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metaid_0000095
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metaid_0000085
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metaid_0000099
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metaid_0000016
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metaid_0000006
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metaid_0000084
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metaid_0000017
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871093
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metaid_0000098
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873159
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metaid_0000008
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873292
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871526
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MODEL7743631122
length unit: length
parameter: metaid_0000071
reaction: metaid_0000185
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parameter: metaid_0000070
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reaction: metaid_0000171
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notes: NFkB model M(34,60,82) This is a model of NFkB pathway functioning from hierarchy of models of decreasing complexity, created to demonstrate application of model reduction methods proposed in Radulescu O, Gorban A., Zinovyev A., Lilienbaum. A. Robust simplifications of multiscale models in systems biology. Manuscript submitted. The models are provided in CellDesigner v3.5 format. The name of the model M(x,y,z) should be deciphered as following: x - number of species y - number of reactions z - number of parameters Simulation protocol: The model can be simulated in CellDesigner directly, or in any simulator supporting events. The simulation period should be set up in 40 hours (t=144000 sec). The 'signal' event applies signal to the pathway at the moment t=20 hours=72000 sec. For additional information please contact Andrei.Zinovyev at curie.fr This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
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is described by: http://identifiers.org/pubmed/18854041
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871478
stoichiometry: 1.0
species: metaid_0000137
type: SpeciesReference

metaid_0000171
kinetic law: 872078
product: 872066
reactant: 872054
fast: false
reversible: false
type: Reaction

metaid_0000144
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: PromIkBa:RNAP3:p50p65
type: Species

metaid_0000117
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: IKKn
type: Species

metaid_0000130
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: NFkB:IKKa:Ikb_alpha
type: Species

metaid_0000181
kinetic law: 872463
product: 872451
reactant: 872439
fast: false
reversible: false
type: Reaction

871442
stoichiometry: 1.0
species: metaid_0000142
type: SpeciesReference

metaid_0000030
constant: true
value: 0.0
type: Parameter

metaid_0000047
constant: true
value: 0.0041
type: Parameter

metaid_0000031
constant: true
value: 4.0E-4
type: Parameter

872331
stoichiometry: 1.0
species: metaid_0000111
type: SpeciesReference

metaid_0000103
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: mRNAp105
type: Species

871298
stoichiometry: 1.0
species: metaid_0000144
type: SpeciesReference

metaid_0000158
kinetic law: 871454
product: 871442
reactant: 871430
reactant: 871418
fast: false
reversible: false
type: Reaction

metaid_0000057
constant: true
value: 6.4E-5
type: Parameter

873123
stoichiometry: 1.0
species: metaid_0000121
type: SpeciesReference

metaid_0000199
kinetic law: 873207
product: 873195
reactant: 873183
fast: false
reversible: false
type: Reaction

871754
stoichiometry: 1.0
species: metaid_0000128
type: SpeciesReference

metaid_0000143
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: InactivePRaseonIkB_alpha
type: Species

metaid_0000170
kinetic law: 872042
product: 872030
reactant: 872018
fast: false
reversible: false
type: Reaction

metaid_0000118
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: sa20_degraded
type: Species

metaid_0000180
kinetic law: 872427
product: 872415
reactant: 872403
fast: false
reversible: false
type: Reaction

metaid_0000104
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: p50
type: Species

metaid_0000046
constant: true
value: 0.01
type: Parameter

872787
stoichiometry: 1.0
species: metaid_0000114
type: SpeciesReference

metaid_0000157
kinetic law: 871406
product: 871394
reactant: 871382
reactant: 871370
fast: false
reversible: false
type: Reaction

metaid_0000056
constant: true
value: 5.0E-5
type: Parameter

872451
stoichiometry: 1.0
species: metaid_0000115
type: SpeciesReference

metaid_0000142
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: PromIkBa:RNAP3:FTAz
type: Species

872931
stoichiometry: 1.0
species: metaid_0000132
type: SpeciesReference

metaid_0000129
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: NFkB:IkB_alpha
type: Species

metaid_0000198
kinetic law: 873171
product: 873159
reactant: 873147
fast: false
reversible: false
type: Reaction

metaid_0000119
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: IKK
type: Species

metaid_0000132
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: IKKa:IKB_alpha
type: Species

metaid_0000183
kinetic law: 872535
product: 872523
reactant: 872511
fast: false
reversible: false
type: Reaction

metaid_0000045
constant: true
value: 0.6
type: Parameter

metaid_0000101
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: sa438_degraded
type: Species

metaid_0000059
constant: true
value: 1.0E-4
type: Parameter

871286
stoichiometry: 1.0
species: metaid_0000141
type: SpeciesReference

metaid_0000141
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 6.66666666666667E-6
in compartment: metaid_0000094
name: PromIkBa:RNAP3
type: Species

873075
stoichiometry: 1.0
species: metaid_0000111
type: SpeciesReference

metaid_0000197
kinetic law: 873135
product: 873123
reactant: 873111
fast: false
reversible: false
type: Reaction

873111
stoichiometry: 1.0
species: metaid_0000112
type: SpeciesReference

872054
stoichiometry: 1.0
species: metaid_0000104
type: SpeciesReference

metaid_0000131
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: NFkB
type: Species

metaid_0000182
kinetic law: 872499
product: 872487
reactant: 872475
fast: false
reversible: false
type: Reaction

metaid_0000159
kinetic law: 871502
product: 871490
product: 871478
reactant: 871466
fast: false
reversible: false
type: Reaction

metaid_0000044
constant: true
value: 0.06
type: Parameter

871742
stoichiometry: 1.0
species: metaid_0000143
type: SpeciesReference

metaid_0000102
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: sa3_degraded
type: Species

872607
stoichiometry: 1.0
species: metaid_0000131
type: SpeciesReference

metaid_0000058
constant: true
value: 10.0
type: Parameter

872871
stoichiometry: 1.0
species: metaid_0000131
type: SpeciesReference

metaid_0000169
kinetic law: 872006
product: 871994
product: 871982
reactant: 871970
fast: false
reversible: false
type: Reaction

metaid_0000140
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: Promp105:RNAP1:FTAx:p50p65:IkBa
type: Species

metaid_0000134
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: NFkB
type: Species

metaid_0000196
kinetic law: 873099
product: 873087
reactant: 873075
fast: false
reversible: false
type: Reaction

metaid_0000148
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000094
name: p65
type: Species

metaid_0000127
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: mRNAIKB_alpha
type: Species

metaid_0000113
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: sa444_degraded
type: Species

metaid_0000168
kinetic law: 871958
product: 871946
reactant: 871934
fast: false
reversible: false
type: Reaction

871334
stoichiometry: 1.0
species: metaid_0000097
type: SpeciesReference

metaid_0000176
kinetic law: 872258
product: 872246
reactant: 872234
fast: false
reversible: false
type: Reaction

metaid_0000195
kinetic law: 873063
product: 873051
reactant: 873039
reactant: 873027
fast: false
reversible: false
type: Reaction

metaid_0000107
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: sa13_degraded
type: Species

metaid_0000154
kinetic law: 871262
product: 871250
reactant: 871238
reactant: 871225
fast: false
reversible: false
type: Reaction

metaid_0000186
kinetic law: 872667
product: 872655
reactant: 872643
fast: false
reversible: false
type: Reaction

metaid_0000184
kinetic law: 872583
product: 872571
reactant: 872559
reactant: 872547
fast: false
reversible: false
type: Reaction

metaid_0000133
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: NFkB:IkB_alpha
type: Species

871141
stoichiometry: 1.0
species: metaid_0000144
type: SpeciesReference

metaid_0000147
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: PromIkBa:RNAP3:FTAz:p50p65:IkB_alpha
type: Species

metaid_0000114
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: IKKi
type: Species

872475
stoichiometry: 1.0
species: metaid_0000116
type: SpeciesReference

metaid_0000128
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: ActivePRaseonIkB_alpha
type: Species

metaid_0000175
kinetic law: 872222
product: 872210
reactant: 872198
fast: false
reversible: false
type: Reaction

872066
stoichiometry: 1.0
species: metaid_0000101
type: SpeciesReference

metaid_0000167
kinetic law: 871922
product: 871910
reactant: 871898
fast: false
reversible: false
type: Reaction

metaid_0000108
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: IkB_alpha
type: Species

metaid_0000194
kinetic law: 873015
product: 873003
reactant: 872991
fast: false
reversible: false
type: Reaction

873147
stoichiometry: 1.0
species: metaid_0000108
type: SpeciesReference

metaid_0000153
kinetic law: 871213
product: 871201
reactant: 871189
reactant: 871177
fast: false
reversible: false
type: Reaction

873087
stoichiometry: 1.0
species: metaid_0000120
type: SpeciesReference

metaid_0000185
kinetic law: 872631
product: 872619
product: 872607
reactant: 872595
fast: false
reversible: false
type: Reaction

metaid_0000136
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: Promp105:RNAP1:p50p65:IkBa
type: Species

metaid_0000069
constant: true
value: 18.4
type: Parameter

metaid_0000125
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: InactivePRaseonp105
type: Species

metaid_0000173
kinetic law: 872150
product: 872138
reactant: 872126
fast: false
reversible: false
type: Reaction

metaid_0000115
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: sa19_degraded
type: Species

metaid_0000146
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: IkBa:RNAP3:FTAz:p50p65
type: Species

metaid_0000193
kinetic law: 872979
product: 872967
reactant: 872955
fast: false
reversible: false
type: Reaction

metaid_0000105
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: p65
type: Species

metaid_0000166
kinetic law: 871886
product: 871874
reactant: 871862
fast: false
reversible: false
type: Reaction

872955
stoichiometry: 1.0
species: metaid_0000131
type: SpeciesReference

871430
stoichiometry: 1.0
species: metaid_0000141
type: SpeciesReference

metaid_0000174
kinetic law: 872186
product: 872174
reactant: 872162
fast: false
reversible: false
type: Reaction

872138
stoichiometry: 1.0
species: metaid_0000106
type: SpeciesReference

metaid_0000156
kinetic law: 871358
product: 871346
reactant: 871334
reactant: 871322
fast: false
reversible: false
type: Reaction

metaid_0000188
kinetic law: 872763
product: 872751
reactant: 872739
reactant: 872727
fast: false
reversible: false
type: Reaction

871346
stoichiometry: 1.0
species: metaid_0000140
type: SpeciesReference

metaid_0000049
constant: true
value: 6.0E-5
type: Parameter

metaid_0000135
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: Promp105:RNAP1:p50p65
type: Species

metaid_0000126
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: ActivePRaseonp105
type: Species

metaid_0000116
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: IKKa
type: Species

metaid_0000068
constant: true
value: 4.8E-4
type: Parameter

metaid_0000172
kinetic law: 872114
product: 872102
reactant: 872090
fast: false
reversible: false
type: Reaction

metaid_0000145
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000094
name: PromIkBa:RNAP3:p50p65:IkBa
type: Species

871490
stoichiometry: 1.0
species: metaid_0000133
type: SpeciesReference

871898
stoichiometry: 1.0
species: metaid_0000100
type: SpeciesReference

metaid_0000165
kinetic law: 871850
product: 871838
reactant: 871826
fast: false
reversible: false
type: Reaction

metaid_0000106
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: sa9_degraded
type: Species

metaid_0000192
kinetic law: 872943
product: 872931
reactant: 872919
reactant: 872907
fast: false
reversible: false
type: Reaction

metaid_0000187
kinetic law: 872715
product: 872703
product: 872691
reactant: 872679
fast: false
reversible: false
type: Reaction

871946
stoichiometry: 1.0
species: metaid_0000102
type: SpeciesReference

metaid_0000155
kinetic law: 871310
product: 871298
reactant: 871286
reactant: 871274
fast: false
reversible: false
type: Reaction

873183
stoichiometry: 1.0
species: metaid_0000131
type: SpeciesReference

metaid_0000048
constant: true
value: 5.0E-5
type: Parameter

873231
stoichiometry: 1.0
species: metaid_0000123
type: SpeciesReference