[Biojava-l] IDL

[Ewan Birney]

On Fri, 11 Feb 2000, David Martin wrote:

> 
> 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. 
> 

Oh boy .... I have been down this route sometimes before. As nice
as all this thought is, at the end of the day, a string of letter
(or - if you are really pushing it, an array of static flyweight
objects) is *really a good* way to represent dna, rna and protein
sequences.

Forcing the whole of biology into one concept of a "biological-thingy"
onto things which are different and *which you don't want to do the
same computational techniques on it* (eg, you can't do sensible dynamic
programming on metabolic pathways) is ... bad software engineering.

To be honest, if you want to discuss this you want to be talking 
ontology.

<snip>

> 
> 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)
> 

I certainly do not expect biojava to be a clone of bioperl, but I do
expect both of them to be well designed, and so a natural expectation
is that the broad outline of the design will be same in the two projects. 

This should make things like biocorba quite doable...


> ..d
> 
>  > 
> 
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