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Conf Proc IEEE Eng Med Biol Soc. 2011;2011:940-4. doi: 10.1109/IEMBS.2011.6090212.

A general CellML simulation code generator using ODE solving scheme description.

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Department of Bioinformatics, Ritsumeikan Univerisity, Shiga-ken 525-8577, Japan.


To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify target computation resources or numerical calculation methods or simulation conditions. Typical biological function simulation software consists of 1) model equation, 2) boundary conditions and 3) ODE solving scheme. Introducing the description model file such as CellML is useful for generalizing the first point and partly second point, however, third point is difficult to handle. We introduce a simulation software generation system which use markup language based description of ODE solving scheme together with cell model description file. By using this software, we can easily generate biological simulation program code with different ODE solving schemes. To show the efficiency of our system, experimental results of several simulation models with different ODE scheme and different computation resources are shown.

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