INDUSTRY

HiCOMB 2007, 6th IEEE International Workshop on High Performance Computational Biology held in conjunction with the International Parallel and Distributed Processing Symposium March 26, 2007, Long Beach, California. HiCOMB 2007 Schedule (Please see its Web site for any updated scheduling information.) 8:45- 9:00: WELCOME Ananth Grama and Shankar Subramaniam, Program Co-Chairs David A. Bader and Srinivas Aluru, Workshop Co-Chairs 9:00-10:00: KEYNOTE TALK Optical Mapping of the Maize Genome Michael S. Waterman 10:00-10:15: BREAK 10:15-12:15: SESSION 1: Biomolecular Simulation Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures Jeremy Meredith, Sadaf Alam, Jeffrey S. Vetter Data-Driven Time-Parallelization in the AFM Simulation of Proteins Lei Ji, Hugh Nymeyer, Ashok Srinivasan, Yanan Yu Biomolecular Path Sampling Enabled by Processing in Network Storage Paul Brenner, Justin Wozniak, Jesus Izaguirre, Aaron Striegel, Douglas Thain, Jeff Peng On the path to enable multi-scale biomolecular simulations on Petaflop supercomputer with multi-core processors Sadaf Alam, Pratul Agarwal 12:15- 1:30: LUNCH (on your own) 1:30- 3:00: SESSION 2: Bioinformatics and Homology Search Exploring the viability of the Cell Broadband Engine for bioinformatics applications Vipin Sachdeva, Mike Kistler, Evan Speight, Tzy-Hwa Kathy Tzeng Preliminary results in accelerating profile HMM search on FPGAs Arpith Jacob, Joseph Lancaster, Jeremy Buhler, Roger Chamberlain High Performance Database Searching with HMMer on FPGAs Tim Oliver, Leow Yuan Yeow, Bertil Schmidt 3:00- 3:30: BREAK 3:30- 5:00: SESSION 3: Protein Interaction Networks and Virus Structure A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multicore Parallel Algorithms David A. Bader, Kamesh Madduri RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology Michela Taufer, Ming-Ying Leung, Kyle L. Johnson, Abel Licon An Automated Data Processing Pipeline for Virus Structure Determination at High Resolution Chen Yu, Dan C. Marinescu, John P. Morrison, Brian C. Clayton, David A. Power 5:00: END OF WORKSHOP -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2007 Keynote Talk Optical Mapping of the Maize Genome Michael S. Waterman University of Southern California Abstract: A new technology, optical mapping, is used to infer the genome map of the location of short sequence patterns called restriction sites. The technology, developed by David Schwartz, allows the visualization of the maps of randomly located single molecules of length from one-half to one million base pairs. The genome map is constructed from overlapping these shorter maps. The substantial mathematical and computational challenges come from modeling the measurement errors and from the process of map assembly. We will report on our experience with assembling the maize genome. Speaker Biography: Michael Waterman holds an Endowed Associates Chair at USC. He came to USC in 1982 after positions at Los Alamos National Laboratory and Idaho State University. He has a bachelors in Mathematics from Oregon State University, and a Ph.D. in Statistics and Probability is from Michigan State University. He was named a Guggenheim Fellow (1995), was elected to the American Academy of Art and Sciences (1995), and was elected to the National Academy of Sciences (2001). Also he is a Fellow of the American Association for the Advancement of Science and Fellow of the Institute of Mathematical Statistics. He has held visiting positions at the University of Hawaii (1979-80), the University of California at San Francisco (1982), Mt. Sinai Medical School (1988), Chalmers University (2000), and in 2000-2001 he held the Aisenstadt Chair at University of Montreal. He is Professor-at-large at the Keck Graduate Institute of Life Sciences and in fall 2000 he became the first Fellow of Celera Genomics In 2002 he received a Gairdner Foundation International Award and in 2005 he was elected to the French Acadimie des Sciences. Beginning Fall 2003, Professor Waterman became Faculty Master of Parkside International Residence College. PIRC is a residental college that is home to over 600 undergraduates and serves as a center for internationally oriented culutral, academic and social events. Professor Waterman works in the area of Computational Biology, concentrating on the creation and application of mathematics, statistics and computer science to molecular biology, particularly to DNA, RNA and protein sequence data. He is the co-developer of the Smith-Waterman algorithm for sequence comparison and of the Lander-Waterman formula for physical mapping. He is a founding editor of Journal of Computational Biology, is on the editorial board of seven journals, and is co-author of the texts Computational Genome Analysis: An Introduction and Introduction to Computational Biology: Maps, Sequences and Genomes. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Workshop Co-Chairs: ------------------- David A. Bader, Georgia Institute of Technology Srinivas Aluru, Iowa State University Program Co-Chairs: ------------------ Ananth Grama, Purdue University Shankar Subramaniam, University of California, San Diego Program Committee: ------------------ Alberto Apostolico, Accademia dei Lincei & Georgia Tech Joel Bader, Johns Hopkins University Vineet Bafna, University of California San Diego Jesus Izaguirre, University of Notre Dame George Karypis, University of Minnesota Daisuke Kihara, Purdue University Vipin Kumar, University of Minnesota Satoru Miyano, HGC, University of Tokyo Ben Raphael, Brown University Naren Ramakrishnan, Virginia Tech Joel Saltz, Ohio State Mona Singh, Princeton University Tandy Warnow, University of Texas, Austin -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-