12th IEEE International Workshop on High Performance Computational Biology
Monday, May 20, 2013
Boston, Massachusetts, USA

  In conjunction with the International Parallel and Distributed Processing Symposium

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News

  • 03/15/2013 - Advance program is now available!
  • 01/14/2013 - Registration is now open. You can register for the entire IPDPS, or just "One Day (Monday or Friday Only)".
  • 12/26/2012 - The HiCOMB deadline extended to January 4, 2013.
  • 11/16/2012 - We are happy to announce that Prof. George Karniadakis will deliver this year keynote talk!
  • 10/12/2012 - Updated call for papers announced! Deadlines have been changed in tune with IPDPS.
  • 09/10/2012 - Call for Papers is now available.

HiCOMB 2013 Keynote Talk

Parallel Multiscale Simulations of Brain Aneurysms

George Karniadakis, Brown University

Abstract: Interfacing atomistic-based with continuum-based simulation codes is now required in many multiscale physical and biological systems. We present the computational advances that have enabled the first multiscale simulation on 300,000 processors by coupling a high-order (spectral element) Navier-Stokes solver with a stochastic (coarse-grained) Molecular Dynamics solver based on Dissipative Particle Dynamics (DPD). The key contributions are proper interface conditions for overlapped domains, topology-aware communication, SIMDization, multiscale visualization and a new domain partitioning for atomistic solvers. We study blood flow in a patient-specific cerebrovasculature with a brain aneurysm, and analyze the interaction of blood cells with the arterial walls endowed with a glycocalyx causing thrombus formation and eventual aneurysm rupture. The macro-scale dynamics (about 10 billion unknowns) are resolved by Nektar - a spectral element solver; the micro-scale flow and cell dynamics within the aneurysm are resolved by an in-house version of DPD-LAMMPS (for an equivalent of about 100 billions molecules).

Speaker Biography: George Karniadakis received his S.M. (1984) and Ph.D. (1987) from Massachusetts Institute of Technology. He was appointed Lecturer in the Department of Mechanical Engineering at MIT in 1987 and subsequently he joined the Center for Turbulence Research at Stanford/Nasa Ames. He joined Princeton University as Assistant Professor in the Department of Mechanical and Aerospace Engineering and as Associate Faculty in the Program of Applied and Computational Mathematics. He was a Visiting Professor at Caltech (1993) in the Aeronautics Department. He joined Brown University as Associate Professor of Applied Mathematics in the Center for Fluid Mechanics on January 1, 1994. He became a full professor on July 1, 1996. He has been a Visiting Professor and Senior Lecturer of Ocean/Mechanical Engineering at MIT since September 1, 2000. He was Visiting Professor at Peking University (Fall 2007). He is a Fellow of the Society for Industrial and Applied Mathematics (SIAM, 2010-), Fellow of the American Physical Society (APS, 2004-), Fellow of the American Society of Mechanical Engineers (ASME, 2003-) and Associate Fellow of the American Institute of Aeronautics and Astronautics (AIAA, 2006-). He received the CFD award (2007) by the US Association in Computational Mechanics. Karniadakis is the lead PI of an OSD/AFOSR MURI on Uncertainty Quantification and Director of a new DOE Center of Mathematics for Mesoscale Modeling of Materials (CM4).

HiCOMB 2013 Call For Papers

High-performance computing became an integral part of research and development in bioinformatics and computational biology. 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 data-intensive and compute-intensive problems arising from molecular biology and related life sciences areas. We are especially interested in parallel and distributed algorithms, memory-efficient algorithms, large scale data mining techniques, including approaches for big data and cloud computing, algorithms on multicores and GPUs, and design of high-performance software for biological applications.

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:

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 PDF copy of the paper here. Submitted manuscripts may not exceed ten (10) single-spaced double-column pages using 10-point size font on 8.5x11 inch pages (IEEE conference style), including figures, tables, and references (see IPDPS Call for Papers for more details). 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 papers due: January 4, 2013 11:59PM PST, December 28, 2012
Authors notification:February 15, 2013, February 4
Camera-ready papers due:February 28, 2013, February 15

Download HiCOMB 2013 Call for Papers


Workshop Co-Chairs

David A. Bader
College of Computing
Georgia Institute of Technology
Atlanta, GA 30332, USA
Phone: +1 404 894-3152
Email:
Srinivas Aluru
Dept. of Electrical & Computer Enginering
Iowa State University
Ames, IA 50011, USA
Phone: +1 515 294-3539
Email:

Program Chair

Jaroslaw Zola
Rutgers Discovery Informatics Institute
Dept. of Electrical & Computer Enginering
Rutgers University
Piscataway, NJ 08854, USA
Email:

Program Committee


HiCOMB Archive

11th International Workshop on High Performance Computational Biology - HiCOMB 2012
10th International Workshop on High Performance Computational Biology - HiCOMB 2011
9th International Workshop on High Performance Computational Biology - HiCOMB 2010
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