Subject: Call for Participation for HiCOMB 2005 Workshop -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- CALL FOR PARTICIPATION HiCOMB 2005 4th 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 4, 2005 Omni Interlocken Resort, Denver, CO -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- HiCOMB 2005 Schedule April 4, 2005 Omni Interlocken Resort, Denver, CO -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- (Please see www.hicomb.org for any updated scheduling information.) 8:30- 8:40: Welcome Nancy M. Amato, Program Chair David A. Bader and Srinivas Aluru, Workshop Co-Chairs 8:40-10:10: SESSION 1: Sequence Alignment ESTmapper: Efficiently Aligning DNA Sequences to Genomes, Xue Wu, Woei-Jyh (Adam) Lee and Chau-Wen Tseng RC-BLAST: Towards an Open Source Hardware Implementation, Krishna Muriki, Keith Underwood and Ron Sass Comparison of Different Versions of Current BLAST Software on Nucleotide Sequences, I. Elizabeth Cha and Eric Rouchka 10:10-10:30: BREAK 10:30-12:00: SESSION 2: Programming Techniques & Tools A Case Study on Pattern-based Systems for High Performance, Weiguo Liu and Bertil Schmidt BioFilter: An architecture for parallel deployment and dynamic chaining of standalone bioinformatics tools, Thomas Brettin and Avinash Kewalramani An Efficient Program for Phylogenetic Inference Using Simulated Annealing, Alexandros Stamatakis 12:00- 1:30: LUNCH (on your own) 1:30- 2:30: SESSION 3: Sequence Analysis High-Performance Direct Pairwise Comparison of Large Genomic Sequences, Chris Mueller, Mehmet Dalkilic and Andrew Lumsdaine Statistical Methods for the Discovery of Co-operative Transcription Factors: the Co-bind code revised, Giovanni Lavorgna, Alessandro Marongiu, Simone Melchionna, Paolo Palazzari, Vittorio Rosato, and Paolo Verrecchia 2:30- 2:50: BREAK 2:50- 3:50: SESSION 4: Protein Structure FROST: Revisited and Distributed, Vincent Poirriez, Antoine Marin, Rumen Andonov and Jean-Francois Gibrat Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing, Michela Taufer, Chahm An, Andre Kerstens, and Charles L. Brooks III 3:50- 4:00: BREAK 4:00- 5:00: KEYNOTE TALK Folding@Home: Advances in biophysics and biomedicine from world-wide grid computing Vijay Pande, Stanford University -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- KEYNOTE TALK Folding@Home: Advances in biophysics and biomedicine from world-wide grid computing Vijay Pande Stanford University Abstract Simulations of biological molecules offers a lot of promise to complement and extend current experiments in the areas of biophysics and biomedicine. However, there are some serious limitations that must be overcome before computational methods are universally accepted. For example, one must be able to examine timescales that are thousands to billions of times longer than most typical simulations. How can one surmount such fundamental computational barriers? I will discuss our solutions to this problem, which combine novel physical chemistry theory and computational paradigms. In addition, I will discuss recent applications of these methods to fundamental questions in biophysics and biomedical applications, including protein folding, protein-protein association, protein-ligand binding, and protein misfolding & aggregation. Biography Prof. Pande's current research centers on the development and application of novel grid computing simulation techniques to address problems in chemical biology. In particular, he has pioneered novel distributed computing methodology to break fundamental barriers in the simulation of kinetics and thermodynamics of proteins and nucleic acids. As director of the Folding@Home project (http://folding.stanford.edu), Prof. Pande has, for the first time, directly simulated protein folding dynamics with quantitative comparisons with experiment, often considered a "holy grail" of computational biology. His current research also includes novel simulation methods for high precision drug binding affinity calculations, protein design, and synthetic bio-mimetic polymers. Prof. Pande received a BA in Physics Princeton University in 1992. There, he was first introduced to biophysical questions, especially in his undergraduate thesis research with Prof. Philip Anderson, a Nobel Laureate in physics. In 1995, he received his PhD in physics from MIT, studying as a NSF Fellow under Profs. Toyoichi Tanaka and Alexander Grosberg. At MIT, Prof. Pande's research centered on statistical mechanical models of protein folding and design, suggesting novel ways to design protein sequences to have the desired stability and folding properties. As a Miller Fellow working with Prof. Daniel Rokhsar at UC Berkeley, Prof. Pande extended this methodology to examine atomistic protein models, laying the foundations for his later work at Stanford University. Prof. Pande has won numerous awards, including most recently being named to MIT'S TR100 (top young innovators in 2002), a Frederick E. Terman Fellowship (2002), and a Henry and Camile Dreyfus Teacher-Scholar (2003). Prof. Pande is currently an Assistant Professor of Chemistry and (by courtesy) of Structural Biology. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Workshop Co-Chairs: ------------------- Prof. Srinivas Aluru Prof. David A. Bader Iowa State University University of New Mexico Program Chair: -------------- Nancy M. Amato, Texas A&M University Program Committee: ------------------ Frank Dehne (Griffith University) Ken Dill (University of California at San Francisco) Roland Dunbrack (Fox Chase Cancer Center) Guang Gao (University of Delaware) Atilla Gursoy (Koc University) Bruce Hendrickson (Sandia National Laboratory) Sorin Istrail (Celera) Joseph JaJa (University of Maryland) Laxmikant V. Kale (University of Illinois at Urbana-Champaign) Michael Langston (University of Tennessee) Jose Moreira (IBM T.J. Watson) Franco P. Preparata (Brown University) Geppino Pucci (University of Padova) Lawrence Rauchwerger (Texas A&M University) John Reif (Duke University) Joel Saltz (Ohio State University) Marc Snir (University of Illinois at Urbana-Champaign) Siang Wun Song (Univ. of Sao Paulo) Michael Thorpe (Arizona State University) Jerry Tsai (Texas A&M University) Tiffani Williams (Radcliffe Institute of Advanced Study) -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-