[Bioperl-l] Another implementation

Ewan Birney birney@ebi.ac.uk
Tue, 12 Sep 2000 21:11:00 +0100 (GMT)

On Tue, 12 Sep 2000, David Block wrote:

> Hello all!
> It's almost time for us at the PBI to release our graphical Perl/BioTk
> based Annotation Workbench, built on top of MySQL.  We built it first, and
> I quickly added methods now near the end to implement SeqI, PrimarySeqI,
> and SeqFeatureI.  So, we have bioperl objects that live on top of MySQL.

Whey hey! sounds great. Jason and other database people - this will be
great to see if this works as advertised etc...

Does the Perl/BioTK work off SeqI/PrimarySeqI/SeqFeatureI stuff or does it
straight to DBI to the database? It would be great if the BioTK stuff
could work against the SeqI interfaces - we could then just point it at
other SeqI implementing databases (eg, Flat file indexed GenBank or my
ever favourite ensembl)

> Two questions - 
> 1) what's the easiest way to test them?  I've written a few test scripts,
> but they're not up to CPAN standards, and they're definitely not part of
> the cvs commit cycle yet.  Since my objects implement the bioperl
> interfaces, can I just run them through the bioperl tests?  and how do I
> do that?

I enjoy the perl test suite system. Inside ensembl we have quite a
comprehensive test system which loads and then drops databases so that we
can test things. (written by the mecurial James Gilbert). Take a look at


> 2) anybody want a look-see?  email me and I'll send you the code - it is
> of course open, but we don't have an organized anon ftp or anon cvs yet.
> We do, however, have a wiki ;)
> http://bioinfo.pbi.nrc.ca/dblock/wiki/

We need weave all the wiki's together at some point... ;) 

> enjoy all!
> Dave Block
> (and Mark Wilkinson)
> National Research Council - Plant Biotechnology Institute
> Saskatoon, Saskatchewan, Canada
> http://bioinfo.pbi.nrc.ca
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420