Tenth IEEE International Workshop on High Performance Computational Biology
Monday, May 16, 2011
Anchorage, Alaska
(Held in conjunction with the International Parallel and
Distributed Processing Symposium)
Monday, May 16, 2011
Anchorage, Alaska
(Held in conjunction with the International Parallel and
Distributed Processing Symposium)
Abstract:
In this talk I will discuss the current state and future trends in
data-intensive genomics driven biological research and how large-scale
computing will enable the development of predictive theory from this
wealth of data. Sequencing centers will soon be producing data volumes
comparable to those in high energy physics and astronomy (multiple
petabytes per year), thus requiring new scalable approaches to
analysis. I'll discuss three such areas. The first is the development
and implementation of the RAST (Rapid Annotation via Subsytem
Technology) system for automated genome annotation that has been used
by thousands of researchers to annotate and analyze over ten thousand
genomes, more than any other system. I'll also address how this system
can scale in the future to handle hundreds of thousands of genomes.
The second is the ModelSEED, which is the first system to support
automated high-throughput construction of metabolic models directly
from genomes. The modelSEED is a key capability in our long-term goal
to predict phenotypes from genotypes. Our group is currently building
computational models for all "complete" bacterial and archaea genomes
(over one thousand models). The third is the analysis and assembly of
environmental metagenomes. Next generation sequencing technology will
make it possible to generate over a billion DNA reads per
environmental sample. From these reads we can reconstruct many aspects
of the community, including the distribution of organisms, the
metabolic potential of the community, and the complete genomes of the
most abundant taxa.
Speaker Biography:
Rick Stevens is Associate Laboratory Director responsible for
Computing, Environment and Life Sciences research at Argonne National
Laboratory and is a professor of computer science at the University of
Chicago. He also holds senior fellow appointment Recently
Prof. Stevens has been co-leading the DOE laboratory planning effort
for exascale computing research aiming to develop computer systems one
thousand times faster than current supercomputers and apply these
systems to fundamental problems in science including genomic analysis,
whole cell modeling, climate models and problems in fundamental
physics and energy technology development. He has authored and
co-authored more than 120 papers and he is a fellow of the American
Association for the Advancement of Science. His research groups have
won many national awards over the years, including an R&D 100 award
for the Access Grid. He sits on many government, university, and
industry advisory boards.
High-performance computing is fast becoming an integral part of research and application 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 algorithms, memory-efficient algorithms, large scale data mining techniques, 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:
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. 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.
| Workshop Paper Due: | December 27, 2010 |
| Author Notification: | January 20, 2011 |
| Camera-ready Paper Due: | February 21, 2011 |
|
Srinivas Aluru Dept. of Electrical & Computer Engg. and Lawrence H. Baker Center for Bioinformatics & Biological Statistics Iowa State University 3227 Coover Hall Ames, IA 50011, USA Phone: +1.515.294.3539 Email: |
David A. Bader College of Computing Georgia Institute of Technology Atlanta, GA 30332 USA Phone: +1.404.894.3152 Email: |
|
Ananth Kalyanaraman School of Electrical Engineering and Computer Science Washington State University Pullman, WA 99164 Email: ananth@eecs.wsu.edu http://www.eecs.wsu.edu/~ananth/ |
For up-to-date information about this workshop, please visit
http://www.hicomb.org/.