Re: Stochastic simulation in SBML
29 Nov '11 12:40
I would interpret such a reaction in the stochastic sense as your option
2. This is indeed how COPASI does it.
One particular issue is the Avogadro's number, which is not 6.02e23 as
you indicate, but a much more precise number. Actually this number is
improved from time to time (it is a fundamental physical constant which
people keep estimating better and better). The precision of this number
makes a big difference in models with small volumes and small
concentratoins (when converting from molar to number of molecules). I
think SBML should at least recommend the number of significant digits of
this number to use, and a good source for the best estimate of this number.
On 11/29/2011 07:50 PM, Chris J. Myers wrote:
> Hi All,
> Currently, the SBML specification does not describe how to perform stochastic simulation on an SBML model. This has led to different tools implementing it differently making stochastic models not portable from one tool to another. Therefore, we would like to come up with a precise semantics for stochastic simulation to solve this problem. There is a subtlety though that complicates things. Consider the following model:
> Species A has an initial amount of 1 mole while species B has an initial amount of 0 moles. There is one reaction with A as a reactant and B as a product. The question is what happens to the state when this reaction occurs.
> 1) 1 mole of A is converted into 1 mole of B
> Pro: simple interpretation that is independent of units (namely, units can be dropped without any change in behavior).
> Con: typical interpretation of stochastic formulations is that reactions update molecule counts.
> 2) 1 molecule of A is converted into 1 molecule of B
> Pro: matches the typical interpretation.
> Con: the behavior is no longer independent of units (namely, a unit conversion must be performed implicitly).
> In an implementation of (2), one would need to convert the species initial amounts into units of individual molecule counts. In the case of moles, this would mean multiplying each species by Avogadro's number (6.02e23). If the units are changed to nanoMoles, then a different conversion is necessary.
> So, the question is which is more important:
> 1) Avoiding having implicit unit conversions and having units affect simulation behavior.
> 2) Keeping an individual molecule interpretation of stochastic reactions.
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Chair in Computational Systems Biology
School of Computer Science
Manchester Centre for Integrative Systems Biology
University of Manchester
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