Re: stoichiometries of modifiers
26 Apr '05 20:25
Without going into all of the theory, let me just say that there exists
a probabilistic version of the quasi steady state approximation. Rao &
Arkin have written a paper on one version of it as applied to the Master
equation. And, like I mentioned in a previous post, the XML parsed
MathML syntax (or something similar) that represents equations in SBML
is not (at least for my purposes) an adequate way of storing the rate
laws. Again, I like the idea of using a mapping of unique integers to
their corresponding rate law forms, but I'd be happy with anything that
Pedro Mendes wrote:
>On Tuesday 26 April 2005 08:36 pm, Howard Salis wrote:
>>Like the previous email, I was referring to what happens when you make
>>the QSS approximation and write down the Michaelis Menten-like rate law.
>>Like you said, I is then a modifier, and the rate law depends on its
>>stoichiometry (among other things). If that information is not encoded
>>in the SBML file, then a simulator using a continuous time MC method
>>will not be able to simulate the system as intended by the modeler.
>the information is encoded in the SBML file exactly as a rate law. It will
>contain one or more terms for I with several constants. The stoichiometry
>of I in the elementary reactions is reflected in these terms. However in
>this overall reaction I has stoichiometry zero.
>I believe from this last explanation, your problem is not having the correct
>rate equation that reflects the behavior of the system with very small
>numbers of molecules. In these conditions the steady-state approximation
>(or the fast equilibrium one) is not appropriate and so you will have to
>derive an overall rate equation in some other way, if at all possible. I
>would suggest that you include all of the elementary steps. In that case,
>my previous point holds (I would not be a modifier). If you want an overall
>rate law that is appropriate for the conditions you described then the
>solution does not pass by assigning stoichiometric coefficients to
>modifiers. This is not a problem of SBML.
>Hope that this helps with the solution.