metaid_0000018
substance units: metaid_0000003
name: NFkBn
initial amount: NaN
is version of: P25799
type: Species
has only substance units: false
initial concentration: 0.0
constant: false
in compartment: metaid_0000008
boundary condition: false

221146
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

metaid_0000040
is version of: GO:0008134
product: 219834
kinetic law: 219846
reactant: 219821
reactant: 219809
fast: false
is version of: GO:0005515
reversible: true
name: int_2ain
type: Reaction

219954
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

220230
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000054
kinetic law: 220350
product: 220338
reactant: 220326
is version of: GO:0044257
fast: false
reversible: false
name: deg_bn_n
type: Reaction

metaid_0000028
has only substance units: false
in compartment: metaid_0000008
constant: false
substance units: metaid_0000003
is version of: O54910
name: IkBen
boundary condition: false
type: Species
initial amount: NaN
initial concentration: 0.0

307058
units: metaid_0000006
value: 1.98
name: tr2a_i
type: LocalParameter

metaid_0000080
kinetic law: 221350
product: 221338
reactant: 221326
is version of: GO:0000060
fast: false
reversible: true
name: loc_e
type: Reaction

219590
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

306979
units: metaid_0000005
value: 6.0E-5
name: d4_3
type: LocalParameter

306991
units: metaid_0000005
value: 0.012
name: tp2a
type: LocalParameter

307004
units: metaid_0000005
value: 0.18
name: deg2_c
type: LocalParameter

metaid_0000068
kinetic law: 220868
product: 220856
product: 220844
reactant: 220832
is version of: GO:0006412
fast: false
reversible: false
name: tsl_e
type: Reaction

219882
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

220580
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

307043
units: metaid_0000005
value: 0.18
name: deg3_c
type: LocalParameter

metaid_0000041
kinetic law: 219870
reactant: 219858
is version of: GO:0044257
fast: false
reversible: false
name: deg_a
type: Reaction

metaid_0000019
has part: Q60680
in compartment: metaid_0000007
constant: false
initial amount: NaN
has part: O88351
initial concentration: 0.0
has only substance units: false
boundary condition: false
substance units: metaid_0000003
name: IkBbIKK
has part: Q60778
type: Species
has part: O88522

metaid_0000055
kinetic law: 220374
reactant: 220362
is version of: GO:0044257
fast: false
reversible: false
name: deg_b_n
type: Reaction

219542
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

307057
units: metaid_0000005
value: 0.0
name: IKK_deg
type: LocalParameter

metaid_0000029
constant: false
in compartment: metaid_0000007
has part: P25799
initial concentration: 0.01
type: Species
initial amount: NaN
has part: O54910
substance units: metaid_0000003
has only substance units: false
name: IkBeNFkB
boundary condition: false

221001
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

220146
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

220652
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

220724
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

220469
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

221242
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

307042
units: metaid_0000005
value: 6.0E-5
name: d6_3
type: LocalParameter

307003
units: metaid_0000005
value: 0.18
name: deg2_n
type: LocalParameter

metaid_0000069
kinetic law: 220916
product: 220904
reactant: 220892
reactant: 220880
is version of: GO:0005515
fast: false
reversible: true
name: int_ei
type: Reaction

306964
units: metaid_0000005
value: 0.2448
name: tr1a
type: LocalParameter

221050
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

metaid_0000042
kinetic law: 219894
reactant: 219882
is version of: GO:0044257
fast: false
reversible: false
name: deg_a_n
type: Reaction

219615
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000016
in compartment: metaid_0000007
is version of: P25799
has only substance units: false
initial amount: NaN
name: NFkB
type: Species
initial concentration: 0.0
constant: false
substance units: metaid_0000003
boundary condition: false

307046
units: metaid_0000005
value: 6.0E-5
name: deg6_n
type: LocalParameter

220989
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

metaid_0000082
kinetic law: 221411
reactant: 221399
is version of: GO:0044257
fast: false
reversible: false
name: IKK_deg
type: Reaction

metaid_0000052
kinetic law: 220278
product: 220266
reactant: 220254
is: GO:0008384
is: http://identifiers.org/ec-code/2.7.11.10
fast: false
reversible: false
name: deg_bi
type: Reaction

220904
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

220458
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

219494
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

306977
units: metaid_0000006
value: 30.0
name: a4_3
type: LocalParameter

307006
units: metaid_0000005
value: 6.0E-5
name: d5_3
type: LocalParameter

219518
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000043
kinetic law: 219930
product: 219918
reactant: 219906
is version of: GO:0044257
fast: false
reversible: false
name: deg_an_n
type: Reaction

307045
units: metaid_0000005
value: 0.18
name: deg3_n
type: LocalParameter

307019
units: metaid_0000005
value: 0.0168
name: tr3b
type: LocalParameter

metaid_0000017
name: IKK
in compartment: metaid_0000007
has part: O88351
initial amount: NaN
type: Species
has part: Q60680
has only substance units: false
initial concentration: 0.001
substance units: metaid_0000003
boundary condition: false
has part: O88522
constant: false

metaid_0000081
kinetic law: 221387
product: 221375
reactant: 221362
is version of: GO:0006611
fast: false
reversible: false
name: loc_en
type: Reaction

221290
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

307055
units: metaid_0000005
value: 0.414
name: k2_e
type: LocalParameter

metaid_0000053
kinetic law: 220314
product: 220302
reactant: 220290
is version of: GO:0044257
fast: false
reversible: false
name: deg_bn
type: Reaction

307054
units: metaid_0000005
value: 0.012
name: tp2e
type: LocalParameter

220664
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

306966
units: metaid_0000006
value: 1.35
name: a1
type: LocalParameter

307005
units: metaid_0000006
value: 30.0
name: a5_3
type: LocalParameter

metaid_0000003
unit: 219422
name: micromole
type: SBMLUnitsDef

219858
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000058
kinetic law: 220494
product: 220481
reactant: 220469
reactant: 220458
is version of: GO:0005515
fast: false
reversible: true
name: int_2bni
type: Reaction

221338
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

metaid_0000014
in compartment: metaid_0000008
boundary condition: false
has part: P25799
initial concentration: 0.0
type: Species
substance units: metaid_0000003
constant: false
initial amount: NaN
has only substance units: false
name: IkBaNFkBn
has part: Q9Z1E3

307018
units: metaid_0000005
value: 0.2448
name: tr1b
type: LocalParameter

metaid_0000024
constant: false
name: IkBb
is version of: Q60778
has only substance units: false
initial amount: NaN
initial concentration: 0.0
type: Species
boundary condition: false
in compartment: metaid_0000007
substance units: metaid_0000003

307028
units: metaid_0000005
value: 0.2448
name: tr1e
type: LocalParameter

219578
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

307048
units: metaid_0000005
value: 6.0E-5
name: deg6_c
type: LocalParameter

metaid_0000044
kinetic law: 219966
product: 219954
reactant: 219942
is version of: GO:0044257
fast: false
reversible: false
name: deg_an
type: Reaction

220616
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000064
kinetic law: 220736
product: 220724
is: GO:0006351
fast: false
reversible: false
name: txn_b
type: Reaction

219990
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

306995
units: metaid_0000005
value: 0.018
name: tp1b
type: LocalParameter

306975
units: metaid_0000005
value: 0.075
name: d1_2
type: LocalParameter

metaid_0000085
constant: false
value: 0.0
name: Total_IkBbeta
type: Parameter

metaid_0000078
kinetic law: 221266
product: 221254
reactant: 221242
is: GO:0008384
is: http://identifiers.org/ec-code/2.7.11.10
fast: false
reversible: false
name: deg_ei
type: Reaction

220062
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

307008
units: metaid_0000005
value: 0.105
name: d2_2
type: LocalParameter

metaid_0000004
unit: 219458
unit: 219446
unit: 219434
name: uM_per_min
type: SBMLUnitsDef

220676
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000083
kinetic law: 221447
modifier: 221435
product: 221423
is version of: GO:0006351
fast: false
reversible: false
name: itxn_a
type: Reaction

220038
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000015
has part: O88351
initial concentration: 0.0
in compartment: metaid_0000007
constant: false
has part: Q60680
has only substance units: false
boundary condition: false
initial amount: NaN
has part: Q9Z1E3
name: IkBaIKKNFkB
type: Species
has part: O88522
substance units: metaid_0000003
has part: P25799

metaid_0000025
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000003
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000008
name: IkBbt
type: Species

307027
units: metaid_0000005
value: 0.0168
name: tr3e
type: LocalParameter

220700
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

metaid_0000059
reactant: 220518
fast: false
product: 220530
is version of: GO:0008134
kinetic law: 220543
reactant: 220506
name: int_bn_n
reversible: true
type: Reaction
is version of: GO:0005515

metaid_0000045
kinetic law: 220002
product: 219990
reactant: 219978
is: GO:0008384
is: http://identifiers.org/ec-code/2.7.11.10
fast: false
reversible: false
name: deg_ai
type: Reaction

307007
units: metaid_0000006
value: 2.88
name: a8
type: LocalParameter

306980
units: metaid_0000005
value: 0.12
name: deg1_c
type: LocalParameter

metaid_0000065
kinetic law: 220772
product: 220760
reactant: 220748
is version of: GO:0000060
fast: false
reversible: true
name: loc_n
type: Reaction

220410
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

306974
units: metaid_0000006
value: 11.1
name: a7
type: LocalParameter

220976
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

metaid_0000084
constant: false
value: 0.0
name: Total_IkBalpha
type: Parameter

306994
units: metaid_0000005
value: 0.414
name: k2_b
type: LocalParameter

metaid_0000079
is: GO:0008384
product: 221290
product: 221302
reversible: false
fast: false
name: deg_ein
reactant: 221278
type: Reaction
is: http://identifiers.org/ec-code/2.7.11.10
is: GO:0051092
kinetic law: 221314

metaid_0000005
unit: 219470
name: per_min
type: SBMLUnitsDef

219506
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

219566
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

307016
units: metaid_0000005
value: 0.105
name: d2_1
type: LocalParameter

metaid_0000026
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000003
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000008
name: IkBet
type: Species

metaid_0000012
boundary condition: false
in compartment: metaid_0000007
initial concentration: 0.0
substance units: metaid_0000003
type: Species
has only substance units: false
name: IkBaIKK
constant: false
has part: O88351
has part: O88522
has part: Q9Z1E3
has part: Q60680
initial amount: NaN

220206
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000056
kinetic law: 220398
reactant: 220386
is version of: GO:0044257
fast: false
reversible: false
name: deg_b
type: Reaction

metaid_0000046
name: deg_ain
fast: false
reversible: false
reactant: 220014
product: 220026
is: GO:0051092
is: http://identifiers.org/ec-code/2.7.11.10
is: GO:0008384
type: Reaction
product: 220038
kinetic law: 220050

221326
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

220386
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

306973
units: metaid_0000005
value: 6.0E-5
name: d4_2
type: LocalParameter

220808
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

metaid_0000066
kinetic law: 220796
product: 220784
is: GO:0006351
fast: false
reversible: false
name: txn_e
type: Reaction

306983
units: metaid_0000005
value: 6.0E-5
name: deg4_n
type: LocalParameter

219942
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

220074
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000076
kinetic law: 221194
product: 221182
reactant: 221170
is version of: GO:0044257
fast: false
reversible: false
name: deg_en_n
type: Reaction

220760
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

ORG:
  orgname: UCSD
n:
  given: Hoffman
  family: Alexander

metaid_0000006
unit: 219506
unit: 219494
unit: 219482
name: per_uM_per_min
type: SBMLUnitsDef

220628
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

306963
units: metaid_0000005
value: 0.0168
name: tr3a
type: LocalParameter

220434
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

221423
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

221254
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000027
in compartment: metaid_0000007
constant: false
has only substance units: false
boundary condition: false
initial amount: NaN
type: Species
substance units: metaid_0000003
is version of: O54910
name: IkBe
initial concentration: 0.0

metaid_0000013
has part: Q9Z1E3
substance units: metaid_0000003
initial concentration: 0.06
type: Species
name: IkBaNFkB
constant: false
has only substance units: false
initial amount: NaN
boundary condition: false
has part: P25799
in compartment: metaid_0000007

307015
units: metaid_0000006
value: 0.36
name: a2
type: LocalParameter

metaid_0000057
type: Reaction
is version of: GO:0005515
reactant: 220410
reactant: 220422
name: int_2bin
fast: false
is version of: GO:0008134
product: 220434
reversible: true
kinetic law: 220446

220134
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

307049
units: metaid_0000005
value: 0.036
name: r3
type: LocalParameter

metaid_0000047
kinetic law: 220086
product: 220074
reactant: 220062
is version of: GO:0000060
fast: false
reversible: true
name: loc_a
type: Reaction

metaid_0000067
kinetic law: 220820
reactant: 220808
is version of: GO:0006402
fast: false
reversible: false
name: mdeg_e
type: Reaction

306982
units: metaid_0000005
value: 0.12
name: deg1_n
type: LocalParameter

306972
units: metaid_0000006
value: 30.0
name: a4_2
type: LocalParameter

220422
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000007
is: GO:0005737
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

306992
units: metaid_0000005
value: 0.828
name: k2_a
type: LocalParameter

306962
units: metaid_0000004
value: 1.848E-4
name: tr2a
type: LocalParameter

metaid_0000077
kinetic law: 221230
product: 221218
reactant: 221206
is version of: GO:0044257
fast: false
reversible: false
name: deg_en
type: Reaction

metaid_0000086
constant: false
value: 0.0
name: Total_IkBeps
type: Parameter

metaid_0000008
is: GO:0005634
constant: true
size: 1.0
spatial dimensions: 3.0
name: nucleus
type: Compartment

metaid_0000074
kinetic law: 221134
reactant: 221122
is version of: GO:0044257
fast: false
reversible: false
name: deg_e
type: Reaction

220952
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

219664
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

306984
units: metaid_0000005
value: 6.0E-5
name: deg4_c
type: LocalParameter

306970
units: metaid_0000006
value: 30.0
name: a4_1
type: LocalParameter

219821
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

307035
units: metaid_0000006
value: 30.0
name: a6_2
type: LocalParameter

metaid_0000033
kinetic law: 219530
product: 219518
is: GO:0006351
fast: false
reversible: false
name: txn_a
type: Reaction

metaid_0000023
in compartment: metaid_0000008
boundary condition: false
type: Species
constant: false
initial concentration: 0.0
initial amount: NaN
has only substance units: false
substance units: metaid_0000003
name: IkBbn
is version of: Q60778

220014
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

220110
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

307025
units: metaid_0000004
value: 3.048E-5
name: tr2e
type: LocalParameter

metaid_0000037
reactant: 219677
is version of: GO:0032088
reactant: 219664
kinetic law: 219701
type: Reaction
name: int_an
product: 219689
reversible: true
fast: false
is version of: GO:0005515

219918
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

220362
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

221302
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

221170
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

metaid_0000009
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000003
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000008
name: IkBat
type: Species

220170
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000075
kinetic law: 221158
reactant: 221146
is version of: GO:0044257
fast: false
reversible: false
name: deg_e_n
type: Reaction

220568
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

220302
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

220604
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

306971
units: metaid_0000005
value: 6.0E-5
name: d4_1
type: LocalParameter

306999
units: metaid_0000005
value: 0.024
name: r2
type: LocalParameter

220506
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

221086
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

221375
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

307036
units: metaid_0000005
value: 6.0E-5
name: d6_2
type: LocalParameter

220481
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000032
type: Species
has part: O88522
initial amount: NaN
in compartment: metaid_0000007
initial concentration: 0.0
has only substance units: false
boundary condition: false
has part: O88351
constant: false
substance units: metaid_0000003
has part: O54910
name: IkBeIKK
has part: Q60680

metaid_0000036
kinetic law: 219652
product: 219638
reactant: 219627
reactant: 219615
is version of: GO:0005515
fast: false
reversible: true
name: int_ai
type: Reaction

219834
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

220928
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

metaid_0000060
reactant: 220568
kinetic law: 220592
type: Reaction
reactant: 220555
reversible: true
fast: false
is version of: GO:0005515
is version of: GO:0032088
name: int_bn
product: 220580

metaid_0000022
has only substance units: false
in compartment: metaid_0000007
substance units: metaid_0000003
type: Species
constant: false
has part: P25799
boundary condition: false
has part: Q60778
initial amount: NaN
initial concentration: 0.03
name: IkBbNFkB

220218
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

306996
units: metaid_0000005
value: 0.012
name: tp2b
type: LocalParameter

221025
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

306986
units: metaid_0000005
value: 0.072
name: r1
type: LocalParameter

219906
stoichiometry: 1.0
species: metaid_0000014
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metaid_0000062
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notes: O'Dea, E.L., Barken, D., Peralta, R.Q., Tran K.T., Werner, S.L., Kearns, J.D., Levchenko, A., Hoffmann, A. A homeostatic model of IkB metabolism to control constitutive activity. Molecular Systems Biology, 3:111, pp. 1-7. 2007 Questions concerning the paper should be addressed to the corresponding author. Alexander Hoffmann (ahoffmann@ucsd.edu) 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. 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. Please address questions about this SBML model to Jeff Kearns (jkearns@ucsd.edu). BioModels DB curation: The model reproduces the values of diffferent species depicted in Fig 3A and 3B (wt) of the paper corresponding to Model1.1. To depict the the total IkB alpha, beta epsilon species, three additional parameters and their corresponding assignment rules have been introduced in this model by the creator. Model succesfully tested on MathSBML. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
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W3 CDTF: Tue Sep 04 11:35:41 BST 2007

given: Harish
family: Dharuri

ORG:
  orgname: California Institute of Technology

W3 CDTF: Wed May 16 11:07:34 BST 2012