Case study of a functional genomics application for an FPGA-based coprocessor

Tom Van Court; Martin C. Herbordt; Richard J. Barton

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Case study of a functional genomics application for an FPGA-based coprocessor

机译：基于FPGA的协处理器的功能基因组学应用案例研究

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Although microarrays are already having a tremendous impact on biomedical science, they still present great computational challenges. We examine a particular problem involving the computation of linear regressions on a large number of vector combinations in a high-dimensional parameter space, a problem that was found to be virtually intractable on a PC cluster. We observe that characteristics of this problem map particularly well to FPGAs and confirm this with an implementation that results in a 1600-fold speed-up over an optimized serial implementation. Some of the other contributions involve the data routing structure, the analysis of bit-width allocation, and the handling of missing data. Since this problem is representative of many in functional genomics, part of the overall significance of this work is that it points to a new area of applicability for FPGA coprocessors.

机译：尽管微阵列已经对生物医学产生了巨大的影响，但它们仍然带来了巨大的计算挑战。我们研究了一个特定的问题，该问题涉及在高维参数空间中对大量矢量组合进行线性回归的计算，该问题在PC群集上实际上很难解决。我们观察到该问题的特征特别适合FPGA，并通过实现比经过优化的串行实现高1600倍的实现来证实这一点。其他一些贡献涉及数据路由结构，位宽分配分析以及丢失数据的处理。由于这个问题是许多功能基因组学的代表，因此这项工作的总体意义的一部分是，它指向了FPGA协处理器的新应用领域。

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来源
《Microprocessors and microsystems》 |2004年第6期|p.213-222|共10页
作者
Tom Van Court; Martin C. Herbordt; Richard J. Barton;
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作者单位

Department of Electrical and Computer Engineering, Boston University, 413 Photonics Building, 8 Saint Mary's Street, Boston, MA 02215, USA;

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收录信息美国《科学引文索引》(SCI);美国《工程索引》(EI);
原文格式 PDF
正文语种 eng
中图分类计算技术、计算机技术;
关键词
computational coprocessor; FPGA application; bioinformatics; microarray data analysis; steiner system;

机译：计算协处理器;FPGA应用;生物信息学;微阵列数据分析;斯坦纳系统;

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3. Functional Genomics, Metabolic Engineering and Mutagenesis Study of Lactic Acid Bacterial Strains in Traditional Food Fermentation, Human Health and Their Potential Applications [J] . Mulatu Workie Advances in Life Science and Technology . 2020,第2期

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4. Case Study of a Functional Genomics Application for an FPGA-Based Coprocessor [C] . Tom Van Court, Martin C. Herbordt, Richard J. Barton Field-Programmable Logic and Applications . 2003

机译：基于FPGA的协处理器的功能基因组学应用案例研究
5. Bioinformatics applications through visualization of variations on protein structures, comparative functional genomics, and comparative modeling for protein structure studies [D] . Uzun, Alper 2009

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6. The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus [O] . Antonis Rokas, John G. Gibbons, Xiaofan Zhou, -1

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7. Case study of a functional genomics application for an FPGA-based coprocessor [O] . Tom Van Court, Martin C. Herbordt, Richard J. Barton 2003

机译：基于FpGa的协处理器的功能基因组学应用案例研究

Case study of a functional genomics application for an FPGA-based coprocessor

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