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Practical Tools For Innovation
O'Reilly Bioinformatics Technology Conference
January 28-31, 2002 -- Tucson, AZ
Chambered Nautilus


BioCORBA: Integrating Cross-Language Bioinformatics Solutions

Jason Stajich, Duke University

Track: Discovery
Date: Tuesday, January 29
Time: 2:15pm - 3:00pm
Location: Canyon II

Bioinformatics problems rarely have a one-language, one-platform solution. CORBA provides middleware connection for language and platform neutral solutions. BioCORBA provides a toolkit of generic biological objects suitable for creating specialized servers and clients in any language.

Developing a Standard
A consortium of developers from OMG, EBI, and the Open Bioinformatics Foundation helped create an interface design for standard objects in biological computing. There are bindings for BioCORBA to the BioPerl, BioJava, and BioPython (Bio{*}) open-source toolkits. Additional implementations have been written to the EBI analysis services and to proprietary systems by vendors such as NetGenetics. OMG is considering a proposal for BioCORBA to be the next Biological Sequence Analysis standard.

Transparent Data and Analysis Access
Developers with the Ensembl team at the EBI have built a CORBA layer derived from BioCORBA to allow development in Java, Python, and C with the Ensembl's Perl API. Other BioCORBA implementations allow users to submit and retrieve sequence analysis jobs transparently. Bindings in the Bio{*} toolkit allow one to program with the generic objects. This allows queries and analysis to be written independent of whether a job is submitted to a remote queue or local process. Home | Conferences Home | Bioinformatics Conference Home
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