The O'Reilly Peer-to-Peer and Web Services Conference
oreilly.comO'Reilly Network
ConferencesInternationalSafari: Books Online


Arrow Home
Arrow Registration
Arrow Speakers
Arrow Keynotes
Arrow Tutorials
Arrow Sessions
Arrow BOFs
Arrow Community Meetings
Arrow Events
Arrow Exhibitors
Arrow Sponsors
Arrow Hotel/Travel
Arrow See & Do
Arrow Press
Arrow Mail List

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

Session

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.


oreilly.com Home | Conferences Home | Bioinformatics Conference Home
Registration | Speakers | Keynotes | Tutorials | Sessions | BOFs
Exhibitors | Sponsors | Hotel/Travel | Press | Mail List


© 2001, O'Reilly Media, Inc.