Re: Stochastic simulation in SBML
29 Nov '11 14:07
--- On Tue, 29/11/11, Chris J. Myers <firstname.lastname@example.org> wrote:
> Hi Darren,
> > Is that really still true? I know it used to be true,
> but the DSMTS:
> > http://code.google.com/p/dsmts/
> > seems to have helped most developers to interpret many
> models correctly (along with the aforementioned book).
> I just checked and all of the examples have model substance
> units of item, so they do not expose this particular issue.
That is true - there are issues of "precision" involved when using other substance units, which is the reason there aren't currently any models in moles in the suite, though the avagadro csymbol should in principle partly solve this. However, there is a detailed worked example of converting a simple SBML model between moles and items in Chapter 7 of my book. L2v4 in the first edition and L3v1 in the second edition.
> > If you really wanted to do this very cleanly, so that
> you could continue to "ignore" units, you could introduce
> another conversion factor representing the conversion from
> "item" to substance units. ie. an amount representing the
> substance to be converted in a single reaction "tick". For a
> model using item units this would be 1, and for a model
> using moles it would be the reciprocal of avagadro (or you
> could set it up so that it is avagadro, depending on how you
> formulate it).
> I think this is a great solution.
As I said, I don't think it solves all problems, but it does solve some, and is arguably better than introducing an explicit dependence on units in the math spec. I would certainly be supportive of the introduction of such a new conversion factor.
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