The model reproduces FIG 11A and FIG 11B of the paper. However, please note that FIG 11B is a plot of normalised amounts versus time. The "stoichiometry" field has been used to convert fluxes from membrane species to volume species. The value of 0.0009967 is a product of (Surface to Volume_M*(1/Avagadro's number)*1E21. 0.6 is the surface to volume ratio of the plasma membrane, 1E21 is required for a unit surface to volume ratio and the Avagadro's number is present in the denominator to convert molecules to moles. The model was successfully tested using MathSBML and SBML ODESolver.
All the kinetic laws have the unit items per second
, which requires the one reaction taking place in the cytoplasm - IP3Phosphatase
- to include an explicit conversion factor both in the kinetic law and the stoichiometry of IP3_C
. The kinetic law is multiplied and the stoichiometry divided by the number of molecules per micro-mole. This conversion factor is only required for correct units and can be replaced by 1, if it should lead to numerical problems.
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.