[Biopython-dev] Pathway module

[Cayte]

----- Original Message -----
From: "Tarjei Mikkelsen" <tarjei_mikkelsen at hotmail.com>
To: <biopython-dev at biopython.org>
Sent: Sunday, November 04, 2001 8:42 PM
Subject: [Biopython-dev] Pathway module


>
> I've committed the following modules to the CVS tree:
>
> Bio.Pathway
> Bio.KEGG.Map
> Bio.MetaTool.Input
>
> Together they form my first (and rather rudimentary) attempt at creating
> classes for representing and working with metabolic and signalling
pathways.
>
> Bio.Pathway contains classes for representing collections of biochemical
> reactions of the type A + B <-> C (Reaction/System), and classes for
> representing explicit networks of arbitrary interactions
> (Interaction/Network).
>
> Bio.KEGG.Map contains a parser for reading a KEGG metabolic pathway map
into
> Reaction/System objects.
>
> Bio.MetaTool.Input contains a function for converting a System object into
a
> string that can be used as input tothe MetaTool program.
>
> Sample usage can be deduced from the correponding test files.
>
> This is very much a prototype so I welcome anyone interested to have a
look
> and poke at it (and rip it apart). I don't recommend that it is included
in
> the actual Biopython distribution until it is a bit more fleshed out and
> tested, but I'll leave that up to whoever makes those decisions.
>
  Great!!! I hope to have time to look into it Wednesday.

                                     Cayte