title: SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks.
abstract: Metabolomics analysis tools can provide quantitative information on the concentration of metabolites in an organism. In this paper, we propose the minimum pathway model generator tool for simulating the dynamics of metabolite concentrations (SS-mPMG) and a tool for parameter estimation by genetic algorithm (SS-GA). SS-mPMG can extract a subsystem of the metabolic network from the genome-scale pathway maps to reduce the complexity of the simulation model and automatically construct a dynamic simulator to evaluate the experimentally observed behavior of metabolites. Using this tool, we show that stochastic simulation can reproduce experimentally observed dynamics of amino acid biosynthesis in Arabidopsis thaliana. In this simulation, SS-mPMG extracts the metabolic network subsystem from published databases. The parameters needed for the simulation are determined using a genetic algorithm to fit the simulation results to the experimental data. We expect that SS-mPMG and SS-GA will help researchers to create relevant metabolic networks and carry out simulations of metabolic reactions derived from metabolomics data.
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma-shi, Nara 630-0192 Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Katsuragi
authors.forename: Naoaki
authors.initials: N
authors.lastname: Ono
authors.forename: Keiichi
authors.initials: K
authors.lastname: Yasumoto
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.forename: Masami Y
authors.initials: MY
authors.lastname: Hirai
authors.forename: Kansuporn
authors.initials: K
authors.lastname: Sriyudthsak
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sawada
authors.forename: Yui
authors.initials: Y
authors.lastname: Yamashita
authors.forename: Yukako
authors.initials: Y
authors.lastname: Chiba
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Onouchi
authors.forename: Toru
authors.initials: T
authors.lastname: Fujiwara
authors.forename: Satoshi
authors.initials: S
authors.lastname: Naito
authors.forename: Fumihide
authors.initials: F
authors.lastname: Shiraishi
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000378:metabolism*; D003198:Computer Simulation; D007700:Kinetics; D053858:Metabolic Networks and Pathways; D055432:Metabolomics; D008954:Models, Biological; D025341:Principal Component Analysis; D013269:Stochastic Processes
keywords: Arabidopsis thaliana; Bioinformatics; Genetic algorithm; Metabolism; Stochastic simulation