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...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Book Chapter |
| Language: | English |
| Published: |
Springer International Publishing
2016
|
| Subjects: | |
| Online Access: | 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 |
| _version_ | 1796991557482577920 |
|---|---|
| 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 |
| collection | UMP |
| 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. |
| first_indexed | 2024-03-06T12:07:14Z |
| format | Book Chapter |
| id | UMPir14395 |
| institution | Universiti Malaysia Pahang |
| language | English |
| last_indexed | 2024-03-06T12:07:14Z |
| publishDate | 2016 |
| publisher | Springer International Publishing |
| record_format | dspace |
| spelling | UMPir143952018-02-08T02:31:28Z 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 Chapter 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 |
| 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 |
| title | 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_short | 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 |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | 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 |
| work_keys_str_mv | AT lizhenya exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT sinnottrichardo exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT choonyeewen exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT sjaugimuhammadfarhan exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT mohdsaberimohamad exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT safaaideris exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT suhaiminapis exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT omatusigeru exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT corchadojuanmanuel exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT zuwairieibrahim exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications AT zulkiflimdyusof exploringthehighperformancecomputingenablementofasuiteofgeneknockoutbasedgeneticengineeringapplications |