Accession Number:

ADA499723

Title:

Multi-Threaded DNA Tag/Anti-Tag Library Generator for Multi-Core Platforms

Descriptive Note:

Final technical rept. Jun 2008-Feb 2009

Corporate Author:

NORTH CAROLINA UNIV AT CHARLOTTE DEPT OF ELECTRICAL AND COMPUTER ENGINEERING

Personal Author(s):

Report Date:

2009-05-01

Pagination or Media Count:

37.0

Abstract:

Report Developed under CRADA 08-RI-CRADA-06. The report describes a new approach to the problem of generating DNA taganti-tag libraries used in experimental computing methods involving bio-molecules, and 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 multi-core CPUs increasingly prevalent in todays commodity workstation computers. We explored and exploited algorithm and architecture trade-offs while developing a multi-threaded code that uses shared memory communication, and minimal synchronization between threads. We also describe experiments that evaluated performance and demonstrated 5X-8X speedups on workstations with dual quad-core CPUs. We observe that coding effort using the C language and Pthreads parallel programming model is greatly reduced compared to two previous approaches that used the VHDL language run on reconfigurable hardware FPGAs, and the C language with MPI API run on a cluster of computers.

Subject Categories:

  • Biochemistry
  • Computer Programming and Software

Distribution Statement:

APPROVED FOR PUBLIC RELEASE