MODEL7743444866
type: SBMLModel
parameter: 407528
curated: false
parameter: 407682
species: 407187
reaction: 407386
parameter: 407678
parameter: 407530
parameter: 407516
parameter: 407564
reaction: 407426
parameter: 407712
area units: area
parameter: 407580
parameter: 407552
species: 406925
parameter: 407634
species: 407092
reaction: 407276
species: 407063
parameter: 407670
species: 406978
parameter: 407586
compartment: 406894
parameter: 407624
parameter: 407654
species: 406988
parameter: 407700
reaction: 407362
parameter: 407526
species: 407178
parameter: 407578
parameter: 407608
parameter: 407642
species: 407102
parameter: 407676
parameter: 407562
parameter: 407548
parameter: 407706
reaction: 407373
parameter: 407534
parameter: 407612
reaction: 407401
parameter: 407550
parameter: 407632
reaction: 407439
species: 406915
parameter: 407570
parameter: 407600
notes: NFkB model M(14,25,33) This is a model of NFkB pathway functioning from hierarchy of models of decreasing complexity, created to demonstrate application of model reduction methods Radulescu O, Gorban A., Zinovyev A., Lilienbaum. A. Robust simplifications of multiscale models in The models are provided in CellDesigner v3.5 format. The name of the model M(x,y,z) should be x - number of species y - number of reactions 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 For additional information please contact 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.
reaction: 407322
parameter: 407584
parameter: 407618
parameter: 407652
species: 407073
parameter: 407638
species: 407140
species: 407083
parameter: 407576
parameter: 407606
parameter: 407640
parameter: 407674
reaction: 407225
parameter: 407592
reaction: 407348
parameter: 407704
parameter: 407610
species: 407130
parameter: 407544
parameter: 407668
reaction: 407236
parameter: 407598
parameter: 407666
time units: 754168
parameter: 407538
reaction: 407287
parameter: 407616
parameter: 407650
species: 407149
parameter: 407636

407528
type: Parameter
constant: true
value: 0.24

407682
type: Parameter
constant: true
value: 8.0E-13

407187
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406894
name: NFkB

406894
type: Compartment
constant: true
size: NaN
spatial dimensions: 3.0
name: nucleus

407386
type: Reaction
kinetic law: 830405
modifier: 830393
product: 830381
reactant: 830369
fast: false
reversible: false

406967
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: A20

406893
type: Compartment
constant: true
size: NaN
spatial dimensions: 3.0

830381
type: SpeciesReference
stoichiometry: 1.0
species: 406988

406988
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: IKKi

830369
type: SpeciesReference
stoichiometry: 1.0
species: 407073

407073
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: IKKa

407678
type: Parameter
constant: true
value: 0.055

407530
type: Parameter
constant: true
value: 0.1

407516
type: Parameter
constant: false
value: 0.0

407564
type: Parameter
constant: true
value: 0.5

407426
type: Reaction
kinetic law: 830537
product: 830525
reactant: 830513
reactant: 830501
fast: false
reversible: false

830525
type: SpeciesReference
stoichiometry: 1.0
species: 407168

407168
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: IKKa:IKB_alpha

830513
type: SpeciesReference
stoichiometry: 1.0
species: 407073

830501
type: SpeciesReference
stoichiometry: 1.0
species: 406925

406925
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: IkB_alpha

407712
type: Parameter
constant: true
value: 0.003
name: =kr58/kf58

407580
type: Parameter
constant: true
value: 1.0E-4

407552
type: Parameter
constant: true
value: 0.5

407634
type: Parameter
constant: true
value: 0.001

407092
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: sa20_degraded

407276
type: Reaction
kinetic law: 830033
product: 830021
reactant: 830009
fast: false
reversible: false

830021
type: SpeciesReference
stoichiometry: 1.0
species: 407073

830009
type: SpeciesReference
stoichiometry: 1.0
species: 407083

407083
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: IKKn

407063
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: sa19_degraded

407670
type: Parameter
constant: true
value: 4.8E-4

406978
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: sa444_degraded

407586
type: Parameter
constant: true
value: 5.0E-4

407624
type: Parameter
constant: true
value: 6.4E-5

407654
type: Parameter
constant: true
value: 0.055

407700
type: Parameter
constant: true
value: 0.0061
name: =kf68/kf64

407362
type: Reaction
kinetic law: 830309
product: 830297
reactant: 830285
fast: false
reversible: false

830297
type: SpeciesReference
stoichiometry: 1.0
species: 406978

830285
type: SpeciesReference
stoichiometry: 1.0
species: 406988

407526
type: Parameter
constant: true
value: 1.25E-4

407178
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406894
name: NFkB:IkB_alpha

407578
type: Parameter
constant: true
value: 10.0

407608
type: Parameter
constant: true
value: 6.0E-5

407642
type: Parameter
constant: true
value: 4.8E-4

407102
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406894
name: IKK

407676
type: Parameter
constant: true
value: 18.4

407562
type: Parameter
constant: true
value: 1.0E-4

407548
type: Parameter
constant: true
value: 0.0025

407706
type: Parameter
constant: true
value: 8.172E-10
name: =P0*k50*k60/k56

407373
type: Reaction
kinetic law: 830357
product: 830345
product: 830333
reactant: 830321
fast: false
reversible: false

830345
type: SpeciesReference
stoichiometry: 1.0
species: 406956

406956
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: mRNAA20

830333
type: SpeciesReference
stoichiometry: 1.0
species: 406967

830321
type: SpeciesReference
stoichiometry: 1.0
species: 406956

407534
type: Parameter
constant: true
value: 0.1

407612
type: Parameter
constant: true
value: 6.4E-5

407401
type: Reaction
kinetic law: 830441
product: 830429
reactant: 830417
fast: false
reversible: false

830429
type: SpeciesReference
stoichiometry: 1.0
species: 407083

830417
type: SpeciesReference
stoichiometry: 1.0
species: 407102

407550
type: Parameter
constant: true
value: 8.0E-5

407632
type: Parameter
constant: true
value: 0.003

407439
type: Reaction
kinetic law: 830573
product: 830561
reactant: 830549
fast: false
reversible: false

830561
type: SpeciesReference
stoichiometry: 5.0
species: 407187

830549
type: SpeciesReference
stoichiometry: 1.0
species: 407159

407159
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: NFkB

406915
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: sa13_degraded

407570
type: Parameter
constant: true
value: 0.0

407600
type: Parameter
constant: true
value: 0.6

407322
type: Reaction
kinetic law: 830177
product: 830165
reactant: 830153
fast: false
reversible: false

830165
type: SpeciesReference
stoichiometry: 1.0
species: 407073

830153
type: SpeciesReference
stoichiometry: 1.0
species: 407168

407584
type: Parameter
constant: true
value: 0.1

407618
type: Parameter
constant: true
value: 0.016

407652
type: Parameter
constant: true
value: 18.4

407638
type: Parameter
constant: true
value: 2.0E-4

407140
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.166
in compartment: 406893
name: NFkB:IkB_alpha

407576
type: Parameter
constant: true
value: 0.0

407606
type: Parameter
constant: true
value: 5.0E-5

407640
type: Parameter
constant: true
value: 0.62

407674
type: Parameter
constant: true
value: 0.055

407225
type: Reaction
kinetic law: 829865
product: 829853
reactant: 829841
fast: false
reversible: false

829853
type: SpeciesReference
stoichiometry: 1.0
species: 406936

406936
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: sa12_degraded

829841
type: SpeciesReference
stoichiometry: 1.0
species: 407130

407130
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: mRNAIKB_alpha

407592
type: Parameter
constant: true
value: 0.06

407348
type: Reaction
kinetic law: 830273
product: 830261
product: 830249
reactant: 830237
fast: false
reversible: false

830261
type: SpeciesReference
stoichiometry: 1.0
species: 407073

830249
type: SpeciesReference
stoichiometry: 1.0
species: 407159

830237
type: SpeciesReference
stoichiometry: 1.0
species: 407149

407149
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: NFkB:IKKa:Ikb_alpha

407704
type: Parameter
constant: true
value: 1.0E-10
name: dummy

407610
type: Parameter
constant: true
value: 1.3E-4

407544
type: Parameter
constant: true
value: 0.5

407668
type: Parameter
constant: true
value: 0.62

407236
type: Reaction
kinetic law: 829901
product: 829889
reactant: 829877
fast: false
reversible: false

829889
type: SpeciesReference
stoichiometry: 1.0
species: 406915

829877
type: SpeciesReference
stoichiometry: 1.0
species: 406925

407598
type: Parameter
constant: true
value: 0.06

407666
type: Parameter
constant: true
value: 4.8E-4

407538
type: Parameter
constant: true
value: 2.0E-5

407287
type: Reaction
kinetic law: 830069
product: 830057
reactant: 830045
fast: false
reversible: false

830057
type: SpeciesReference
stoichiometry: 1.0
species: 407159

830045
type: SpeciesReference
stoichiometry: 1.0
species: 407140

407616
type: Parameter
constant: true
value: 1.0E-4

407650
type: Parameter
constant: true
value: 0.055

407636
type: Parameter
constant: true
value: 2.0E-4

407198
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406894
name: IKB_alpha

407478
type: Reaction
kinetic law: 830693
product: 830681
reactant: 830669
fast: false
reversible: false

830681
type: SpeciesReference
stoichiometry: 1.0
species: 407111

407111
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: sa96_degraded

830669
type: SpeciesReference
stoichiometry: 1.0
species: 406956

407688
type: Parameter
constant: true
value: 2.0E-4

407574
type: Parameter
constant: true
value: 0.01

407604
type: Parameter
constant: true
value: 0.0041

407656
type: Parameter
constant: true
value: 0.0038

407672
type: Parameter
constant: true
value: 18.4

407412
type: Reaction
kinetic law: 830489
product: 830477
reactant: 830465
reactant: 830453
fast: false
reversible: false

830477
type: SpeciesReference
stoichiometry: 1.0
species: 407140

830465
type: SpeciesReference
stoichiometry: 1.0
species: 407159

830453
type: SpeciesReference
stoichiometry: 1.0
species: 406925

407590
type: Parameter
constant: true
value: 0.006

407520
type: Parameter
constant: true
value: 1.0E-5

407644
type: Parameter
constant: true
value: 0.62

407692
type: Parameter
constant: true
value: 6.66E-6
name: concentration of promoters

407702
type: Parameter
constant: true
value: 0.003
name: =kr66/kf66

407542
type: Parameter
constant: true
value: 0.0

407334
type: Reaction
kinetic law: 830225
product: 830213
reactant: 830201
reactant: 830189
fast: false
reversible: false

830213
type: SpeciesReference
stoichiometry: 1.0
species: 407149

830201
type: SpeciesReference
stoichiometry: 1.0
species: 407140

830189
type: SpeciesReference
stoichiometry: 1.0
species: 407073

407680
type: Parameter
constant: true
value: 0.0038

407708
type: Parameter
constant: true
value: 1.1957E-8
name: =P0*kr58*k62/kf58

407596
type: Parameter
constant: true
value: 0.02

407452
type: Reaction
kinetic law: 830609
product: 830597
reactant: 830585
fast: false
reversible: false

830597
type: SpeciesReference
stoichiometry: 1.0
species: 407140

830585
type: SpeciesReference
stoichiometry: 5.0
species: 407178

407664
type: Parameter
constant: true
value: 0.62

407710
type: Parameter
constant: true
value: 0.0061
name: =kf60/kf56

407698
type: Parameter
constant: true
value: 6.7E-8
name: =k39*k36*kr66*k70*P0/(k37*kf66*(k38+k39))

407536
type: Parameter
constant: true
value: 1.25E-4

407614
type: Parameter
constant: true
value: 10.0

407500
type: Reaction
kinetic law: 830765
product: 830753
reactant: 830741
fast: false
reversible: false

830753
type: SpeciesReference
stoichiometry: 5.0
species: 406904

406904
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406894
name: IkB_alpha

830741
type: SpeciesReference
stoichiometry: 1.0
species: 406925

407686
type: Parameter
constant: true
value: 8.0E-13

407572
type: Parameter
constant: true
value: 4.0E-4

407602
type: Parameter
constant: true
value: 0.01

407568
type: Parameter
constant: true
value: 5.0E-4

407558
type: Parameter
constant: true
value: 5.0E-7

407622
type: Parameter
constant: true
value: 5.0E-5

407556
type: Parameter
constant: true
value: 3.0E-4

407690
type: Parameter
constant: true
value: 2.0E-4

407524
type: Parameter
constant: true
value: 0.0015

407248
type: Reaction
kinetic law: 829949
product: 829937
product: 829925
reactant: 829913
fast: false
reversible: false

829937
type: SpeciesReference
stoichiometry: 1.0
species: 407130

829925
type: SpeciesReference
stoichiometry: 1.0
species: 406925

829913
type: SpeciesReference
stoichiometry: 1.0
species: 407130

406946
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406894
name: A20

407540
type: Parameter
constant: true
value: 0.5

407594
type: Parameter
constant: true
value: 5.0E-4

407560
type: Parameter
constant: true
value: 0.0

407299
type: Reaction
kinetic law: 830105
product: 830093
reactant: 830081
fast: false
reversible: false

830093
type: SpeciesReference
stoichiometry: 1.0
species: 407063

830081
type: SpeciesReference
stoichiometry: 1.0
species: 407083

407662
type: Parameter
constant: true
value: 8.0E-13

407628
type: Parameter
constant: true
value: 1.0E-4

407546
type: Parameter
constant: true
value: 0.0

407261
type: Reaction
kinetic law: 829997
modifier: 829985
product: 829973
reactant: 829961
fast: false
reversible: false

829973
type: SpeciesReference
stoichiometry: 1.0
species: 406956

829961
type: SpeciesReference
stoichiometry: 1.0
species: 406946

407648
type: Parameter
constant: true
value: 18.4

407696
type: Parameter
constant: true
value: 2.2925E-7
name: =k36*k39*P0*k34*kf68/(k37*kf64*(k38+k39))

407513
type: Event
event assignment: 830801
delay: 830789
trigger: 830777
use values from trigger time: true
name: signal

830777
type: Trigger
persistant: true
initial value: true

407684
type: Parameter
constant: true
value: 0.0038

407532
type: Parameter
constant: true
value: 1.2

407518
type: Parameter
constant: true
value: 1.25E-4

407566
type: Parameter
constant: true
value: 0.001

407630
type: Parameter
constant: true
value: 0.025

407489
type: Reaction
kinetic law: 830729
product: 830717
reactant: 830705
fast: false
reversible: false

830717
type: SpeciesReference
stoichiometry: 1.0
species: 407121

407121
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 406893
name: sa97_degraded

830705
type: SpeciesReference
stoichiometry: 1.0
species: 406967

407714
type: Parameter
constant: true
value: 1.0E-10
name: dummy

407582
type: Parameter
constant: true
value: 5.0E-4

407620
type: Parameter
constant: true
value: 0.0053

407554
type: Parameter
constant: true
value: 4.0E-4

407522
type: Parameter
constant: true
value: 0.1

407464
type: Reaction
kinetic law: 830657
product: 830645
reactant: 830633
reactant: 830621
fast: false
reversible: false

830645
type: SpeciesReference
stoichiometry: 1.0
species: 407178

830633
type: SpeciesReference
stoichiometry: 1.0
species: 406904

830621
type: SpeciesReference
stoichiometry: 1.0
species: 407187

407658
type: Parameter
constant: true
value: 8.0E-13

407207
type: Reaction
kinetic law: 829829
modifier: 829817
modifier: 829805
product: 829793
reactant: 829781
fast: false
reversible: false

829793
type: SpeciesReference
stoichiometry: 1.0
species: 407130

829781
type: SpeciesReference
stoichiometry: 1.0
species: 407198

407311
type: Reaction
kinetic law: 830141
product: 830129
reactant: 830117
fast: false
reversible: false

830129
type: SpeciesReference
stoichiometry: 1.0
species: 407092

830117
type: SpeciesReference
stoichiometry: 1.0
species: 407073

407588
type: Parameter
constant: true
value: 0.1

407626
type: Parameter
constant: true
value: 10.0

407660
type: Parameter
constant: true
value: 0.0038

407646
type: Parameter
constant: true
value: 4.8E-4

407694
type: Parameter
constant: true
value: 7.07E-5
name: =k43*k45*P0 / k46