MODEL7743576806
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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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is described by: http://identifiers.org/pubmed/18854041

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constant: true
value: 1.1957E-8
name: =P0*kr58*k62/kf58

metaid_0000039
type: Parameter
constant: true
value: 0.1

metaid_0000079
type: Parameter
constant: true
value: 0.62

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

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

metaid_0000012
type: Parameter
constant: true
value: 0.1

metaid_0000069
type: Parameter
constant: true
value: 18.4

metaid_0000043
type: Parameter
constant: true
value: 0.02

metaid_0000009
type: Parameter
constant: true
value: 0.24

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

metaid_0000162
type: Reaction
kinetic law: 851020
product: 851008
reactant: 850996
reactant: 850984
fast: false
reversible: false

851008
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000133

850996
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000120

850984
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000112

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

850456
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000120

850444
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000121

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

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

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

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

metaid_0000047
type: Parameter
constant: true
value: 0.0041

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

metaid_0000166
type: Reaction
kinetic law: 851176
product: 851164
reactant: 851152
fast: false
reversible: false

851164
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000124

851152
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000115

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

metaid_0000063
type: Parameter
constant: true
value: 2.0E-4

metaid_0000060
type: Parameter
constant: true
value: 0.025

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

metaid_0000027
type: Parameter
constant: true
value: 0.5

metaid_0000067
type: Parameter
constant: true
value: 0.62

metaid_0000041
type: Parameter
constant: true
value: 0.06

metaid_0000165
type: Reaction
kinetic law: 851140
product: 851128
reactant: 851116
reactant: 851104
fast: false
reversible: false

851128
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000134

851116
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000105

851104
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000135

metaid_0000062
type: Parameter
constant: true
value: 0.001

metaid_0000150
type: Reaction
kinetic law: 850504
product: 850492
reactant: 850480
fast: false
reversible: false

850492
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000132

850480
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000130

metaid_0000096
type: Parameter
constant: true
value: 0.003
name: =kr66/kf66

metaid_0000045
type: Parameter
constant: true
value: 0.6

metaid_0000169
type: Reaction
kinetic law: 851284
product: 851272
reactant: 851260
fast: false
reversible: false

851272
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000126

851260
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000132

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

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

metaid_0000040
type: Parameter
constant: true
value: 0.006

metaid_0000006
type: Parameter
constant: true
value: 0.1

metaid_0000154
type: Reaction
kinetic law: 850660
product: 850648
reactant: 850636
reactant: 850624
fast: false
reversible: false

850648
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000131

850636
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000130

850624
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000120

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

851369
type: Trigger
persistant: true
initial value: true