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: | , , , , , , , , , , |
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| Format: | Conference or Workshop Item |
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Springer Verlag
2016
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| _version_ | 1796862116503748608 |
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| author | Li, Z. Sinnott, R .O. Choon, Y. W. Sjaugi, M. F. Mohammad, M. S. Deris, S. Napis, S. Omatu, S. Corchado, J. M. Ibrahim, Z. Yusof, Z. M. |
| author_facet | Li, Z. Sinnott, R .O. Choon, Y. W. Sjaugi, M. F. Mohammad, M. S. Deris, S. Napis, S. Omatu, S. Corchado, J. M. Ibrahim, Z. Yusof, Z. M. |
| author_sort | Li, Z. |
| collection | ePrints |
| 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 | 2024-03-05T20:06:42Z |
| format | Conference or Workshop Item |
| id | utm.eprints-73686 |
| institution | Universiti Teknologi Malaysia - ePrints |
| last_indexed | 2024-03-05T20:06:42Z |
| publishDate | 2016 |
| publisher | Springer Verlag |
| record_format | dspace |
| spelling | utm.eprints-736862017-11-28T08:38:32Z http://eprints.utm.my/73686/ Exploring the high performance computing-enablement of a suite of gene-knockout based genetic engineering applications Li, Z. Sinnott, R .O. Choon, Y. W. Sjaugi, M. F. Mohammad, M. S. Deris, S. Napis, S. Omatu, S. Corchado, J. M. Ibrahim, Z. Yusof, Z. M. QA75 Electronic computers. Computer science 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 Verlag 2016 Conference or Workshop Item PeerReviewed Li, Z. and Sinnott, R .O. and Choon, Y. W. and Sjaugi, M. F. and Mohammad, M. S. and Deris, S. and Napis, S. and Omatu, S. and Corchado, J. M. and Ibrahim, Z. and Yusof, Z. M. (2016) Exploring the high performance computing-enablement of a suite of gene-knockout based genetic engineering applications. In: International Conference on Practical Applications of Computational Biology and Bioinformatics PACBB, 2016, 1-3 June 2016, Sevilla, Spain. https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976353266&doi=10.1007%2f978-3-319-40126-3_14&partnerID=40&md5=dba8960a365196122be51a1306d54ab5 |
| spellingShingle | QA75 Electronic computers. Computer science Li, Z. Sinnott, R .O. Choon, Y. W. Sjaugi, M. F. Mohammad, M. S. Deris, S. Napis, S. Omatu, S. Corchado, J. M. Ibrahim, Z. Yusof, Z. M. 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 | QA75 Electronic computers. Computer science |
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