[Biopython-dev] Pathway module

[Cayte]

>
> if you are not aware, look up BIND on the net. This is written by
> Christopher Hogue's group (yes, the same would has writtn chapter in the
> Baxevanis text Bioinformatics).
>
>
    I found the text and my first impression is that its too ambitious for
what we are doing.  We are not supporting kinetics or simulation.  Our
mandate, as I understand it, is to provide tools that make it easier to work
with databses like BIND, to complement not duplicate their functionality.
BINDS supports detail at the atomic level, this enzyme weaks three electons
on the 4th carbon.

   We could use a subset, maybe Interaction, Pathway and Action objects.
But we would either carry a lot of extra baggage  or hsve lots of empty
fields.  Even if the fields are empty  we would need code to fish through
them and pull out the data of interest.

  On the positive side, it would be extensible and compatible with a
standard format.  But I'd be concerned that the format is so rich, you'd
lose the forest for the trees.

  What do others think?

                                                                    Cayte


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