TY - GEN
T1 - Exploring the high performance computing-enablement of a suite of gene-knockout based genetic engineering applications
AU - Li, Zhenya
AU - Sinnott, Richard O.
AU - Choon, Yee Wen
AU - Sjaugi, Muhammad Farhan
AU - Mohammad, Mohd Saberi
AU - Deris, Safaai
AU - Napis, Suhaimi
AU - Omatu, Sigeru
AU - Corchado, Juan Manuel
AU - Ibrahim, Zuwairie
AU - Yusof, Zulkifli Md
N1 - Publisher Copyright:
© Springer International Publishing Switzerland 2016.
PY - 2016
Y1 - 2016
N2 - 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.
AB - 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.
KW - Bees algorithm
KW - Flux balance
KW - Gene knockout
KW - Genetic engineering
KW - High performance computing
KW - HPC
UR - https://www.scopus.com/pages/publications/84976353266
UR - https://www.scopus.com/pages/publications/84976353266#tab=citedBy
U2 - 10.1007/978-3-319-40126-3_14
DO - 10.1007/978-3-319-40126-3_14
M3 - Conference contribution
AN - SCOPUS:84976353266
SN - 9783319401256
T3 - Advances in Intelligent Systems and Computing
SP - 133
EP - 139
BT - 10th International Conference on Practical Applications of Computational Biology and Bioinformatics
A2 - Fdez-Riverola, Florentino
A2 - De Paz, Juan F.
A2 - Rocha, Miguel P.
A2 - Mayo, Francisco J. Domínguez
A2 - Mohamad, Mohd Saberi
PB - Springer Verlag
T2 - International Conference on Practical Applications of Computational Biology and Bioinformatics PACBB, 2016
Y2 - 1 June 2016 through 3 June 2016
ER -