Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications

Genetic engineering provides methods to modify the genes of microorganisms to achieve desired effects. This can be done for improved organism growth rate or increasing production yield of a desired gene product. Gene knockout is a technique that can improve the specific characteristics of microorgan...

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Main Authors:	Li, Zhenya, Sinnott, Richard O., Choon, Yee Wen, Sjaugi, Muhammad Farhan, Mohd Saberi, Mohamad, Safaai, Deris, Suhaimi, Napis, Omatu, Sigeru, Corchado, Juan Manuel, Zuwairie, Ibrahim, Zulkifli, Md. Yusof
Format:	Book Section
Language:	English
Published:	Springer International Publishing 2016
Subjects:	TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://umpir.ump.edu.my/id/eprint/14395/ http://umpir.ump.edu.my/id/eprint/14395/ http://umpir.ump.edu.my/id/eprint/14395/ http://umpir.ump.edu.my/id/eprint/14395/1/Exploring%20the%20High%20Performance%20Computing-Enablement%20of%20a%20Suite%20of%20Gene-Knockout%20Based%20Genetic%20Engineering%20Applications.pdf

id	ump-14395
recordtype	eprints
spelling	ump-143952018-02-08T02:31:28Z http://umpir.ump.edu.my/id/eprint/14395/ Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications Li, Zhenya Sinnott, Richard O. Choon, Yee Wen Sjaugi, Muhammad Farhan Mohd Saberi, Mohamad Safaai, Deris Suhaimi, Napis Omatu, Sigeru Corchado, Juan Manuel Zuwairie, Ibrahim Zulkifli, Md. Yusof TK Electrical engineering. Electronics Nuclear engineering Genetic engineering provides methods to modify the genes of microorganisms to achieve desired effects. This can be done for improved organism growth rate or increasing production yield of a desired gene product. Gene knockout is a technique that can improve the specific characteristics of microorganisms by disabling selected sets of genes. However, microorganisms are complex and predicting the effects of gene modification is difficult. Several algorithms have been proposed to support a range of gene knockout strategies, including BAFBA, BHFBA and DBFBA. In this paper, scaling these algorithms and methods to utilise High Performance Computing (HPC) resources have been explored. The applications have been parallelized on HPC and the scalability and performance of these approaches were explored and documented. Springer International Publishing 2016 Book Section PeerReviewed application/pdf en http://umpir.ump.edu.my/id/eprint/14395/1/Exploring%20the%20High%20Performance%20Computing-Enablement%20of%20a%20Suite%20of%20Gene-Knockout%20Based%20Genetic%20Engineering%20Applications.pdf Li, Zhenya and Sinnott, Richard O. and Choon, Yee Wen and Sjaugi, Muhammad Farhan and Mohd Saberi, Mohamad and Safaai, Deris and Suhaimi, Napis and Omatu, Sigeru and Corchado, Juan Manuel and Zuwairie, Ibrahim and Zulkifli, Md. Yusof (2016) Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications. In: 10th International Conference on Practical Applications of Computational Biology & Bioinformatics. Advances in Intelligent Systems and Computing, 477 . Springer International Publishing, Switzerland, pp. 133-139. ISBN 978-3-319-40125-6 http://dx.doi.org/10.1007/978-3-319-40126-3_14 DOI: 10.1007/978-3-319-40126-3_14
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Malaysia Pahang
building	UMP Institutional Repository
collection	Online Access
language	English
topic	TK Electrical engineering. Electronics Nuclear engineering
spellingShingle	TK Electrical engineering. Electronics Nuclear engineering Li, Zhenya Sinnott, Richard O. Choon, Yee Wen Sjaugi, Muhammad Farhan Mohd Saberi, Mohamad Safaai, Deris Suhaimi, Napis Omatu, Sigeru Corchado, Juan Manuel Zuwairie, Ibrahim Zulkifli, Md. Yusof Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications
description	Genetic engineering provides methods to modify the genes of microorganisms to achieve desired effects. This can be done for improved organism growth rate or increasing production yield of a desired gene product. Gene knockout is a technique that can improve the specific characteristics of microorganisms by disabling selected sets of genes. However, microorganisms are complex and predicting the effects of gene modification is difficult. Several algorithms have been proposed to support a range of gene knockout strategies, including BAFBA, BHFBA and DBFBA. In this paper, scaling these algorithms and methods to utilise High Performance Computing (HPC) resources have been explored. The applications have been parallelized on HPC and the scalability and performance of these approaches were explored and documented.
format	Book Section
author	Li, Zhenya Sinnott, Richard O. Choon, Yee Wen Sjaugi, Muhammad Farhan Mohd Saberi, Mohamad Safaai, Deris Suhaimi, Napis Omatu, Sigeru Corchado, Juan Manuel Zuwairie, Ibrahim Zulkifli, Md. Yusof
author_facet	Li, Zhenya Sinnott, Richard O. Choon, Yee Wen Sjaugi, Muhammad Farhan Mohd Saberi, Mohamad Safaai, Deris Suhaimi, Napis Omatu, Sigeru Corchado, Juan Manuel Zuwairie, Ibrahim Zulkifli, Md. Yusof
author_sort	Li, Zhenya
title	Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications
title_short	Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications
title_full	Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications
title_fullStr	Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications
title_full_unstemmed	Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications
title_sort	exploring the high performance computing-enablement of a suite of gene-knockout based genetic engineering applications
publisher	Springer International Publishing
publishDate	2016
url	http://umpir.ump.edu.my/id/eprint/14395/ http://umpir.ump.edu.my/id/eprint/14395/ http://umpir.ump.edu.my/id/eprint/14395/ http://umpir.ump.edu.my/id/eprint/14395/1/Exploring%20the%20High%20Performance%20Computing-Enablement%20of%20a%20Suite%20of%20Gene-Knockout%20Based%20Genetic%20Engineering%20Applications.pdf
first_indexed	2023-09-18T22:18:06Z
last_indexed	2023-09-18T22:18:06Z
_version_	1777415473103634432

Exploring the High Performance Computing-Enablement of a Suite of Gene-Knockout Based Genetic Engineering Applications

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