An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks.
Computer simulation is an important technique to capture the dynamics of biochemical networks. Numerical optimization is the key to estimate the values of kinetic parameters so that the dynamic model reproduces the behaviors of the existing experimental data. It is required to develop general strategies for the optimization of complex biochemical networks with a huge space of search parameters, under the condition that kinetic and quantitative data are hardly available. We propose an integrative and practical strategy for optimizing a complex dynamic model by using qualitative and incomplete experimental data. The key technologies are the divide and conquer method for reducing the search space, handling of multiple objective functions representing different types of biological behaviors, and design of rule-based objective functions that are suitable for qualitative and error-prone experimental data. This strategy is applied to optimizing a dynamic model of the yeast cell cycle to demonstrate the feasibility of it.
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, Japan.
Kazuhiro
K
Maeda
Yuya
Y
Fukano
Shunsuke
S
Yamamichi
Daichi
D
Nitta
Hiroyuki
H
Kurata
D000465:Algorithms; D002453:Cell Cycle; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism; D005658:Fungi / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods; D007700:Kinetics; D008954:Models, Biological; D008962:Models, Theoretical; D013997:Time Factors
D004247:DNA