Computational Mass Spectrometry in a Reconfigurable Coherent Coprocessing Architecture

The significant growth in the quantity of data in biology and related fields has spawned the need for novel computational solutions. The authors show how a key search task in proteomics, the large-scale study of proteins, can be accelerated by several orders of magnitude by the use of FPGA-based hardware.

[1]  Tony M. Brewer,et al.  Instruction Set Innovations for the Convey HC-1 Computer , 2010, IEEE Micro.

[2]  Keith D. Underwood,et al.  RC-BLAST: towards a portable, cost-effective open source hardware implementation , 2005, IEEE International Parallel and Distributed Processing Symposium.

[3]  Martin C. Herbordt,et al.  Single Pass, BLAST-Like, Approximate String Matching on FPGAs , 2006, 2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines.

[4]  P. Pevzner,et al.  InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. , 2005, Analytical chemistry.

[5]  Dekel Tsur,et al.  Identification of post-translational modifications via blind search of mass-spectra , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

[6]  Kunle Olukotun,et al.  FARM: A Prototyping Environment for Tightly-Coupled, Heterogeneous Architectures , 2010, 2010 18th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines.

[7]  William Lynch,et al.  Smith-Waterman implementation on a FSB-FPGA module using the Intel Accelerator Abstraction Layer , 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

[8]  Guang R. Gao,et al.  Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform , 2007, HPRCTA.