Bioperl: Bio* integration with AceDB

[Jason Stajich]

On Fri, 16 Jun 2000, Ewan Birney wrote:
> On Thu, 15 Jun 2000, David Block wrote:
> 
> > Reports from Acedb2000:
> > 
> > A few of us met in the coffee room to discuss what needed to be/ could be
> > done to better integrate with the Bio::* (Perl, Java, Corba, XML) effort.
> > We came up with a few useful projects that need some volunteers to tackle
> > them.  Of course, this also needs to be coordinated with the Bio* people.
> 
> Sounds great ;)
> 
> > 
> > Notes from the discussion:
> > BioJava has been focussed on data processing, rather than UI.  They
> > inherited AceDB client code.
> > 
> > What is needed is an abstract data layer for objects that crosses
> > boundaries.  BioCorba is using a common sequence definition derived from
> > Bio::Perl.
> 
> Biocorba has a bioperl bias, but has been implemented by all three groups
> (bioperl, biopython, biojava) though not heavily used. 
> 
> > 
> > Project:  Analyze the different sequence objects floating around and
> > determine how to integrate them (there has to be a core of essential
> > information that everyone is passing around).
> > 
> > We then need a sequence transducer class (subclassed from Bio::SeqIO) that
> > reads/writes Bio::Perl objects and .ace files and translates between them.
> > 
> 
> The Bio::SeqIO::ace would be great. Also viewing an AceDB as a
> Bio::DB::SeqI (a sequence database) would also be great. If that was done
> the "for free" you would get a biocorba server implemented in Perl , as
> the bioperl corba server is written to work on top of the Bio::DB::SeqI 
> interface (jason - feel free to correct me!)

Yep.  A biocorba seqDB is constructed with a Bio::DB::SeqI
object so if you follow this you can make an acedb file a seqdb that is
accessible in biocorba.

I'm working on detailed documentation and a step-by-step for setting up
Biocorba clients and servers to make it easier to know how to use it.

> 
> > Project:  Create a SeqAlign object in Bio::Perl that reads homol sections
> > from AceDB.
> > 
> 
> I don't think you want to make SeqAlign objects from AceDB homols, but
> rather Bio::SeqFeature::FeaturePair objects.
> 
> 
> > Project:  Using Bio::Perl blast parsing objects, store historical info/
> > parameters/ essential results from blast hits in AceDB.  With Blast used
> > for annotation, it would be helpful to have a way to reproduce the blast
> > search and look at some of the primary data without having to store
> > thousands of blast reports on your hard drive.
> > 
> > Anyone interested, reply to me, or post to BioPerl.
> > 
> > Dave Block
> > NRC PBI Saskatoon
> > 
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> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
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Jason Stajich
Center for Human Genetics
Duke University Medical Center
jason@chg.mc.duke.edu
(919)684-1806 (office)
(919)684-2275 (fax)
http://wwwchg.mc.duke.edu/




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