COPASI214
fast: false
reversible: false
name: re130
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_57f2654c_865b_4ebd_9c33_12246b673a20
stoichiometry: 1.0
species: COPASI27
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#baf1fe41_93e5_4140_a645_dbc493298f3e
stoichiometry: 1.0
species: COPASI37
type: SpeciesReference

COPASI55
notes: percent of de-activated T-cells that become memory T-cells
constant: true
value: 0.1
name: @vT
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_25d9baf2_b0d4_47f1_9598_36f3d035f48b
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_71375f83_c5bc_46bb_96c2_03b678e7970e
stoichiometry: 1.0
species: COPASI30
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_23854a6f_252c_4a91_8cbe_e541dc4b251f
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI207
name: re122
type: Reaction
reversible: false
fast: false

COPASI109
constant: false
value: 0.0
name: Th1 NS (rel)
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_03a3cf1a_851e_4f8f_acf0_7322d9beb2fe
value: 0.167494
name: k1
type: LocalParameter

COPASI41
constant: false
boundary condition: true
has only substance units: false
initial concentration: 5.17752018460542E7
initial amount: NaN
in compartment: COPASI5
name: TotalT
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#a28cede6_0659_4fbf_9201_81f96dbc9d9b
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI69
constant: false
value: 7.0E-13
name: Stim_t_Th1
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_80d2280d_271a_4f80_b441_291e85a21ce7
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

COPASI213
reversible: false
type: Reaction
name: re129
fast: false

COPASI56
constant: false
value: 0.00572
name: toemT
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_1f592179_f24f_4ea6_bb9e_99c0c935e53c
fast: false
reversible: false
name: nTh1 deg
type: Reaction

COPASI208
fast: false
type: Reaction
reversible: false
name: re123

http://identifiers.org/biomodels.db/BIOMD0000000480#_454c1560_bcff_4cd1_8786_818fa9c3985f
name: time
type: SBMLUnitsDef

COPASI108
constant: false
value: 0.0
name: iTreg NS (rel)
type: Parameter

COPASI42
notes: Multiplied by 0.01 to account for the fact that the data is in percent.
constant: false
boundary condition: true
has only substance units: false
initial concentration: 51775.2018460542
initial amount: NaN
in compartment: COPASI5
name: TotalT-s
type: Species

COPASI205
name: re094
reversible: false
fast: false
type: Reaction

COPASI188
name: re104
reversible: false
fast: false
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#d439eba7_e3b8_4f73_8d8f_062de086cc94
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_36b5f76a_e858_4d5c_8077_d74d6e292d90
stoichiometry: 1.0
species: COPASI31
type: SpeciesReference

COPASI216
fast: false
reversible: false
name: re132
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_95bd90d9_bf53_4378_a8f7_e6d3ecff2c6d
stoichiometry: 1.0
species: COPASI39
type: SpeciesReference

COPASI67
constant: false
value: 3.0E-7
name: Stim_cmT_Th17
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_0e7dba24_0fc1_4a0b_87cc_2d6fbc3582ea
stoichiometry: 1.0
species: COPASI36
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_88416954_9f9c_4220_8043_287059c69dda
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_254d8b00_e28b_48cc_882b_1317a3bb3972
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI168
reversible: false
name: re084
type: Reaction
fast: false

http://identifiers.org/biomodels.db/BIOMD0000000480#d594a3a0_9c24_480c_a877_be713d607899
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI57
constant: false
value: 0.00858
name: tcmT
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_5e091f0f_dc72_4feb_8623_0916ef803479
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

COPASI189
fast: false
reversible: false
name: re119
type: Reaction

COPASI215
fast: false
reversible: false
name: re131
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_39b3a8ca_0dfe_442e_877b_f0b3380ff6a2
stoichiometry: 1.0
species: COPASI38
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_3b040665_013a_4a57_88fa_50980618a6fc
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_241e8133_1b71_4656_9265_f9d3010a3406
stoichiometry: 2.0
species: COPASI10
type: SpeciesReference

COPASI206
name: re092
reversible: false
fast: false
type: Reaction

COPASI68
constant: false
value: 1.0E-6
name: Stim_cmT_iTreg
type: Parameter

COPASI40
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI5
name: TotalDC
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#f5803b7b_7980_4d9e_b726_f70220325324
fast: false
reversible: false
name: nTh17 trans
type: Reaction

COPASI58
constant: false
value: 512.0
name: pt
type: Parameter

COPASI169
type: Reaction
reversible: false
fast: false
name: re085

http://identifiers.org/biomodels.db/BIOMD0000000480#_6afcfdfe_d173_4cb3_a603_f691604a3c25
value: 0.1
name: k1
type: LocalParameter

COPASI30
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI4
name: Ep
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#fd72e221_9a89_4184_9bae_08f6c1dc107b
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

COPASI65
constant: false
value: 1.0E-6
name: Stim_emT_iTreg
type: Parameter

COPASI175
fast: false
reversible: false
name: re095
type: Reaction

COPASI224
fast: false
reversible: false
name: re140
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_950fd617_fdcc_4e33_bb1b_215803d7c2e6
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

COPASI51
notes: probability that nT will be stimulated to iTreg when contacted by tDC
constant: true
value: 1.0E-6
name: atreg
type: Parameter

COPASI210
fast: false
reversible: false
name: re124
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#d53e7100_6783_45e8_83c1_22ecf6094d6f
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_30cab2c0_3b6b_4c1f_89e8_fc70a2ab375c
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_38bdbb73_c046_488b_9b08_99dbfc2d5a19
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI31
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI4
name: Edead
type: Species

COPASI166
type: Reaction
reversible: false
name: re082
fast: false

COPASI45
notes: probability that TEM or TCM will be stimulated to iTreg when contacted by tDC
constant: true
value: 1.0
name: aTreg
type: Parameter

COPASI176
fast: false
reversible: false
name: re096
type: Reaction

COPASI223
fast: false
name: re139
type: Reaction
reversible: false

http://identifiers.org/biomodels.db/BIOMD0000000480#c72b43ac_4743_4d4b_a585_ac1f769115e8
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI66
constant: false
value: 7.0E-7
name: Stim_cmT_Th1
type: Parameter

COPASI46
notes: probability that TEM or TCM will be stimulated to Th17 when contacted by eDC
constant: true
value: 0.3
name: aTh17
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#c3e518f3_c336_43d0_b15f_d0b372ff3fe6
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#df60611c_c5e8_4bfe_9764_69a57566d6e9
stoichiometry: 1.0
species: COPASI39
type: SpeciesReference

COPASI52
notes: probability that nT will be stimulated to Th1 when contacted by eDC
constant: false
value: 7.0E-7
name: ath1
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_030b2da1_af5d_4449_9d72_7b193da7fdf4
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#c5dde09b_7f12_499c_bac0_f12b32ef72d3
value: 0.119124
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000480#f669457c_bdc8_4516_94b7_79cf3e1dc00d
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI32
constant: false
boundary condition: false
has only substance units: false
initial concentration: 4501139.56260765
initial amount: NaN
in compartment: COPASI4
name: iDC
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_7ebee493_056b_4a3b_bd92_709f630ae93d
value: 0.1
name: k1
type: LocalParameter

COPASI167
reversible: false
type: Reaction
fast: false
name: re083

http://identifiers.org/biomodels.db/BIOMD0000000480#_43de0c3a_088c_4494_91ba_880eb3287e23
stoichiometry: 1.0
species: COPASI32
type: SpeciesReference

COPASI177
fast: false
reversible: false
name: re097
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#df109681_5ac6_4e3f_b0f4_42e08279dd13
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_6f249dd6_eef8_49f7_a8de_f00405146c4f
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI63
constant: false
value: 3.0E-7
name: Stim_emT_Th17
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_659dd5c1_7dd4_4b6c_899c_bb780f70a3d9
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#bc3deefa_6192_4c0e_9f10_73eee5f050f8
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI222
fast: false
reversible: false
name: re138
type: Reaction

COPASI209
fast: false
reversible: false
name: re116
type: Reaction

COPASI212
type: Reaction
name: re128
fast: false
reversible: false

COPASI150
use values from trigger time: true
name: 3rd Dose
type: Event

COPASI53
notes: probability that nT will be stimulated to Th17 when contacted by eDC
constant: true
value: 3.0E-7
name: ath17
type: Parameter

COPASI163
fast: false
reversible: false
name: re079
type: Reaction

COPASI33
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI5
name: eDC
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#ff30e710_9c5e_4b61_969a_88cbf21c3797
fast: false
reversible: false
name: nTh1 creation
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#b5afec0c_d956_43c4_9df1_6965372664ab
constant: true
value: 0.3
name: Initial for aTh17
type: Parameter

COPASI178
fast: false
reversible: false
name: re098
type: Reaction

COPASI43
notes: probalility that HP induces effector responce in M0 and iDC
constant: true
value: 0.5
name: vHP
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_35f9ea26_bf34_414c_b72e_b1da34a774db
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_650fc790_791a_4448_9f4a_5a66cc914486
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#ce3323b7_f91a_4ba9_95f9_02d8fb181676
stoichiometry: 1.0
species: COPASI37
type: SpeciesReference

COPASI64
constant: false
value: 7.0E-7
name: Stim_emT_Th1
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_2f134ce9_45f9_4d08_8433_72dcdcb9545d
stoichiometry: 1.0
species: COPASI36
type: SpeciesReference

COPASI221
fast: false
reversible: false
name: re137
type: Reaction

COPASI54
notes: Rate at which activated T-cells become de-activated in the LP
constant: true
value: 0.143
name: @uT
type: Parameter

COPASI211
fast: false
reversible: true
name: re127
type: Reaction

COPASI164
type: Reaction
name: re080
reversible: false
fast: false

COPASI165
name: re081
type: Reaction
fast: false
reversible: false

COPASI34
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI5
name: tDC
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_7ac41c98_99ea_40f7_a1f9_7f9be0b36ef9
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI44
constant: false
value: 0.5
name: vHP2
type: Parameter

COPASI179
fast: false
reversible: false
name: re099
type: Reaction

COPASI191
fast: false
reversible: false
name: re107
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_164eb3a2_a284_441a_b883_d2963bed7747
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_57f7d8f3_77b6_43f6_9f5c_6eee704ba39b
value: 0.00346737
name: k1
type: LocalParameter

COPASI143
constant: false
value: 7.0E-7
name: Stim_cmT_Th1LB
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#c354e968_e7a8_496f_b1ed_d542236ab56f
fast: false
reversible: false
name: Th17 to Treg
type: Reaction

COPASI22
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI3
name: HP
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#a36cde65_a54b_41e2_8ea3_dee72bacd2a6
stoichiometry: 1.0
species: COPASI29
type: SpeciesReference

COPASI181
fast: false
reversible: false
name: re060
type: Reaction

COPASI161
type: Reaction
fast: false
reversible: false
name: re077

COPASI133
constant: true
value: 100000.0
name: ri_I
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_4b29ce22_8af9_44ac_81ce_017fad65f24e
stoichiometry: 1.0
species: COPASI32
type: SpeciesReference

COPASI152
reversible: false
fast: false
name: re066
type: Reaction

COPASI101
notes: rate of M1 and M2 removal
constant: true
value: 0.0218776162394955
name: uMA
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_0365fa17_8bc1_45dd_badf_2d2585f584e6
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#c2138fa6_2e6a_4f95_9afe_e67a57eed8e2
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

COPASI142
constant: false
value: 7.0E-7
name: Stim_emT_Th1LB
type: Parameter

COPASI171
fast: false
reversible: false
name: re088
type: Reaction

COPASI61
notes: birth rate of HP
constant: true
value: 2.0
name: lHP
type: Parameter

COPASI115
constant: true
value: 0.5
name: @ud
type: Parameter

COPASI123
constant: false
value: 6416.67253955392
name: new_Th17_GLN
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_8f27a670_b35e_4a14_929a_6929a97ed1c5
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI9
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: LB Dose
type: Species

COPASI192
type: Reaction
reversible: false
fast: false
name: re061

http://identifiers.org/biomodels.db/BIOMD0000000480#b576c0ad_a89f_4817_8628_09f1464b21c9
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI21
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1198199.01671451
initial amount: NaN
in compartment: COPASI3
name: emT
type: Species

COPASI182
fast: false
reversible: false
name: re057
type: Reaction

COPASI131
constant: true
value: 2.0
name: v21
type: Parameter

COPASI132
constant: true
value: 1.0
name: v12
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_3dca656d_0fb0_4604_b6a5_23b6d004b722
value: 0.1
name: k1
type: LocalParameter

COPASI162
fast: false
reversible: false
name: re078
type: Reaction

COPASI200
fast: false
reversible: false
name: re117
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_61135983_5c7f_419f_ac12_d46e8d9c175a
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI100
notes: Rate at which M0 becomes M1 or M2 when in contact with cytokine-secreting immune cells
constant: true
value: 1.0
name: vm
type: Parameter

COPASI151
reversible: false
name: re055
fast: false
type: Reaction

COPASI141
constant: false
value: 3.0E-7
name: Stim_emT_Th17LB
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_9570a5b4_e442_477b_9915_fd3ceb192620
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_7bd417e5_c46b_4511_8df0_dad20fff9817
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI62
notes: turnover rate of E cells
constant: true
value: 1.0
name: @uE
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_64b5cf05_450b_4960_980d_1a549263ba7f
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: nTh1
type: Species

COPASI172
fast: false
reversible: false
name: re089
type: Reaction

COPASI114
constant: false
value: 0.0
name: Th17 S (rel)
type: Parameter

COPASI122
constant: false
value: 14972.2359256258
name: new_Th1_GLN
type: Parameter

COPASI10
constant: false
boundary condition: false
has only substance units: false
initial concentration: 150000.0
initial amount: NaN
in compartment: COPASI2
name: nTh1_LP
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_29e0205f_f2b0_46e3_98ad_4e1ecc0cddfe
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI193
type: Reaction
name: re062
reversible: false
fast: false

COPASI120
constant: false
value: 0.313385
name: iDCtoeDC_LB
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_034c3f54_147f_4f99_89a7_c78467e0cc2a
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

COPASI155
fast: false
type: Reaction
reversible: false
name: re074

COPASI20
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI3
name: tDC
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_99834f14_2a48_4e9a_84f5_da64227dd963
stoichiometry: 1.0
species: COPASI31
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_2653a386_20af_4b7c_b161_d0e2cc8d93fe
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI103
constant: false
value: 0.1287
name: T_deactivation
type: Parameter

COPASI135
constant: true
value: 0.001
name: phi_HP
type: Parameter

COPASI121
constant: false
value: 0.0
name: new_iTreg_GLN
type: Parameter

COPASI173
name: re091
type: Reaction
fast: false
reversible: false

http://identifiers.org/biomodels.db/BIOMD0000000480#_0ae9bd34_d39e_4034_8308_b53746ece67f
stoichiometry: 1.0
type: SpeciesReference

COPASI140
constant: false
value: 0.7
name: aTh1LB
type: Parameter

COPASI113
constant: false
value: 0.0
name: Th1 S (rel)
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#c25b162c_68d6_499a_ba62_4cf0d6f1dcf0
fast: false
reversible: false
name: nTreg_LP deg
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#f6dc818d_b088_4a78_9dd0_ef4dcbe1de0f
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_0e6bd71d_1d55_47d6_82d3_7fd7e81c794a
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI194
reversible: false
type: Reaction
name: re067
fast: false

http://identifiers.org/biomodels.db/BIOMD0000000480#e867e062_089d_4d86_8878_cb8161af55d4
stoichiometry: 1.0
species: COPASI36
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#e4f2e6f5_d541_4522_8dd6_7288e1571b1d
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: nTh17
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#b5bbb971_5193_4f96_b71b_22f3c99c64e2
stoichiometry: 1.0
species: COPASI32
type: SpeciesReference

COPASI180
fast: false
reversible: false
name: re100
type: Reaction

COPASI154
type: Reaction
fast: false
name: re105
reversible: false

COPASI153
reversible: false
fast: false
type: Reaction
name: re059

COPASI160
name: re072
type: Reaction
reversible: false
fast: false

COPASI102
constant: true
value: 2.0
name: n
type: Parameter

COPASI90
notes: extent to which iTreg inhibits T-cell proliferation
constant: true
value: 0.01
name: m_reg
type: Parameter

COPASI134
constant: true
value: 100000.0
name: ir_I
type: Parameter

COPASI50
notes: rate of cell flow in lymph from LP to GLN
constant: true
value: 1.0
name: @eEI
type: Parameter

COPASI174
fast: false
type: Reaction
name: re093
reversible: false

COPASI60
notes: death rate of HP
constant: true
value: 1.0
name: uHP
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_306c337b_a110_430a_9719_afa878fbb7a4
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI112
constant: false
value: 0.0
name: iTreg S (rel)
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#d25f1bc7_e22c_4710_afac_8a94f46cbee6
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

COPASI185
fast: false
reversible: false
name: re052
type: Reaction

COPASI157
fast: false
name: re058
reversible: false
type: Reaction

COPASI6
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.34E-8
initial amount: NaN
in compartment: COPASI2
name: HP
type: Species

COPASI147
constant: true
value: 0.0
name: vEC
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_80eb68c5_0c8c_48f5_9868_91f7473bcc2d
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_2645f119_fe58_4992_947d_cd56fa6bccb7
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

COPASI195
fast: false
reversible: false
name: re053
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_7c44deee_ee9d_4279_a1d4_ade666f0d6fb
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_832b7a7f_f594_4e0a_80be_67635a44acf4
fast: false
reversible: false
name: nTreg trans
type: Reaction

COPASI218
fast: false
reversible: false
name: re134
type: Reaction

COPASI119
constant: false
value: 0.5
name: iDCtotDC_LB
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#adfa719d_9c2e_44d7_82d3_e6751a5f649d
name: volume
type: SBMLUnitsDef

COPASI105
notes: in-flow rate of M0
constant: true
value: 100000.0
name: lm
type: Parameter

COPASI203
fast: false
reversible: false
name: re121
type: Reaction

COPASI156
type: Reaction
name: re063
fast: false
reversible: false

COPASI186
fast: false
reversible: false
name: re065
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_9d3992d3_3999_4975_b8bf_ef67dc9ed959
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI5
constant: true
size: 1.0
spatial dimensions: 3.0
name: Gastric Lymph Node
type: Compartment

http://identifiers.org/biomodels.db/BIOMD0000000480#a5410e5b_a18a_49fe_87a8_12e479657550
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_755412ff_8a99_4aed_af81_8090a3873ebf
fast: false
reversible: false
name: nTh1_LP deg
type: Reaction

COPASI196
reversible: false
type: Reaction
name: re068
fast: false

COPASI146
constant: false
value: 3.0E-13
name: Stim_t_Th17LB
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_2fe1c015_3c41_4c7f_a980_e6e07538bacd
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

COPASI217
fast: false
reversible: false
name: re133
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_453dc888_1f87_4906_acef_798c14b6d869
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_4a7a8738_0504_496a_9d19_d043f67e2066
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI104
notes: fraction of iDC in LP that are in contact with epithilial barrier and have contact with lumen environment
constant: true
value: 0.01
name: iDC percentage
type: Parameter

COPASI118
constant: true
value: 1.0
name: k_LB
type: Parameter

COPASI204
name: re071
fast: false
reversible: false
type: Reaction

COPASI187
fast: false
name: re103
type: Reaction
reversible: false

COPASI159
reversible: false
type: Reaction
name: re073
fast: false

COPASI130
constant: true
value: 2.5
name: K_17r
type: Parameter

COPASI183
fast: false
reversible: false
name: re102
type: Reaction

COPASI145
constant: false
value: 7.0E-13
name: Stim_t_Th1LB
type: Parameter

COPASI197
fast: false
reversible: false
name: re069
type: Reaction

COPASI8
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: LB
type: Species

COPASI107
notes: The selection factor for viable H. pylori following inoculation
constant: true
value: 1.0E-6
name: HP Dose Response
type: Parameter

COPASI117
constant: false
value: 0.5
name: vLB2
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_5bf12e5b_9ea4_4ff3_80d4_dab105b9fb21
stoichiometry: 1.0
type: SpeciesReference

COPASI198
fast: false
reversible: false
name: re111
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_3586293c_ca0d_4eed_8b99_eef7946cecb4
value: 94.3761
name: V
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000480#d518ae6b_eafa_40b1_9eca_e9b9a0710306
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

COPASI201
fast: false
reversible: false
name: re118
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#fc358d04_7bc3_42ee_ae8f_9dfcd14fd5ef
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI158
name: re070
reversible: false
fast: false
type: Reaction

COPASI7
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0534
initial amount: NaN
in compartment: COPASI2
name: HP Dose
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_904edb12_eeac_460e_9f0f_f24ac6a76ace
stoichiometry: 1.0
species: COPASI39
type: SpeciesReference

COPASI184
fast: false
reversible: false
name: re101
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_3eac09ce_c614_44bc_8df8_6bde823d1170
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI144
constant: false
value: 3.0E-7
name: Stim_cmT_Th17LB
type: Parameter

COPASI116
constant: true
value: 0.5
name: vLB
type: Parameter

COPASI219
fast: false
reversible: false
name: re135
type: Reaction

COPASI170
fast: false
reversible: false
name: re087
type: Reaction

COPASI199
fast: false
reversible: false
name: re112
type: Reaction

COPASI202
fast: false
reversible: false
name: re120
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#f13868f5_eeae_4613_9763_66982df42c43
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_277eeda9_2be0_4c9d_be89_e19649746910
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

COPASI106
notes: in-flow rate if iDC
constant: true
value: 1000000.0
name: ld
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#c50fcefa_bbe5_4738_9056_6e114a46a88e
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: nTreg
type: Species

COPASI74
notes: Number of nT recruited by each eDC in GLN
constant: true
value: 100.0
name: @et
type: Parameter

COPASI29
constant: false
boundary condition: false
has only substance units: false
initial concentration: 10000.0
initial amount: NaN
in compartment: COPASI4
name: E
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#fc918728_13e7_4c13_b8d2_ac8e31ed9ded
stoichiometry: 1.0
species: COPASI29
type: SpeciesReference

COPASI15
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI3
name: iTreg
type: Species

COPASI84
notes: out-flow rate of iDC
constant: true
value: 1.0
name: udi_LP
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#e57abce1_0192_45b7_ac85_398cf74ed225
value: 0.158489
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_7b851c00_b8c3_4d6b_9bbe_f8dd2db8671c
value: 0.107647
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_971815b3_a95f_48f4_84e7_492f122695e9
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

COPASI94
constant: false
value: 0.313385
name: iDCtoeDC_Lumen
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_4fdc138c_58d8_4f0f_b39c_b34a3137d7d8
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#fd1ff247_e663_405d_be97_695fbf62fcc9
fast: false
reversible: false
name: nTh1_LP expansion
type: Reaction

COPASI73
notes: rate at which EC and Ep are killed by cytotoxic factors secreted by Th17 and Th1
constant: true
value: 1.0E-4
name: uCE
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_293d37ea_0114_4bb3_847a_cdabe54cc63f
stoichiometry: 1.0
species: COPASI29
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_4c277780_ca44_4faf_9221_ad366e36e651
value: 1.35871
name: k
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000480#dee6782c_e67f_441a_95be_c78a6b01de45
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#d3f09160_c86d_4091_8305_075ee7a7484f
exponent: 1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

http://identifiers.org/biomodels.db/BIOMD0000000480#feed3377_876d_4d58_afe4_b8b88d4ab085
stoichiometry: 1.0
species: COPASI37
type: SpeciesReference

COPASI16
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI3
name: Th17
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_182db432_68bf_49ca_8617_c6788fb53ba3
fast: false
reversible: false
name: nTh17 deg
type: Reaction

COPASI83
notes: contact rate between iTreg and eDC
constant: true
value: 1.0E-6
name: kTD
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_18f285aa_3140_4e7b_a0f6_467a19ee32be
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI93
constant: false
value: 1.0E-6
name: HP_Ep_Lumen
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#f7b681d9_9069_49cb_b94a_3b2af9b82d15
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#bf6a161f_ee70_405f_920e_c2e6fbe47140
value: 0.00260615
name: k1
type: LocalParameter

COPASI72
notes: extent to which Ep secretes M1 and Th17-inducing cytokines
constant: true
value: 1000.0
name: Bc
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#cac5225e_ebf7_4849_a22e_e1987db5f65a
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_58e25b25_97c4_4277_82d1_a9d64723db62
stoichiometry: 1.0
species: COPASI29
type: SpeciesReference

COPASI27
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI3
name: eDCLB
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_2e3ebd34_9b83_46e8_953a_cd5d502785f2
value: 0.1
name: k1
type: LocalParameter

COPASI128
constant: true
value: 10000.0
name: et_i
type: Parameter

BIOMD0000000480
species: COPASI16
species: COPASI23
parameter: COPASI54
reaction: COPASI153
parameter: COPASI56
parameter: COPASI70
parameter: COPASI62
parameter: COPASI44
is version of: GO:0006955
reaction: COPASI166
compartment: COPASI5
reaction: COPASI154
species: COPASI30
function def: COPASI232
reaction: COPASI168
parameter: COPASI71
reaction: COPASI156
reaction: COPASI218
reaction: COPASI180
reaction: COPASI206
parameter: COPASI91
function def: COPASI227
species: COPASI20
reaction: COPASI214
name: 1 sub 3 activators 3 parameters
reaction: COPASI202
species: COPASI18
parameter: COPASI87
name: Constant Flux, 3 activators
reaction: COPASI222
parameter: COPASI138
occurs in: http://identifiers.org/taxonomy/10090
species: COPASI7
parameter: COPASI102
event: COPASI150
species: COPASI32
parameter: COPASI74
parameter: COPASI66
name: 1sub 1 activator 1 parameter
reaction: COPASI158
name: 1 sub 2 act 2 params 1 const
parameter: COPASI93
parameter: COPASI75
reaction: COPASI178
parameter: COPASI90
species: COPASI24
reaction: COPASI184
reaction: COPASI172
parameter: COPASI95
species: COPASI12
is: MODEL1307130000
reaction: COPASI192
parameter: COPASI133
reaction: COPASI224
parameter: COPASI49
parameter: COPASI120
parameter: COPASI61
parameter: COPASI106
parameter: COPASI43
parameter: COPASI68
species: COPASI36
name: 1sub 2 activators 2 parameters
parameter: COPASI63
parameter: COPASI78
parameter: COPASI121
parameter: COPASI97
reaction: COPASI194
function def: COPASI231
parameter: COPASI99
reaction: COPASI196
parameter: COPASI137
reaction: COPASI221
parameter: COPASI51
area units: area
species: COPASI21
species: COPASI19
parameter: COPASI142
parameter: COPASI65
parameter: COPASI130
species: COPASI13

COPASI17
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI3
name: M1
type: Species

COPASI86
notes: contact rate in lumen
constant: true
value: 1.0E-6
name: k_lumen
type: Parameter

COPASI148
constant: true
value: 1.0
name: Bc2
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#cc17581f_6b9e_4ea7_a035_b068f819841b
value: 0.1
name: k1
type: LocalParameter

COPASI92
notes: contact rate in GLN
constant: true
value: 1.0E-6
name: kGLN
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_322bb898_fd92_4f88_9d46_6048f34a23ff
stoichiometry: 1.0
species: COPASI39
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_64aaa04f_c6f3_4348_be65_dc0bc4a96863
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_545bbd60_55d3_413a_8cf8_c167aedda3d2
stoichiometry: 1.0
species: COPASI39
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_11c051c6_9cec_49be_8f6b_f02110f78556
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

COPASI28
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI3
name: pEC
type: Species

COPASI129
constant: true
value: 1.0
name: K_r17
type: Parameter

COPASI71
constant: false
value: 1.0E-12
name: Stim_t_iTreg
type: Parameter

COPASI85
notes: out-flow rate of M0
constant: true
value: 1.0
name: um
type: Parameter

COPASI18
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI3
name: M2
type: Species

COPASI91
notes: extent to which HP inhibits T-cell proliferation
constant: true
value: 0.01
name: m_HP
type: Parameter

COPASI149
use values from trigger time: true
name: 2nd Dose
type: Event

http://identifiers.org/biomodels.db/BIOMD0000000480#de03c20a_2b4a_4f94_9bea_baad8036d2bf
stoichiometry: 1.0
species: COPASI32
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#f6c67ec1_8685_47a1_8517_50bcfa377ae4
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#f7e7f735_602d_48ed_a1bf_d073f095d123
stoichiometry: 1.0
species: COPASI33
type: SpeciesReference

COPASI126
constant: false
value: 92.0216844836741
name: new_emT_Th17
type: Parameter

COPASI110
constant: false
value: 0.0
name: Th17 NS (rel)
type: Parameter

COPASI70
constant: false
value: 3.0E-13
name: Stim_t_Th17
type: Parameter

COPASI25
constant: false
boundary condition: true
has only substance units: false
initial concentration: 1000000.0
initial amount: NaN
in compartment: COPASI3
name: TotalM
type: Species

COPASI136
constant: true
value: 0.0714
name: uLB
type: Parameter

COPASI80
notes: extent to which Ep secretes microbicides (defensin)
constant: true
value: 1.0
name: Bd
type: Parameter

COPASI190
fast: false
reversible: false
name: re106
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#e7fd773f_e2c7_42d3_9e15_613d790ac256
persistant: true
initial value: true
type: Trigger

http://identifiers.org/biomodels.db/BIOMD0000000480#f0569de2_c0a2_4224_9619_6313315fe55e
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_46fccb2e_87c9_4d31_b2f3_e9e6ea99abee
stoichiometry: 1.0
species: COPASI30
type: SpeciesReference

COPASI98
constant: false
value: 5.0E-7
name: M0toM1_LP
type: Parameter

COPASI11
constant: false
boundary condition: false
has only substance units: false
initial concentration: 150000.0
initial amount: NaN
in compartment: COPASI2
name: nTh17_LP
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_3af59e5a_c4be_42a8_a593_c50b7e3f447c
stoichiometry: 2.0
species: COPASI6
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#bd349a4c_4837_4b61_8b1c_a9e2a16a9231
stoichiometry: 1.0
species: COPASI37
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_6ea38677_030d_4569_a8c2_811c38995ee5
stoichiometry: 1.0
species: COPASI31
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_7a72abf8_b54c_44de_bfe5_9eac2180666c
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI127
constant: true
value: 10000.0
name: er_i
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_63a9b5dd_d8f1_4ee4_8b21_93d4e8916b1e
fast: false
reversible: false
name: nTh17 creation
type: Reaction

COPASI111
constant: true
value: 10.0
name: Stimulation
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_997040af_4919_4cb0_8bbf_65ed7b40d0ab
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#f15756ca_654e_4110_af76_0085158326ed
value: 0.00214783
name: k1
type: LocalParameter

COPASI26
constant: false
boundary condition: true
has only substance units: false
initial concentration: 1198199.01671451
initial amount: NaN
in compartment: COPASI3
name: TotalT
type: Species

COPASI137
constant: true
value: 3.0E-7
name: ath17LB
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_163df5e7_8f69_4ce6_ba29_7e70daef7515
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#f4fd7cc2_9d14_4ed3_9999_07f4d7601e77
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_957cd050_a9ae_4fe6_b147_eb8cfff04d52
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI97
constant: false
value: 5.0E-7
name: iDCtotDC_LP
type: Parameter

COPASI12
constant: false
boundary condition: false
has only substance units: false
initial concentration: 150000.0
initial amount: NaN
in compartment: COPASI2
name: nTreg_LP
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#c06de2a0_1588_4b62_abb8_d7570bbd5616
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#a0e46d0e_10b6_46d1_8e72_26ee7c8900b6
stoichiometry: 1.0
species: COPASI39
type: SpeciesReference

COPASI82
notes: number of resting immune cells recruited by M1, eDC to LP
constant: true
value: 1000.0
name: er
type: Parameter

COPASI13
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI3
name: eDC
type: Species

COPASI124
constant: false
value: 0.0
name: new_emT_iTreg
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_9ad0aa39_ba78_457d_9eca_f71594578f7c
name: substance
type: SBMLUnitsDef

COPASI138
constant: false
value: 7.0E-7
name: ath1LB
type: Parameter

COPASI23
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1000000.0
initial amount: NaN
in compartment: COPASI3
name: iDC
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#eeeafa28_47bb_4c15_b677_3918a1898208
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI96
constant: false
value: 0.313385
name: iDCtoeDC_LP
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_5de3cf44_1c88_494c_8bd8_7519fdb91819
stoichiometry: 1.0
species: COPASI30
type: SpeciesReference

COPASI14
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI3
name: Th1
type: Species

COPASI125
constant: false
value: 214.717263795239
name: new_emT_Th1
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#dad5b3e2_3d9c_4a8f_8289_8724bfc617a8
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI139
constant: true
value: 0.3
name: aTh17LB
type: Parameter

COPASI81
notes: extent to which Ep secretes chemoattractants
constant: true
value: 1000.0
name: Br
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#eeb179ef_3700_4089_9bd5_5d2a190eebff
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

COPASI24
constant: false
boundary condition: true
has only substance units: false
initial concentration: 5501140.56260765
initial amount: NaN
in compartment: COPASI3
name: TotalDC
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#f5148d2c_7dae_4452_a990_047095280b6e
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#c268b981_fbec_4d61_aba3_ee3af8f422b4
stoichiometry: 1.0
species: COPASI36
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_5a4d9177_c7e8_4537_9f23_71e0a59baa11
value: 0.11695
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_955b04ad_d1fe_495b_a47e_1dad28e2c398
stoichiometry: 1.0
species: COPASI20
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#ac2ff58e_b459_4da2_b2d6_20b6f8fcb9e1
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

COPASI95
constant: false
value: 5.0E-7
name: iDCtotDC_Lumen
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_330d86c8_98fd_4ab6_addb_23cb170cedd2
value: 0.105682
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_3dddb374_2094_4fcd_abd6_f2183f4d6962
stoichiometry: 1.0
species: COPASI38
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#c5f89545_097a_4181_9693_fb01f085d693
stoichiometry: 1.0
species: COPASI22
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_2093ba05_fc2f_418f_a7d2_e0c64ad298ff
constant: true
value: 0.62677
name: k_LP1
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_85e93437_3dcc_4e5e_a2bd_b86417eccbe4
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#a098b3a1_5531_4faf_98a7_fb63262ffd83
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_2bae6557_2282_4393_955f_b01c72fa459b
stoichiometry: 1.0
species: COPASI33
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_2a06a5a5_42b6_46f9_9c12_e15595442b34
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_5a415121_ffa3_4935_b68e_61a79ed5ce40
stoichiometry: 1.0
species: COPASI38
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_6480bb6a_f563_40da_9aab_3269079bbacb
fast: false
reversible: false
name: nTreg deg
type: Reaction

COPASI36
constant: false
boundary condition: false
has only substance units: false
initial concentration: 4.17752018460542E7
initial amount: NaN
in compartment: COPASI5
name: cmT
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#e297f88a_cb57_4551_a13c_8bb612101fb6
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#eed58661_d5cb_4aad_85e8_325b20303906
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#ecda0afa_a5dc_4aab_ad20_fbcf85cb6301
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

COPASI35
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0E7
initial amount: NaN
in compartment: COPASI5
name: nT
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_9cee4856_a6e4_4a03_856e_cdac4afc855b
persistant: true
initial value: true
type: Trigger

COPASI49
notes: rate of T-cell flow from GLN to LP
constant: true
value: 0.5
name: @eIE
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#ef2cbd72_4586_49d8_9d3b_d71213587fac
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_59305961_a142_47d9_a997_e94d01a8185f
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI220
fast: false
reversible: false
name: re136
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#_4fd1d071_e631_41e2_aee4_3bb1ea45748f
stoichiometry: 1.0
species: COPASI30
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_26ff964b_3bc0_49e1_b9b5_02107b828a7d
fast: false
reversible: false
name: nTreg creation
type: Reaction

COPASI38
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI5
name: Th1
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_558b7d60_f21c_4b74_85d7_e25c171c8974
stoichiometry: 1.0
species: COPASI37
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_50a7afd7_e611_482b_8bc1_f43c76bf2d33
stoichiometry: 1.0
species: COPASI19
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#b02eeff8_4273_4618_bb91_5f2aa6d5873a
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

COPASI48
notes: contact rate between bacteria and Epithelium (invasion of mucous layer)
constant: true
value: 1.0E-6
name: kEB
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_79423314_d24b_4e23_a40d_0f9ae1f64c90
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_7149dbdc_cb65_42ce_9d8f_082adf146ef0
stoichiometry: 1.0
species: COPASI35
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#d821f9b4_75ff_43bc_9a1c_3a8aeeb25b21
stoichiometry: 1.0
type: SpeciesReference

COPASI99
constant: false
value: 5.0E-7
name: M0toM2_LP
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#ed21abe7_d078_49b7_8fe8_c16164f8e2c3
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI79
notes: rate at which E and Ep are killed by cytotoxic factors secreted by M1
constant: true
value: 1.0E-4
name: uM1
type: Parameter

COPASI37
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI5
name: Th17
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#a2745000_e04e_4fae_bf0b_8e790f05e349
stoichiometry: 1.0
species: COPASI12
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#f59e74c6_834a_4dd8_95b8_4c960935cc81
stoichiometry: 1.0
species: COPASI38
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_0c1b666a_b743_47f8_98d8_5ba02d839712
stoichiometry: 1.0
type: SpeciesReference

COPASI47
notes: probability that TEM or TCM will be stimulated to Th1 when contacted by eDC
constant: false
value: 0.7
name: aTh1
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#ea9fe196_423c_4a47_870e_3004af549d5b
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_83264ac7_728f_4f43_bbd7_a5f26a8cdaf5
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

COPASI4
constant: true
size: 1.0
spatial dimensions: 3.0
name: Epithelium
type: Compartment

http://identifiers.org/biomodels.db/BIOMD0000000480#f591fa57_7383_49fb_bfe4_f7f62b9413a9
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_825e45ac_9d15_4a67_a959_2b228d86248b
stoichiometry: 1.0
species: COPASI37
type: SpeciesReference

COPASI88
notes: number of nascent T-cells from one stimulated TEM- uninhibited
constant: true
value: 512.0
name: @pt_0
type: Parameter

COPASI19
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1000000.0
initial amount: NaN
in compartment: COPASI3
name: M0
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000480#_6f3a9e4c_49c1_43f1_9b19_743f93e8b51b
fast: false
reversible: false
name: nTh1 trans
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000480#fae77a63_410b_493f_bc38_23c485f0386b
stoichiometry: 1.0
species: COPASI36
type: SpeciesReference

COPASI78
constant: false
value: 1.0E-6
name: cyto_change
type: Parameter

COPASI3
constant: true
size: 1.0
spatial dimensions: 3.0
name: Lamina Propia
type: Compartment

COPASI59
constant: false
value: 128.0
name: pT
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_494d494b_9e45_4d32_9bfe_36540d101d07
stoichiometry: 2.0
species: COPASI22
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_0dc77b96_6035_4c5a_a6c6_5fd631e4ea35
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_003fd8cd_15d3_4440_b740_86e6587a5932
stoichiometry: 1.0
species: COPASI29
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_71f78b16_7d02_4371_b7c8_4fa5771e4416
stoichiometry: 1.0
species: COPASI34
type: SpeciesReference

COPASI87
notes: contact rate in LP
constant: true
value: 1.0E-6
name: k_LP
type: Parameter

COPASI39
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI5
name: iTreg
type: Species

COPASI77
notes: extent to which Ep becomes more permissive to bacterial passage
constant: true
value: 1.0
name: Bp
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_714ff6b1_3fd3_4aee_abc4_e0f070684e58
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#c4fe7487_b24d_43c2_8e57_9495fa12962d
fast: false
reversible: false
name: nTh17_LP deg
type: Reaction

COPASI2
constant: true
size: 1.0
spatial dimensions: 3.0
name: Lumen
type: Compartment

http://identifiers.org/biomodels.db/BIOMD0000000480#_13d3e7d2_674f_4a92_b490_6eb70e1085c7
constant: true
value: 3.0E-7
name: Initial for ath17
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_44dcc571_7024_4904_b43e_07032c2d4864
stoichiometry: 1.0
species: COPASI13
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#a1140e27_f9c7_40bc_94d5_e0ea16dfd3d8
stoichiometry: 1.0
species: COPASI15
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_45008aec_45a3_4a1d_b086_d774c10a7b6c
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_8b8cd863_c957_4ec1_aa85_897c4299f467
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_3b3b6871_cea0_4b02_b3fb_e79924285d04
stoichiometry: 1.0
species: COPASI21
type: SpeciesReference

COPASI76
notes: in-flow rate of nT in to GLN
constant: true
value: 1.0E8
name: @lt
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#a6c6e96f_fd71_4e47_9800_5491a94d77f2
stoichiometry: 1.0
species: COPASI32
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#_8935347b_98e3_4fd3_bbbb_951c72a302d7
stoichiometry: 1.0
species: COPASI34
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000480#c0af71a1_f703_43b4_b2fd_1c905ba43a45
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI5
name: eDCLB
type: Species

COPASI89
notes: number of nascent T-cells from one stimulated TCM or nT- uninhibited
constant: true
value: 128.0
name: @pT_0
type: Parameter

COPASI75
notes: out-flow rate of nT from GLN
constant: true
value: 1.0
name: @ut
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000480#_6f3baac6_97e3_46cd_84bb_8062d9cba6db
stoichiometry: 1.0
species: COPASI36
type: SpeciesReference

ORG:
  orgname: Center for Modeling Immunity to Enteric Pathogens
n:
  given: Adria
  family: Carbo

orgname: EMBL-EBI

given: Vijayalakshmi
family: Chelliah

W3 CDTF: Wed Oct 09 14:40:27 BST 2013

W3 CDTF: Tue Sep 17 13:08:08 BST 2013