[Biojava-l] IDL

David Martin david.martin@biotek.uio.no
Fri, 11 Feb 2000 20:14:07 +0100

I have a few pennys worth to throw in here..

Firstly I think that IDL is definitely the way to go to get a good design
and interoperatability between the various bio* development efforts.

Now for the fun..

At present the IDL is focussed exclusively on linear sequences of amino
acids or nucleotides (of whichever flavour). This may prove to be a
mistake in future as not all biological sequences are linear.

I am thinking of the bio* IDL being useable across the whole spectrum of
biocomputing rather than basic sequence analysis. 

If we start at the basic level, everything in molecular biology (in its
broadest sense) is a unit at some scale. It typically forms part of a
sequence of such units where one or more units precede it and it precedes
one or more units.
We are looking at the nodes of a unidirected graph.

Taking it from the abstract and putting some examples up, think of the

A Metabolic pathway.

A carbohydrate chain.

A regulatory pathway

Peptide nucleic acids.

Cyclic biopolymers

Suddenly we start to get a bit fractal. Instead of every point being a
link in a chain, it is a node in a graph. That graph may then contain
other graphs.

Ie an enzyme is a point in a  metabolic pathway graph and a node in a gene
expression graph.
The enzyme contains units that themselves are graphs (peptides linked by
disulphide bridges, carbohydrate derived sidechains)
The building blocks of these units are themselves graphs (the arrangement
of atoms in an amino acid, the cyclic nature of carbohydrates and nucleic

This starts to make analysis a bit more interesting but has the advantage
of allowing the basic bio*.object to have the functionality required to
operate in a nonlinear world.

Maybe you already have very good reasons for not taking this approach, but
it is occasionally neccessary to do something a bit different to extend
our capabilities rather than biojava being a clone of bioperl (worthy a
goal though that is)



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