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HiCOMB 2003 Keynote Talk

Blue Gene: Massively Parallel Computing for Biomolecular Simulation

This talk will give an overview of and current update on IBM's Blue Gene project, which was announced in 1999 as a multi-year initiative to advance our understanding of biological phenomena such as protein folding via large scale simulation and to push the boundaries in parallel machine architecture. The first member of the Blue Gene family, BG/L, is being developed in collaboration with the Lawrence Livermore National Laboratory and will be a 65,000 node machine with a projected peak performance of 180/360TF. Following an overview of the machine architecture and the science related to protein dynamics that we hope to probe with this machine, some of the issues involved in mapping a biomolecular simulation application onto such a machine will be discussed along with some options for taking advantage of the BG/L interconnection networks (torus and global tree). The simple performance models being used to prioritize our development efforts will be described including communications estimates for the three dimensional FFT required for our treatment of periodic electrostatics.

Biography: Robert S. Germain manages the Biomolecular Dynamics and Scalable Modeling group within the Computational Biology Center at the IBM Thomas J. Watson Research Center. He received his A.B. in physics from Princeton University in 1982 and his M.S. and Ph.D. in physics from Cornell University in 1986 and 1989 respectively. After receiving his doctorate, Germain joined the Watson Research Center as a Research Staff Member in the Physical Sciences Department. From 1995 to 1998, he was project leader for development of a large scale fingerprint identification system using an indexing scheme (FLASH) developed in IBM Research. Following this project, as manager of the Scalable Similarity Searching group, he assumed responsibility for managing ongoing work in flexible molecular matching and moment-based molecular similarity (CoMMA). Since 2000, Dr. Germain has been responsible for the science and application portions of the Blue Gene project. His current research interests include the parallel implementation of algorithms for high performance scientific computing, the development of new programming models for parallel computing, and applications of high performance computing to challenging scientific problems in computational biology. Dr. Germain is a member of the IEEE and the American Physical Society.

Papers to be presented at HiCOMB 2003:

• Sequence Alignment on the Cray MTA-2
  Shahid H. Bokhari and Jon R. Sauer
• Using Hybrid Alignment for Iterative Sequence Database Searches
  Yuheng Li, Mario Lauria, and Ralf Bundschuh
• A Fast Algorithm for the Exhaustive Analysis of 12-Nucleotide-Long DNA Sequences: Applications to Human Genomics
  Vicente Arnau and Ignacio Marín
• Realtime Primer Design for DNA chips
  Harald Simmler, H. Singpiel, and R. Männer
• Accurate method for fast design of diagnostic oligonucleotide probe sets for DNA microarrays
  Andreas Krause, Markus Kräutner, and Harald Meier
• Gene Clustering using Self-Organizing Maps and Particle Swarm Optimization
  X. Xiao, E. Dow, R. Eberhart, Z. Ben Miled, and R. J. Oppelt
• Protein Structure Prediction by Applying an Evolutionary Algorithm
  Richard O. Day, Gary B. Lamont, and Ruth Pachter
• PROSIDIS: a Special Purpose Processor for PROtein SImilarity DIScovery
  A. Marongiu, P. Palazzari, and V. Rosato
• Parallelisation of IBD computation for determining genetic disease map
  Nouhad J. Rizk
• Parallel Detection of Regulatory Elements with gMP
  Bertil Schmidt, Lin Feng, Amey Laud, and Yusdi Santoso
• Solving the Protein Threading Problem in Parallel
  Nicola Yanev and Rumen Andonov
• Phylogenetic Tree Inference on PC Architectures with AxML/PAxML
  Alexandros P. Stamatakis and Thomas Ludwig

Workshop Co-Chairs
 

David A. Bader Electrical & Computer Engr. Dept. University of New Mexico Albuquerque, NM 87131 USA Phone: +1.505.277.6724 Fax: +1.505.277.1439 email: dbader@eece.unm.edu

Srinivas Aluru Dept. of Electrical & Computer Engg. and Lawrence H. Baker Center for Bioinformatics          & Biological Statistics Iowa State University 3218 Coover Hall Ames, IA 50011, USA Phone: +1.515.294.3539 Fax: +1.515.294.8432 email: aluru@iastate.edu

Program Committee
 

Suchendra Bhandarkar, University of Georgia Alok Choudhary, Northwestern University David W. Deerfield II, Pittsburgh Supercomputing Center Gao Guang, University of Delaware Bruce Hendrickson, Sandia National Laboratories Joseph Ja'Ja', University of Maryland Suraj Kothari, Iowa State University Timothy Mattson, Intel Corporation John Reynders, Celera Joel Saltz, Ohio State University Quinn Snell, Brigham Young University Stefan Unger, Sun Microsystems Geert Wenes, National Center for Genome Resources Albert Y. Zomaya, University of Western Australia

For up-to-date information about this workshop, please visit http://www.hicomb.org/.