[Bioperl-l] Another implementation

[Ewan Birney]

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

http://www.ensembl.org/cgi-bin/cvsweb/cvsweb.cgi/~checkout~/ensembl/modules/t/EnsTestDB.pm?rev=1.7

> 
> 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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> 

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