-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- CALL FOR PARTICIPATION HiCOMB 2010 9th 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/ April 19, 2010 Atlanta, Georgia -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2010 Schedule (Please see www.hicomb.org for any updated scheduling information.) 8:45- 9:00: WELCOME David A. Bader and Srinivas Aluru, Workshop Co-Chairs George Karypis, Program Chair 9:00-10:00: KEYNOTE TALK Analysis and Design of Organizational Computational Science Christopher A. Lynberg Centers for Disease Control and Prevention IT Research & Development 10:00-10:30: BREAK 10:30-12:30: SESSION 1: Emerging HPC Architectures Acceleration of Spiking Neural Networks in Emerging Multi-core and GPU Architectures Mohammad A. Bhuiyan, Vivek K. Pallipuram, and Melissa Smith GPU-Accelerated Multi-scoring Functions Protein Loop Structure Sampling Yaohang Li and Weihang Zhu A Tile-based Parallel Viterbi Algorithm for Biological Sequence Alignment on GPU with CUDA Zhihui Du, Zhaoming Yin, and David A. Bader Fast Binding Site Mapping using GPU and CUDA Bharat Sukhwani and Martin Herbordt 12:30- 1:30: LUNCH (on your own) 1:30- 3:00: SESSION 2: Sequence Analysis Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform Doruk Bozdag, Ayat Hatem, and Umit V. Catalyurek pFANGS: Parallel High Speed Sequence Mapping for Next Generation 454-Roche Sequencing Reads Sanchit Misra, Ramanathan Narayanan, Wei-keng Liao, Alok Choudhary, and Simon Lin Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild- populations Saad Sheikh, Ashfaq Khokhar, and Tanya Berger-Wolf 3:00- 3:30: BREAK 3:30- 5:00: SESSION 3: HPC for Bioinformatics Hybrid MPI/Pthreads Parallelization of the RAxML Phylogenetics Code Wayne Pfeiffer and Alexandros Stamatakis Measuring Properties of Molecular Surfaces Using Ray Casting Mike Phillips, Iliyan Georgiev, Anna Dehof, Lukas Marsalek, Hans-Peter Lenhof, Andreas Hildebrandt, and Philipp Slusallek On the Parallelisation of MCMC-based Image Processing Jonathan M R Byrd, Stephen A Jarvis, and Abhir H. Bhalerao 5:00: END OF WORKSHOP -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2010 Keynote Talk Analysis and Design of Organizational Computational Science Christopher A. Lynberg Centers for Disease Control and Prevention IT Research & Development Abstract: "CDC's ultimate goal: to better prevent illness, disability, and death" inevitably leads to increased national productivity thus benefitting individuals and society as a whole. Viable public health science drives CDC's progress toward attaining its health goals. CDC scientist are increasingly turning towards modeling and simulation as the third pillar of science, aside from theory and experiment, which led to the need to formalize computational science strategies within the agency. The architectural blueprinting of Computational Science provides CDC with a foundation for modernizing its computational science while also harmonizing the business, science, computational science, computer science, and information technology domains of CDC. While important movement toward this formalization has been made, challenges continue to exist that may also be experienced by other organizations. Speaker Biography: Christopher A. Lynberg is a computer scientist responsible for enterprise information technology research and development at CDC. His work began at CDC in 1988 and broadly covers any aspect of IT R&D, and has been responsible for the R&D and enterprise implementations of networking, operating systems, messaging and directory systems, setting standards, technical evaluations, R&D reports, white papers, and proposals to advance CDC's business and scientific information technologies.. Prior to his work at CDC he developed parallelized demodulation algorithms. Prior to working for the DoD he worked in biological research labs at the University of Iowa and UCLA developing monoclonal antibodies against prostate cancer, identifying the target cells of HIV, and researching dioxin biochemistry. Education. BS Microbiology/Chemistry 1980: University of Iowa BS Electrical Engineering 1987: University of Iowa -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Workshop Co-Chairs: ------------------- David A. Bader, Georgia Institute of Technology Srinivas Aluru, Iowa State University Program Chair: ------------------ George Karypis, University of Minnesota Program Committee: ------------------ Pratul K. Agarwal, Oak Ridge National Laboratory, USA Inanc Birol, Genome Sciences Centre, British Columbia, Canada Georg Fuellen, University of Rostock, Rostock, Germany Ananth Grama, Purdue University, Indiana, USA Mark Miller, San Diego Supecomputer Center, California, USA Sandeep Patel, University of Delaware, USA Andrew Rau-Chaplin, Dalhousie University, Nova Scotia, Canada Huzefa Rangwala, George Mason University, Virginia, USA Jared Simpson, Wellcome Trust Sanger Institute, Cambridge, UK Alexandros Stamatakis, Technische Universitat Munchen, Munich, Germany John Stone, University of Illinois at Urbana-Champaign, USA Evripidis Sotiriadis, Tech. Univ. of Crete, Greece Denis Trystram, LIG, France Chau-Wen Tseng, University of Maryland, College Park, USA Ian Watson, Lilly, Indiana, USA Tiffani Williams, Texas A\&M University, Texas, USA Ying Zhao, Tsinghua University, Beijing, China Albert Zomaya, University of Sydney, Sydney, Australia -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-