simulation platform

1. biological function model simulation program generator CellCompiler

   
   In the biological function model simulation platform project, we are constructing software tools which can be used by the researchers who are not familiar with computer software. One of the tool called CellCompiler can generate simulation program (in C language) automatically from biological simulation model equaions which are written by CellML. The system automatically generate C program by using a CellML model file and also numerical solution of differential equations such as Euler method, Backward Euler, Runge Kutta, implicit Runge Kutta.

2. numerical calculation scheme description language  TecML

   CellCompiler is a software tool which generates simulation program of biological models whose equations are written by CellML. And the system uses numerical solutions of differential equation such as Euler method, Backward Euler method, Runge Kutta method. Also, the system can use multistep methods such as Adams Bashforth method, and also any kind of numerical schemes which are written in the recurrence relation equations. Thus the system can generate simulation programs including multiple loops for handling multiple models which has different time steps. These numerical schemes are written in the XML type file called TecML.

3. simulation platform DynaBioS

   In the heart motion simulation, both the cell level simulation software simBio which is developed at the medical school in Kyoto University, and the FEM solver marc (MSC software) are coupled together. To couple these software, coupling simulation platform DynaBioS was developed. DynaBioS can handle simulation software which do not have coupling simulation interface, so the researchers can use their familiar simulation software to develop their models which may reduce bugs.