Re: Ancillary equations in SBML models
09 Aug '08 01:06
> Let me step back for a moment. Speaking just for myself, my
> understanding of people's desire is/was that the SBML
> reaction's list of reactants, products and modifiers should
> (1) refer to identifiers that explicitly appear in the
> kinetic law expressions, NOT (2) to an "extended set" (if
> you will) of any species that may enter into the expression
> through any means. When I read it, I still think (1) is the
> natural interpretation, but I'm amazed this issue hasn't
> come up before, because now that you bring it up, I have to
> agree that the first sentence in section 4.13.2 (L2v3r2)
> really can be read as meaning (2).
> Now, a very good question is, how many other people
> interpreted the lists of reactions, products and modifiers
> according to (2)? Should we run a poll to ascertain this?
I for one definitely read it to read as (1).
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