NFkB binary IKK IkBeps complex formation
NFkB-binary IKK IkBalpha complex formation
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.
NFkB binary IKK IkBbeta complex formation
IKK-binary IkBalpha NFkB complex formation
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.
IKK binary IkBeps NFkB complex formation
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.
IKK binary IkBbeta NFkB complex formation