WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways
WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways
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DOI：
10.1142/s0219720006002132
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发表时间：
2006-06-01
影响因子：
1
通讯作者：
Okamoto, Masahiro
中科院分区：
文献类型：
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作者：
Sekiguchi, Tatsuya;Okamoto, Masahiro
我们已经实现了一个高效的，用户友好的生化反应模拟器，称为基于Web的BEST-KIT（生化工程系统分析工具-KIT），用于分析大规模的非线性网络，如代谢途径。用户可以很容易地设计和分析一个任意的反应方案，通过互联网和一个高效的图形用户界面，而无需考虑的数学方程。反应方案可以包括几种反应类型，其由质量作用定律（质量平衡）和稳态下酶动力学的近似速度函数表示，例如Michaelis-Menten，Hill合作，竞争性抑制。然而，由于基于Web的BEST-KIT中的所有模块都是以Java（TM）applet风格开发的，因此除了准备好的方程之外，用户不能随意使用原始数学方程。在本研究中，我们开发了一个新版本的BEST-KIT（用于Microsoft（R）Windows（R），称为WinBEST-KIT），允许用户定义原始数学方程，并将这些方程非常容易地定制为用户定义的反应符号。以下强大的系统分析方法准备系统分析：时程计算，参数扫描，估计未知的动力学参数的值的基础上实验观察到的反应物时程数据，反应物对虚拟外部扰动的动态响应，和实时模拟（虚拟干实验室）。
We have implemented an efficient, user-friendly biochemical reaction simulator called Web-based BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing large-scale nonlinear networks such as metabolic pathways. Users can easily design and analyze an arbitrary reaction scheme through the Internet and an efficient graphical user interface without considering the mathematical equations. The reaction scheme can include several reaction types, which are represented by both the mass action law (mass balance) and approximated velocity functions of enzyme kinetics at steady state, such as Michaelis-Menten, Hill cooperative, Competitive inhibition. However, since all modules in Web-based BEST-KIT have been developed in Java (TM) applet style, users cannot optionally make use of original mathematical equations in addition to the prepared equations. In the present study, we have developed a new version of BEST-KIT (for Microsoft (R) Windows (R), called WinBEST-KIT) to allow users to define original mathematical equations and to customize these equations very easily as user-defined reaction symbols. The following powerful system-analytical methods are prepared for system analysis: time-course calculation, parameter scanning, estimation of the values of unknown kinetic parameters based on experimentally observed time-course data of reactants, dynamic response of reactants against virtual external perturbations, and real-time simulation (Virtual Dry Lab).