IKK binary IkBbeta NFkB complex formation
The model corresponds to the knock out model of beta-/-, epsilon -/- and reproduces the upper panel in Fig 2C. In order to reproduce the other knock out models the transcription rate of the species that are not present must be set to zero and the rate of the one that is present must be set as seven times its corresponding value for the wild type model. This is done so as to compensate for the loss of other isoforms. 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 IkBeps 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.
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.
NFkB-binary IKK IkBalpha complex formation
IKK-binary IkBalpha NFkB complex formation
IKK binary IkBeps NFkB complex formation
NFkB binary IKK IkBbeta complex formation