Bioperl: Sequence Analysis RFP critiques requested

Ewan Birney
Tue, 27 Oct 1998 12:04:03 +0000 (GMT)

On Tue, 27 Oct 1998, Steve Chervitz wrote:

> Five different groups have submitted specs to be considered for
> adoption as standards. I encourage everyone to take a look at these
> submissions and to direct any critiques & suggestions to this Bioperl
> mailing list and/or me. These documents could have a major impact on
> future software tools related to sequence analysis. 

Just to second steve's mail, I think it is very interesting to read
(both steve and myself are authors for different submissions) the models.
There are interesting things about both the convergence and divergence
of the data models. This is what we are most interested in finding out
the pluses and minuses about. Let's face it - most of the 'component
based' software in bioinformatics is written in perl (not the algorithms,
but the gluey-scripting-analysis flow type scripts) and fair proportion of 
that is written by people on this list, so we do represent a good body
of opinion to comment on it. Let's tell them what they've got wrong!

I'll post my comments here once I manage to get through alot of the UML.
(some of it is pretty...dense...).

> The Neomorphic submission incorporates some ideas of Bioperl
> developers, but additional ideas & comments are always welcome.

I'd also like say that the ebi submission had some bioperl input via
myself - in particular splitting the sequence object into heavy weight
and light weight objects. The align module was partially inspired by
Georg's UnivAlign along with ideas I have in Wise2. So bioperl has 
already had an influence on the process <grin>

Ewan Birney

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