VISUALIZATION

HiCOMB 2003 - 2nd IEEE International Workshop On High Performance Computational Biology www.hicomb.org held in conjunction with the International Parallel and Distributed Processing Symposium www.ipdps.org April 22, 2003 Nice Acropolis Convention Center, Nice, France 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. Please see www.hicomb.org for speaker's biography and any updated scheduling information. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2003 Schedule April 22, 2003 Nice Acropolis Convention Center, Nice, France -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 8:45am -- 9:00am Introduction and Welcome David A. Bader and Srinivas Aluru 9:00am -- 10:00am KEYNOTE TALK Blue Gene: Massively Parallel Computing for Biomolecular Simulation Robert S. German, IBM 10:00am -- 10:30am BREAK 10:30am -- 12:00pm SESSION 1 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 Mari'n 12:00pm -- 1:30pm LUNCH 1:30pm -- 3:00pm SESSION 2 Realtime Primer Design for DNA chips Harald Simmler, H. Singpiel, and R. Ma"nner Accurate method for fast design of diagnostic oligonucleotide probe sets for DNA microarrays Andreas Krause, Markus Kra"utner, 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 3:00pm -- 3:30pm BREAK 3:30pm -- 5:00pm SESSION 3 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 5:00pm -- 5:30pm BREAK 5:30pm -- 7:00pm SESSION 4 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 7:00pm WRAPUP -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Workshop Co-Chairs: ------------------- Prof. Srinivas Aluru Prof. David A. Bader Electrical & Computer Engg. Electrical & Computer Engg. Iowa State University University of New Mexico 3218 Coover Hall Albuquerque, NM 87131 USA Ames, IA 50014 USA Email: dbader@eece.unm.edu Email: aluru@iastate.edu Tel: 505-277-6724 Tel: 515-294-3539 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 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-