[Bioperl-l] question about the nature of bioperl

[mwilkinson@gene.pbi.nrc.ca]

I would have to second what  Ewan says.  Personally, I don't use *all* of
BioPerl... does anyone... and who cares??  What I am sure of is that the bits that
I do use always (ha ha) work beautifully, and that saves me time.  It may be
bloated, but at least it's modular - I can use just the bits that I need to and
ignore the rest... in fact, sometimes I simply cut-n-paste what I know to be
working code from the BioPerl modules into my own scripts, rather than using the OO
approach.

The repository is a **resource**...and a good one, because the people building it
care.  I don't ask my local public library to "cut down because they are getting
too many books" .  Similarly, I would not fault BioPerl for becoming massive - if
you look at it as a resource, rather than an mammoth unified project, you will see
what I mean.  I think the most sensible way to judge something is by its utility,
and it certainly is useful! (this is starting to sound like a GeneOntology
argument...)

> Then I put alongside two projects I have personally work on which reuse
> bioperl code - Pfam database at Sanger and the Ensembl project. In both
> cases in fact the bioperl parts are somewhat deep and probably ossified
> (or in the process of ossification), but that's ok - they still work.

Genquire also would never have gotten off the ground without BioPerl!

Cheers all!  And thanks, Jason, for fixing those Blast parsing bugs...

Mark
...who doesn't work at Berkeley and has to write his own code ;-)

--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson, RA Bioinformatics
National Research Council, Plant Biotechnology Institute
110 Gymnasium Place, Saskatoon, SK, Canada

phone : (306) 975 5279
pager : (306) 934 2322
mobile: markw_mobile@illuminae.com