Reconfigurable hardware-software codesign methodology for protein identification

Venkateshwarlu Y. Gudur; Sandeep Thallada; Abhinay R. Deevi; Venkata Krishna Gande; Amit Acharyya; Vasundhra Bhandari; Paresh Sharma; Saqib Khursheed; Ganesh R. Naik

doi:10.1109/EMBC.2016.7591227

Reconfigurable hardware-software codesign methodology for protein identification

Venkateshwarlu Y. Gudur, Sandeep Thallada, Abhinay R. Deevi, Venkata Krishna Gande, Amit Acharyya, Vasundhra Bhandari, Paresh Sharma, Saqib Khursheed, Ganesh R. Naik

Western Sydney University

Research output: Chapter in Book / Conference Paper › Conference Paper › peer-review

2 Citations (Scopus)

Abstract

![CDATA[In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated processing and on-the-fly reconfigurable system design methodology to bring flexibility to its usage in the medical science community without the need of changing the entire hardware every time with the advent of new biomarker or protein. The proteome database of human at UniProtKB (Proteome ID up000005640) comprising of 42132 canonical and isoform proteins with variable database-size are used for testing the proposed design and the performance of the proposed system has been found to compare favorably with the state-of-the-art approaches with the additional advantage of real-time reconfigurability.]]

Original language	English
Title of host publication	Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '16), 16-20 August 2016, Orlando, Florida, USA
Publisher	IEEE
Pages	2456-2459
Number of pages	4
ISBN (Print)	9781457702204
DOIs	https://doi.org/10.1109/EMBC.2016.7591227
Publication status	Published - 2016
Event	IEEE Engineering in Medicine and Biology Society. Annual International Conference - Duration: 11 Jul 2022 → …

Publication series

Name
ISSN (Print)	1558-4615

Conference

Conference	IEEE Engineering in Medicine and Biology Society. Annual International Conference
Period	11/07/22 → …

Keywords

biochemical markers
proteins
sequential machine theory
system design

Access to Document

10.1109/EMBC.2016.7591227

Cite this

Gudur, V. Y., Thallada, S., Deevi, A. R., Gande, V. K., Acharyya, A., Bhandari, V., Sharma, P., Khursheed, S., & Naik, G. R. (2016). Reconfigurable hardware-software codesign methodology for protein identification. In Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '16), 16-20 August 2016, Orlando, Florida, USA (pp. 2456-2459). IEEE. https://doi.org/10.1109/EMBC.2016.7591227

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title = "Reconfigurable hardware-software codesign methodology for protein identification",

abstract = "![CDATA[In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated processing and on-the-fly reconfigurable system design methodology to bring flexibility to its usage in the medical science community without the need of changing the entire hardware every time with the advent of new biomarker or protein. The proteome database of human at UniProtKB (Proteome ID up000005640) comprising of 42132 canonical and isoform proteins with variable database-size are used for testing the proposed design and the performance of the proposed system has been found to compare favorably with the state-of-the-art approaches with the additional advantage of real-time reconfigurability.]]",

keywords = "biochemical markers, proteins, sequential machine theory, system design",

author = "Gudur, {Venkateshwarlu Y.} and Sandeep Thallada and Deevi, {Abhinay R.} and Gande, {Venkata Krishna} and Amit Acharyya and Vasundhra Bhandari and Paresh Sharma and Saqib Khursheed and Naik, {Ganesh R.}",

year = "2016",

doi = "10.1109/EMBC.2016.7591227",

language = "English",

isbn = "9781457702204",

publisher = "IEEE",

pages = "2456--2459",

booktitle = "Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '16), 16-20 August 2016, Orlando, Florida, USA",

note = "IEEE Engineering in Medicine and Biology Society. Annual International Conference ; Conference date: 11-07-2022",

}

Gudur, VY, Thallada, S, Deevi, AR, Gande, VK, Acharyya, A, Bhandari, V, Sharma, P, Khursheed, S & Naik, GR 2016, Reconfigurable hardware-software codesign methodology for protein identification. in Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '16), 16-20 August 2016, Orlando, Florida, USA. IEEE, pp. 2456-2459, IEEE Engineering in Medicine and Biology Society. Annual International Conference, 11/07/22. https://doi.org/10.1109/EMBC.2016.7591227

Reconfigurable hardware-software codesign methodology for protein identification. / Gudur, Venkateshwarlu Y.; Thallada, Sandeep; Deevi, Abhinay R. et al.
Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '16), 16-20 August 2016, Orlando, Florida, USA. IEEE, 2016. p. 2456-2459.

Research output: Chapter in Book / Conference Paper › Conference Paper › peer-review

TY - GEN

T1 - Reconfigurable hardware-software codesign methodology for protein identification

AU - Gudur, Venkateshwarlu Y.

AU - Thallada, Sandeep

AU - Deevi, Abhinay R.

AU - Gande, Venkata Krishna

AU - Acharyya, Amit

AU - Bhandari, Vasundhra

AU - Sharma, Paresh

AU - Khursheed, Saqib

AU - Naik, Ganesh R.

PY - 2016

Y1 - 2016

N2 - ![CDATA[In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated processing and on-the-fly reconfigurable system design methodology to bring flexibility to its usage in the medical science community without the need of changing the entire hardware every time with the advent of new biomarker or protein. The proteome database of human at UniProtKB (Proteome ID up000005640) comprising of 42132 canonical and isoform proteins with variable database-size are used for testing the proposed design and the performance of the proposed system has been found to compare favorably with the state-of-the-art approaches with the additional advantage of real-time reconfigurability.]]

AB - ![CDATA[In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated processing and on-the-fly reconfigurable system design methodology to bring flexibility to its usage in the medical science community without the need of changing the entire hardware every time with the advent of new biomarker or protein. The proteome database of human at UniProtKB (Proteome ID up000005640) comprising of 42132 canonical and isoform proteins with variable database-size are used for testing the proposed design and the performance of the proposed system has been found to compare favorably with the state-of-the-art approaches with the additional advantage of real-time reconfigurability.]]

KW - biochemical markers

KW - proteins

KW - sequential machine theory

KW - system design

UR - http://handle.westernsydney.edu.au:8081/1959.7/uws:41586

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DO - 10.1109/EMBC.2016.7591227

M3 - Conference Paper

SN - 9781457702204

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BT - Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '16), 16-20 August 2016, Orlando, Florida, USA

PB - IEEE

T2 - IEEE Engineering in Medicine and Biology Society. Annual International Conference

Y2 - 11 July 2022

ER -

Gudur VY, Thallada S, Deevi AR, Gande VK, Acharyya A, Bhandari V et al. Reconfigurable hardware-software codesign methodology for protein identification. In Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '16), 16-20 August 2016, Orlando, Florida, USA. IEEE. 2016. p. 2456-2459 doi: 10.1109/EMBC.2016.7591227

Reconfigurable hardware-software codesign methodology for protein identification

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