[Bioperl-l] RE: gbrowse running on biosql

[Hilmar Lapp]

Cool Lincoln. Regarding BioDatabaseAdaptor as a RandomAccessI I'll have to check that since I'm messing around with everything in there ...

	-hilmar

> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Monday, September 09, 2002 6:09 AM
> To: Hilmar Lapp; Bioperl
> Cc: Biosql
> Subject: gbrowse running on biosql
> 
> 
> Hi Guys,
> 
> I've got gbrowse running on top of biosql via a Bio::DasI 
> adaptor.  It took 
> about six hours, three of which were to come up to speed on 
> biosql, half an 
> hour to write the adaptor layer, and another 2.5 hours to 
> find and fix all 
> the latent bugs that a new adaptor exposed in gbrowse!
> 
> Basically, the adaptor allows you to type in the accession 
> number of a 
> BioEntry, and get a graphical rendition of its feature table, 
> all nicely 
> scrollable and zooomable.  Other features, like the various 
> pretty dumpers 
> and the restriction map generator, seem to work.  If you're 
> interested in 
> trying it, you need to CVS update bioperl-live and the 
> Generic Genome Browser 
> CVS (www.gmod.org).  There's a sample configuration file 
> called "biosql.conf" 
> that you must modify slightly for your local configuration.
> 
> The main limitation of this adaptor is that it uses the 
> Bio::DB::BioSQL::BioDatabaseAdaptor module, which is a pure 
> RandomAccessI 
> interface.  This means that I can't intelligently fetch 
> features from a 
> restricted coordinate range, but instead have to fetch 
> *everything* and then 
> filter them for the region of interest.  This limits the 
> usefulness of 
> gbrowse to moderate size entries (under a megabase, I guess). 
>  If someone can 
> point me to a way to construct virtual entries that contain 
> feature tables 
> that have been filtered by coordinate and/or by primary_tag, 
> this would allow 
> the interface to scale considerably.
> 
> Also, I need volunteers to translate gbrowse's messages file 
> into Spanish, 
> Russian, Korean, Japanese and Swedish.  If someone would like 
> to help out 
> with this I'll send you a messages file in English, and you 
> just replace the 
> English with your favorite language.  It shouldn't take more 
> than 10 minutes.
> 
> Lincoln
> 
> On Friday 06 September 2002 04:23 pm, Hilmar Lapp wrote:
> > I'm thinking about creating a Bio::BioEntry object (no definitive
> > name yet) that would basically map to a bare-bones row in the
> > Bioentry table in BioSQL (you know that's where I'm coming from
> > presently don't you).
> >
> > BioEntry would be different from PrimarySeq in not having a sequence
> > associated with it. Nonetheless, it would have a stable ID and live
> > in a namespace; it also has an optional description. Hence,
> > technically,
> >
> > 	Bio::BioEntry is-a Bio::IdentifiableI
> > 	Bio::BioEntry is-a Bio::DescribableI
> >
> > and that's about it.
> >
> > Note that I'm not describing an ontology term, there is no hierarchy
> > or whatever here.
> >
> > I'm undecided yet whether or not this is really going to help me,
> > but as a preliminary poll, if anyone has thoughts on this please
> > share.
> >
> > 	-hilmar
> 
> -- 
> Lincoln Stein
> lstein@cshl.org
>