MODEL7743358405
type: SBMLModel
is described by: http://identifiers.org/pubmed/18854041
parameter: 554627
parameter: 554613
curated: false
parameter: 554657
reaction: 554516
species: 554346
parameter: 554653
species: 554386
area units: area
species: 554427
species: 554406
parameter: 554609
parameter: 554633
parameter: 554661
parameter: 554619
parameter: 554669
parameter: 554637
parameter: 554675
species: 554396
reaction: 554502
reaction: 554553
parameter: 554647
species: 554416
species: 554366
parameter: 554629
parameter: 554639
species: 554316
species: 554306
parameter: 554623
reaction: 554564
reaction: 554489
species: 554376
parameter: 554605
parameter: 554615
parameter: 554663
volume units: metaid_0000217
parameter: 554643
reaction: 554474
substance units: 106194
species: 554355
reaction: 554437
compartment: 554285
compartment: 554287
reaction: 554450
time units: 754168
species: 554296
parameter: 554625
parameter: 554635
parameter: 554671
reaction: 554575
parameter: 554617
reaction: 554540
parameter: 554665
parameter: 554673
reaction: 554586
parameter: 554611
parameter: 554645
parameter: 554655
species: 554326
parameter: 554649
parameter: 554659
parameter: 554641
parameter: 554651
parameter: 554603
length unit: length
parameter: 554621
parameter: 554631
parameter: 554607
reaction: 554529
parameter: 554667
species: 554336
notes: NFkB model M(8,12,19) 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.
name: Radulescu2008_NFkB_hierarchy_M_8_12_19

554627
type: Parameter
constant: true
value: 18.4

554613
type: Parameter
constant: true
value: 1.25E-4

554657
type: Parameter
constant: true
value: 4.0E-4

554516
type: Reaction
kinetic law: 821257
product: 821245
product: 821233
reactant: 821221
fast: false
reversible: false

821245
type: SpeciesReference
stoichiometry: 1.0
species: 554346

554346
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: mRNAA20

554285
type: Compartment
constant: true
size: NaN
spatial dimensions: 3.0

821233
type: SpeciesReference
stoichiometry: 1.0
species: 554355

554355
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: A20

821221
type: SpeciesReference
stoichiometry: 1.0
species: 554346

554653
type: Parameter
constant: true
value: 0.001

554386
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: sa97_degraded

554427
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554287
name: IkB_alpha

554287
type: Compartment
constant: true
size: NaN
spatial dimensions: 3.0
name: nucleus

554406
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: IkB_alpha

554609
type: Parameter
constant: true
value: 0.1

554633
type: Parameter
constant: true
value: 0.0

554661
type: Parameter
constant: true
value: 0.0

554619
type: Parameter
constant: true
value: 1.0

554669
type: Parameter
constant: true
value: 0.015
name: =k5/k4

554637
type: Parameter
constant: true
value: 0.0

554675
type: Parameter
constant: true
value: 0.015
name: =k5/k4

554396
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554287
name: NFkB/IkB_alpha

554502
type: Reaction
kinetic law: 821209
modifier: 821197
product: 821185
reactant: 821173
fast: false
reversible: false

554416
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554287
name: NFKB

821185
type: SpeciesReference
stoichiometry: 1.0
species: 554346

821173
type: SpeciesReference
stoichiometry: 1.0
species: 554336

554336
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554287
name: A20

554553
type: Reaction
kinetic law: 821377
product: 821365
reactant: 821353
fast: false
reversible: false

821365
type: SpeciesReference
stoichiometry: 1.0
species: 554376

554376
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: sa96_degraded

821353
type: SpeciesReference
stoichiometry: 1.0
species: 554346

554647
type: Parameter
constant: true
value: 0.0

554366
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.166
in compartment: 554285
name: NFKB.IKBA

554629
type: Parameter
constant: true
value: 0.0

554639
type: Parameter
constant: true
value: 0.5

554316
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: sa12_degraded

554306
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: sa13_degraded

554623
type: Parameter
constant: true
value: 1.25E-4

554564
type: Reaction
kinetic law: 821413
product: 821401
reactant: 821389
fast: false
reversible: false

821401
type: SpeciesReference
stoichiometry: 1.0
species: 554386

821389
type: SpeciesReference
stoichiometry: 1.0
species: 554355

554489
type: Reaction
kinetic law: 821161
product: 821149
product: 821137
reactant: 821125
fast: false
reversible: false

821149
type: SpeciesReference
stoichiometry: 1.0
species: 554326

554326
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554285
name: mRNAIKBA

821137
type: SpeciesReference
stoichiometry: 1.0
species: 554406

821125
type: SpeciesReference
stoichiometry: 1.0
species: 554326

554605
type: Parameter
constant: true
value: 1.25E-4

554615
type: Parameter
constant: true
value: 0.2

554663
type: Parameter
constant: true
value: 5.0E-7

554643
type: Parameter
constant: true
value: 3.0E-4

554474
type: Reaction
kinetic law: 821113
modifier: 821101
modifier: 821089
product: 821077
reactant: 821065
fast: false
reversible: false

821077
type: SpeciesReference
stoichiometry: 1.0
species: 554306

821065
type: SpeciesReference
stoichiometry: 1.0
species: 554406

554437
type: Reaction
kinetic law: 821017
modifier: 821005
product: 820993
reactant: 820981
fast: false
reversible: false

820993
type: SpeciesReference
stoichiometry: 1.0
species: 554326

820981
type: SpeciesReference
stoichiometry: 1.0
species: 554296

554296
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 554287
name: IKBA

554450
type: Reaction
kinetic law: 821053
product: 821041
reactant: 821029
fast: false
reversible: false

821041
type: SpeciesReference
stoichiometry: 1.0
species: 554316

821029
type: SpeciesReference
stoichiometry: 1.0
species: 554326

554625
type: Parameter
constant: true
value: 2.0E-5

554635
type: Parameter
constant: true
value: 0.0025

554671
type: Parameter
constant: true
value: 2.0E-5
name: =k3*k9/k4

554575
type: Reaction
kinetic law: 821449
product: 821437
reactant: 821425
fast: false
reversible: false

821437
type: SpeciesReference
stoichiometry: 5.0
species: 554427

821425
type: SpeciesReference
stoichiometry: 1.0
species: 554406

554617
type: Parameter
constant: true
value: 0.1

554540
type: Reaction
kinetic law: 821341
product: 821329
reactant: 821317
reactant: 821305
fast: false
reversible: false

821329
type: SpeciesReference
stoichiometry: 1.0
species: 554396

821317
type: SpeciesReference
stoichiometry: 1.0
species: 554427

821305
type: SpeciesReference
stoichiometry: 1.0
species: 554416

554665
type: Parameter
constant: true
value: 3.397E-9
name: =kf15*k3*k9/k4/kf13

554673
type: Parameter
constant: true
value: 1.359E-4
name: =kf15/kf13

554586
type: Reaction
kinetic law: 821509
modifier: 821497
modifier: 821485
product: 821473
reactant: 821461
fast: false
reversible: false

821473
type: SpeciesReference
stoichiometry: 5.0
species: 554416

821461
type: SpeciesReference
stoichiometry: 1.0
species: 554366

554611
type: Parameter
constant: true
value: 0.0015

554645
type: Parameter
constant: true
value: 5.0E-7

554655
type: Parameter
constant: true
value: 5.0E-4

554649
type: Parameter
constant: true
value: 1.0E-4

554659
type: Parameter
constant: true
value: 0.01

554641
type: Parameter
constant: true
value: 4.0E-4

554651
type: Parameter
constant: true
value: 0.5

554603
type: Parameter
constant: true
value: 0.0025

554621
type: Parameter
constant: true
value: 0.1

554631
type: Parameter
constant: true
value: 18.4

554607
type: Parameter
constant: false
value: 2.5E-6

554529
type: Reaction
kinetic law: 821293
product: 821281
reactant: 821269
fast: false
reversible: false

821281
type: SpeciesReference
stoichiometry: 1.0
species: 554366

821269
type: SpeciesReference
stoichiometry: 5.0
species: 554396

554667
type: Parameter
constant: true
value: 1.359E-4
name: =kf15/kf13