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Advance Program for HiCOMB 2008

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HiCOMB 2008 Keynote Talk

HPC-based Policy Informatics: A Public Health Epidemiology Example

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

Papers to be presented at HiCOMB 2008:

• Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison
  D. Lavenier
• 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
• Parallelized preprocessing algorithms for high-density oligonucleotide array data
  M. Schmidberger, U. Mansmann
• On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks
  M. Taufer, T. Solorio, A. Licon, D. Mireles, M.-Y. Leung
• A Parallel Architecture for Regulatory Motif Algorithm Assessment
  D. Quest, K. Dempsey, D. Bastola, H. Ali
• Design and Development of a FPGA-based Cascade Markov Model for Recognition of Steroid Hormone Response Elements
  M. Stepanova, F. Lin, V. Lin
• Supporting High Performance Bioinformatics Flat-File Data Processing
  X. Zhang, G. Agrawal
• 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
• Impacts of Multicores on Large-scale Molecular Dynamics Simulations
  S. Alam, J. Vetter, P. Agarwal, H. Ong, S. Hampton

HiCOMB 2008 Call For Papers

Computational Biology is fast emerging as an important discipline 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. 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

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

• 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

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

Call for Papers for HiCOMB 2008:

• ASCII Format
• PDF Format

Previous meetings

• 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)