WinBEST-KIT: Windows-based Biochemical Reaction Simulator for Analyzing Complicated Metabolic Pathways

Features

  1. Reaction schemes can be created by operations that are similar to using a drawing tool
    The reaction scheme that represents the biochemical reaction system can be created by using lines to connect reactant symbols (which represent reactants) and reaction step symbols (which represent reaction steps). A wide variety of editing functions (cut, copy, paste, undo, etc.) are also provided.
  2. Reaction schemes can be created by using the same layout as metabolic pathways
    Reaction schemes can be divided up into multiple functions, and each function can be edited individually by using multiple editing windows, and multiple reactant symbols with the same name can be placed. This makes it possible to create reaction schemes that have the same layouts as the metabolic pathways, such as the ones seen in biochemical textbooks.
  3. Reaction schemes can be created that contain a combination of the mass action law and the steady-state approximations of enzyme kinetics
    Reaction scheme can be created that combine detailed models based on the mass action law along with the steady-state approximations of enzyme kinetics such as Michaelis-Menten equation. The major steady-state approximations of enzyme kinetics are provided as standard reaction step symbols.
  4. Original mathematical equations can be used as reaction steps
    Users can define the original mathematical equations representing unknown kinetic mechanisms and customize them as the reaction steps of GUI components (custom reaction step symbols can be registered to WinBEST-KIT).
  5. Automatic derivation of mass balance equations and automatic simulation
    The mathematical models of biochemical reaction systems are represented by initial concentration of reactants, mass balance equations (simultaneous differential equations), and kinetic parameters of reaction steps. WinBEST-KIT can be automatically performed the derivation of mass balance equations that represents a created reaction scheme. Because of this, the user does not need to be aware of the cumbersome simultaneous differential equations. Since the numerical calculations needed for the simulation are also performed automatically, the user also does not need to be aware of the numerical calculation methods or programming language.
  6. High-speed simulations using a compiler
    When performing simulations, the numerical calculations can be performed using an external compiler. Although the compiler needs to be installed, the complex work of compilation is afterward performed automatically. If you want to try out using WinBEST-KIT alone, the numerical calculations can be performed by the built-in interpreter.
  7. Wide variety of analysis functions
    WinBEST-KIT provides a wide variety of analysis functions in addition to regular time-course simulation, including parameter estimation, parameter scanning, and a real-time simulation called Virtual Lab. The analysis results that can be displayed include time-course graphs, phase plane diagrams, numerical data, and mass balance equations.