A general CellML simulation code generator using ODE solving scheme description

Akira Amano, Naoki Soejima, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Title of host publication33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
Pages940-944
Number of pages5
DOIs
Publication statusPublished - 2011
Externally publishedYes
Event33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011 - Boston, MA, United States
Duration: Aug 30 2011Sep 3 2011

Publication series

NameProceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
ISSN (Print)1557-170X

Other

Other33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
CountryUnited States
CityBoston, MA
Period8/30/119/3/11

All Science Journal Classification (ASJC) codes

  • Signal Processing
  • Biomedical Engineering
  • Computer Vision and Pattern Recognition
  • Health Informatics

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