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Issue No.04 - July/August (2011 vol.28)
pp: 58-67
Devi Sravanthi Yalamarthy , University of California, San Diego
Joel Coburn , University of California, San Diego
Rajesh K. Gupta , University of California, San Diego
Glen Edwards , Convey Computer
Mark Kelly , Convey Computer
<p><it>Editor's note:</it></p><p>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.</p><p align="right"><it>&#x2014;George A. Constantinides (Imperial College London) and Nicola Nicolici (McMaster University)</it></p>
design and test, coherent coprocessing, reconfigurable computing, hardware accelerator, FPGA
Devi Sravanthi Yalamarthy, Joel Coburn, Rajesh K. Gupta, Glen Edwards, Mark Kelly, "Computational Mass Spectrometry in a Reconfigurable Coherent Coprocessing Architecture", IEEE Design & Test of Computers, vol.28, no. 4, pp. 58-67, July/August 2011, doi:10.1109/MDT.2011.47
1. D. Tsur et al., "Identification of Post-Translational Modifications via Blind Search of Mass-Spectra," Proc. IEEE Computational Systems Bioinformatics Conf. (CSB 05), IEEE CS Press, 2005, pp. 157-166.
2. S. Tanner et al., "Inspect: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra," Analytical Chemistry, vol. 77, no. 14, 2005, pp. 4626-4639.
3. T. Oguntebi et al., "FARM: A Prototyping Environment for Tightly-Coupled, Heterogeneous Architectures," Proc. 18th Ann. Int'l IEEE Symp. Field-Programmable Custom Computing Machines (FCCM 10), IEEE CS Press, 2010, pp. 221-228.
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