metaid_0000101
constant: true
value: 0.003
name: =kr58/kf58
type: Parameter

metaid_0000019
constant: true
value: 0.0025
type: Parameter

metaid_0000045
constant: true
value: 0.6
type: Parameter

metaid_0000055
constant: true
value: 0.0053
type: Parameter

metaid_0000095
constant: true
value: 0.0061
name: =kf68/kf64
type: Parameter

metaid_0000118
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: sa20_degraded
type: Species

MODEL7743528808
parameter: metaid_0000059
reaction: metaid_0000148
parameter: metaid_0000031
species: metaid_0000125
reaction: metaid_0000139
parameter: metaid_0000058
parameter: metaid_0000082
name: Radulescu2008_NFkB_hierarchy_M_14_30_41
parameter: metaid_0000069
parameter: metaid_0000043
reaction: metaid_0000151
species: metaid_0000113
parameter: metaid_0000066
species: metaid_0000127
parameter: metaid_0000094
reaction: metaid_0000152
parameter: metaid_0000078
parameter: metaid_0000051
parameter: metaid_0000071
species: metaid_0000108
parameter: metaid_0000044
species: metaid_0000120
species: metaid_0000133
parameter: metaid_0000013
parameter: metaid_0000083
reaction: metaid_0000156
parameter: metaid_0000056
parameter: metaid_0000008
curated: false
parameter: metaid_0000080
parameter: metaid_0000067
notes: NFkB model M(14,30,41) 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.
compartment: metaid_0000104
parameter: metaid_0000033
parameter: metaid_0000092
parameter: metaid_0000084
reaction: metaid_0000135
parameter: metaid_0000045
species: metaid_0000115
species: metaid_0000123
substance units: 106194
parameter: metaid_0000017
parameter: metaid_0000099
parameter: metaid_0000096
parameter: metaid_0000011
parameter: metaid_0000010
parameter: metaid_0000081
reaction: metaid_0000154
parameter: metaid_0000073
parameter: metaid_0000035
species: metaid_0000122
parameter: metaid_0000015
parameter: metaid_0000097
species: metaid_0000128
parameter: metaid_0000006
parameter: metaid_0000085
reaction: metaid_0000158
parameter: metaid_0000047
species: metaid_0000130
species: metaid_0000110
reaction: metaid_0000140
species: metaid_0000116
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species: metaid_0000121
species: metaid_0000109
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parameter: metaid_0000048
parameter: metaid_0000020
reaction: metaid_0000137
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parameter: metaid_0000019
parameter: metaid_0000032
species: metaid_0000129
parameter: metaid_0000037
time units: 754168
parameter: metaid_0000028
parameter: metaid_0000040
parameter: metaid_0000102
parameter: metaid_0000060
parameter: metaid_0000049

metaid_0000157
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product: 840650
reactant: 840638
fast: false
reversible: false
type: Reaction

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

840153
stoichiometry: 1.0
species: metaid_0000116
type: SpeciesReference

metaid_0000130
constant: false
boundary condition: false
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initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000104
name: NFkB:IkB_alpha
type: Species

metaid_0000140
kinetic law: 839947
modifier: 839935
product: 839923
reactant: 839911
fast: false
reversible: false
type: Reaction

840127
stoichiometry: 1.0
species: metaid_0000116
type: SpeciesReference

840398
stoichiometry: 1.0
species: metaid_0000117
type: SpeciesReference

metaid_0000108
constant: false
boundary condition: false
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initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: IkB_alpha
type: Species

metaid_0000085
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value: 0.0038
type: Parameter

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species: metaid_0000131
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840446
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species: metaid_0000126
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839972
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species: metaid_0000116
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metaid_0000046
constant: true
value: 0.01
type: Parameter

metaid_0000018
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value: 0.0
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metaid_0000100
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value: 0.0061
name: =kf60/kf56
type: Parameter

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

840166
stoichiometry: 1.0
species: metaid_0000126
type: SpeciesReference

metaid_0000086
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value: 8.0E-13
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metaid_0000117
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initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: IKKn
type: Species

metaid_0000156
kinetic law: 840626
product: 840614
reactant: 840602
reactant: 840590
fast: false
reversible: false
type: Reaction

metaid_0000096
constant: true
value: 0.003
name: =kr66/kf66
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839874
stoichiometry: 1.0
species: metaid_0000108
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metaid_0000003
constant: false
value: 0.0
type: Parameter

840230
stoichiometry: 1.0
species: metaid_0000116
type: SpeciesReference

metaid_0000141
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product: 839972
reactant: 839960
fast: false
reversible: false
type: Reaction

metaid_0000131
constant: false
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initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000104
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metaid_0000107
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initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: sa13_degraded
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metaid_0000043
constant: true
value: 0.02
type: Parameter

metaid_0000017
constant: true
value: 0.5
type: Parameter

metaid_0000103
constant: true
size: NaN
spatial dimensions: 3.0
type: Compartment

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

840818
stoichiometry: 1.0
species: metaid_0000130
type: SpeciesReference

840290
stoichiometry: 1.0
species: metaid_0000111
type: SpeciesReference

metaid_0000007
constant: true
value: 0.0015
type: Parameter

metaid_0000142
kinetic law: 840023
product: 840010
reactant: 839997
fast: false
reversible: false
type: Reaction

840049
stoichiometry: 1.0
species: metaid_0000115
type: SpeciesReference

metaid_0000159
kinetic law: 840734
product: 840722
reactant: 840710
fast: false
reversible: false
type: Reaction

839802
stoichiometry: 1.0
species: metaid_0000109
type: SpeciesReference

metaid_0000097
constant: true
value: 1.0E-10
name: dummy
type: Parameter

metaid_0000106
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000104
name: csa17_degraded
type: Species

metaid_0000083
constant: true
value: 18.4
type: Parameter

metaid_0000016
constant: true
value: 0.0
type: Parameter

metaid_0000044
constant: true
value: 0.06
type: Parameter

metaid_0000102
constant: true
value: 1.0E-10
name: dummy
type: Parameter

metaid_0000104
constant: true
size: NaN
spatial dimensions: 3.0
name: nucleus
type: Compartment

839960
stoichiometry: 1.0
species: metaid_0000117
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839681
stoichiometry: 1.0
species: metaid_0000128
type: SpeciesReference

metaid_0000058
constant: true
value: 10.0
type: Parameter

metaid_0000070
constant: true
value: 0.055
type: Parameter

metaid_0000006
constant: true
value: 0.1
type: Parameter

metaid_0000143
kinetic law: 840062
product: 840049
reactant: 840036
fast: false
reversible: false
type: Reaction

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

840114
stoichiometry: 1.0
species: metaid_0000129
type: SpeciesReference

metaid_0000119
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000104
name: IKK
type: Species

metaid_0000158
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product: 840686
reactant: 840674
fast: false
reversible: false
type: Reaction

metaid_0000105
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boundary condition: false
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initial concentration: NaN
initial amount: 0.0
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name: IkB_alpha
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840338
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species: metaid_0000116
type: SpeciesReference

metaid_0000098
constant: true
value: 8.172E-10
name: =P0*k50*k60/k56
type: Parameter

metaid_0000030
constant: true
value: 0.0
type: Parameter

metaid_0000084
constant: true
value: 0.055
type: Parameter

839886
stoichiometry: 1.0
species: metaid_0000125
type: SpeciesReference

metaid_0000015
constant: true
value: 0.5
type: Parameter

metaid_0000071
constant: true
value: 18.4
type: Parameter

metaid_0000041
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value: 0.06
type: Parameter

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

metaid_0000061
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value: 0.003
type: Parameter

metaid_0000081
constant: true
value: 18.4
type: Parameter

839632
stoichiometry: 1.0
species: metaid_0000131
type: SpeciesReference

metaid_0000014
constant: true
value: 2.0E-5
type: Parameter

metaid_0000021
constant: true
value: 0.5
type: Parameter

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

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

metaid_0000072
constant: true
value: 0.055
type: Parameter

839730
stoichiometry: 1.0
species: metaid_0000132
type: SpeciesReference

metaid_0000052
constant: true
value: 10.0
type: Parameter

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

metaid_0000062
constant: true
value: 0.001
type: Parameter

metaid_0000013
constant: true
value: 1.25E-4
type: Parameter

840638
stoichiometry: 1.0
species: metaid_0000111
type: SpeciesReference

840422
stoichiometry: 1.0
species: metaid_0000108
type: SpeciesReference

metaid_0000082
constant: true
value: 0.055
type: Parameter

metaid_0000022
constant: true
value: 4.0E-4
type: Parameter

metaid_0000032
constant: true
value: 0.01
type: Parameter

840854
persistant: true
initial value: true
type: Trigger

840010
stoichiometry: 1.0
species: metaid_0000128
type: SpeciesReference

metaid_0000092
constant: true
value: 7.07E-5
name: =k43*k45*P0 / k46
type: Parameter

840386
stoichiometry: 1.0
species: metaid_0000119
type: SpeciesReference

metaid_0000073
constant: true
value: 0.0038
type: Parameter

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

metaid_0000012
constant: true
value: 0.1
type: Parameter

840179
stoichiometry: 1.0
species: metaid_0000127
type: SpeciesReference

839644
stoichiometry: 1.0
species: metaid_0000106
type: SpeciesReference

metaid_0000093
constant: true
value: 2.2925E-7
name: =k36*k39*P0*k34*kf68/(k37*kf64*(k38+k39))
type: Parameter

metaid_0000033
constant: true
value: 0.0
type: Parameter

840710
stoichiometry: 1.0
species: metaid_0000108
type: SpeciesReference

metaid_0000040
constant: true
value: 0.006
type: Parameter

840686
stoichiometry: 1.0
species: metaid_0000121
type: SpeciesReference

metaid_0000074
constant: true
value: 8.0E-13
type: Parameter

metaid_0000054
constant: true
value: 0.016
type: Parameter

metaid_0000060
constant: true
value: 0.025
type: Parameter

840036
stoichiometry: 1.0
species: metaid_0000117
type: SpeciesReference

metaid_0000129
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: IKKa:IKB_alpha
type: Species

metaid_0000011
constant: true
value: 1.2
type: Parameter

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

metaid_0000109
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: sa12_degraded
type: Species

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

840530
stoichiometry: 5.0
species: metaid_0000131
type: SpeciesReference

840434
stoichiometry: 1.0
species: metaid_0000128
type: SpeciesReference

metaid_0000034
constant: true
value: 10.0
type: Parameter

metaid_0000094
constant: true
value: 6.7E-8
name: =k39*k36*kr66*k70*P0/(k37*kf66*(k38+k39))
type: Parameter

metaid_0000148
kinetic law: 840278
product: 840266
reactant: 840254
fast: false
reversible: false
type: Reaction

840266
stoichiometry: 1.0
species: metaid_0000113
type: SpeciesReference

840614
stoichiometry: 1.0
species: metaid_0000130
type: SpeciesReference

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

metaid_0000163
event assignment: 840878
delay: 840866
trigger: 840854
use values from trigger time: true
name: signal
type: Event

metaid_0000025
constant: true
value: 0.0
type: Parameter

metaid_0000010
constant: true
value: 0.1
type: Parameter

metaid_0000110
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000104
name: A20
type: Species

metaid_0000076
constant: true
value: 8.0E-13
type: Parameter

metaid_0000139
kinetic law: 839898
product: 839886
product: 839874
reactant: 839862
fast: false
reversible: false
type: Reaction

839742
stoichiometry: 1.0
species: metaid_0000125
type: SpeciesReference

840075
stoichiometry: 1.0
species: metaid_0000116
type: SpeciesReference

840302
stoichiometry: 1.0
species: metaid_0000112
type: SpeciesReference

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

metaid_0000149
kinetic law: 840326
product: 840314
product: 840302
reactant: 840290
fast: false
reversible: false
type: Reaction

metaid_0000120
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: sa96_degraded
type: Species

metaid_0000162
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product: 840830
reactant: 840818
fast: false
reversible: false
type: Reaction

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

840218
stoichiometry: 1.0
species: metaid_0000128
type: SpeciesReference

metaid_0000026
constant: true
value: 1.0E-4
type: Parameter

metaid_0000075
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value: 0.0038
type: Parameter

metaid_0000111
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: mRNAA20
type: Species

metaid_0000065
constant: true
value: 0.62
type: Parameter

metaid_0000121
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boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: sa97_degraded
type: Species

metaid_0000037
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value: 0.1
type: Parameter

metaid_0000161
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product: 840794
reactant: 840782
fast: false
reversible: false
type: Reaction

839997
stoichiometry: 1.0
species: metaid_0000126
type: SpeciesReference

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

metaid_0000136
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modifier: 839766
modifier: 839754
product: 839742
reactant: 839730
fast: false
reversible: false
type: Reaction

840650
stoichiometry: 1.0
species: metaid_0000120
type: SpeciesReference

840830
stoichiometry: 1.0
species: metaid_0000124
type: SpeciesReference

840205
stoichiometry: 1.0
species: metaid_0000127
type: SpeciesReference

metaid_0000151
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product: 840398
reactant: 840386
fast: false
reversible: false
type: Reaction

839669
stoichiometry: 1.0
species: metaid_0000133
type: SpeciesReference

840794
stoichiometry: 1.0
species: metaid_0000123
type: SpeciesReference

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

metaid_0000050
constant: true
value: 1.3E-4
type: Parameter

metaid_0000122
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: csa21_degraded
type: Species

metaid_0000064
constant: true
value: 2.0E-4
type: Parameter

840722
stoichiometry: 5.0
species: metaid_0000105
type: SpeciesReference

metaid_0000160
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product: 840758
reactant: 840746
fast: false
reversible: false
type: Reaction

metaid_0000090
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value: 2.0E-4
type: Parameter

metaid_0000038
constant: true
value: 5.0E-4
type: Parameter

840350
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species: metaid_0000114
type: SpeciesReference

metaid_0000137
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product: 839802
reactant: 839790
fast: false
reversible: false
type: Reaction

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

metaid_0000150
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modifier: 840362
product: 840350
reactant: 840338
fast: false
reversible: false
type: Reaction

840470
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species: metaid_0000108
type: SpeciesReference

metaid_0000138
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product: 839838
reactant: 839826
fast: false
reversible: false
type: Reaction

metaid_0000063
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value: 2.0E-4
type: Parameter

metaid_0000077
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value: 0.62
type: Parameter

metaid_0000123
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boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: csa18_degraded
type: Species

metaid_0000039
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type: Parameter

metaid_0000134
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product: 839644
reactant: 839632
fast: false
reversible: false
type: Reaction

840554
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species: metaid_0000130
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839862
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species: metaid_0000125
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840782
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species: metaid_0000126
type: SpeciesReference

metaid_0000144
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product: 840088
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fast: false
reversible: false
type: Reaction

metaid_0000153
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product: 840494
reactant: 840482
reactant: 840470
fast: false
reversible: false
type: Reaction

840758
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species: metaid_0000122
type: SpeciesReference

840518
stoichiometry: 1.0
species: metaid_0000128
type: SpeciesReference

metaid_0000124
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has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000104
name: csa9_degraded
type: Species

metaid_0000059
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value: 1.0E-4
type: Parameter

839923
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species: metaid_0000111
type: SpeciesReference

metaid_0000049
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value: 6.0E-5
type: Parameter

metaid_0000114
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boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: IKKi
type: Species

metaid_0000116
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has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: IKKa
type: Species

metaid_0000099
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value: 1.1957E-8
name: =P0*kr58*k62/kf58
type: Parameter

metaid_0000135
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modifier: 839705
modifier: 839693
product: 839681
reactant: 839669
fast: false
reversible: false
type: Reaction

metaid_0000145
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product: 840127
reactant: 840114
fast: false
reversible: false
type: Reaction

839838
stoichiometry: 1.0
species: metaid_0000107
type: SpeciesReference

metaid_0000089
constant: true
value: 2.0E-4
type: Parameter

metaid_0000152
kinetic law: 840458
product: 840446
reactant: 840434
reactant: 840422
fast: false
reversible: false
type: Reaction

metaid_0000069
constant: true
value: 18.4
type: Parameter

metaid_0000125
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boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: mRNAIKB_alpha
type: Species

840482
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species: metaid_0000116
type: SpeciesReference

metaid_0000079
constant: true
value: 0.62
type: Parameter

metaid_0000115
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boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: sa19_degraded
type: Species

839790
stoichiometry: 1.0
species: metaid_0000125
type: SpeciesReference

839911
stoichiometry: 1.0
species: metaid_0000110
type: SpeciesReference

840566
stoichiometry: 1.0
species: metaid_0000126
type: SpeciesReference

metaid_0000027
constant: true
value: 0.5
type: Parameter

metaid_0000132
constant: false
boundary condition: false
has only substance units: false
initial concentration: 4.9E-324
initial amount: NaN
in compartment: metaid_0000104
name: IKB_alpha
type: Species

840746
stoichiometry: 1.0
species: metaid_0000128
type: SpeciesReference

840314
stoichiometry: 1.0
species: metaid_0000111
type: SpeciesReference

metaid_0000088
constant: true
value: 8.0E-13
type: Parameter

metaid_0000127
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: NFkB:IKKa:Ikb_alpha
type: Species

metaid_0000155
kinetic law: 840578
product: 840566
reactant: 840554
fast: false
reversible: false
type: Reaction

metaid_0000146
kinetic law: 840192
product: 840179
reactant: 840166
reactant: 840153
fast: false
reversible: false
type: Reaction

metaid_0000126
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: NFkB:IkB_alpha
type: Species

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

840254
stoichiometry: 1.0
species: metaid_0000114
type: SpeciesReference

metaid_0000028
constant: true
value: 0.001
type: Parameter

840602
stoichiometry: 1.0
species: metaid_0000105
type: SpeciesReference

metaid_0000112
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: A20
type: Species

metaid_0000008
constant: true
value: 1.25E-4
type: Parameter

840674
stoichiometry: 1.0
species: metaid_0000112
type: SpeciesReference

metaid_0000047
constant: true
value: 0.0041
type: Parameter

839826
stoichiometry: 1.0
species: metaid_0000108
type: SpeciesReference

metaid_0000133
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000104
name: NFkB
type: Species

metaid_0000087
constant: true
value: 0.0038
type: Parameter

metaid_0000154
kinetic law: 840542
product: 840530
reactant: 840518
fast: false
reversible: false
type: Reaction

metaid_0000128
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: NFkB
type: Species

metaid_0000147
kinetic law: 840242
product: 840230
product: 840218
reactant: 840205
fast: false
reversible: false
type: Reaction

metaid_0000067
constant: true
value: 0.62
type: Parameter

metaid_0000113
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: sa444_degraded
type: Species

840088
stoichiometry: 1.0
species: metaid_0000118
type: SpeciesReference

metaid_0000029
constant: true
value: 5.0E-4
type: Parameter

840494
stoichiometry: 1.0
species: metaid_0000129
type: SpeciesReference

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

metaid_0000009
constant: true
value: 0.24
type: Parameter