Bioperl: Bio* integration with AceDB

David Block
Thu, 15 Jun 2000 16:31:05 -0600 (CST)

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.

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

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.

Project:  Create a SeqAlign object in Bio::Perl that reads homol sections
from AceDB.

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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