[Bioperl-l] analysis pipeline for small and medium size labs

[Lukasz Huminiecki]

Bioinformatics becoming more and more database-centric?
Sounds great to me :))

Elia, your point about the pipeline being accessible for a wider research
cummunity is an excellent one. When I started using pipeline for Ensembl I
thought it's the single piece of the system that potentially could become
a very powerful and widely used standalone pool for small and medium size
research groups. The trick is to make it simple and reliable - we are not
all as computer savvy as you, Ensembl experts!

I got quite shocked to find out that in Dublin both Ensembl and bioperl
are virtually unused and basically everybody writes their own parsers,
little glue scripts, small pipelines etc, etc. What a waste!
Popularising a simple, reliable and popular framework system like
bioperl/ensembl pipeline would be a great winner for you
with great respect from the whole community.

just a small opinion from a biology-oriented person


Lukasz



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Lukasz Huminiecki, D.Phil.

Molecular Evolution Lab
Smurfit Institute
Department of Genetics
Trinity College Dublin
Dublin 2
Ireland

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On Tue, 12 Mar 2002, Elia Stupka wrote:

>On a similar topic I love all the stuff Chris (Mungall) can do with
>postgres where basically fasta, gff, gtf, reverse complement,etc, all
>become postgres views of the data, if you want to have a look see the
>biosql-schema cvs module, biosql repository of bioperl, in
>sql/biosql-postrgres.sql or something like that, quite nice!
>
>Elia
>
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