A program code generator for multiphysics biological simulation using markup languages

Akira Amano, Masanari Kawabata, Yoshiharu Yamashita, Florencio Rusty Punzalan, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda

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

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 the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Original languageEnglish
Title of host publication2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012
Pages6624-6627
Number of pages4
DOIs
Publication statusPublished - Dec 14 2012
Event34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2012 - San Diego, CA, United States
Duration: Aug 28 2012Sep 1 2012

Publication series

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

Other

Other34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2012
CountryUnited States
CitySan Diego, CA
Period8/28/129/1/12

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Markup languages
Language
Software
Boundary conditions

All Science Journal Classification (ASJC) codes

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

Cite this

Amano, A., Kawabata, M., Yamashita, Y., Rusty Punzalan, F., Shimayoshi, T., Kuwabara, H., & Kunieda, Y. (2012). A program code generator for multiphysics biological simulation using markup languages. In 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012 (pp. 6624-6627). [6347513] (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). https://doi.org/10.1109/EMBC.2012.6347513

A program code generator for multiphysics biological simulation using markup languages. / Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi.

2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012. 2012. p. 6624-6627 6347513 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

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

Amano, A, Kawabata, M, Yamashita, Y, Rusty Punzalan, F, Shimayoshi, T, Kuwabara, H & Kunieda, Y 2012, A program code generator for multiphysics biological simulation using markup languages. in 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012., 6347513, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, pp. 6624-6627, 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2012, San Diego, CA, United States, 8/28/12. https://doi.org/10.1109/EMBC.2012.6347513
Amano A, Kawabata M, Yamashita Y, Rusty Punzalan F, Shimayoshi T, Kuwabara H et al. A program code generator for multiphysics biological simulation using markup languages. In 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012. 2012. p. 6624-6627. 6347513. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). https://doi.org/10.1109/EMBC.2012.6347513
Amano, Akira ; Kawabata, Masanari ; Yamashita, Yoshiharu ; Rusty Punzalan, Florencio ; Shimayoshi, Takao ; Kuwabara, Hiroaki ; Kunieda, Yoshitoshi. / A program code generator for multiphysics biological simulation using markup languages. 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012. 2012. pp. 6624-6627 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).
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