[Bioperl-l] Another implementation

[David Block]

On Tue, 12 Sep 2000, Ewan Birney wrote:

> 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...

We're looking forward to seeing that too :)

> 
> 
> 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)

The problem I am seeing now is that we import data from our non-standard
database, and importing stuff from other dbs may break parts of our
non-bioperl code.  I will attempt to make this more robust.

On the other hand, we would like to make this DAS compliant as well, so
then it just wouldn't matter, would it?

Our database is quite hairy right now, but the whole thing is built around
a few primary tables, primarily a GFF-like feature table.  I'll figure out
a visual DB schema if anyone is interested.  The database came first, and
this application is adapting to it, rather than the other way around.
> > 
> > Dave Block
> > (and Mark Wilkinson)
> > National Research Council - Plant Biotechnology Institute
> > Saskatoon, Saskatchewan, Canada
> > http://bioinfo.pbi.nrc.ca
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
Dave "I had better look at installation procedures now" Block