[Bioperl-l] Talking at BOSC???

[Ewan Birney]

For people who haven't seen the flyers, the due date for BOSC for
registration is the end of this month - as is ISMB's registration.
BOSC is running just before ISMB.


I'd love to see a strong bioperl presence giving talks at BOSC - we are
after all the oldest of the open source bioinformatics projects (well... 
depends if you count EGCG... hey ho). If you are coming to BOSC and one
of the bioperl developers, please consider submitting an abstract.


I will be submitting an abstract on Bioperl-db: Rough Draft below




Bioperl-db
----------

Ewan Birney


Bioperl-db is a first attempt at making a clean, simple, relational
database representation of sequence orientated bioinformatics objects. It
uses the Bioperl (and therefore the associated biocorba and bio* projects
in general) object model as a source for its design. It provides storage
for a number of associated pieces of information

   - Different "databases" (data collections) of sequences
   - Raw sequence information 
   - Sequence feature information 
   - annotation of sequences including
     - references
     - comments
     - database links

As well as providing this relational structure, bioperl-db comes with Perl
bindings that comply to the Bioperl "interface" definitions for the
appropiate objects, and the database code can store Bioperl interface
definitions. This object layer was modelled after the Ensembl/GadFly
"Adaptor" style interface and in particular provides for "lazy"
fetch-on-demand access of the data,
 

The result is a flexible system which can, for example,

   - read a flat file of sequences into the database

   - provide client/server access to sequence data objects, using 
     the SQL client/server connection

   - provide other bioperl interface using functions, eg, 
     running the Annotation Workbench or the Bioperl CORBA server
     from it

   - read from a different bioperl interface into the database,
     eg, a different BioCorba server can be cached locally 
     using this mechanism


I will discuss the design and implementation of the bioperl-db package





  




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