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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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307024
type: LocalParameter
units: metaid_0000005
value: 0.0048
name: k1_1

307022
type: LocalParameter
units: metaid_0000005
value: 5.4
name: k1_2

220760
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

220748
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

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

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

220386
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

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

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

221218
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

221206
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

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

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

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

220856
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

220844
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

220832
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

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

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

219677
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

219664
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

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

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

219689
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

metaid_0000051
type: Reaction
product: 220230
is: GO:0008384
is: GO:0051092
kinetic law: 220242
fast: false
name: deg_bin
reactant: 220206
reversible: false
is: http://identifiers.org/ec-code/2.7.11.10
product: 220218

220230
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

306997
type: LocalParameter
units: metaid_0000005
value: 0.12
name: r5

220206
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

220218
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000049
type: Reaction
kinetic law: 220158
product: 220146
reactant: 220134
is version of: GO:0006611
fast: false
reversible: false
name: loc_bn

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

220146
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

220134
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

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

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

219882
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

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

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

221375
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

221362
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000063
type: Reaction
kinetic law: 220712
reactant: 220700
is version of: GO:0006402
fast: false
reversible: false
name: mdeg_b

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

220700
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

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

307001
type: LocalParameter
units: metaid_0000005
value: 6.0E-5
name: deg5_n

220338
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

220326
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

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

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

221146
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

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

220568
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

307014
type: LocalParameter
units: metaid_0000005
value: 6.0E-5
name: d5_1

307013
type: LocalParameter
units: metaid_0000006
value: 30.0
name: a5_1

220555
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

220580
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

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

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

220784
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

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

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

219518
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000072
type: Reaction
kinetic law: 221062
product: 221050
reactant: 221037
reactant: 221025
is version of: GO:0005515
fast: false
reversible: true
name: int_2eni

307040
type: LocalParameter
units: metaid_0000005
value: 0.105
name: d3_2

307038
type: LocalParameter
units: metaid_0000006
value: 4.2
name: a9

221050
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

221037
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

221025
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000078
type: Reaction
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

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

221254
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

221242
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

metaid_0000045
type: Reaction
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

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

219990
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

219978
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

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

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

220410
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

220422
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

220434
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

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

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

metaid_0000038
type: Reaction
kinetic law: 219749
is version of: GO:0005515
fast: false
product: 219737
is version of: GO:0008134
reactant: 219725
reversible: true
reactant: 219713
name: int_an_n

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

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

219737
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

219725
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

219713
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

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

307032
type: LocalParameter
units: metaid_0000005
value: 0.105
name: d3_1

307030
type: LocalParameter
units: metaid_0000006
value: 0.54
name: a3

220904
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

220892
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

220880
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000070
type: Reaction
reversible: true
name: int_en
is version of: GO:0032088
is version of: GO:0005515
fast: false
product: 220952
reactant: 220928
kinetic law: 220964
reactant: 220940

220952
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

220928
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

307034
type: LocalParameter
units: metaid_0000005
value: 6.0E-5
name: d6_1

307033
type: LocalParameter
units: metaid_0000006
value: 30.0
name: a6_1

220940
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000061
type: Reaction
kinetic law: 220640
product: 220628
reactant: 220616
reactant: 220604
is version of: GO:0005515
fast: false
reversible: true
name: int_bi

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

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

220628
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

220616
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

220604
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

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

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

219918
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

219906
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000034
type: Reaction
kinetic law: 219554
reactant: 219542
is version of: GO:0006402
fast: false
reversible: false
name: mdeg_a

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

219542
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

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

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

221399
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

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

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

220362
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000040
type: Reaction
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

219834
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

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

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

219821
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

219809
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

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

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

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri

W3 CDTF: Tue Sep 04 11:35:41 BST 2007