A review on modelling methods, Pathway simulation software and recent development on differential evolution algorithms for metabolic pathways in systems biology

Chuii Khim Chong; Mohd Saberi Mohamad; Safaai Deris; Mohd Shahir Shamsir; Yee Wen Choon; Lian En Chai

doi:10.2174/157489360905141014154242

A review on modelling methods, Pathway simulation software and recent development on differential evolution algorithms for metabolic pathways in systems biology

Chuii Khim Chong, Mohd Saberi Mohamad, Safaai Deris, Mohd Shahir Shamsir, Yee Wen Choon, Lian En Chai

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Abstract

The process of analysing metabolic pathways mathematically in systems biology requires accurate parameters which represent the simulated in-vivo processes. Differential Evolution algorithm (DE) has been provenable to outperform other estimation algorithms, and has been used to achieve an accurate estimation of the required parameters. The total number of DE-variants has increased recently, which makes researchers face difficulties in obtaining complete overview of current DE-variants. To provide a holistic view to the area of mathematical modelling in System Biology, through this paper, we present an overview of modelling methods, parameter estimation by utilizing DE-variants to analyse metabolic pathways, and exiting pathway simulation software.

Original language	English
Pages (from-to)	509-521
Number of pages	13
Journal	Current Bioinformatics
Volume	9
Issue number	5
DOIs	https://doi.org/10.2174/157489360905141014154242
Publication status	Published - Mar 1 2014
Externally published	Yes

Keywords

Differential evolution
Modelling
System biology

ASJC Scopus subject areas

Biochemistry
Molecular Biology
Genetics
Computational Mathematics

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10.2174/157489360905141014154242

Cite this

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abstract = "The process of analysing metabolic pathways mathematically in systems biology requires accurate parameters which represent the simulated in-vivo processes. Differential Evolution algorithm (DE) has been provenable to outperform other estimation algorithms, and has been used to achieve an accurate estimation of the required parameters. The total number of DE-variants has increased recently, which makes researchers face difficulties in obtaining complete overview of current DE-variants. To provide a holistic view to the area of mathematical modelling in System Biology, through this paper, we present an overview of modelling methods, parameter estimation by utilizing DE-variants to analyse metabolic pathways, and exiting pathway simulation software.",

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AU - Chong, Chuii Khim

AU - Mohamad, Mohd Saberi

AU - Deris, Safaai

AU - Shamsir, Mohd Shahir

AU - Choon, Yee Wen

AU - Chai, Lian En

PY - 2014/3/1

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A review on modelling methods, Pathway simulation software and recent development on differential evolution algorithms for metabolic pathways in systems biology

Abstract

Keywords

ASJC Scopus subject areas

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