Accelerating Genomic Data Analytics with Composable Hardware Acceleration Framework
Publication
, Journal Article
Ham, TJ; Lee, Y; Seo, SH; Song, UG; Lee, JW; Bruns-Smith, D; Sweeney, B; Asanovic, K; Oh, YH; Wills, LW
Published in: IEEE Micro
May 1, 2021
This article presents a framework, Genesis (genome analysis), to efficiently and flexibly accelerate generic data manipulation operations that have become performance bottlenecks in the genomic data processing pipeline utilizing FPGAs-as-a-service. Genesis conceptualizes genomic data as a very large relational database and uses extended SQL as a domain-specific language to construct data manipulation queries. To accelerate the queries, we designed a Genesis hardware library of efficient coarse-grained primitives that can be composed into a specialized dataflow architecture. This approach explores a systematic and scalable methodology to expedite domain-specific end-to-end accelerated system development and deployment.
Duke Scholars
Published In
IEEE Micro
DOI
EISSN
1937-4143
ISSN
0272-1732
Publication Date
May 1, 2021
Volume
41
Issue
3
Start / End Page
42 / 49
Related Subject Headings
- Computer Hardware & Architecture
- 4606 Distributed computing and systems software
- 4009 Electronics, sensors and digital hardware
- 1006 Computer Hardware
- 0906 Electrical and Electronic Engineering
Citation
APA
Chicago
ICMJE
MLA
NLM
Ham, T. J., Lee, Y., Seo, S. H., Song, U. G., Lee, J. W., Bruns-Smith, D., … Wills, L. W. (2021). Accelerating Genomic Data Analytics with Composable Hardware Acceleration Framework. IEEE Micro, 41(3), 42–49. https://doi.org/10.1109/MM.2021.3072385
Ham, T. J., Y. Lee, S. H. Seo, U. G. Song, J. W. Lee, D. Bruns-Smith, B. Sweeney, K. Asanovic, Y. H. Oh, and L. W. Wills. “Accelerating Genomic Data Analytics with Composable Hardware Acceleration Framework.” IEEE Micro 41, no. 3 (May 1, 2021): 42–49. https://doi.org/10.1109/MM.2021.3072385.
Ham TJ, Lee Y, Seo SH, Song UG, Lee JW, Bruns-Smith D, et al. Accelerating Genomic Data Analytics with Composable Hardware Acceleration Framework. IEEE Micro. 2021 May 1;41(3):42–9.
Ham, T. J., et al. “Accelerating Genomic Data Analytics with Composable Hardware Acceleration Framework.” IEEE Micro, vol. 41, no. 3, May 2021, pp. 42–49. Scopus, doi:10.1109/MM.2021.3072385.
Ham TJ, Lee Y, Seo SH, Song UG, Lee JW, Bruns-Smith D, Sweeney B, Asanovic K, Oh YH, Wills LW. Accelerating Genomic Data Analytics with Composable Hardware Acceleration Framework. IEEE Micro. 2021 May 1;41(3):42–49.
Published In
IEEE Micro
DOI
EISSN
1937-4143
ISSN
0272-1732
Publication Date
May 1, 2021
Volume
41
Issue
3
Start / End Page
42 / 49
Related Subject Headings
- Computer Hardware & Architecture
- 4606 Distributed computing and systems software
- 4009 Electronics, sensors and digital hardware
- 1006 Computer Hardware
- 0906 Electrical and Electronic Engineering