Re: Stochastic simulation in SBML
29 Nov '11 16:30
I think that we do not have the choice between option 1) and 2) below.
The model and its simulation should be representing the 'physical
reality' thus option 1) is clearly wrong. Also we must not think about
stochastic vs deterministic simulation as there are methods of
integration which use both strategies in parallel.
We can argue that solution 2) requires implicit unit conversion but I
agree with Darren that to properly implement any stochastic simulation
one needs to be able to convert the given substance unit into items.
This is not implicit it is explicit especially in L3 where we have
defined the Avogadro constant. This interpretation leaves models in
which the substance is measured in kg out, but I do not see any problem
Therefore I do not see any need to act, except to elaborate on the
examples and to provide further test case which use other units than
items. Here I would like to thank Darren for the excellent test suite,
which the COPASI team uses extensively to validate its different
stochastic and hybrid algorithms.
On Tue, 29 Nov 2011 12:50:19 -0700
"Chris J. Myers" <firstname.lastname@example.org> 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
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