TITLE:

HIGH PERFORMANCE COMPUTATIONAL ANALYSIS OF DNA SEQUENCES FROM DIFFERENT ENVIRONMENTS

DATE:

Friday, September 12th, 2008

TIME:

3:30 PM

LOCATION:

GMCS 214

SPEAKER:

Robert Edwards, Assistant Professor, Computer Sciences Department and Computational Sciences Research Center, San Diego State University

ABSTRACT:

New high-throughput DNA sequencing technologies have revolutionized how scientists study the organisms around us. In particular microbiology, the study of the smallest, unseen organisms that pervade our lives has embraced these new techniques to characterize and analyze the cellular constituents, and use this information to develop novel tools, techniques, and therapeutics. Next generation DNA sequencing platforms resulted in huge increases in the amount of raw data that can be rapidly generated.

The computational analysis of more than 10,000,000,000 bp of DNA sequence data revealed the advanced computational requirements required for DNA sequence analysis platforms, and suggests the level of analysis that will be essential as microbiologists move to understand how these tiny organisms affect our every day lives. The results from this analysis indicate that data analysis has strictly linear complexity, and that currently most analyses are held up in queues. With sufficient resources, computations could be completed in a few hours for a typical data set. These data also suggest execution times that delimit timely completion of computational analyses, and provide bounds for problematic processes. Methods and approaches that are being deployed to defray the computational cost associated with analyzing DNA sequences will be described, including more computers, teragrid computations, and cloud computing.

HOST:

Jose Castillo

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