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BIOMD0000000480 - Carbo2013 - Mucosal Immune Response during H.pylori Infection

  
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Reference Publication
Publication ID: 10.1371/journal.pone...
Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe M, Eubank S, Wendelsdorf K, Bisset K, Hoops S, Deng X, Alam M, Kronsteiner B, Mei Y, Hontecillas R.
Predictive computational modeling of the mucosal immune responses during Helicobacter pylori infection.
PLoS ONE 2013; 8(9): e73365
Nutritional Immunology and Molecular Medicine Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America ; Center for Modeling Immunity to Enteric Pathogens Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America.  [more]
Model
Original Model: BIOMD0000000480.origin
Submitter: Adria Carbo
Submission ID: MODEL1307130000
Submission Date: 13 Jul 2013 01:54:30 UTC
Last Modification Date: 08 Apr 2016 18:37:09 UTC
Creation Date: 17 Sep 2013 13:08:08 UTC
Encoders:  Vijayalakshmi Chelliah
   Adria Carbo
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:hasTaxon Taxonomy Mus musculus
set #3
bqbiol:isVersionOf Gene Ontology defense response to Gram-negative bacterium
Gene Ontology T cell mediated immunity
set #4
bqbiol:isVersionOf Human Disease Ontology bacterial infectious disease
Notes
Model
Publication ID: 10.1371/journal.pone... Submission Date: 13 Jul 2013 01:54:30 UTC Last Modification Date: 08 Apr 2016 18:37:09 UTC Creation Date: 17 Sep 2013 13:08:08 UTC
Mathematical expressions
Reactions
re055 re066 re059 re105
re074 re063 re058 re070
re073 re072 re077 re078
re079 re080 re081 re082
re083 re084 re085 re087
re088 re089 re091 re093
re095 re096 re097 re098
re099 re100 re060 re057
re102 re101 re052 re065
re103 re104 re119 re106
re107 re061 re062 re067
re053 re068 re069 re111
re112 re117 re118 re120
re121 re071 re094 re092
re122 re123 re116 re124
re127 re128 re129 re130
re131 re132 re133 re134
re135 re136 re137 re138
re139 re140 nTh1 creation nTh1 trans
nTh1_LP deg nTh1_LP expansion nTh1 deg nTh17 creation
nTh17 trans nTh17_LP deg nTh17 deg nTreg creation
nTreg trans nTreg_LP deg nTreg deg Th17 to Treg
Rules
Assignment Rule (variable: vHP2) Assignment Rule (variable: aTh1) Assignment Rule (variable: ath1) Assignment Rule (variable: tcmT)
Assignment Rule (variable: toemT) Assignment Rule (variable: TotalDC) Assignment Rule (variable: TotalM) Assignment Rule (variable: TotalT)
Assignment Rule (variable: TotalDC) Assignment Rule (variable: TotalT) Assignment Rule (variable: TotalT-s) Assignment Rule (variable: pt)
Assignment Rule (variable: pT) Assignment Rule (variable: Stim_emT_Th17) Assignment Rule (variable: Stim_emT_Th1) Assignment Rule (variable: Stim_emT_iTreg)
Assignment Rule (variable: Stim_cmT_Th1) Assignment Rule (variable: Stim_cmT_Th17) Assignment Rule (variable: Stim_cmT_iTreg) Assignment Rule (variable: Stim_t_Th1)
Assignment Rule (variable: Stim_t_Th17) Assignment Rule (variable: Stim_t_iTreg) Assignment Rule (variable: cyto_change) Assignment Rule (variable: HP_Ep_Lumen)
Assignment Rule (variable: iDCtoeDC_Lumen) Assignment Rule (variable: iDCtotDC_Lumen) Assignment Rule (variable: iDCtoeDC_LP) Assignment Rule (variable: iDCtotDC_LP)
Assignment Rule (variable: M0toM1_LP) Assignment Rule (variable: M0toM2_LP) Assignment Rule (variable: new_iTreg_GLN) Assignment Rule (variable: T_deactivation)
Assignment Rule (variable: iTreg NS (rel)) Assignment Rule (variable: Th1 NS (rel)) Assignment Rule (variable: Th17 NS (rel)) Assignment Rule (variable: iTreg S (rel))
Assignment Rule (variable: Th1 S (rel)) Assignment Rule (variable: Th17 S (rel)) Assignment Rule (variable: vLB2) Assignment Rule (variable: iDCtotDC_LB)
Assignment Rule (variable: iDCtoeDC_LB) Assignment Rule (variable: new_emT_iTreg) Assignment Rule (variable: ath1LB) Assignment Rule (variable: aTh1LB)
Assignment Rule (variable: Stim_emT_Th1LB) Assignment Rule (variable: new_emT_Th1) Assignment Rule (variable: Stim_emT_Th17LB) Assignment Rule (variable: new_emT_Th17)
Assignment Rule (variable: Stim_cmT_Th1LB) Assignment Rule (variable: Stim_cmT_Th17LB) Assignment Rule (variable: Stim_t_Th1LB) Assignment Rule (variable: new_Th1_GLN)
Assignment Rule (variable: Stim_t_Th17LB) Assignment Rule (variable: new_Th17_GLN)    
Events
2nd Dose 3rd Dose    
Physical entities
Compartments Species
Lumen HP HP Dose LB
LB Dose nTh1 nTh1_LP
nTh17 nTh17_LP nTreg
nTreg_LP    
Lamina Propia eDC Th1 iTreg
Th17 M1 M2
M0 tDC emT
HP iDC TotalDC
TotalM TotalT eDCLB
pEC    
Epithelium E Ep Edead
iDC    
Gastric Lymph Node eDC tDC nT
cmT Th17 Th1
iTreg TotalDC TotalT
TotalT-s eDCLB  
Global parameters
vHP vHP2 aTreg aTh17
aTh1 kEB @eIE @eEI
atreg ath1 ath17 @uT
@vT toemT tcmT pt
pT uHP lHP @uE
Stim_emT_Th17 Stim_emT_Th1 Stim_emT_iTreg Stim_cmT_Th1
Stim_cmT_Th17 Stim_cmT_iTreg Stim_t_Th1 Stim_t_Th17
Stim_t_iTreg Bc uCE @et
@ut @lt Bp cyto_change
uM1 Bd Br er
kTD udi_LP um k_lumen
k_LP @pt_0 @pT_0 m_reg
m_HP kGLN HP_Ep_Lumen iDCtoeDC_Lumen
iDCtotDC_Lumen iDCtoeDC_LP iDCtotDC_LP M0toM1_LP
M0toM2_LP vm uMA n
T_deactivation iDC percentage lm ld
HP Dose Response iTreg NS (rel) Th1 NS (rel) Th17 NS (rel)
Stimulation iTreg S (rel) Th1 S (rel) Th17 S (rel)
@ud vLB vLB2 k_LB
iDCtotDC_LB iDCtoeDC_LB new_iTreg_GLN new_Th1_GLN
new_Th17_GLN new_emT_iTreg new_emT_Th1 new_emT_Th17
er_i et_i K_r17 K_17r
v21 v12 ri_I ir_I
phi_HP uLB ath17LB ath1LB
aTh17LB aTh1LB Stim_emT_Th17LB Stim_emT_Th1LB
Stim_cmT_Th1LB Stim_cmT_Th17LB Stim_t_Th1LB Stim_t_Th17LB
vEC Bc2 k_LP1 Initial for aTh17
Initial for ath17      
Reactions (88)
 
 re055 [E] → [Ep];   {HP} , {E} , {HP}
 
 re066 [HP] → [HP];   {Edead} , {HP} , {Edead}
 
 re059 [Ep] → [Edead];   {Th1} , {Th17} , {M1} , {Ep} , {Th1} , {Th17} , {M1}
 
 re105 [iDC] + [HP] → [eDC];   {iDC} , {HP}
 
 re074 [emT] → [iTreg];   {M2} , {tDC} , {emT} , {M2} , {tDC}
 
 re063 [iDC] + [HP] → [eDC];   {iDC} , {HP}
 
 re058 [E] → [Edead];   {Th1} , {Th17} , {M1} , {E} , {Th1} , {Th17} , {M1}
 
 re070 [M0] → [M1];   {M1} , {eDC} , {Th1} , {Th17} , {Ep} , {M0} , {M1} , {eDC} , {Th1} , {Th17} , {Ep}
 
 re073 [M0] → [M2];   {M2} , {iTreg} , {tDC} , {M0} , {M2} , {iTreg} , {tDC}
 
 re072 [M2] → [M1];   {Th1} , {M1} , {eDC} , {Th17} , {Ep} , {M2} , {Th1} , {M1} , {eDC} , {Th17} , {Ep}
 
 re077 [iDC] + [HP] → [tDC];   {iDC} , {HP}
 
 re078 [eDC] → [eDC];   {eDC}
 
 re079 [tDC] → [tDC];   {tDC}
 
 re080 [nT] → [Th17];   {eDC} , {eDCLB} , {nT} , {eDC} , {eDCLB}
 
 re081 [nT] → [Th1];   {eDC} , {nT} , {eDC}
 
 re082 [nT] → [iTreg];   {tDC} , {nT} , {tDC}
 
 re083 [cmT] → [Th17];   {eDC} , {eDCLB} , {cmT} , {eDC} , {eDCLB}
 
 re084 [cmT] → [Th1];   {eDC} , {eDCLB} , {cmT} , {eDC} , {eDCLB}
 
 re085 [cmT] → [iTreg];   {tDC} , {cmT} , {tDC}
 
 re087 [Th17] → [Th17];   {Th17}
 
 re088 [Th1] → [Th1];   {Th1}
 
 re089 [iTreg] → [iTreg];   {iTreg}
 
 re091 [iTreg] → [Th17];   {Th1} , {eDC} , {Th17} , {iTreg} , {Th1} , {eDC} , {Th17}
 
 re093 [iTreg] → [Th17];   {Th17} , {eDC} , {M1} , {Th1} , {Ep} , {iTreg} , {Th17} , {eDC} , {M1} , {Th1} , {Ep}
 
 re095 [Th17] → [emT];   {Th17}
 
 re096 [Th1] → [emT];   {Th1}
 
 re097 [iTreg] → [emT];   {iTreg}
 
 re098 [Th17] → [cmT];   {Th17}
 
 re099 [Th1] → [cmT];   {Th1}
 
 re100 [iTreg] → [cmT];   {iTreg}
 
 re060 [Ep] → [E];   {Ep}
 
 re057 [Edead] → [E];   {Edead}
 
 re102 [HP] → 2.0 × [HP];   {HP}
 
 re101 [HP] → ;   {HP}
 
 re052 [HP] → 2.0 × [HP];   {HP}
 
 re065 [HP] → ;   {HP}
 
 re103 [emT] → [Th1];   {M1} , {eDC} , {eDCLB} , {emT} , {M1} , {eDC} , {eDCLB}
 
 re104 [emT] → [Th17];   {M1} , {eDC} , {eDCLB} , {emT} , {M1} , {eDC} , {eDCLB}
 
 re119 [Th17] → ;   {Th17}
 
 re106  → [nT];   {eDC} , {eDC}
 
 re107 [nT] → ;   {nT}
 
 re061 [HP] → [HP];   {Ep} , {HP} , {Ep}
 
 re062 [iDC] + [HP] → [tDC];   {iDC} , {HP}
 
 re067 [HP] → ;   {Ep} , {M1} , {HP} , {Ep} , {M1}
 
 re053 [HP] → ;   {Ep} , {HP} , {Ep}
 
 re068  → [iDC];   {Ep} , {M1} , {eDC} , {Ep} , {M1} , {eDC}
 
 re069  → [M0];   {M1} , {Ep} , {eDC} , {M1} , {Ep} , {eDC}
 
 re111 [iDC] → ;   {iDC}
 
 re112 [M0] → ;   {M0}
 
 re117 [M1] → ;   {M1}
 
 re118 [M2] → ;   {M2}
 
 re120 [Th1] → ;   {Th1}
 
 re121 [iTreg] → ;   {iTreg}
 
 re071 [M1] → [M2];   {iTreg} , {M2} , {tDC} , {M1} , {iTreg} , {M2} , {tDC}
 
 re094 [Th17] → [iTreg];   {iTreg} , {tDC} , {M2} , {Th17} , {iTreg} , {tDC} , {M2}
 
 re092 [Th17] → [iTreg];   {iTreg} , {tDC} , {Th17} , {iTreg} , {tDC}
 
 re122 [M0] + [HP] → [M1];   {M0} , {HP}
 
 re123 [M0] + [HP] → [M2];   {M0} , {HP}
 
 re116 [eDC] → ;   {eDC}
 
 re124 [tDC] → ;   {tDC}
 
 re127 [iDC] ↔ [iDC];   {iDC} , {iDC}
 
 re128 [iDC] → [tDC];   {LB} , {iDC} , {LB}
 
 re129 [iDC] → [eDC];   {LB} , {iDC} , {LB}
 
 re130 [LB] → ;   {LB}
 
 re131  → [iTreg];  
 
 re132  → [Th1];  
 
 re133  → [Th17];  
 
 re134  → [iTreg];  
 
 re135  → [Th1];  
 
 re136  → [Th17];  
 
 re137 [eDCLB] → [eDCLB];   {eDCLB}
 
 re138 [eDCLB] → ;   {eDCLB}
 
 re139 [E] → [Ep];   {Th1} , {Th17} , {eDC} , {M1} , {Ep} , {E} , {Th1} , {Th17} , {eDC} , {M1} , {Ep}
 
 re140 [eDCLB] → ;   {eDCLB}
 
 nTh1 creation [nT] → [nTh1];   {nT}
 
 nTh1 trans [nTh1] → [nTh1_LP];   {nTh1}
 
 nTh1_LP deg [nTh1_LP] → ;   {nTh1_LP}
 
 nTh1_LP expansion [nTh1_LP] → 2.0 × [nTh1_LP];   {nTh1_LP}
 
 nTh1 deg [nTh1] → ;   {nTh1}
 
 nTh17 creation [nT] → [nTh17];   {nT}
 
 nTh17 trans [nTh17] → [nTh17_LP];   {nTh17}
 
 nTh17_LP deg [nTh17_LP] → ;   {nTh17_LP}
 
 nTh17 deg [nTh17] → ;   {nTh17}
 
 nTreg creation [nT] → [nTreg];   {nT}
 
 nTreg trans [nTreg] → [nTreg_LP];   {nTreg}
 
 nTreg_LP deg [nTreg_LP] → ;   {nTreg_LP}
 
 nTreg deg [nTreg] → ;   {nTreg}
 
 Th17 to Treg [nTh17_LP] → [nTreg_LP];   {nTh17_LP}
 
Rules (54)
 
 Assignment Rule (name: parameter_2) vHP2 = 1-parameter_1
 
 Assignment Rule (name: parameter_5) aTh1 = 1-ModelValue_3
 
 Assignment Rule (name: parameter_11) ath1 = 1E-6-ModelValue_10
 
 Assignment Rule (name: parameter_16) tcmT = parameter_13*parameter_14*0.6
 
 Assignment Rule (name: parameter_15) toemT = parameter_13*0.4*parameter_14
 
 Assignment Rule (name: species_2) TotalDC = s9+species_1+s25+s4
 
 Assignment Rule (name: species_3) TotalM = s22+s19+s21
 
 Assignment Rule (name: species_4) TotalT = s13+s16+s15+s17
 
 Assignment Rule (name: species_6) TotalDC = s26+s27
 
 Assignment Rule (name: species_8) TotalT = s31+s30+s33+s29+s28
 
 Assignment Rule (name: species_9) TotalT-s = 0.01*(s31+s30+s33+(s28+s29)/parameter_70)
 
 Assignment Rule (name: parameter_17) pt = parameter_49*1/(1+parameter_51*s33)
 
 Assignment Rule (name: parameter_18) pT = parameter_50*1/(1+parameter_51*s15+parameter_52*s6)
 
 Assignment Rule (name: parameter_22) Stim_emT_Th17 = parameter_4*parameter_48
 
 Assignment Rule (name: parameter_23) Stim_emT_Th1 = parameter_48*parameter_5
 
 Assignment Rule (name: parameter_24) Stim_emT_iTreg = parameter_3*parameter_48
 
 Assignment Rule (name: parameter_25) Stim_cmT_Th1 = parameter_5*parameter_53
 
 Assignment Rule (name: parameter_26) Stim_cmT_Th17 = parameter_4*parameter_53
 
 Assignment Rule (name: parameter_27) Stim_cmT_iTreg = parameter_3*parameter_53
 
 Assignment Rule (name: parameter_28) Stim_t_Th1 = parameter_11*parameter_53
 
 Assignment Rule (name: parameter_29) Stim_t_Th17 = parameter_12*parameter_53
 
 Assignment Rule (name: parameter_30) Stim_t_iTreg = parameter_10*parameter_53
 
 Assignment Rule (name: parameter_37) cyto_change = parameter_7*parameter_36
 
 Assignment Rule (name: parameter_54) HP_Ep_Lumen = parameter_7*parameter_39
 
 Assignment Rule (name: parameter_55) iDCtoeDC_Lumen = parameter_1*parameter_107
 
 Assignment Rule (name: parameter_56) iDCtotDC_Lumen = parameter_2*parameter_47
 
 Assignment Rule (name: parameter_57) iDCtoeDC_LP = parameter_1*parameter_107
 
 Assignment Rule (name: parameter_58) iDCtotDC_LP = parameter_2*parameter_48
 
 Assignment Rule (name: parameter_59) M0toM1_LP = parameter_1*parameter_48
 
 Assignment Rule (name: parameter_60) M0toM2_LP = parameter_2*parameter_48
 
 Assignment Rule (name: parameter_79) new_iTreg_GLN = parameter_17*(parameter_27*s29+parameter_30*s28)*s27
 
 Assignment Rule (name: parameter_64) T_deactivation = (1-parameter_14)*parameter_13
 
 Assignment Rule (name: parameter_67) iTreg NS (rel) = s33/species_8
 
 Assignment Rule (name: parameter_68) Th1 NS (rel) = s31/species_8
 
 Assignment Rule (name: parameter_69) Th17 NS (rel) = s30/species_8
 
 Assignment Rule (name: parameter_71) iTreg S (rel) = s33/species_9
 
 Assignment Rule (name: parameter_72) Th1 S (rel) = s31/species_9
 
 Assignment Rule (name: parameter_73) Th17 S (rel) = s30/species_9
 
 Assignment Rule (name: parameter_75) vLB2 = 1-parameter_74
 
 Assignment Rule (name: parameter_77) iDCtotDC_LB = parameter_75*parameter_76
 
 Assignment Rule (name: parameter_78) iDCtoeDC_LB = parameter_74*parameter_107
 
 Assignment Rule (name: parameter_82) new_emT_iTreg = parameter_18*parameter_24*(s25+s21)*s17
 
 Assignment Rule (name: parameter_96) ath1LB = 1E-6-parameter_95
 
 Assignment Rule (name: parameter_98) aTh1LB = 1-parameter_97
 
 Assignment Rule (name: parameter_100) Stim_emT_Th1LB = parameter_48*parameter_98
 
 Assignment Rule (name: parameter_83) new_emT_Th1 = parameter_18*(parameter_23*(s19+s9)*s17+s17*species_18*parameter_100)
 
 Assignment Rule (name: parameter_99) Stim_emT_Th17LB = parameter_48*parameter_97
 
 Assignment Rule (name: parameter_84) new_emT_Th17 = parameter_18*(parameter_22*(s19+s9)*s17+s17*species_18*parameter_99)
 
 Assignment Rule (name: parameter_101) Stim_cmT_Th1LB = parameter_53*parameter_98
 
 Assignment Rule (name: parameter_102) Stim_cmT_Th17LB = parameter_53*parameter_97
 
 Assignment Rule (name: parameter_103) Stim_t_Th1LB = parameter_53*parameter_96
 
 Assignment Rule (name: parameter_80) new_Th1_GLN = parameter_17*((parameter_25*s29+parameter_28*s28)*s26+(s29*parameter_101+s28*parameter_103)*species_20)
 
 Assignment Rule (name: parameter_104) Stim_t_Th17LB = parameter_95*parameter_53
 
 Assignment Rule (name: parameter_81) new_Th17_GLN = parameter_17*((parameter_26*s29+parameter_29*s28)*s26+species_20*(s29*parameter_102+s28*parameter_104))
 
Events (2)
 
 2nd Dose
HP = s1+species_7*parameter_6
LB = species_10+species_11
 
 3rd Dose
HP = s1+species_7*parameter_6
LB = species_10+species_11
 
Functions (13)
 
 Constant flux (irreversible) lambda(v, v)
 
 1 reactant, 3 activators, KVW lambda(Vf, r1, A1, n1, A2, n2, A3, n3, Vf*r1*(n1*A1+n2*A2+n3*A3))
 
 1sub 1 activator 1 parameter lambda(substrate, a1, k1, substrate*a1*k1)
 
 1sub 2 activators 2 parameters lambda(substrate, k1, a1, k2, a2, substrate*(k1*a1+k2*a2))
 
 Constant Flux, 3 activators lambda(c, k, A, n, kA, B, kB, C, kC, c+k*(A^n/(A^n+kA^n)+B^n/(B^n+kB^n)+C^n/(C^n+kC^n)))
 
 Constant Flux, 1 activator lambda(k, A, n, kA, c, c+k*A^n/(A^n+kA^n))
 
 1 sub 5 activators lambda(k, substrate, A, n, kA, B, kB, C, kC, D, kD, E, kE, k*substrate*(A^n/(A^n+kA^n)+B^n/(B^n+kB^n)+C^n/(C^n+kC^n)+D^n/(D^n+kD^n)+E^n/(E^n+kE^n)))
 
 1 sub 3 activators lambda(k, substrate, A, n, kA, B, kB, C, kC, k*substrate*(A^n/(A^n+kA^n)+B^n/(B^n+kB^n)+C^n/(C^n+kC^n)))
 
 1 sub 2 activators lambda(k, substrate, A, n, kA, B, kB, k*substrate*(A^n/(A^n+kA^n)+B^n/(B^n+kB^n)))
 
 bact repo lambda(k, sub, c, k*sub/(c+sub))
 
 iDC_Ep replenishment lambda(V, s, k, P, V*(s-k*P))
 
 1 sub 2 act 2 params 1 const lambda(substrate, k, k1, a1, k2, a2, substrate*k*(k1*a1+k2*a2))
 
 1 sub 3 activators 3 parameters lambda(substrate, k1, a1, k2, a2, k3, a3, substrate*(k1*a1+k2*a2+k3*a3))
 
 Lumen Spatial dimensions: 3.0  Compartment size: 1.0
 
 HP
Compartment: Lumen
Initial concentration: 5.34E-8
 
 HP Dose
Compartment: Lumen
Initial concentration: 0.0534
Constant
 
 LB
Compartment: Lumen
Initial concentration: 1.0
 
 LB Dose
Compartment: Lumen
Initial concentration: 1.0
 
 nTh1
Compartment: Lumen
Initial concentration: 1.0
 
 nTh1_LP
Compartment: Lumen
Initial concentration: 150000.0
 
 nTh17
Compartment: Lumen
Initial concentration: 1.0
 
 nTh17_LP
Compartment: Lumen
Initial concentration: 150000.0
 
 nTreg
Compartment: Lumen
Initial concentration: 1.0
 
 nTreg_LP
Compartment: Lumen
Initial concentration: 150000.0
 
 Lamina Propia Spatial dimensions: 3.0  Compartment size: 1.0
 
 eDC
Compartment: Lamina Propia
Initial concentration: 1.0
 
 Th1
Compartment: Lamina Propia
Initial concentration: 0.0
 
 iTreg
Compartment: Lamina Propia
Initial concentration: 0.0
 
 Th17
Compartment: Lamina Propia
Initial concentration: 0.0
 
 M1
Compartment: Lamina Propia
Initial concentration: 0.0
 
 M2
Compartment: Lamina Propia
Initial concentration: 0.0
 
 M0
Compartment: Lamina Propia
Initial concentration: 1000000.0
 
 tDC
Compartment: Lamina Propia
Initial concentration: 0.0
 
 emT
Compartment: Lamina Propia
Initial concentration: 1198199.01671451
 
 HP
Compartment: Lamina Propia
Initial concentration: 0.0
 
 iDC
Compartment: Lamina Propia
Initial concentration: 1000000.0
 
  TotalDC
Compartment: Lamina Propia
Initial concentration: 5501140.56260765
 
  TotalM
Compartment: Lamina Propia
Initial concentration: 1000000.0
 
  TotalT
Compartment: Lamina Propia
Initial concentration: 1198199.01671451
 
 eDCLB
Compartment: Lamina Propia
Initial concentration: 1.0
 
 pEC
Compartment: Lamina Propia
Initial concentration: 1.0
 
 Epithelium Spatial dimensions: 3.0  Compartment size: 1.0
 
 E
Compartment: Epithelium
Initial concentration: 10000.0
 
 Ep
Compartment: Epithelium
Initial concentration: 0.0
 
 Edead
Compartment: Epithelium
Initial concentration: 0.0
 
 iDC
Compartment: Epithelium
Initial concentration: 4501139.56260765
 
 Gastric Lymph Node Spatial dimensions: 3.0  Compartment size: 1.0
 
 eDC
Compartment: Gastric Lymph Node
Initial concentration: 0.0
 
 tDC
Compartment: Gastric Lymph Node
Initial concentration: 0.0
 
 nT
Compartment: Gastric Lymph Node
Initial concentration: 1.0E7
 
 cmT
Compartment: Gastric Lymph Node
Initial concentration: 4.17752018460542E7
 
 Th17
Compartment: Gastric Lymph Node
Initial concentration: 0.0
 
 Th1
Compartment: Gastric Lymph Node
Initial concentration: 0.0
 
 iTreg
Compartment: Gastric Lymph Node
Initial concentration: 0.0
 
  TotalDC
Compartment: Gastric Lymph Node
Initial concentration: 0.0
 
  TotalT
Compartment: Gastric Lymph Node
Initial concentration: 5.17752018460542E7
 
  TotalT-s
Compartment: Gastric Lymph Node
Initial concentration: 51775.2018460542
 
 eDCLB
Compartment: Gastric Lymph Node
Initial concentration: 1.0
 
Global Parameters (109)
 
 vHP
Value: 0.5
Constant
 
  vHP2
Value: 0.5
 
 aTreg
Value: 1.0
Constant
 
 aTh17
Value: 0.3
Constant
 
  aTh1
Value: 0.7
 
 kEB
Value: 1.0E-6
Constant
 
 @eIE
Value: 0.5
Constant
 
 @eEI
Value: 1.0
Constant
 
 atreg
Value: 1.0E-6
Constant
 
  ath1
Value: 7.0E-7
 
 ath17
Value: 3.0E-7
Constant
 
 @uT
Value: 0.143
Constant
 
 @vT
Value: 0.1
Constant
 
  toemT
Value: 0.00572
 
  tcmT
Value: 0.00858
 
  pt
Value: 512.0
 
  pT
Value: 128.0
 
 uHP
Value: 1.0
Constant
 
 lHP
Value: 2.0
Constant
 
 @uE
Value: 1.0
Constant
 
  Stim_emT_Th17
Value: 3.0E-7
 
  Stim_emT_Th1
Value: 7.0E-7
 
  Stim_emT_iTreg
Value: 1.0E-6
 
  Stim_cmT_Th1
Value: 7.0E-7
 
  Stim_cmT_Th17
Value: 3.0E-7
 
  Stim_cmT_iTreg
Value: 1.0E-6
 
  Stim_t_Th1
Value: 7.0E-13
 
  Stim_t_Th17
Value: 3.0E-13
 
  Stim_t_iTreg
Value: 1.0E-12
 
 Bc
Value: 1000.0
Constant
 
 uCE
Value: 1.0E-4
Constant
 
 @et
Value: 100.0
Constant
 
 @ut
Value: 1.0
Constant
 
 @lt
Value: 1.0E8
Constant
 
 Bp
Value: 1.0
Constant
 
  cyto_change
Value: 1.0E-6
 
 uM1
Value: 1.0E-4
Constant
 
 Bd
Value: 1.0
Constant
 
 Br
Value: 1000.0
Constant
 
 er
Value: 1000.0
Constant
 
 kTD
Value: 1.0E-6
Constant
 
 udi_LP
Value: 1.0
Constant
 
 um
Value: 1.0
Constant
 
 k_lumen
Value: 1.0E-6
Constant
 
 k_LP
Value: 1.0E-6
Constant
 
 @pt_0
Value: 512.0
Constant
 
 @pT_0
Value: 128.0
Constant
 
 m_reg
Value: 0.01
Constant
 
 m_HP
Value: 0.01
Constant
 
 kGLN
Value: 1.0E-6
Constant
 
  HP_Ep_Lumen
Value: 1.0E-6
 
  iDCtoeDC_Lumen
Value: 0.313385
 
  iDCtotDC_Lumen
Value: 5.0E-7
 
  iDCtoeDC_LP
Value: 0.313385
 
  iDCtotDC_LP
Value: 5.0E-7
 
  M0toM1_LP
Value: 5.0E-7
 
  M0toM2_LP
Value: 5.0E-7
 
 vm
Value: 1.0
Constant
 
 uMA
Value: 0.0218776162394955
Constant
 
 n
Value: 2.0
Constant
 
  T_deactivation
Value: 0.1287
 
 iDC percentage
Value: 0.01
Constant
 
 lm
Value: 100000.0
Constant
 
 ld
Value: 1000000.0
Constant
 
 HP Dose Response
Value: 1.0E-6
Constant
 
  iTreg NS (rel)  
 
  Th1 NS (rel)  
 
  Th17 NS (rel)  
 
 Stimulation
Value: 10.0
Constant
 
  iTreg S (rel)  
 
  Th1 S (rel)  
 
  Th17 S (rel)  
 
 @ud
Value: 0.5
Constant
 
 vLB
Value: 0.5
Constant
 
  vLB2
Value: 0.5
 
 k_LB
Value: 1.0
Constant
 
  iDCtotDC_LB
Value: 0.5
 
  iDCtoeDC_LB
Value: 0.313385
 
  new_iTreg_GLN  
 
  new_Th1_GLN
Value: 14972.2359256258
 
  new_Th17_GLN
Value: 6416.67253955392
 
  new_emT_iTreg  
 
  new_emT_Th1
Value: 214.717263795239
 
  new_emT_Th17
Value: 92.0216844836741
 
 er_i
Value: 10000.0
Constant
 
 et_i
Value: 10000.0
Constant
 
 K_r17
Value: 1.0
Constant
 
 K_17r
Value: 2.5
Constant
 
 v21
Value: 2.0
Constant
 
 v12
Value: 1.0
Constant
 
 ri_I
Value: 100000.0
Constant
 
 ir_I
Value: 100000.0
Constant
 
 phi_HP
Value: 0.001
Constant
 
 uLB
Value: 0.0714
Constant
 
 ath17LB
Value: 3.0E-7
Constant
 
  ath1LB
Value: 7.0E-7
 
 aTh17LB
Value: 0.3
Constant
 
  aTh1LB
Value: 0.7
 
  Stim_emT_Th17LB
Value: 3.0E-7
 
  Stim_emT_Th1LB
Value: 7.0E-7
 
  Stim_cmT_Th1LB
Value: 7.0E-7
 
  Stim_cmT_Th17LB
Value: 3.0E-7
 
  Stim_t_Th1LB
Value: 7.0E-13
 
  Stim_t_Th17LB
Value: 3.0E-13
 
 vEC
Constant
 
 Bc2
Value: 1.0
Constant
 
   k_LP1
Value: 0.62677
Constant
 
 Initial for aTh17
Value: 0.3
Constant
 
 Initial for ath17
Value: 3.0E-7
Constant
 
re127 (2)
 
   V
Value: 94.3761
Constant
 
   k
Value: 1.35871
Constant
 
nTh1 creation (1)
 
   k1
Value: 0.00260615
Constant
 
nTh1 trans (1)
 
   k1
Value: 0.105682
Constant
 
nTh1_LP deg (1)
 
   k1
Value: 0.158489
Constant
 
nTh1_LP expansion (1)
 
   k1
Value: 0.1
Constant
 
nTh1 deg (1)
 
   k1
Value: 0.107647
Constant
 
nTh17 creation (1)
 
   k1
Value: 0.00214783
Constant
 
nTh17 trans (1)
 
   k1
Value: 0.11695
Constant
 
nTh17_LP deg (1)
 
   k1
Value: 0.1
Constant
 
nTh17 deg (1)
 
   k1
Value: 0.1
Constant
 
nTreg creation (1)
 
   k1
Value: 0.00346737
Constant
 
nTreg trans (1)
 
   k1
Value: 0.1
Constant
 
nTreg_LP deg (1)
 
   k1
Value: 0.1
Constant
 
nTreg deg (1)
 
   k1
Value: 0.119124
Constant
 
Th17 to Treg (1)
 
   k1
Value: 0.167494
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000480

Curator's comment: (updated: 17 Sep 2013 13:04:49 GMT)

Figure 2A of the corresponding publication has been reproduced here. The model was simulated using SBML odeSolver and the plot was generated using Gnuplot.
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