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metaid_0000018
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metaid_0000100
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metaid_0000162
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reversible: false
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metaid_0000099
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850120
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850324
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850060
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metaid_0000128
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851116
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metaid_0000117
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metaid_0000056
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metaid_0000096
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850552
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metaid_0000053
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850276
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850372
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850936
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metaid_0000014
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MODEL7743576806
parameter: metaid_0000051
species: metaid_0000116
reaction: metaid_0000139
parameter: metaid_0000044
notes: Radulescu2008 - NF-κB hierarchy ℳ(16,34,46) This is a model of NF-κB pathway functioning from hierarchy of models of decreasing complexity, created to demonstrate application of model reduction methods proposed in the associated publication. 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. This model is described in the article: Robust simplifications of multiscale biochemical networks. Radulescu O, Gorban AN, Zinovyev A, Lilienbaum A. BMC Syst Biol 2008 Oct; 2(1):86 Abstract: BACKGROUND: Cellular processes such as metabolism, decision making in development and differentiation, signalling, etc., can be modeled as large networks of biochemical reactions. In order to understand the functioning of these systems, there is a strong need for general model reduction techniques allowing to simplify models without loosing their main properties. In systems biology we also need to compare models or to couple them as parts of larger models. In these situations reduction to a common level of complexity is needed. RESULTS: We propose a systematic treatment of model reduction of multiscale biochemical networks. First, we consider linear kinetic models, which appear as "pseudo-monomolecular" subsystems of multiscale nonlinear reaction networks. For such linear models, we propose a reduction algorithm which is based on a generalized theory of the limiting step that we have developed in 1. Second, for non-linear systems we develop an algorithm based on dominant solutions of quasi-stationarity equations. For oscillating systems, quasi-stationarity and averaging are combined to eliminate time scales much faster and much slower than the period…
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type: SBMLModel
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is described by: http://identifiers.org/pubmed/18854041
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850684
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851008
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851272
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850492
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metaid_0000119
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850192
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850564
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type: Species

850672
stoichiometry: 1.0
species: metaid_0000131
type: SpeciesReference

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

metaid_0000108
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000103
name: p50
type: Species

851068
stoichiometry: 5.0
species: metaid_0000134
type: SpeciesReference

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

850048
stoichiometry: 1.0
species: metaid_0000137
type: SpeciesReference

metaid_0000084
constant: true
value: 0.055
type: Parameter

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

850852
stoichiometry: 1.0
species: metaid_0000120
type: SpeciesReference

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

metaid_0000046
constant: true
value: 0.01
type: Parameter

metaid_0000148
kinetic law: 850432
modifier: 850420
product: 850408
reactant: 850396
fast: false
reversible: false
type: Reaction

metaid_0000158
kinetic law: 850840
product: 850828
reactant: 850816
reactant: 850804
fast: false
reversible: false
type: Reaction

850396
stoichiometry: 1.0
species: metaid_0000114
type: SpeciesReference

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

metaid_0000161
kinetic law: 850972
product: 850960
reactant: 850948
reactant: 850936
fast: false
reversible: false
type: Reaction

metaid_0000085
constant: true
value: 0.0038
type: Parameter

metaid_0000075
constant: true
value: 0.0038
type: Parameter

metaid_0000171
kinetic law: 851356
product: 851344
reactant: 851332
fast: false
reversible: false
type: Reaction

metaid_0000045
constant: true
value: 0.6
type: Parameter

metaid_0000170
kinetic law: 851320
product: 851308
reactant: 851296
fast: false
reversible: false
type: Reaction

851308
stoichiometry: 1.0
species: metaid_0000127
type: SpeciesReference

metaid_0000149
kinetic law: 850468
product: 850456
reactant: 850444
fast: false
reversible: false
type: Reaction

850180
stoichiometry: 1.0
species: metaid_0000109
type: SpeciesReference

metaid_0000159
kinetic law: 850888
modifier: 850876
product: 850864
reactant: 850852
fast: false
reversible: false
type: Reaction

851224
stoichiometry: 1.0
species: metaid_0000112
type: SpeciesReference

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

metaid_0000160
kinetic law: 850924
product: 850912
reactant: 850900
fast: false
reversible: false
type: Reaction

metaid_0000003
constant: false
value: 0.0
type: Parameter

850648
stoichiometry: 1.0
species: metaid_0000131
type: SpeciesReference

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

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

850636
stoichiometry: 1.0
species: metaid_0000130
type: SpeciesReference

metaid_0000146
kinetic law: 850336
product: 850324
reactant: 850312
fast: false
reversible: false
type: Reaction

850348
stoichiometry: 1.0
species: metaid_0000129
type: SpeciesReference

850444
stoichiometry: 1.0
species: metaid_0000121
type: SpeciesReference

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

metaid_0000034
constant: true
value: 10.0
type: Parameter

851188
stoichiometry: 1.0
species: metaid_0000116
type: SpeciesReference

850156
stoichiometry: 1.0
species: metaid_0000109
type: SpeciesReference

metaid_0000087
constant: true
value: 0.0038
type: Parameter

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

metaid_0000073
constant: true
value: 0.0038
type: Parameter

851236
stoichiometry: 5.0
species: metaid_0000105
type: SpeciesReference

metaid_0000147
kinetic law: 850384
product: 850372
product: 850360
reactant: 850348
fast: false
reversible: false
type: Reaction

metaid_0000047
constant: true
value: 0.0041
type: Parameter

metaid_0000033
constant: true
value: 0.0
type: Parameter

metaid_0000060
constant: true
value: 0.025
type: Parameter

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

metaid_0000172
event assignment: 851393
delay: 851381
trigger: 851369
use values from trigger time: true
name: signal
type: Event

850588
stoichiometry: 1.0
species: metaid_0000133
type: SpeciesReference

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