Generic Cell Cycle Model
Parameters
The rate constants are 'effective' values because they capture only the time scales of processes (rate constant units are min-1). For each mutant, we use the same equations and parameter values except for those parameter changes that are changed by the mutation (ie. for gene deletion we set the synthesis rate of the mutated protein to zero). J's are dimensionless Michaelis constants. (The mammalian parameters shown here were rescaled in the the published parameter list, to have their dimension min-1. The parameters presented here are for a timescale 10 minutes = 1 hour, following Novak & Tyson, 2004 )
Some rate constants are not needed for different organisms. These parameters
were set to 0 when we performed calculations, except those which would give
a division by zero, these we set to an artificial number. Still these modules
were uncoupled from the cell cycle engine in the different organisms (.set
files on show the used parameter sets with these artificial numbers included).
To create the bifurcation diagram of APC-A mutants we deleted the equation of
APCP and used APCP = 0.1 (10% of total activity) as a parameter.
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