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874773
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062490
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873894
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061206
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873874
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063518
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062818
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875033
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061012
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062382
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species: 873514
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062902
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060490
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062057
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061412
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873854
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873694
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874814
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874774
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059858
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874834
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062999
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060865
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873834
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873794
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873494
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873414
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061218
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874973
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061828
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061085
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061512
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061024
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059651
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062806
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060878
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060976
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061815
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062069
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062430
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874974
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060234
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059663
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062914
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species: 873894
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060331
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062248
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062781
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061695
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061097
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061791
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060344
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062927
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060246
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061635
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059591
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061549
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059712
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061000
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060840
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061181
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874813
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874434
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062308
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874154
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874174
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059675
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062587
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874354
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874474
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062172
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060258
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061623
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062199
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060853
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062987
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873734
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059700
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061194
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062370
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874374
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873934
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059736
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061145
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874654
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062514
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060502
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059772
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873674
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875053
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061731
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061671
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061338
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875013
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reactant: 063325
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059482
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063265
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061449
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062575
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874853
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873474
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874514
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063119
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species: 873554
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060562
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060732
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062866
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062478
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059822
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060417
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874594
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060356
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species: 873514
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874574
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060283
units: 059543
value: 6.0E-5
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061157
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062526
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059494
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063253
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059809
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species: 873374
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060550
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063458
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062878
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060744
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063107
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060405
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873434
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874554
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874534
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063385
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061121
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063373
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061060
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061486
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061755
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060006
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060526
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063445
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060295
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873594
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062466
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059519
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060964
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059834
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061767
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060514
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874854
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060018
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874234
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061133
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873714
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060210
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874833
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063397
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061474
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059748
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species: 873354
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059507
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060952
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874874
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062454
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061424
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874254
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062854
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060720
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059932
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874454
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873534
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063409
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873514
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059797
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063277
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061437
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873754
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063337
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061362
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874733
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060635
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874114
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061278
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059882
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874314
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060780
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060307
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062647
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060054
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874334
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062045
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059603
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062830
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061326
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061985
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059567
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063047
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874873
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062732
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059969
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874734
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063482
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873654
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874634
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062345
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059982
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060623
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061374
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063325
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060150
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062081
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873454
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061900
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063229
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061973
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059555
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059944
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063035
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062033
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062695
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062538
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060683
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062744
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060611
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MODEL8478881246
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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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