[Biopython-dev] Pathway Module

[Cayte]

> This might be obvious, but it occurred to me that there are two
> different "pathway" concepts that are useful in different circumstances:
>
> The first, a System, is as a set of reactions that are
> implicitly connected through their products and substrates. This is
> essentially equivalent to a stochiometric matrix, which is useful for
> things like flux/mode analysis.
>
> The second, a Pathway, is a set of species/metabolites that are
> explicitly linked through reactions. This is equivalent to a graph,
> which is useful for things like route searches, neighbor analysis
> and so on.
>
> You can convert from a System to a Pathway by specifying which of
> the products and substrates from the System reactions are to be
> used as nodes in the Pathway graph. The reverse conversion is trivial.
>
> I think that in our module it might be useful to make a distinction
> between these two concepts. The reason being that they are each useful
> for different kind of analyses, and that databases like KEGG, WIT
> and BIND seem to contain many more individual reactions - which can
> be grouped into a System - than are used in their "curated" pathways.
>
> Does this make sense?
>
   The user is boss.  If the separation of  modules is the most efficient
way to support  the typical user scenarios, I think we should go with it.

                                                   Cayte
>
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