Development of the parameter-fitting module for web-based biochemical reaction simulator BEST-KIT

Chem-Bio Informatics Journal

Tadahiro Shimonobou²  Masahiro Okamoto³  Jun Yoshimura³  Tatsuya Sekiguchi¹ 

[1] Department of Information Engineering, Faculty of Engineering, Maebashi Institute of Technology;Department of Biochemical Engineering & Science, Faculty of Computer Science & Systems Engineering, Kyushu Institute of Technology;Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University

关键词: Web-based simulator;    Webベースのシミュレータ;    computer simulation;    コンピュータシミュレーション;    optimization;    �?適化;    metabolic pathway;    代謝経路;    bioinformatics;    バイオインフォマティックス;   

DOI  :  10.1273/cbij.3.114

学科分类：生物化学/生物物理

来源: Chem-Bio Informatics Society

【 摘 要 】

References(23)Cited-By(6)We have implemented an efficient, user-friendly, and web-based "biosimulator" named BEST-KIT (Biochemical Engineering System analyzing Tool-KIT: http://www.best-kit.org) for analyzing large-scale nonlinear reaction networks such as metabolic pathways. The BEST-KIT mainly consists of a module, "MassAction++, " that can construct and analyze a reaction scheme represented by both mass action law (mass balance) and approximated velocity functions of enzyme kinetics at steady state. This module was developed in Java applet style and can be carried out on "any" platform machine through a web browser. In this study, we developed the parameter-estimation module for MassAction++. This module can estimate the values of unknown kinetic parameters based on the experimentally observed time-course data of state variables. We adopted three optimization techniques, the modified Powell method, the genetic algorithm, and the Hybrid method, which incorporates the genetic algorithm into the modified Powell method. The user can use an appropriate method for each purpose.

【 授权许可】

Unknown