[Bioperl-l] Another implementation

[Ewan Birney]

On Tue, 12 Sep 2000, David Block wrote:

> 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.

This (should) be a non-issue for separating out any viewing code.

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

depends. DAS is great for distributing annotation, but if we want to reuse
your bioTK stuff, then DAS doesn't help us here. 


> 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
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------