-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- CALL FOR PARTICIPATION HiCOMB 2008 7th 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 14, 2008 Miami, Florida -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2008 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 Bertil Schmidt, Program Chair 9:00-10:00: KEYNOTE TALK HPC-based Policy Informatics: A Public Health Epidemiology Example Christopher L. Barrett Virginia Bio-Informatics Institute and Dept of Computer Science Virginia Tech 10:00-10:30: BREAK 10:30-12:30: SESSION 1: High Performance Systems for Bioinformatics Design and Development of a FPGA-based Cascade Markov Model for Recognition of Steroid Hormone Response Elements M. Stepanova, F. Lin, V. Lin A Parallel Architecture for Regulatory Motif Algorithm Assessment D. Quest, K. Dempsey, D. Bastola, H. Ali Parallelized preprocessing algorithms for high-density oligonucleotide array data M. Schmidberger, U. Mansmann Supporting High Performance Bioinformatics Flat-File Data Processing X. Zhang, G. Agrawal 12:30- 1:30: LUNCH (on your own) 1:30- 3:00: SESSION 2: Sequence Analysis Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison D. Lavenier Sample-Align-D: A High Performance Multiple Sequence Alignment System using Phylogenetic Sampling and Domain Decomposition F. Saeed, A. Khokhar Adaptive Locality-Effective Kernel Methods for Phosphorylation Site Prediction P. Yoo, Y.S. Ho, B.B. Zhou, A. Zomaya 3:00- 3:30: BREAK 3:30- 5:00: SESSION 3: Biological Systems and Structures Impacts of Multicores on Large-scale Molecular Dynamics Simulations S. Alam, J. Vetter, P. Agarwal, H. Ong, S. Hampton Parallel, Scalable, Memory-Efficient Backtracking for Combinatorial Modeling of Large-Scale Biological Systems B.-H. Park, M. Schmidt, K. Thomas, T. Karpinets, N.F. Samatova On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks M. Taufer, T. Solorio, A. Licon, D. Mireles, M.-Y. Leung 5:00: END OF WORKSHOP -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2008 Keynote Talk HPC-based Policy Informatics: A Public Health Epidemiology Example Christopher L. Barrett Virginia Bio-Informatics Institute and Dept of Computer Science Virginia Tech Abstract: This talk outlines an HPC enabled, interaction-based approach to policy informatics and the detailed behavioral analysis of large complex systems. Policy problems typically consist of a large number of interacting physical, technological, and, importantly, human/societal components. Obvious examples of such systems involve biological systems, functioning societal infrastructures such as urban regional transportation systems, electrical power markets and grids, the Internet, ad-hoc communication and computing systems, public health, etc. All such systems share the essential feature of being networks; that is, individual agents/entities/ components interact in particular ways with a specified set of components. It has become widely appreciated that computer simulation aided support tools provide a compelling and practical approach for studying such systems. Quantitative changes in HPC capability have created qualitative changes in the way information can be integrated in analysis of these large heterogenous systems. In particular, we will discuss examples of, and some issuses with, expanded use of knowledge held as procedural information in combination with measured data. The approach we describe has three thrusts: (i) detailed representation: an interaction-based, high performance computing oriented, modeling environment for situation assessment and course of action analysis, (ii) Simfrastructure: a service oriented HPC-based cyber-architecture for coordinating models, data and decision support systems, and (iii) synthetic information: integrating diverse measured and simulated data to synthesize new composite system knowledge. After a brief overview, I will describe the our approach within the context of a specific application: development of modeling and decision support environments to study public health planning related to epidemics of infectious diseases. Speaker Biography: Christopher Louis Barrett is the Director of Network Dynamics and Simulation Science Laboratory of the Virginia Bioinformatics Institute at Virginia Tech and Professor of Computer Science. His work includes the development of large-scale, high performance simulation systems, the development of a distributed computing approach for detailed simulation-based study of large socio-technical systems and formal approaches to interaction-based systems. Before moving to Virginia Tech in 2004, he led the Basic and Applied Simulation Science Group at Los Alamos National Laboratory. He has also been a guest professor at KTH, Stockholm Sweden, and serves on several scientific advisory boards. Dr. Barrett holds MS and PhD degrees from the California Institute of Technology. Dr. Barrett and his group have developed many large simulation environments, among them, distributed communication and sensor systems, TRANSIMS, EPISIMS, Marketecture, Urban Infrastructure Suite and co-established the National Infrastructure Simulation and Analysis Center (NISAC) at DHS. Additionally, they have developed and continue to study Sequential Dynamical Systems (SDS) which provide a formal foundation for interaction-based systems and agent-based simulations. Education. Post PhD certification, US Navy Aerospace, Experimental Psychology, 1986 PhD, Bioinformation Systems/Engineering Science, California Institute of Technology, 1985 MS, California Institute of Technology, Engineering Science, 1983 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Workshop Co-Chairs: ------------------- David A. Bader, Georgia Institute of Technology Srinivas Aluru, Iowa State University Program Chair: ------------------ Bertil Schmidt, NICTA, University of Melbourne Program Committee: ------------------ Alexandros Stamatakis, EPFL, Switzerland Michela Taufer, University of Delaware, USA Albert Zomaya, University of Sydney, Australia Jaroslaw Zola, Iowa State, USA Ananth Kalyanaraman, Washington State, USA Dominique Lavenier, IRISA, France Weiguo Liu, NTU, Singapore Heiko Schroder, RMIT, Australia Feng Lin, NTU, Singapore Vipin Chaudhary, SUNY Buffalo, USA Jeremy Buhler, Washington University, USA Martin Middendorf, University of Leipzig, Germany Bharadwaj Veeravalli, National University of Singapore, Singapore -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-