MODEL1008110000
type: SBMLModel
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parameter: 058554
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species: 058357
units def: 867736
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reaction: 058460
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is described by: http://identifiers.org/pubmed/16166517
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notes: This is the model described in the article: Stimulus specificity of gene expression programs determined by temporal control of IKK activity. by Werner SL, Barken D, Hoffmann A. Science. 2005 Sep 16;309(5742):1857-61; PMID: 16166517 , DOI= 10.1126/science.1113319 Abstract: A small number of mammalian signaling pathways mediate a myriad of distinct physiological responses to diverse cellular stimuli. Temporal control of the signaling module that contains IkappaB kinase (IKK), its substrate inhibitor of NF-kappaB (IkappaB), and the key inflammatory transcription factor NF-kappaB can allow for selective gene activation. We have demonstrated that different inflammatory stimuli induce distinct IKK profiles, and we examined the underlying molecular mechanisms. Although tumor necrosis factor-alpha (TNFalpha)-induced IKK activity was rapidly attenuated by negative feedback, lipopolysaccharide (LPS) signaling and LPS-specific gene expression programs were dependent on a cytokine-mediated positive feedback mechanism. Thus, the distinct biological responses to LPS and TNFalpha depend on signaling pathway-specific mechanisms that regulate the temporal profile of IKK activity. The model was implemented according to the description in the supplemental materials and by comparison to the matlab files provided by Prof. Hoffmann. It includes a delay for the induced transcription of IκBε mRNA. For the IKK input one of the randomly generated profiles was used. In its current form the model could not reproduce the time courses given in the article, as first the IKK activity profiles cannot easily be described by the same fitting functions in SBML and second the time delay limits simulation to tools, for which the current converters do not provide full SBML export. Originally created by libAntimony v1.4 (using libSBML 3.4.1) This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels…
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fast: false
reversible: false

870063
type: SpeciesReference
stoichiometry: 1.0
species: 058349

870051
type: SpeciesReference
stoichiometry: 1.0
species: 058348

870039
type: SpeciesReference
stoichiometry: 1.0
species: 058377

058579
type: Parameter
constant: true
value: 6.0E-5

058411
type: Reaction
kinetic law: 869047
product: 869035
product: 869023
reactant: 869011
fast: false
reversible: false

869035
type: SpeciesReference
stoichiometry: 1.0
species: 058349

869023
type: SpeciesReference
stoichiometry: 1.0
species: 058376

869011
type: SpeciesReference
stoichiometry: 1.0
species: 058377

058544
type: Parameter
constant: true
value: 30.0

058432
type: Reaction
kinetic law: 869666
reactant: 869654
fast: false
reversible: false

869654
type: SpeciesReference
stoichiometry: 1.0
species: 058353

058387
type: Reaction
kinetic law: 868115
product: 868102
reactant: 868090
reactant: 868077
fast: false
reversible: false

868102
type: SpeciesReference
stoichiometry: 1.0
species: 058359

868090
type: SpeciesReference
stoichiometry: 1.0
species: 058349

868077
type: SpeciesReference
stoichiometry: 1.0
species: 058358

058467
type: Reaction
kinetic law: 870524
product: 870512
fast: false
reversible: false

870512
type: SpeciesReference
stoichiometry: 1.0
species: 058361

058450
type: Reaction
kinetic law: 870185
product: 870173
reactant: 870161
fast: false
reversible: false

870173
type: SpeciesReference
stoichiometry: 1.0
species: 058351

870161
type: SpeciesReference
stoichiometry: 1.0
species: 058374

058569
type: Parameter
constant: true
value: 6.0E-5

058392
type: Reaction
kinetic law: 868318
product: 868305
reactant: 868292
reactant: 868279
fast: false
reversible: false

868305
type: SpeciesReference
stoichiometry: 1.0
species: 058377

868292
type: SpeciesReference
stoichiometry: 1.0
species: 058349

868279
type: SpeciesReference
stoichiometry: 1.0
species: 058376

058619
type: Parameter
constant: true
value: 0.2448

058447
type: Reaction
kinetic law: 870112
product: 870099
reactant: 870087
fast: false
reversible: false

870099
type: SpeciesReference
stoichiometry: 1.0
species: 058351

870087
type: SpeciesReference
stoichiometry: 1.0
species: 058357

058624
type: Parameter
constant: true
value: 0.0168

058465
type: Reaction
kinetic law: 870476
modifier: 870464
product: 870452
fast: false
reversible: false

870452
type: SpeciesReference
stoichiometry: 1.0
species: 058369

058555
type: Parameter
constant: true
value: 30.0

058440
type: Reaction
kinetic law: 869859
product: 869847
reactant: 869835
fast: false
reversible: false

869847
type: SpeciesReference
stoichiometry: 1.0
species: 058349

869835
type: SpeciesReference
stoichiometry: 1.0
species: 058364

058603
type: Parameter
constant: true
value: 6.0E-5

058406
type: Reaction
kinetic law: 868853
product: 868841
product: 868828
reactant: 868816
fast: false
reversible: false

868841
type: SpeciesReference
stoichiometry: 1.0
species: 058349

868828
type: SpeciesReference
stoichiometry: 1.0
species: 058358

868816
type: SpeciesReference
stoichiometry: 1.0
species: 058359

058388
type: Reaction
kinetic law: 868164
product: 868152
reactant: 868140
reactant: 868127
fast: false
reversible: false

868152
type: SpeciesReference
stoichiometry: 1.0
species: 058359

868140
type: SpeciesReference
stoichiometry: 1.0
species: 058348

868127
type: SpeciesReference
stoichiometry: 1.0
species: 058356

058408
type: Reaction
kinetic law: 868949
product: 868937
product: 868925
reactant: 868913
fast: false
reversible: false

868937
type: SpeciesReference
stoichiometry: 1.0
species: 058349

868925
type: SpeciesReference
stoichiometry: 1.0
species: 058367

868913
type: SpeciesReference
stoichiometry: 1.0
species: 058368

058572
type: Parameter
constant: true
value: 6.0E-5

058538
type: Parameter
constant: true
value: 0.11

058437
type: Reaction
kinetic law: 869787
product: 869775
reactant: 869762
fast: false
reversible: false

869775
type: SpeciesReference
stoichiometry: 1.0
species: 058349

869762
type: SpeciesReference
stoichiometry: 1.0
species: 058356

058552
type: Parameter
constant: true
value: 11.1

058625
type: Parameter
constant: true
value: 0.0168

058423
type: Reaction
kinetic law: 869422
product: 869410
reactant: 869398
fast: false
reversible: false

869410
type: SpeciesReference
stoichiometry: 1.0
species: 058356

869398
type: SpeciesReference
stoichiometry: 1.0
species: 058357

058383
type: Reaction
kinetic law: 867965
product: 867953
reactant: 867941
reactant: 867929
fast: false
reversible: false

867953
type: SpeciesReference
stoichiometry: 1.0
species: 058364

867941
type: SpeciesReference
stoichiometry: 1.0
species: 058349

867929
type: SpeciesReference
stoichiometry: 1.0
species: 058362

058594
type: Parameter
constant: true
value: 0.12

058441
type: Reaction
kinetic law: 869895
product: 869883
reactant: 869871
fast: false
reversible: false

869883
type: SpeciesReference
stoichiometry: 1.0
species: 058348

869871
type: SpeciesReference
stoichiometry: 1.0
species: 058376

058407
type: Reaction
kinetic law: 868901
product: 868889
product: 868877
reactant: 868865
fast: false
reversible: false

868889
type: SpeciesReference
stoichiometry: 1.0
species: 058356

868877
type: SpeciesReference
stoichiometry: 1.0
species: 058348

868865
type: SpeciesReference
stoichiometry: 1.0
species: 058359

058614
type: Parameter
constant: true
value: 0.12

058399
type: Reaction
kinetic law: 868608
product: 868596
product: 868584
reactant: 868572
fast: false
reversible: false

868596
type: SpeciesReference
stoichiometry: 1.0
species: 058349

868584
type: SpeciesReference
stoichiometry: 1.0
species: 058353

868572
type: SpeciesReference
stoichiometry: 1.0
species: 058356

058419
type: Reaction
kinetic law: 869313
product: 869301
reactant: 869289
fast: false
reversible: false

869301
type: SpeciesReference
stoichiometry: 1.0
species: 058362

869289
type: SpeciesReference
stoichiometry: 1.0
species: 058363

058549
type: Parameter
constant: true
value: 30.0

058580
type: Parameter
constant: true
value: 0.012

058533
type: Parameter
constant: false
value: NaN

058466
type: Reaction
kinetic law: 870500
product: 870488
fast: false
reversible: false

870488
type: SpeciesReference
stoichiometry: 1.0
species: 058352

058563
type: Parameter
constant: true
value: 6.0E-5

058434
type: Reaction
kinetic law: 869690
reactant: 869678
fast: false
reversible: false

869678
type: SpeciesReference
stoichiometry: 1.0
species: 058362

058611
type: Parameter
constant: true
value: 6.0E-5

058384
type: Reaction
kinetic law: 868014
product: 868002
reactant: 867990
reactant: 867978
fast: false
reversible: false

868002
type: SpeciesReference
stoichiometry: 1.0
species: 058376

867990
type: SpeciesReference
stoichiometry: 1.0
species: 058348

867978
type: SpeciesReference
stoichiometry: 1.0
species: 058371

058389
type: Reaction
kinetic law: 868214
product: 868202
reactant: 868189
reactant: 868177
fast: false
reversible: false

868202
type: SpeciesReference
stoichiometry: 1.0
species: 058368

868189
type: SpeciesReference
stoichiometry: 1.0
species: 058349

868177
type: SpeciesReference
stoichiometry: 1.0
species: 058367

058452
type: Reaction
kinetic law: 870234
reactant: 870221
fast: false
reversible: false

870221
type: SpeciesReference
stoichiometry: 1.0
species: 058363

058418
type: Reaction
kinetic law: 869277
product: 869265
reactant: 869253
fast: false
reversible: false

869265
type: SpeciesReference
stoichiometry: 1.0
species: 058353

869253
type: SpeciesReference
stoichiometry: 1.0
species: 058354

058578
type: Parameter
constant: true
value: 6.0E-5

058414
type: Reaction
kinetic law: 869192
product: 869180
product: 869168
reactant: 869156
fast: false
reversible: false

869180
type: SpeciesReference
stoichiometry: 1.0
species: 058351

869168
type: SpeciesReference
stoichiometry: 1.0
species: 058363

869156
type: SpeciesReference
stoichiometry: 1.0
species: 058366

058530
type: Parameter
constant: true
value: 15.0

058449
type: Reaction
kinetic law: 870149
product: 870137
reactant: 870125
fast: false
reversible: false

870137
type: SpeciesReference
stoichiometry: 1.0
species: 058351

870125
type: SpeciesReference
stoichiometry: 1.0
species: 058366

058585
type: Parameter
constant: true
value: 0.828

058431
type: Reaction
kinetic law: 869642
product: 869630
reactant: 869618
fast: false
reversible: false

869630
type: SpeciesReference
stoichiometry: 1.0
species: 058351

869618
type: SpeciesReference
stoichiometry: 1.0
species: 058349

058630
type: Parameter
constant: true
value: 4.272E-5

058564
type: Parameter
constant: true
value: 0.105

058402
type: Reaction
kinetic law: 868704
product: 868692
product: 868680
reactant: 868668
fast: false
reversible: false

868692
type: SpeciesReference
stoichiometry: 1.0
species: 058349

868680
type: SpeciesReference
stoichiometry: 1.0
species: 058362

868668
type: SpeciesReference
stoichiometry: 1.0
species: 058364