A multi-threaded DNA tag/anti-tag library generator for multi-core platforms

Authors:
Arun Ravindran;Daniel J. Burns
Affiliations:
Department of Electrical and Computer Engineering, University of North Carolina, Charlotte, NC;Air Force Research Laboratory, Information Directorate, Rome, NY
Venue:
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Year:
2009

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Abstract

This paper describes a new approach to the problem of generating DNA tag/anti-tag libraries for use in biological assay methods. This approach couples multi-threaded coding methods and a highly parallel multi-population genetic algorithm to leverage performance gains made possible by the multicore CPUs increasingly prevalent in today's commodity computers. We also describe the results of experiments characterizing the performance of this approach, which can yield up to an 8X speedup on a workstation equipped with dual quad-core CPUs. We observe that the coding effort required to implement this approach using the C language and Pthreads parallel programming model is greatly reduced compared to previous methods using both the VHDL language and reconfigurable hardware (FPGAs), and compared to C with the MPI API run on a cluster of computers.