Code generator for distributed parameter biological model simulation with PDE numerical schemes

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

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

1 Citation (Scopus)

Abstract

The physiological simulation at the tissue and organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and in cases like pharmacokinetics, distributed parameters add to the complexity of the PDE solution. These factors make most PDE solutions and their corresponding program codes tailored for specific problems. We propose a general approach for handling PDEs in computational models using a replacement scheme for discretization. This method allows for the handling of the different PDE types. The replacement scheme involves substituting all the partial differential terms with the numerical solution equations. Once the model equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to determine the simulation loop structure and generate the program code.

Original languageEnglish
Title of host publication2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
Pages1494-1497
Number of pages4
DOIs
Publication statusPublished - 2013
Externally publishedYes
Event2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 - Osaka, Japan
Duration: Jul 3 2013Jul 7 2013

Publication series

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

Other

Other2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
CountryJapan
CityOsaka
Period7/3/137/7/13

All Science Journal Classification (ASJC) codes

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

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