O'Reilly Bioinformatics Technology Conference.
Books Safari Bookshelf Conferences O'Reilly Network

Arrow Home
Arrow Registration
Arrow Speakers
Arrow Keynotes
Arrow Tutorials
Arrow Sessions
Arrow At-a-Glance
Arrow BOFs
Arrow Posters
Arrow Community
Arrow Events
Arrow Exhibitors
Arrow Sponsors
Arrow Hotel/Travel
Arrow Venue Map
Arrow See & Do
Arrow Press
Arrow Join Mailing List 
Arrow Related Reading

Practical Innovation at BioCon 2003


Swarms and Wrappers: Making High-performance Computing Accessible to Bench Scientists
Susan Chacko, Center for Information Technology, National Institutes of Health

Track: End-User Applications
Date: Tuesday, February 04
Time: 5:00pm - 5:45pm
Location: California Ballroom C

Molecular biologists are often the real end-users of bioinformatics software. They may have high-throughput needs, but are not comfortable in traditional high-performance Unix environments.

Biowulf, our 1.2+ teraflop Linux cluster, has a large collection of sequence analysis software that is used extensively by the NIH intramural scientific community.

Most bioinformatics software is not designed for clusters, and most bench scientists are not designed to deal with batch systems and distributed computing.

Chacko’s presentation discusses different approaches to adapting sequence analysis software, such as:

  • MPI wrappers for BLAST and BLAT
  • Enabling delivery of "swarms" of single-threaded jobs
  • Front-end scripts to mask the complexities of PVM and PBS

Download presentation file

oreilly.com Home | O'Reilly Bookstores | How to Order | O'Reilly Contacts
International | About O'Reilly | Affiliated Companies | Privacy Policy

© 2002, O'Reilly Media, Inc.