[Biopython-dev] Pathway Module

[Tarjei S Mikkelsen]

>   I found another paper that may be interesting, at least, to 
> keep the ideas flowing.
> 

Thanks for the pointer. It looks like interesting work. I'll take a look
as soon as I get a chance.

I played around with some quick and dirty code this weekend to test
whether my initial ideas sucked (quick answer: yup ;) )

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?

 Tarjei