SimBiology dynamic parameters

scott — Fri, 10 Oct 2008 22:09:02 -0400

Stochastic simulation in SimBiology is restricted to mass action kinetics. To circumvent this (e.g. to simulate a michaelis-menten type reaction) I'd like to make the rate parameter dependent upon the levels of some of the species in the reaction.

The key, though, is that the parameter value would have to be updated during the simulation with the current species level.

I don't see any field for current value of a species in the simbiology object hierarchy, but it must be stored somewhere during the run. Where would it be and how could I access it to change the parameter value?

Alternatively, is there another way to get around the problem (i.e. to simulate hill or michaelis-menten kinetics using stochastic simulation in simbiology)

Thanks

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SimBiology dynamic parameters