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

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

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Abstract

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.

Item Type: Book Section
Uncontrolled Keywords: High performance computing; HPC; Gene knockout; Genetic engineering; Bees algorithm; Flux balance
Subjects: T Technology > TK Electrical engineering. Electronics Nuclear engineering
Faculty/Division: Faculty of Electrical & Electronic Engineering
Depositing User: Mrs. Neng Sury Sulaiman
Date Deposited: 21 Sep 2016 04:07
Last Modified: 08 Feb 2018 02:31
URI: http://umpir.ump.edu.my/id/eprint/14395
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