IU-led activities in Computational Biology and Bioinformatics at BIBE07



Indiana University is leading two important events at the BIBE07 (BioInformatics and Biomedical Engineering) conference to be held October 14-17 at the Harvard Medical School Conference Center in Boston, MA. Dr. Craig Stewart, Associate Dean for Research Technologies at IU, will give a tutorial lecture on Sunday, October 14, from 4:40-5:15 on two key resources available to the national research community via the NSF-funded TeraGrid: IU's Big Red supercomputer and IU's archival tape storage system. Indiana University's 30.6 TFLOPS IBM e1350 cluster is among the larger supercomputers integrated with the TeraGrid. Big Red has proven particularly popular with users of molecular dynamics codes, and supports NAMD, Amber, and CHARMM. Dr. Stewart will also present information on how to store data in IU's HPSS archival storage system via the TeraGrid. HPSS was initially developed for national weapons labs; it is extremely robust and secure, and offers excellent performance. IU's HPSS installation is unique within the TeraGrid in that data are by default copied to two geographically separated tape silos, providing extreme reliability in data storage. Use of HPSS via the TeraGrid is relatively simple, and a short amount of time will be devoted to instructing participants in how to access HPSS via gridftp and the TeraGrid. The tutorial lecture will also include information about new services being offered by IU, including the hosting of servers that deliver data and services through Service Oriented Architecture protocols such as WSDL. Some of the first services hosted will be bioinformatics services delivered by Web Services.

IU is also coordinating a workshop on PetaScale Applications in Biology, to be held on the afternoon of October 15. Papers to be presented in this workshop include:
  • R. Henschel and M. Mueller. I/O Induced scalability limits of bioinformatics applications
  • M. Freindorf et al. Large-Scale QM/MM Calculations of electronic excitations in yellow protein: toward petascale levels of protein calculations
  • J. Tilson et al. MotifNework: Genome-wide domain analysis using grid-enabled workflows
  • Baden et al. Toward petascale simulation of cellular microphysiology.
  • S. Alam et al. Performance evaluation of a scalable molecular dynamics simulation framework on a massively-parallel system.

BIBE07 promises an exciting agenda overall, and the contributions from IU as regards computational biology and bioinformatics should add to the benefits of attending a highly valuable conference.

Schedule

  • Where Boston, MA; Harvard Medical School Conference Center
  • When  Oct 14
  • Time   4:40pm-5:15pm

Registration

This workshop is free and open for all conference attendees, but registration is required and limited. To register, contact the UITS-RT-HPC group using the UITS web email form: http://uits.iu.edu/scripts/email.php4?entry=58

Online notes

We will use online notes available at http://rc.uits.indiana.edu/hpc/workshops/bibe2007/notes.html for this workshop.

Who would benefit?

If you would like to learn about the TeraGrid, or you are a new TeraGrid user, and you have a specific allocation on IU's Big Red cluster or you have a roaming allocation that allows you to login to Big Red.

Pre-requisites

Very basic UNIX skills are needed -- if you've worked on a UNIX-based system before, then you should be fine.