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The last few days has been a fascinating exchange of ideas and
temperaments. One question I have is how would one use the compositional
information in a dynamical model? The compositional information that we
do tend to use is built right into the stoichiometry matrix. I would be
interested to learn about the kinds of applications that need detailed
composition (above and beyond what we already have) in a dynamic model?


Michael Hucka wrote:
> myers> I'm not sure though how strongly I would push to
> myers> have such a concept in the core. I would not argue
> myers> against it, since it is useful. If this idea is
> myers> absorbed into the groups package, then I would like
> myers> to see it modified to accept a number which can be
> myers> interpreted as the number molecules in a complex as
> myers> described above.
>
> Hi Chris,
>
> Although this is an attractive idea, there is a significant
> problem in coming up with a universal way of counting the
> entities (or summing the amounts of all the species). Your
> example didn't involve a simple sum of X = A + B + C ...,
> but multipliers (X = A + 2B ...), which means there must be
> a scheme for people to express exactly how they want things
> counted up. That in turn means arbitrary formulas. Where
> would such formulas go, and how would it differ from using
> parameters and assignment rules today? (I'm not being
> dismissive here, just trying to think the ideas through.)
>
> MH
>
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