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notes: This model corresponds to the IkB-NFkB signaling in wild type cells and reproduces the dynamics of the species as depicted in Figure 2 F of the paper. The authors mention that the simulation is carried out in three phases, where the steady state values of the species in one phase are fed to the succeding phase. This model captures the simulation dynamics of two phases and makes use of the event section to introduce the stimulus and thereby transition to the next phase. Accordingly, a few terms have been introduced that make this transition possible, this in no way compromises the original model. Also, the simulation plots are not an exact reproduction of the figures in the paper, they do however match the simulation results that the authors shared with us. Model was successfully tested on MathSBML. 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.
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notes: The sum of "flag_for_after_signal" and "fr_after_trigger" insures that the value of the fraction of "IkBbeta_nuc_ NFkB_nuc" capable of nuclear export is equal to one before the signal is introduced and then follows the rate rule for "fr_after_trigger" after the signal is introduced.

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name: IkBeps transcript degradation

208351
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000064

metaid_0000108
type: Reaction
kinetic law: 208615
reactant: 208603
is version of: GO:0044257
fast: false
reversible: false
name: IkBbeta degradation

208603
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

metaid_0000094
type: Reaction
kinetic law: 208267
reactant: 208255
is version of: GO:0006402
fast: false
reversible: false
name: IkBalpha transcript degradation

208255
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000143
type: Parameter
constant: false
value: 0.5

metaid_0000139
type: Parameter
constant: false
value: NaN

metaid_0000111
type: Reaction
is version of: GO:0005515
reactant: 208663
product: 208687
name: IKK-IkBeps complex formation
is version of: GO:0043623
fast: false
kinetic law: 208699
reversible: true
reactant: 208675

208663
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

208687
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000053

208675
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

metaid_0000066
type: Reaction
kinetic law: 207485
product: 207473
reactant: 207461
reactant: 207449
is version of: GO:0005515
fast: false
reversible: true
name: NFkB-IkBalpha complex formation

207473
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000043

207461
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

207449
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

W3 CDTF: Thu Jul 05 15:50:23 BST 2012

metaid_0000123
type: Reaction
reactant: 209001
kinetic law: 209025
is version of: GO:0005515
name: IKK binary IkBeps NFkB complex formation
product: 209013
fast: false
reversible: true
is version of: GO:0043623
reactant: 208988

209001
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

209013
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000054

208988
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

metaid_0000008
type: Parameter
constant: true
value: 0.03

metaid_0000003
type: Parameter
constant: true
value: 30.0

metaid_0000130
type: Event
event assignment: 209241
event assignment: 209229
event assignment: 209217
trigger: 209205
notes: The events section is used to set the IKK signal, the system is allowed to equilibrate for 2000 minutes and IKK is increased to 0.1 uM. trigger value is a parameter that is zero until equilibration and then is set to 1, this in turn is used in the rate rule section for "fr_after_trigger". The latter term corresponds to fr in the paper.
use values from trigger time: true

209205
type: Trigger
persistant: true
initial value: true

metaid_0000120
type: Reaction
reactant: 208891
name: IKK binary IkBbeta NFkB complex formation
reversible: true
reactant: 208904
is version of: GO:0043623
is version of: GO:0005515
product: 208916
fast: false
kinetic law: 208928

208891
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

208904
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000045

208916
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000052

metaid_0000015
type: Parameter
constant: true
value: 9.25E-5

metaid_0000005
type: Parameter
constant: true
value: 30.0

metaid_0000109
type: Reaction
kinetic law: 208651
product: 208639
reactant: 208627
is version of: GO:0000060
fast: false
reversible: true
name: IkBbeta translocation

208639
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000058

208627
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000044

metaid_0000036
type: Parameter
constant: true
value: 0.2442

metaid_0000010
type: Parameter
constant: true
value: 0.45

metaid_0000126
type: Reaction
kinetic law: 209097
product: 209085
reactant: 209073
is version of: GO:0044257
has part: http://identifiers.org/ec-code/2.7.11.10
fast: false
reversible: false
name: IkBalpha degradation

209085
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

209073
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000048

metaid_0000017
type: Parameter
constant: true
value: 0.0168

metaid_0000074
type: Reaction
product: 207655
reversible: false
fast: false
kinetic law: 207679
name: IkBalpha degradation
product: 207667
is version of: GO:0044257
has part: http://identifiers.org/ec-code/2.7.11.10
reactant: 207643

207655
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

207667
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000050

207643
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000049

metaid_0000070
type: Reaction
kinetic law: 207583
product: 207571
reactant: 207559
reactant: 207547
is version of: GO:0005515
fast: false
reversible: true
name: NFkB-IkBeps complex formation

207571
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000047

207559
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

207547
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000042

metaid_0000022
type: Parameter
constant: true
value: 0.2448

W3 CDTF: Wed May 16 14:37:19 BST 2007

metaid_0000018
type: Parameter
constant: true
value: 1.068E-5

metaid_0000113
type: Reaction
kinetic law: 208735
modifier: 208723
product: 208711
is version of: GO:0006412
fast: false
reversible: false
name: IkBeps synthesis

208711
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000046

metaid_0000004
type: Parameter
constant: true
value: 0.03

metaid_0000086
type: Reaction
reactant: 208052
kinetic law: 208077
name: NFkB-IkBalpha complex formation
is version of: GO:0043623
reversible: true
fast: false
is version of: GO:0005515
reactant: 208040
product: 208065

208052
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000056

208040
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000055

208065
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000057

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