HiCOMB 2003
Second IEEE International Workshop on High Performance Computational Biology

Tuesday, April 22, 2003
Nice Acropolis Convention Center, Nice, France

(Held in conjunction with the International Parallel and Distributed Processing Symposium)


HiCOMB Online Proceedings

Advance Program for HiCOMB 2003

Online Registration for IPDPS

HiCOMB 2003 Keynote Talk

Blue Gene: Massively Parallel Computing for Biomolecular Simulation

Robert S. Germain
Manager, Biomolecular Dynamics and Scalable Modeling
IBM Thomas J. Watson Research Center

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:

Call For Papers (paper submission deadline has passed)

Computational Biology is fast emerging as an important discipline for academic research and industrial application. The large size of biological data sets, inherent complexity of biological problems and the ability to deal with error-prone data all result in large run-time and memory requirements. The goal of this workshop is to provide a forum for discussion of latest research in developing high-performance computing solutions to problems arising from molecular biology. We are especially interested in parallel algorithms, memory- efficient algorithms, large scale data mining techniques, and design of high-performance software. The workshop will feature contributed papers as well as invited talks from reputed researchers in the field.

Topics of interest include but are not limited to:

Submission guidelines:

Papers reporting on original research (both theoretical and experimental) in all areas of bioinformatics and computational biology are sought. Surveys of important recent results and directions are also welcome. To submit a paper, send a postscript copy of the paper by email to one of the workshop co-chairs. The paper should not exceed 12 single-spaced pages (US Letter or A4 size) in 11pt font or larger. All papers will be reviewed. IEEE CS Press will publish the IPDPS symposium and workshop abstracts as a printed volume. The complete symposium and workshop proceedings will also be published by IEEE CS Press as a CD-ROM disk.

Important Dates
November 29, 2002
December 31, 2002
January 24, 2003
Workshop Paper Due
Author Notification
Camera-ready Paper Due

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/.

Call for Papers for HiCOMB 2003:

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Last updated: Tue Mar 25 09:35:49 MST 2003