-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- CALL FOR PARTICIPATION HiCOMB 2009 8th IEEE International Workshop on High Performance Computational Biology http://www.hicomb.org/ held in conjunction with the International Parallel and Distributed Processing Symposium http://www.ipdps.org/ Rome, Italy -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2009 Schedule (Please see www.hicomb.org for any updated scheduling information.) 8:10 - 8:20: Welcome and Workshop Introduction 8:20 - 10:00: SESSION I: HPC and Graphics Processing Units Chair: Srinivas Aluru, Iowa State University - An Efficient Implementation Smith Waterman Algorithm on GPU using CUDA, for Massively Parallel Scanning of Sequence Databases Lukasz Ligowski and Witold Rudnicki - Parallel Reconstruction of Neighbor-Joining Trees for Large Multiple Sequence Alignments using CUDA Yongchao Liu, Bertil Schmidt, and Douglas Maskell - Accelerating Error Correction in High-Throughput Short-Read DNA Sequencing Data with CUDA Haixiang Shi, Bertil Schmidt, Weiguo Liu, and Wolfgang Mueller-Wittig - Long Time-scale Simulations of in vivo Diffusion using GPU Hardware Elijah Roberts, John Stone, Leonardo Sepulveda, Wen-Mei Hwu, and Zaida Luthey-Schulten 10:00: BREAK 10:30: KEYNOTE TALK Chair: Michela Taufer, University of Delaware - De Novo Modeling of GPCR Class A Structures Charles L. Brooks III, University of Michigan at Ann Arbor 11:30 - 12:20: SESSION II: Grid Computing Chair: Michela Taufer, University of Delaware - Folding@home: Lessons From Eight Years of Volunteer Distributed Computing Adam L. Beberg, Guha Jayachandran, Siraj Khaliq, Vijay S. Pande - High-throughput Protein Structure Determination using Grid Computing Jason W. Schmidberger, Blair Bethwaite, Colin Enticott, Mark A. Bate, Steve G. Androulakis, Noel Faux, Cyril F. Reboul, Jennifer M. N. Phan, James C. Whisstock, Wojtek J. Goscinski, Slavisa Garic, David Abramson, and Ashley M. Buckle 12:20: LUNCH 13:45 - 3:00: SESSION III: Parallelization Techniques Chair: Bertil Schmidt, Nanyang Technological University - Dynamic Parallelization for RNA Structure Comparison Eric Aubanel, Patricia Evans, and Eric Snow - A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications Yaohang Li, Dougalas Wardell, and Vincent Freeh - Parallel Monte Carlo Study on Caffeine-DNA Interaction in Aqueous Solution Michael Kalugin and Alexandr Teplukhin 3:00: BREAK 3:30 - 4:45: SESSION IV: Reconfigurable Architectures and Novel Frameworks Chair: Adam Beberg, Stanford University - Exploring FPGAs for Accelerating the Phylogenetic Likelihood Function Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, and Alexandros Stamatakis - HMMer Acceleration Using Systolic Array Based Reconfigurable Architecture Yanteng Sun, Peng Li, Guochang Gu, Yuan Wen, Yuan Liu, and Dong Liu - A Novel Framework for Modeling Ion Channels May Siksik and Vikram Krishnamurthy 4:45: END OF WORKSHOP Please note that all presentations are scheduled for 25 minutes, including 5 minutes of Q&A time. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2009 Keynote Talk De Novo Modeling of GPCR Class A Structures Charles L. Brooks, III University of Michigan, Ann Arbor Abstract: In this talk I will describe recent work to develop novel methods to model GPCR structures from their sequence information and statistically significant side chain contacts within a "template" structure. Our approach utilizes methods of bioinformatics to identify likely high confidence side chain side chain TM helical contacts and then reconstitutes the seven TM helical domain through a simulated annealing protocol with refinement using replica exchange and an implicit solvent/implicit membrane sampling scheme. Results will be presented for de novo prediction of the b2 adenergic receptor, the adenine receptor and a number of other amine receptors. Speaker Biography: Charles L. Brooks III is the Warner-Lambert Professor of Chemistry and Professor of Biophysics at the University of Michigan. Prior to moving to Michigan in 2008, Professor Brooks was professor of Molecular Biology at The Scripps Research Institute since 1994 and professor of Chemistry at Carnegie Mellon University until 1993, where he began as an assistant professor in 1985. Professor Brooks received his undergraduate training in chemistry, physics and mathematics from Alma College. He studied chemical physics at Purdue University, where he received his Ph.D. in 1982, and was a postdoctoral fellow at Harvard University from 1982-85. Professor Brooks' research focuses on the applications of statistical mechanics, quantum chemistry, and computational methods to solve chemically and physically oriented problems in biology. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Workshop Co-Chairs: ------------------- David A. Bader, Georgia Institute of Technology Srinivas Aluru, Iowa State University Program Chair: ------------------ Michela Taufer, University of Delaware Program Committee: ------------------ - Dmitry A. Afonnikov, Institute of Cytology and Genetics SB RAS, Novosibirsk and Novosibirsk State University (Russia) - Pratul K. Agarwal, Oak Ridge National Laboratory (USA) - Nancy Amato, Texas A&M University (USA) - Roger Armen, University of Michigan at Ann Arbor (USA) - Georg Fuellen, Ernst-Moritz-Arndt-University Greifswald (Germany) - Concettina Guerra, Georgia Tech (USA) and University of Padova (Italy) - Ming-Ying Leung, University of Texas at El Paso (USA) - Mark Miller, San Diego Supercomputer Center (USA) - Aiichiro Nakano, University of South California (USA) - Sandeep Patel, University of Delaware (USA) - Geppino Pucci, University of Padova (Italy) - Jacques Rougemont, EPFL (Switzerland) - Alexandros Stamatakis, Ludwig-Maximilians-University Munich (Germany) - Bertil Schmidt, Nanyang Technological University (Singapore) - Heiko Schroder, RMIT University (Australia) - John Stone, University of Illinois at Urbana-Champaign (USA) - Wing-Kin Sung, National University of Singapore (Singapore) - Jim Tisdall, DuPont (USA) - Chau-Wen Tseng, University of Maryland, College Park (USA) -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-