In the field of biological function simulation, many quantitative models are now accumulated in the repository driven by several model markup language groups such as CellML repository. Such quantitative model research are now considered very important for the future research in the biological field. However, the quality of each model is not guaranteed thus in some case, we can not reproduce graphs in the published papers from the uploaded model files. One reason of this problem is the computation environment, or the calculation engine used to simulate each model. Thus we came to think that the description language for describing the calculation scheme is necessary for reproducing the simulation results. If the calculation scheme is very simple, then the scheme is just a description of simple Euler method or Runge-Kutta method, however, if we think of combining different type of models together, the calculation scheme becomes very complex. These schemes are called coupling calculation schemes. Since there are so many variety in the coupling calculation, there is no standard scheme for multiple model combination. In such case, a formal description of the coupling calculation scheme is necessary. TecML is a markup language dedicated for describing numerical calculation schemes which covers simple ODE (ordinary differential equation) schemes, coupling calculation schemes and PDE (partial differential equation).


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



Department of Bioinformatics, College of Life Sciences
Ritsumeikan University

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