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[Colloquium] Metagenomics and High Performance Computing

May 6, 2010

Watch Colloquium: 

Quicktime file (484 MB)
AVI file (502 MB)

  • Date: Thursday, May 6, 2010 
  • Time: 11 am — 12:15 pm 
  • Place: Mechanical Engineering, Room 218

Bill Feiereisen
Director of High Performance Computing
DoD for Lockheed Martin Corporation

Abstract: It has become a cliche to state that the biological sciences have become information sciences. Vastly increased volumes of experimentally acquired genomic and proteomic data hint at rich new insights in many areas of the biological sciences, but the demands they place on computing for their analysis are just as great. This is one of the many reasons why scientists from the more traditional areas of high performance computing have been attracted into biology. However, the character of this computing has changed — away from modeling and simulation, upon which much of our high performance computing expertise is based, to the extraction of scientific insight from data analysis.

This talk discusses my journey in moving from traditional computational simulation into high performance bioinformatics. The motivation occurs through global climate modeling and the very large contribution that the microbial biology of the ocean has upon the carbon dioxide budget in ocean models. Current microbial models incorporated into ocean models presume knowledge of the organisms present and their metabolism. In reality, recent “metagenomic” ocean surveys have shown that most organisms are not known or understood, nor do we know about their spatial and temporal distribution. So, how would we use this new information to evaluate the performance of current models or build new ones?

Metagenomics is the study of microbial communities in situ. Over 99% of microbes in the ocean cannot be studied in the lab, because they cannot be separated from the symbiosis of their community and survive. Their genomes must be acquired together and teased apart with new computational algorithms. I will discuss work in sequence based and similarity based algorithms to categorize the mixed fragments of DNA for assembly into complete genomes. Comparison of these genome fragments and complete genomes can be performed through multiple alignment algorithms. Both of these algorithmic tasks are now overwhelming our high performance computing capability and point the way to fertile new fields for algorithm developers.

Bio: Bill Feiereisen is the Director of High Performance Computing, DoD for Lockheed Martin Corporation. He was formerly the laboratory Chief Technologist and Division Director of the Computer and Computational Sciences Division at Los Alamos and before that the head of the NASA Advanced Supercomputing Facility at Ames Research Center.

He is active in the broader computer science community, serving on the editorial board of IEEE Computers in Science and Engineering, as the former chairman of the Advisory Committee for the Open Grid Forum, on the council of the NSF Computing Community Consortium and as a founding member of the New Mexico Computing Applications Center. He is a member of numerous review boards and advisory committees.

Bill’s original interests in high performance computing come from computational fluid dynamics and range from turbulence modeling to rarefied gas dynamics with applications to achinery and hypersonic flows. However the computer science of high performance computing that underlies computational science has been a motivator for his work since the nineties. His recent computational interests are in the field of bioinformatics and high performance computing.

He holds a Doctorate and Masters in Mechanical Engineering from Stanford University and a Bachelors Degree from the University of Wisconsin.

In his copious free time he is a wannabe bicycle racer and can usually be found running last in club races in New Mexico.