Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research

Eric A. Stahlberg, T. Steinke, M. C. Smith, S. Chandrasekaran, B. Chapman
SAIC-Frederick, Frederick, Maryland, US National Cancer Institute, USA
WorldComputing, 2011


   title={Heterogeneous Accelerated Bioinformatics–Perspectives for Cancer Research},

   author={Stahlberg, E. and Steinke, T. and Smith, MC and Chandrasekaran, S. and Chapman, B.},



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The demand for even higher performance in bioinformatics data analysis continues to grow rapidly as the volumes of data generated by next generation sequencing equipment soar. Traditional acceleration techniques historically used for faster bioinformatics application will individually be insufficient to meet the demand and increased analysis complexity, requiring an integrated heterogeneous accelerated computing environment. Current accelerated computing programming environments including reconfigurable computing technologies as well as multicore technologies are reviewed in the context of bioinformatics applications, highlighting opportunities and limitations of these technologies. Requirements for successful heterogeneous accelerated computing environments supporting bioinformatics applications are presented.
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