overview
CellCompiler is a tool which generates simulation program code from cell model files and calculation scheme file. For the cell model file, the system now supports CellML and will be supporting PHML. For the calculation scheme file, the system uses TecML file. Since the cell model file only defines equations, the boundary condition to be used in the simulation have to be provided by users. This information is provided as RelML in the system.
We also provide a tool to generate Jacobian Matrix calculation program called JacobianGenerator. The input files for JacobianGenerator are CellML file and a variable definition file called JGML file. The package also contains a program for calculating equilibrium point for CellML files.
References
Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, and Akira Amano
A CellML Simulation Compiler and Code Generator Using ODE Solving Schemes
Source Code for Biology and Medicine, 7:11, 2012
Florencio Rusty Punzalan, Yoshiharu Yamashita, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, Akira Amano
Code Generator for Distributed Parameter Biological Model Simulation with PDE Numerical Schemes
Proc. IEEE EMB Conference 2013, pp.1494-1497, 2013.
Akira Amano, Masanari Kawabata, Yoshiharu Yamashita, Florencio Rusty Punzalan, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda
A Program Code Generator for Multiphysics Biological Simulation using Markup Languages
Proc. IEEE EMB Conference 2012, pp. 6624-6627, 2012.
Akira Amano
Description Language of Calculation Scheme for Automatic Simulation Code Generation
CellML Workshop, 2012.
Masanari Kawabata, Yoshiharu Yamashita, Florencio Rusty Punzalan, Yoshitoshi Kunieda, Akira Amano
A Program Code Generator for Multiphysics Biological Simulation using Markup Languages
International Workshop on Innovative Architecture for Future Generation High-Performance Processors and Systems 2012, 2012.1.10.
Yoshiharu Yamashita, Yuichiro Hayashi, Naoki Soejima, Masanari Kawabata, Punzalan Florencio Rusty, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, Akira Amano
A Parallel CellML Simulation Program Generator with a Nonlinear Simultaneous Equation Solver
International Workshop on Innovative Architecture for Future Generation High-Performance Processors and Systems 2012
Akira AMANO, Naoki SOEJIMA, Takao SHIMAYOSHI, Hiroaki KUWABARA, Yoshitoshi KUNIEDA
A General CellML Simulation Code Generator using ODE Solving Scheme Description
Proc. IEEE EMB Conference 2011, pp. 940-944, 2011.
Contributors
Akira Amano (Ritsumeikan University)
Florencio Punzalan Rusty
Yoshitoshi Kunieda (Ritsumeikan University)
Hiroaki Kuwabara (Ritsumeikan University)
Takao Shimayoshi (Kyoto Univeristy)
Naoki Soejima (Ritsumeikan University)
Masanari Kawabata (Ritsumeikan University)
Yoshiharu Yamashita (Ritsumeikan University)
Contact
Akira AMANO
Department of Bioinformatics, College of Life Sciences
Ritsumeikan University
a-amano(at)fc.ritsumei.ac.jp