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) : Ravinfran, Arun


Full Text : https://apps.dtic.mil/dtic/tr/fulltext/u2/a499723.pdf


Report Date : May 2009


Pagination or Media Count : 37


Abstract : Report Developed under CRADA 08-RI-CRADA-06. The report describes a new approach to the problem of generating DNA tag/anti-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 today's 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.


Descriptors :   *WORK STATIONS , *DEOXYRIBONUCLEIC ACIDS , *BIOMOLECULES , *CODING , GAIN , SYNCHRONIZATION(ELECTRONICS) , COMMUNICATION AND RADIO SYSTEMS , TRADE OFF ANALYSIS , TIME SHARING , APPLICATION PROGRAMMING INTERFACE , FIELD PROGRAMMABLE GATE ARRAYS , MEMORY DEVICES , INTEGRATED CIRCUITS , GENETIC ALGORITHMS , MODELS , PROGRAMMING LANGUAGES


Subject Categories : Biochemistry
      Computer Programming and Software


Distribution Statement : APPROVED FOR PUBLIC RELEASE