#abudukelimu1

FIX: Bcells FLC_drug drug

#reactions
R10_drug_washout:
 {1.0}drug + {1.0}washout = {1.0}washout
  compartment * k1 * drug * washout
R11_FLC_drug_binding:
 {1.0}drug + {1.0}FLC = {1.0}FLC_drug
  compartment * (k1 * drug * FLC - k2 * FLC_drug)
R12_FLC_drug_washout:
 {1.0}FLC_drug + {1.0}washout = {1.0}washout
  compartment * k1 * FLC_drug * washout
R13_CRA_Secretion_DyingFibr:
 {1.0}DyingFibr = {1.0}CRA
  compartment * k1 * DyingFibr
R14_CRAClipOffHealthyFibr:
 {1.0}HealthyFibr + {1.0}MMP7 = {1.0}CRA + {1.0}MMP7 + {1.0}HealthyFibr
  compartment * Rate_Law_for_BAFF_clipoff(k1, HealthyFibr, MMP7)
R15_DyingFibroblast_death:
 {1.0}DyingFibr = $pool
  compartment * k1 * DyingFibr
R16_Healthy_to_Dying_fibroblast:
 {1.0}HealthyFibr + {1.0}TNFalpha = {1.0}DyingFibr + {1.0}TNFalpha
  compartment * k1 * HealthyFibr * TNFalpha
R17_HealthyBacteriaProduction:
 {1.0}HealthyBacteria = {2.0}HealthyBacteria
  compartment * k1 * HealthyBacteria
R18_HealthyFibProduction:
 {1.0}HealthyFibr = {2.0}HealthyFibr
  compartment * k1 * free_space * HealthyFibr
R19_MMP7_release_HealthyFibr:
 {1.0}HealthyFibr = {1.0}HealthyFibr + {1.0}MMP7
  compartment * k1 * HealthyFibr
R1_CRA_degradation:
 {1.0}CRA + {1.0}MMP8 = {1.0}MMP8
  compartment * k1 * CRA * MMP8
R20_MMP8_release_HealthyFibr:
 {1.0}HealthyFibr = {1.0}HealthyFibr + {100.0}MMP8
  compartment * k1 * HealthyFibr
R21_Healthy_to_Dying_Bacteria:
 {1.0}HealthyBacteria + {1.0}Protease = {1.0}DyingBacteria + {1.0}Protease
  compartment * k1 * HealthyBacteria * Protease
R22_CRA_binding:
 {1.0}MastCells_FLC + {1.0}CRA = {1.0}MastCells_FLC_CRA
  compartment * (k1 * MastCells_FLC * CRA - k2 * MastCells_FLC_CRA)
R23_FLC_binding:
 {1.0}FLC + {1.0}MastCells = {1.0}MastCells_FLC
  compartment * (k1 * FLC * MastCells - k2 * MastCells_FLC)
R24_TNFalpha_production:
 {1.0}MastCells_FLC_CRA = {1.0}TNFalpha + {1.0}MastCells_FLC_CRA
  compartment * k1 * MastCells_FLC_CRA
R25_Protease_production:
 {1.0}MastCells_FLC_CRA = {1.0}Protease + {1.0}MastCells_FLC_CRA
  compartment * k1 * MastCells_FLC_CRA
R26_DyingBacteria_secrete_CRA:
 {1.0}DyingBacteria = {1000.0}CRA
  compartment * k1 * DyingBacteria
R27_Dyingbacteria_die:
 {1.0}DyingBacteria = $pool
  compartment * k1 * DyingBacteria
R28_Proteaseinflux:
 $pool = {1.0}Protease
  compartment * Constant_flux__irreversible(k_protease_influx)
R2_CRA_washout:
 {1.0}CRA + {1.0}washout = {1.0}washout
  compartment * k1 * CRA * washout
R3_CRAinflux:
 $pool = {1.0}CRA
  compartment * Constant_flux__irreversible(k_CRA_influx)
R4_FLC_washout:
 {1.0}FLC + {1.0}washout = {1.0}washout
  compartment * k1 * FLC * washout
R5_MMP7_washout:
 {1.0}MMP7 + {1.0}washout = {1.0}washout
  compartment * k1 * MMP7 * washout
R6_MMP8_washout:
 {1.0}MMP8 + {1.0}washout = {1.0}washout
  compartment * k1 * MMP8 * washout
R7_Protease_washout:
 {1.0}Protease + {1.0}washout = {1.0}washout
  compartment * k1 * Protease * washout
R8_TNFalpha_washout:
 {1.0}TNFalpha + {1.0}washout = {1.0}washout
  compartment * k1 * TNFalpha * washout
R9_FLC_production:
 {1.0}CRA + {1.0}Bcells = {1.0}FLC + {1.0}CRA + {1.0}Bcells
  compartment * Rate_Law_for_B_FLC_production(k1, CRA, Bcells)


#parameters
Metabolite_18 = 1000.0
k_CRA_influx = 0.0
k_protease_influx = 0.0
Bcells = 1.0
FLC_drug = 0.0
drug = 0.0
R1_CRA_degradation_k1 = 0.0001
R2_CRA_washout_k1 = 0.01
R4_FLC_washout_k1 = 0.01
R5_MMP7_washout_k1 = 0.01
R6_MMP8_washout_k1 = 0.01
R7_Protease_washout_k1 = 0.01
R8_TNFalpha_washout_k1 = 0.01
R9_FLC_production_k1 = 0.001
R10_drug_washout_k1 = 0.0001
R11_FLC_drug_binding_k1 = 1e-05
R11_FLC_drug_binding_k2 = 1e-05
R12_FLC_drug_washout_k1 = 0.0001
R13_CRA_Secretion_DyingFibr_k1 = 0.001
R14_CRAClipOffHealthyFibr_k1 = 1e-08
R15_DyingFibroblast_death_k1 = 0.2
R16_Healthy_to_Dying_fibroblast_k1 = 5e-07
R17_HealthyBacteriaProduction_k1 = 0.01
R18_HealthyFibProduction_k1 = 4.85e-07
R19_MMP7_release_HealthyFibr_k1 = 1.0
R20_MMP8_release_HealthyFibr_k1 = 0.1
R21_Healthy_to_Dying_Bacteria_k1 = 0.005
R22_CRA_binding_k1 = 0.1
R22_CRA_binding_k2 = 0.1
R23_FLC_binding_k1 = 0.1
R23_FLC_binding_k2 = 0.1
R24_TNFalpha_production_k1 = 5000.0
R25_Protease_production_k1 = 65.0
R26_DyingBacteria_secrete_CRA_k1 = 10.0
R27_Dyingbacteria_die_k1 = 0.1
compartment = 1.0


#initial values
CRA = 0.00999412
DyingBacteria = 0.0
DyingFibr = 0.0
FLC = 0.000999412
HealthyBacteria = 1e-06
HealthyFibr = 999.509
MMP7 = 99951.0
MMP8 = 999509.0
MastCells = 0.0998992
MastCells_FLC = 9.98404e-05
MastCells_FLC_CRA = 9.97816000000001e-07
Protease = 1.0
TNFalpha = 4.75162
washout = 1.0


#assignment rules
!F free_space = Metabolite_18 - (HealthyFibr + DyingFibr)
!F Total_space = Metabolite_18