MODEL8478881246
type: SBMLModel
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notes: This SBML file is a translation of a MatLab model utilized in the following paper. It describes the interplay of IkB and P100 negative feedback to control the cellular localization of the NFkB transcription factor in response to activation of IkB Kinase 1 (IKK1) and IkB Kinase 2 (IKK2). Soumen Basak, Ha Na Kim, Jeffrey D. Kearns, Vinay Tergaonkar, Ellen O'Dea, Shannon L. Werner, Chris A. Benedict, Carl F. Ware, Gourishankar Ghosh, Inder M. Verma, Alexander Hoffmann. "A Fourth IkB Protein in the NFkB Signaling Module." Cell (2007) Questions concerning the paper should be addressed to the corresponding author. Alexander Hoffmann (ahoffmann@ucsd.edu) Technical questions concerning the implementation of the model within SBML should be addressed to Jeff Kearns (jkearns@ucsd.edu) - Introduction: The original model was written and simulated within MathWorks MatLab 2006a using the ode15s (stiff/NDF) solver. It is highly recommended that those wanting to model this system use the MatLab version which we will freely provide upon request. As always, simulation results vary according to the numerical solver used. In addition, there are also shortcomings in the Stimulation Phase of the model (listed below) that maybe resolved with future versions of SBML. - SBML Generation : Translation to SBML Level 2.1 was performed via reconstruction of the model within MathWorks SimBiology Desktop (version 2.1) followed by an Export to SBML. - Running the model : Simulations require two sequential runs of the model. It is recommended that you generate a script to pass the final component concentrations from the first run into the initial concentrations of the second. 1. Equilibrium Phase. - In both phases, total NFkB (0.125 micromole), IKK1 (0.1 micromole), and IKK2 (0.1 micromole) protein remains constant. These exist in free and bound forms. - Synthesis and degradation reactions are included for IkBa, IkBb, IkBe, and P100 mRNA and protein. - Equilibrium state nuclear NFkB (NFkBn) levels fo…
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060078
type: LocalParameter
units: 059567
value: 11.1
name: a_c_2ani

060054
type: SpeciesReference
stoichiometry: 1.0
species: 873474

060042
type: SpeciesReference
stoichiometry: 1.0
species: 873514

060030
type: SpeciesReference
stoichiometry: 1.0
species: 873434

873994
type: Reaction
kinetic law: 059687
product: 059675
fast: false
reversible: false
name: txn_a

059700
type: LocalParameter
units: 059507
value: 1.1848E-4
name: rsu_a

059675
type: SpeciesReference
stoichiometry: 1.0
species: 873354

874993
type: Reaction
kinetic law: 063289
product: 063277
reactant: 063265
reactant: 063253
fast: false
reversible: true
name: int_pn

063313
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_c_pn

063301
type: LocalParameter
units: 059567
value: 30.0
name: a_c_pn

063277
type: SpeciesReference
stoichiometry: 1.0
species: 873914

063265
type: SpeciesReference
stoichiometry: 1.0
species: 873494

063253
type: SpeciesReference
stoichiometry: 1.0
species: 873954

874014
type: Reaction
kinetic law: 059724
reactant: 059712
fast: false
reversible: false
name: mdeg_a

059736
type: LocalParameter
units: 059543
value: 0.0252
name: rd_a

059712
type: SpeciesReference
stoichiometry: 1.0
species: 873354

874234
type: Reaction
kinetic law: 060368
product: 060356
reactant: 060344
fast: false
reversible: false
name: deg_ai

060380
type: LocalParameter
units: 059543
value: 0.0018
name: pd_c_2ai

060356
type: SpeciesReference
stoichiometry: 1.0
species: 873514

060344
type: SpeciesReference
stoichiometry: 1.0
species: 873414

874954
type: Reaction
kinetic law: 063071
product: 063059
reactant: 063047
reactant: 063035
fast: false
reversible: true
name: int_2pqn

063095
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_c_2pqn

063083
type: LocalParameter
units: 059567
value: 30.0
name: a_c_2pqn

063059
type: SpeciesReference
stoichiometry: 1.0
species: 873874

873874
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 059482
initial concentration: NaN
initial amount: 0.0
in compartment: 873334
name: P100IKK1NFkB

063047
type: SpeciesReference
stoichiometry: 1.0
species: 873494

063035
type: SpeciesReference
stoichiometry: 1.0
species: 873854

874794
type: Reaction
kinetic law: 062236
product: 062223
reactant: 062211
fast: false
reversible: false
name: deg_en_n

062248
type: LocalParameter
units: 059543
value: 6.0E-5
name: pd_n_2en

062223
type: SpeciesReference
stoichiometry: 1.0
species: 873534

062211
type: SpeciesReference
stoichiometry: 1.0
species: 873794

874694
type: Reaction
kinetic law: 061647
product: 061635
fast: false
reversible: false
name: txn_e

061659
type: LocalParameter
units: 059507
value: 6.1E-6
name: rsu_e

061635
type: SpeciesReference
stoichiometry: 1.0
species: 873714

873714
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 059482
initial concentration: NaN
initial amount: 0.0
in compartment: 873334
name: IkBet

059639
type: Parameter
constant: true
value: 0.01
name: ikk1_multiplier

874074
type: Reaction
kinetic law: 059920
product: 059907
reactant: 059895
reactant: 059882
fast: false
reversible: true
name: int_an

059944
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_c_an

059932
type: LocalParameter
units: 059567
value: 30.0
name: a_c_an

059907
type: SpeciesReference
stoichiometry: 1.0
species: 873434

059895
type: SpeciesReference
stoichiometry: 1.0
species: 873494

059882
type: SpeciesReference
stoichiometry: 1.0
species: 873374

875053
type: Reaction
kinetic law: 063470
reactant: 063458
fast: false
reversible: false
name: mdeg_p

063482
type: LocalParameter
units: 059543
value: 0.00168
name: rd_p

063458
type: SpeciesReference
stoichiometry: 1.0
species: 873974

874873
type: Reaction
kinetic law: 062611
modifier: 062599
product: 062587
fast: false
reversible: false
name: itxn_p

062623
type: LocalParameter
units: 059603
value: 1.6
name: rsr_pn

062587
type: SpeciesReference
stoichiometry: 1.0
species: 873974

874773
type: Reaction
kinetic law: 062094
product: 062081
reactant: 062069
reactant: 062057
fast: false
reversible: true
name: int_2ein

062120
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_c_2ein

062107
type: LocalParameter
units: 059567
value: 30.0
name: a_c_2ein

062081
type: SpeciesReference
stoichiometry: 1.0
species: 873814

062069
type: SpeciesReference
stoichiometry: 1.0
species: 873494

062057
type: SpeciesReference
stoichiometry: 1.0
species: 873834

874134
type: Reaction
kinetic law: 060138
product: 060126
reactant: 060114
reactant: 060102
fast: false
reversible: true
name: int_2ain

060162
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_c_2ain

060150
type: LocalParameter
units: 059567
value: 30.0
name: a_c_2ain

060126
type: SpeciesReference
stoichiometry: 1.0
species: 873474

060114
type: SpeciesReference
stoichiometry: 1.0
species: 873494

060102
type: SpeciesReference
stoichiometry: 1.0
species: 873414

874034
type: Reaction
kinetic law: 059785
product: 059772
product: 059760
reactant: 059748
fast: false
reversible: false
name: tsl_a

059797
type: LocalParameter
units: 059543
value: 0.02448
name: ps_c_a

059772
type: SpeciesReference
stoichiometry: 1.0
species: 873374

059760
type: SpeciesReference
stoichiometry: 1.0
species: 873354

059748
type: SpeciesReference
stoichiometry: 1.0
species: 873354

874514
type: Reaction
kinetic law: 061109
reactant: 061097
fast: false
reversible: false
name: deg_b

061121
type: LocalParameter
units: 059543
value: 0.18
name: pd_c_b

061097
type: SpeciesReference
stoichiometry: 1.0
species: 873674

874354
type: Reaction
kinetic law: 060707
modifier: 060695
product: 060683
fast: false
reversible: false
name: itxn_b

060720
type: LocalParameter
units: 059603
value: 0.02
name: rsr_bn

060683
type: SpeciesReference
stoichiometry: 1.0
species: 873694

874254
type: Reaction
kinetic law: 060430
product: 060417
product: 060405
reactant: 060392
fast: false
reversible: false
name: deg_ain

060442
type: LocalParameter
units: 059543
value: 0.36
name: pd_c_3ain

060417
type: SpeciesReference
stoichiometry: 1.0
species: 873494

060405
type: SpeciesReference
stoichiometry: 1.0
species: 873514

060392
type: SpeciesReference
stoichiometry: 1.0
species: 873474

874494
type: Reaction
kinetic law: 061072
reactant: 061060
fast: false
reversible: false
name: deg_b_n

061085
type: LocalParameter
units: 059543
value: 0.18
name: pd_n_b

061060
type: SpeciesReference
stoichiometry: 1.0
species: 873654

873574
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 059482
initial concentration: NaN
initial amount: 0.0
in compartment: 873334
name: IkBbIKK

874713
type: Reaction
kinetic law: 061683
reactant: 061671
fast: false
reversible: false
name: mdeg_e

061695
type: LocalParameter
units: 059543
value: 0.00672
name: rd_e

061671
type: SpeciesReference
stoichiometry: 1.0
species: 873714

874893
type: Reaction
kinetic law: 062719
product: 062707
reactant: 062695
fast: false
reversible: true
name: loc_p

062744
type: LocalParameter
units: 059543
value: 0.012
name: ex_p

062732
type: LocalParameter
units: 059543
value: 0.045
name: in_p

062707
type: SpeciesReference
stoichiometry: 1.0
species: 873934

062695
type: SpeciesReference
stoichiometry: 1.0
species: 873954

874374
type: Reaction
kinetic law: 060756
product: 060744
reactant: 060732
fast: false
reversible: true
name: loc_bn

060780
type: LocalParameter
units: 059543
value: 0.414
name: ex_2bn

060768
type: LocalParameter
units: 059543
value: 0.0276
name: in_2bn

060744
type: SpeciesReference
stoichiometry: 1.0
species: 873614

873614
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 059482
initial concentration: NaN
initial amount: 0.0
in compartment: 873334
name: IkBbNFkBn

060732
type: SpeciesReference
stoichiometry: 1.0
species: 873634

874894
type: Reaction
kinetic law: 062793
product: 062781
product: 062769
reactant: 062757
fast: false
reversible: false
name: deg_pqn

062806
type: LocalParameter
units: 059543
value: 0.18
name: pd_c_3pqn

062781
type: SpeciesReference
stoichiometry: 1.0
species: 873554

062769
type: SpeciesReference
stoichiometry: 1.0
species: 873494

062757
type: SpeciesReference
stoichiometry: 1.0
species: 873874

874733
type: Reaction
kinetic law: 061803
product: 061791
reactant: 061779
reactant: 061767
fast: false
reversible: true
name: int_ei

061828
type: LocalParameter
units: 059543
value: 0.105
name: d_c_ei

061815
type: LocalParameter
units: 059567
value: 0.54
name: a_c_ei

061791
type: SpeciesReference
stoichiometry: 1.0
species: 873834

061779
type: SpeciesReference
stoichiometry: 1.0
species: 873514

061767
type: SpeciesReference
stoichiometry: 1.0
species: 873734

874973
type: Reaction
kinetic law: 063143
product: 063131
reactant: 063119
reactant: 063107
fast: false
reversible: true
name: int_2pnq

063167
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_c_2pnq

063155
type: LocalParameter
units: 059567
value: 4.2
name: a_c_2pnq

063131
type: SpeciesReference
stoichiometry: 1.0
species: 873874

063119
type: SpeciesReference
stoichiometry: 1.0
species: 873554

063107
type: SpeciesReference
stoichiometry: 1.0
species: 873914

059651
type: Parameter
constant: true
value: 0.001
name: ikk2_multiplier

874554
type: Reaction
kinetic law: 061242
product: 061230
reactant: 061218
reactant: 061206
fast: false
reversible: true
name: int_2bni

061266
type: LocalParameter
units: 059543
value: 0.105
name: d_c_2bni

061254
type: LocalParameter
units: 059567
value: 2.88
name: a_c_2bni

061230
type: SpeciesReference
stoichiometry: 1.0
species: 873594

061218
type: SpeciesReference
stoichiometry: 1.0
species: 873514

061206
type: SpeciesReference
stoichiometry: 1.0
species: 873634

874774
type: Reaction
kinetic law: 062146
reactant: 062133
fast: false
reversible: false
name: deg_e

062159
type: LocalParameter
units: 059543
value: 0.18
name: pd_c_e

062133
type: SpeciesReference
stoichiometry: 1.0
species: 873734

874454
type: Reaction
kinetic law: 060988
product: 060976
reactant: 060964
fast: false
reversible: false
name: deg_bn

061000
type: LocalParameter
units: 059543
value: 6.0E-5
name: pd_c_2bn

060976
type: SpeciesReference
stoichiometry: 1.0
species: 873494

060964
type: SpeciesReference
stoichiometry: 1.0
species: 873634

874853
type: Reaction
kinetic law: 062502
product: 062490
reactant: 062478
fast: false
reversible: true
name: loc_en

062526
type: LocalParameter
units: 059543
value: 0.414
name: ex_2en

062514
type: LocalParameter
units: 059543
value: 0.138
name: in_2en

062490
type: SpeciesReference
stoichiometry: 1.0
species: 873794

062478
type: SpeciesReference
stoichiometry: 1.0
species: 873774

874753
type: Reaction
kinetic law: 061949
product: 061937
reactant: 061925
reactant: 061913
fast: false
reversible: true
name: int_en_n

061973
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_n_en

061961
type: LocalParameter
units: 059567
value: 30.0
name: a_n_en

061937
type: SpeciesReference
stoichiometry: 1.0
species: 873794

061925
type: SpeciesReference
stoichiometry: 1.0
species: 873534

061913
type: SpeciesReference
stoichiometry: 1.0
species: 873754

874154
type: Reaction
kinetic law: 060186
reactant: 060174
fast: false
reversible: false
name: deg_a

060198
type: LocalParameter
units: 059543
value: 0.12
name: pd_c_a

060174
type: SpeciesReference
stoichiometry: 1.0
species: 873374

875073
type: Reaction
kinetic law: 063506
product: 063494
fast: false
reversible: false
name: txn_p

063518
type: LocalParameter
units: 059507
value: 6.1E-6
name: rsu_p

063494
type: SpeciesReference
stoichiometry: 1.0
species: 873974

874274
type: Reaction
kinetic law: 060478
product: 060466
reactant: 060454
fast: false
reversible: true
name: loc_a

060502
type: LocalParameter
units: 059543
value: 0.012
name: ex_a

060490
type: LocalParameter
units: 059543
value: 0.09
name: in_a

060466
type: SpeciesReference
stoichiometry: 1.0
species: 873394

060454
type: SpeciesReference
stoichiometry: 1.0
species: 873374

874913
type: Reaction
kinetic law: 062842
product: 062830
reactant: 062818
fast: false
reversible: false
name: deg_pqi

062854
type: LocalParameter
units: 059543
value: 0.0012
name: pd_c_2pq

062830
type: SpeciesReference
stoichiometry: 1.0
species: 873554

062818
type: SpeciesReference
stoichiometry: 1.0
species: 873854

874714
type: Reaction
kinetic law: 061743
product: 061731
product: 061719
reactant: 061707
fast: false
reversible: false
name: tsl_e

061755
type: LocalParameter
units: 059543
value: 0.02448
name: ps_c_e

061731
type: SpeciesReference
stoichiometry: 1.0
species: 873734

061719
type: SpeciesReference
stoichiometry: 1.0
species: 873714

061707
type: SpeciesReference
stoichiometry: 1.0
species: 873714

874614
type: Reaction
kinetic law: 061462
product: 061449
reactant: 061437
reactant: 061424
fast: false
reversible: true
name: int_bi

061486
type: LocalParameter
units: 059543
value: 0.105
name: d_c_bi

061474
type: LocalParameter
units: 059567
value: 0.36
name: a_c_bi

061449
type: SpeciesReference
stoichiometry: 1.0
species: 873574

061437
type: SpeciesReference
stoichiometry: 1.0
species: 873514

061424
type: SpeciesReference
stoichiometry: 1.0
species: 873674

874334
type: Reaction
kinetic law: 060659
modifier: 060647
product: 060635
fast: false
reversible: false
name: itxn_a

060671
type: LocalParameter
units: 059603
value: 9.504
name: rsr_an

060635
type: SpeciesReference
stoichiometry: 1.0
species: 873354

874854
type: Reaction
kinetic law: 062562
modifier: 062550
product: 062538
fast: false
reversible: false
name: itxn_e

062575
type: LocalParameter
units: 059603
value: 1.28
name: rsr_en

062538
type: SpeciesReference
stoichiometry: 1.0
species: 873714

874534
type: Reaction
kinetic law: 061169
product: 061157
reactant: 061145
reactant: 061133
fast: false
reversible: true
name: int_2bin

061194
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_c_2bin

061181
type: LocalParameter
units: 059567
value: 30.0
name: a_c_2bin

061157
type: SpeciesReference
stoichiometry: 1.0
species: 873594

061145
type: SpeciesReference
stoichiometry: 1.0
species: 873494

061133
type: SpeciesReference
stoichiometry: 1.0
species: 873574

874574
type: Reaction
kinetic law: 061314
product: 061302
reactant: 061290
reactant: 061278
fast: false
reversible: true
name: int_bn_n

061338
type: LocalParameter
units: 059543
value: 6.0E-5
name: d_n_bn

061326
type: LocalParameter
units: 059567
value: 30.0
name: a_n_bn

061302
type: SpeciesReference
stoichiometry: 1.0
species: 873614

061290
type: SpeciesReference
stoichiometry: 1.0
species: 873534

061278
type: SpeciesReference
stoichiometry: 1.0
species: 873654

874474
type: Reaction
kinetic law: 061036
product: 061024
reactant: 061012
fast: false
reversible: false
name: deg_bn_n

061048
type: LocalParameter
units: 059543
value: 6.0E-5
name: pd_n_2bn

061024
type: SpeciesReference
stoichiometry: 1.0
species: 873534

061012
type: SpeciesReference
stoichiometry: 1.0
species: 873614

874434
type: Reaction
kinetic law: 060940
product: 060927
reactant: 060915
fast: false
reversible: false
name: deg_bi

060952
type: LocalParameter
units: 059543
value: 6.0E-4
name: pd_c_2bi

060927
type: SpeciesReference
stoichiometry: 1.0
species: 873514

060915
type: SpeciesReference
stoichiometry: 1.0
species: 873574