Exploring the high performance computing-enablement of a suite of gene-knockout based genetic engineering applications

Zhenya Li, Richard O. Sinnott, Yee Wen Choon, Muhammad Farhan Sjaugi, Mohd Saberi Mohammad, Safaai Deris, Suhaimi Napis, Sigeru Omatu, Juan Manuel Corchado, Zuwairie Ibrahim, Zulkifli Md Yusof

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish
Title of host publication10th International Conference on Practical Applications of Computational Biology and Bioinformatics
EditorsFlorentino Fdez-Riverola, Juan F. De Paz, Miguel P. Rocha, Francisco J. Domínguez Mayo, Mohd Saberi Mohamad
PublisherSpringer Verlag
Pages133-139
Number of pages7
ISBN (Print)9783319401256
DOIs
Publication statusPublished - 2016
Externally publishedYes
EventInternational Conference on Practical Applications of Computational Biology and Bioinformatics PACBB, 2016 - Sevilla, Spain
Duration: Jun 1 2016Jun 3 2016

Publication series

NameAdvances in Intelligent Systems and Computing
Volume477
ISSN (Print)2194-5357

Conference

ConferenceInternational Conference on Practical Applications of Computational Biology and Bioinformatics PACBB, 2016
Country/TerritorySpain
CitySevilla
Period6/1/166/3/16

Keywords

  • Bees algorithm
  • Flux balance
  • Gene knockout
  • Genetic engineering
  • High performance computing
  • HPC

ASJC Scopus subject areas

  • Control and Systems Engineering
  • General Computer Science

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