Cdiff_Death_m2 = 594.896546415159
Cdiff_Death_m3 = 0.102702503781515
N_Activation_Migration_v = 5.29827880572231e-05
N_Activation_Migration_k1 = 0.120935308788409
N_Activation_Migration_k2 = 0.171190728888258
N_Activation_Migration_k3 = 0.129717307334483
Cdiff_Growth_K = 5e-11
Treg_Migration_k1 = 5.5
Th1_Migration_k1 = 1.459
Th17_Plasticity_k1 = 1.27393226093773
Th17_Plasticity_k2 = 0.0020401460213434
Th17_Migration_k1 = 2.50454427171444
E_Inflame_K = 0.000171079818745428
E_i_Damage_v = 0.065
E_i_Damage_k1 = 0.006
E_i_Damage_k2 = 0.0106698310809694
E_i_Damage_k3 = 1.16013457036959e-06
M_Activation_K = 4.5e-05
M_Activation_e1 = 2.0
M_Activation_e2 = 0.092308585205372
M_Death_k1 = 20.0
Commensal_Regrowth_k1 = 4.5e-10
Commensal_Regrowth_k2 = 0.156287382551622
E_Heal_k1 = 4000.0
tDC_Production_K = 0.0002
tDC_Production_k1 = 559.297141527983
tDC_Production_k2 = 26.8747332769592
tDC_Migration_k1 = 3.65
tDC_Degradation_k = 0.00095
Th17_Differentiation_k1 = 2255.80469507059
Th1_Differentiation_K = 0.0430096
Th1_Differentiation_k2 = 9.65568121975566e-05
Th1_Differentiation_k1 = 0.0648415756801505
Treg_Differentiation_k1 = 53.9130568911728
Commensal_Harmful_Death_K = 2.33225e-05
Commensal_Harmful_Death_A1 = 0.00478
Commensal_Harmful_Death_A2 = 0.18
Commensal_Death_k1 = 0.0933277452272273
E_i_Natural_Death_k1 = 2.5
Epithelium = 4.0
LP = 0.07
Lumen = 1.0
MLN = 1.0


#initial values
Cdiff = 484.0
Commensal_Beneficial = 1.0
Commensal_Dead = 50000000000.0
Commensal_Harmful = 15000000000.0
E = 1052500.0
E_d = 0.0
E_i = 0.0
M_LP = 3250.0
N_Lum = 0.0
Th17_LP = 0.0
Th17_MLN = 0.0
Th1_LP = 0.0
Th1_MLN = 0.0
eDC_LP = 0.0
eDC_MLN = 0.0
iTreg_LP = 0.0
iTreg_MLN = 0.0
tDC_LP = 0.0
tDC_MLN = 0.0


#assignment rules