MODEL7743631122
type: SBMLModel
parameter: metaid_0000071
reaction: metaid_0000185
parameter: metaid_0000063
parameter: metaid_0000070
parameter: metaid_0000089
reaction: metaid_0000171
parameter: metaid_0000022
parameter: metaid_0000083
parameter: metaid_0000014
reaction: metaid_0000197
parameter: metaid_0000090
species: metaid_0000103
parameter: metaid_0000082
reaction: metaid_0000191
reaction: metaid_0000156
species: metaid_0000096
reaction: metaid_0000183
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parameter: metaid_0000026
species: metaid_0000144
reaction: metaid_0000168
reaction: metaid_0000195
species: metaid_0000102
parameter: metaid_0000038
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.
species: metaid_0000127
species: metaid_0000132
parameter: metaid_0000017
parameter: metaid_0000045
reaction: metaid_0000160
parameter: metaid_0000009
area units: area
species: metaid_0000147
species: metaid_0000121
parameter: metaid_0000029
parameter: metaid_0000057
species: metaid_0000105
is described by: http://identifiers.org/pubmed/18854041
parameter: metaid_0000064
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time units: 754168
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metaid_0000071
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metaid_0000185
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872619
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metaid_0000116
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metaid_0000093
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metaid_0000131
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metaid_0000070
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metaid_0000112
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metaid_0000090
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metaid_0000103
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873051
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873039
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873027
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metaid_0000134
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871538
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871526
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metaid_0000138
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871514
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metaid_0000029
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metaid_0000126
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metaid_0000050
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metaid_0000021
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metaid_0000055
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metaid_0000041
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metaid_0000068
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metaid_0000075
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metaid_0000109
type: Species
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boundary condition: false
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initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
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872198
type: SpeciesReference
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species: metaid_0000127

metaid_0000202
type: Event
event assignment: 873316
delay: 873304
trigger: 873292
use values from trigger time: true
name: signal

metaid_0000003
type: Parameter
constant: false
value: 0.0

873292
type: Trigger
persistant: true
initial value: true

metaid_0000087
type: Parameter
constant: true
value: 0.0038

metaid_0000189
type: Reaction
kinetic law: 872811
modifier: 872799
product: 872787
reactant: 872775
fast: false
reversible: false

872787
type: SpeciesReference
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species: metaid_0000114

872775
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000116

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

metaid_0000079
type: Parameter
constant: true
value: 0.62

metaid_0000020
type: Parameter
constant: true
value: 8.0E-5

metaid_0000005
type: Parameter
constant: true
value: 1.0E-5

metaid_0000012
type: Parameter
constant: true
value: 0.1

metaid_0000073
type: Parameter
constant: true
value: 0.0038

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

872703
type: SpeciesReference
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species: metaid_0000111

872691
type: SpeciesReference
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species: metaid_0000112

872679
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000111

metaid_0000080
type: Parameter
constant: true
value: 4.8E-4

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

871250
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000136

871238
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000097

871225
type: SpeciesReference
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species: metaid_0000135

metaid_0000135
type: Species
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

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

872451
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000115

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

872439
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000117

metaid_0000032
type: Parameter
constant: true
value: 0.01

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

872138
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000106

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

872126
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000105

metaid_0000024
type: Parameter
constant: true
value: 5.0E-7

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

873195
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000122

metaid_0000122
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: csa21_degraded

873183
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000131

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

metaid_0000085
type: Parameter
constant: true
value: 0.0038

metaid_0000152
type: Reaction
kinetic law: 871165
product: 871153
reactant: 871141
reactant: 871129
fast: false
reversible: false

871153
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000145

metaid_0000145
type: Species
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

871141
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000144

871129
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000097

metaid_0000092
type: Parameter
constant: true
value: 5.5E-5
name: =k43*k45*prop65RNAP0 / k46

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

872967
type: SpeciesReference
stoichiometry: 5.0
species: metaid_0000134

872955
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000131

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

871874
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000103

871862
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000126

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

871442
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000142

871430
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000141

871418
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000096

metaid_0000036
type: Parameter
constant: true
value: 5.0E-4

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

metaid_0000164
type: Reaction
product: 871754
fast: false
modifier: 871778
kinetic law: 871814
modifier: 871766
modifier: 871790
modifier: 871802
reversible: false
reactant: 871742

871754
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000128

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

871742
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000143

metaid_0000007
type: Parameter
constant: true
value: 0.0015

metaid_0000042
type: Parameter
constant: true
value: 5.0E-4

metaid_0000150
type: Reaction
kinetic law: 871068
product: 871056
reactant: 871044
reactant: 871032
fast: false
reversible: false

871056
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000139

871044
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000134

871032
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000138

metaid_0000019
type: Parameter
constant: true
value: 0.0025

metaid_0000047
type: Parameter
constant: true
value: 0.0041

metaid_0000054
type: Parameter
constant: true
value: 0.016

metaid_0000162
type: Reaction
kinetic law: 871646
product: 871634
product: 871622
reactant: 871610
fast: false
reversible: false

871634
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000133

871622
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000141

871610
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000145

metaid_0000200
type: Reaction
kinetic law: 873243
product: 873231
reactant: 873219
fast: false
reversible: false

873231
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000123

metaid_0000123
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000093
name: csa18_degraded

873219
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000129

metaid_0000040
type: Parameter
constant: true
value: 0.006

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

metaid_0000066
type: Parameter
constant: true
value: 4.8E-4

metaid_0000060
type: Parameter
constant: true
value: 0.025

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

872174
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000127

872162
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000128

metaid_0000052
type: Parameter
constant: true
value: 10.0

metaid_0000086
type: Parameter
constant: true
value: 8.0E-13

metaid_0000078
type: Parameter
constant: true
value: 4.8E-4

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

metaid_0000004
type: Parameter
constant: true
value: 1.25E-4

metaid_0000011
type: Parameter
constant: true
value: 1.2

metaid_0000072
type: Parameter
constant: true
value: 0.055

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

872655
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000113

872643
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000114

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

871201
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000135

871189
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000137

871177
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000134

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

872415
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000131

872403
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000129

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

872102
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000105

872090
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000148

metaid_0000016
type: Parameter
constant: true
value: 0.0

metaid_0000023
type: Parameter
constant: true
value: 3.0E-4

metaid_0000084
type: Parameter
constant: true
value: 0.055

metaid_0000015
type: Parameter
constant: true
value: 0.5

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

873159
type: SpeciesReference
stoichiometry: 5.0
species: metaid_0000097

873147
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000108

metaid_0000091
type: Parameter
constant: true
value: 6.66E-6
name: concentration of promoters

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

871838
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000098

871826
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000134

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

872931
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000132

872919
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000116

872907
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000108

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

871394
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000147

871382
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000146

871370
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000097

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

872571
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000130

872559
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000129

872547
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000116

metaid_0000035
type: Parameter
constant: true
value: 1.0E-4

metaid_0000027
type: Parameter
constant: true
value: 0.5

metaid_0000163
type: Reaction
fast: false
modifier: 871706
modifier: 871718
product: 871670
reversible: false
reactant: 871658
modifier: 871694
kinetic law: 871730
modifier: 871682

871670
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000126

871658
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000125

metaid_0000006
type: Parameter
constant: true
value: 0.1

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

871994
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000103

871982
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000100

871970
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000103

metaid_0000018
type: Parameter
constant: true
value: 0.0

metaid_0000046
type: Parameter
constant: true
value: 0.01

metaid_0000053
type: Parameter
constant: true
value: 1.0E-4

metaid_0000161
type: Reaction
kinetic law: 871598
product: 871586
product: 871574
reactant: 871562
fast: false
reversible: false

871586
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000133

871574
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000142

871562
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000147

metaid_0000058
type: Parameter
constant: true
value: 10.0

metaid_0000065
type: Parameter
constant: true
value: 0.62

metaid_0000051
type: Parameter
constant: true
value: 6.4E-5

metaid_0000077
type: Parameter
constant: true
value: 0.62

metaid_0000179
type: Reaction
kinetic law: 872391
product: 872379
reactant: 872367
fast: false
reversible: false

872379
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000116

872367
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000117

metaid_0000010
type: Parameter
constant: true
value: 0.1