A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli
In the past decades, metabolic engineering has received great attention from different sectors of science due to its important role in enhancing the over expression of the target phenotype by manipulating the metabolic pathway. The advent of metabolic engineering has further laid the foundation for...
| Main Authors: | , , , , , , , |
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| Format: | Book Chapter |
| Language: | English English |
| Published: |
Springer Nature Switzerland
2018
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| Subjects: | |
| Online Access: | http://umpir.ump.edu.my/id/eprint/22155/1/17.%20A%20Hybrid%20of%20Simple%20Constrained%20Artificial%20Bee%20Colony%20Algorithm%20and%20Flux%20Balance%20Analysis.pdf http://umpir.ump.edu.my/id/eprint/22155/2/17.1%20A%20Hybrid%20of%20Simple%20Constrained%20Artificial%20Bee%20Colony%20Algorithm%20and%20Flux%20Balance%20Analysis.pdf |
| _version_ | 1796992894627741696 |
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| author | Hon, Mei Kie Mohd Saberi, Mohamad Abdul Hakim, Mohamed Salleh Choon, Yee Wen Muhammad Akmal, Remli Mohd Arfian, Ismail Omatu, Sigeru Corchado, Juan Manuel |
| author_facet | Hon, Mei Kie Mohd Saberi, Mohamad Abdul Hakim, Mohamed Salleh Choon, Yee Wen Muhammad Akmal, Remli Mohd Arfian, Ismail Omatu, Sigeru Corchado, Juan Manuel |
| author_sort | Hon, Mei Kie |
| collection | UMP |
| description | In the past decades, metabolic engineering has received great attention from different sectors of science due to its important role in enhancing the over expression of the target phenotype by manipulating the metabolic pathway. The advent of metabolic engineering has further laid the foundation for computational biology, leading to the development of computational approaches for suggesting genetic manipulation. Previously, conventional methods have been used to enhance the production of lactate and succinate in E. coli. However, these products are always far below their theoretical maxima. In this research, a hybrid algorithm is developed to seek optimal solutions in order to increase the overproduction of lactate and succinate by gene knockout in E. coli. The hybrid algorithm employed the Simple Constrained Artificial Bee Colony (SCABC) algorithm, using swarm intelligence as an optimization algorithm to optimize the objective function, where lactate and succinate productions are maximized by simulating gene knockout in E. coli. In addition, Flux Balance Analysis (FBA) is used as a fitness function in the SCABC algorithm to assess the growth rate of E. coli and the productivity of lactate and succinate. As a result of the research, the gene knockout list which induced the highest production of lactate and succinate is obtained. |
| first_indexed | 2024-03-06T12:26:19Z |
| format | Book Chapter |
| id | UMPir22155 |
| institution | Universiti Malaysia Pahang |
| language | English English |
| last_indexed | 2024-03-06T12:26:19Z |
| publishDate | 2018 |
| publisher | Springer Nature Switzerland |
| record_format | dspace |
| spelling | UMPir221552019-05-15T04:18:07Z http://umpir.ump.edu.my/id/eprint/22155/ A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli Hon, Mei Kie Mohd Saberi, Mohamad Abdul Hakim, Mohamed Salleh Choon, Yee Wen Muhammad Akmal, Remli Mohd Arfian, Ismail Omatu, Sigeru Corchado, Juan Manuel QA76 Computer software In the past decades, metabolic engineering has received great attention from different sectors of science due to its important role in enhancing the over expression of the target phenotype by manipulating the metabolic pathway. The advent of metabolic engineering has further laid the foundation for computational biology, leading to the development of computational approaches for suggesting genetic manipulation. Previously, conventional methods have been used to enhance the production of lactate and succinate in E. coli. However, these products are always far below their theoretical maxima. In this research, a hybrid algorithm is developed to seek optimal solutions in order to increase the overproduction of lactate and succinate by gene knockout in E. coli. The hybrid algorithm employed the Simple Constrained Artificial Bee Colony (SCABC) algorithm, using swarm intelligence as an optimization algorithm to optimize the objective function, where lactate and succinate productions are maximized by simulating gene knockout in E. coli. In addition, Flux Balance Analysis (FBA) is used as a fitness function in the SCABC algorithm to assess the growth rate of E. coli and the productivity of lactate and succinate. As a result of the research, the gene knockout list which induced the highest production of lactate and succinate is obtained. Springer Nature Switzerland 2018 Book Chapter PeerReviewed pdf en http://umpir.ump.edu.my/id/eprint/22155/1/17.%20A%20Hybrid%20of%20Simple%20Constrained%20Artificial%20Bee%20Colony%20Algorithm%20and%20Flux%20Balance%20Analysis.pdf pdf en http://umpir.ump.edu.my/id/eprint/22155/2/17.1%20A%20Hybrid%20of%20Simple%20Constrained%20Artificial%20Bee%20Colony%20Algorithm%20and%20Flux%20Balance%20Analysis.pdf Hon, Mei Kie and Mohd Saberi, Mohamad and Abdul Hakim, Mohamed Salleh and Choon, Yee Wen and Muhammad Akmal, Remli and Mohd Arfian, Ismail and Omatu, Sigeru and Corchado, Juan Manuel (2018) A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli. In: Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. Advances in Intelligent Systems and Computing . Springer Nature Switzerland, pp. 1-8. ISBN 978-3-319-98702-6 https://link.springer.com/chapter/10.1007/978-3-319-98702-6_1 DOI: https://doi.org/10.1007/978-3-319-98702-6_1 |
| spellingShingle | QA76 Computer software Hon, Mei Kie Mohd Saberi, Mohamad Abdul Hakim, Mohamed Salleh Choon, Yee Wen Muhammad Akmal, Remli Mohd Arfian, Ismail Omatu, Sigeru Corchado, Juan Manuel A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli |
| title | A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli |
| title_full | A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli |
| title_fullStr | A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli |
| title_full_unstemmed | A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli |
| title_short | A hybrid of Simple Constrained artificial bee colony algorithm and flux balance analysis for enhancing Lactate and Succinate in Escherichia Coli |
| title_sort | hybrid of simple constrained artificial bee colony algorithm and flux balance analysis for enhancing lactate and succinate in escherichia coli |
| topic | QA76 Computer software |
| url | http://umpir.ump.edu.my/id/eprint/22155/1/17.%20A%20Hybrid%20of%20Simple%20Constrained%20Artificial%20Bee%20Colony%20Algorithm%20and%20Flux%20Balance%20Analysis.pdf http://umpir.ump.edu.my/id/eprint/22155/2/17.1%20A%20Hybrid%20of%20Simple%20Constrained%20Artificial%20Bee%20Colony%20Algorithm%20and%20Flux%20Balance%20Analysis.pdf |
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