HiCOMB 2010 Keynote Talk

Analysis and Design of Organizational Computational Science

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

Papers to be presented at HiCOMB 2010:

• GPU-Accelerated Multi-scoring Functions Protein Loop Structure Sampling
  Yaohang Li and Weihang Zhu
• Acceleration of Spiking Neural Networks in Emerging Multi-core and GPU Architectures
  Mohammad A. Bhuiyan, Vivek K. Pallipuram and Melissa C. Smith
• 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
• 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
• Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform
  Doruk Bozdag, Ayat Hatem, 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

HiCOMB 2010 Call For Papers

Computational Biology are related disciplines are fast emerging as an important area for academic research and industrial application. The large size of biological data sets, inherent complexity of biological problems and the ability to deal with error-prone data all result in large run-time and memory requirements. The goal of this workshop is to provide a forum for discussion of latest research in developing high-performance computing solutions to problems arising from molecular biology and related life sciences areas. We are especially interested in parallel algorithms, memory-efficient algorithms, large scale data mining techniques, and design of high-performance software. The workshop will feature contributed papers as well as invited talks from reputed researchers in the field.

Topics of interest include but are not limited to:

• Bioinformatic databases
• Computational genomics
• Computational proteomics
• DNA assembly, clustering, and mapping
• Gene expression and microarrays
• Gene identification and annotation
• Parallel algorithms for biological analysis
• Parallel architectures for biological applications
• Molecular evolution
• Molecular sequence analysis
• Phylogeny reconstruction algorithms
• Protein structure prediction and modeling
• String data structures and algorithms
• Parallel algorithms in chemical genetics and chemical informatics

Submission guidelines:

Papers reporting on original research (both theoretical and experimental) in all areas of bioinformatics and computational biology are sought. Surveys of important recent results and directions are also welcome. To submit a paper, upload a postscript or PDF copy of the paper here. The paper should not exceed 12 single-spaced pages (US Letter or A4 size) in 11pt font or larger. All papers will be reviewed. IEEE CS Press will publish the IPDPS symposium and workshop abstracts as a printed volume. The complete symposium and workshop proceedings will also be published by IEEE CS Press on CD-ROM and will also be available in the IEEE Digital Library.

Important Dates

Workshop Co-Chairs

Program Chair

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 Universität 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

For up-to-date information about this workshop, please visit http://www.hicomb.org/.

Call for Papers for HiCOMB 2010:

• ASCII Format
• PDF Format

Previous meetings

• 8th International Workshop on High Performance Computational Biology (HiCOMB 2009)
• 7th International Workshop on High Performance Computational Biology (HiCOMB 2008)
• 6th International Workshop on High Performance Computational Biology (HiCOMB 2007)
• 5th International Workshop on High Performance Computational Biology (HiCOMB 2006)
• 4th International Workshop on High Performance Computational Biology (HiCOMB 2005)
• 3rd International Workshop on High Performance Computational Biology (HiCOMB 2004)
• 2nd International Workshop on High Performance Computational Biology (HiCOMB 2003)
• 1st International Workshop on High Performance Computational Biology (HiCOMB 2002)