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 language | English |
|---|---|
| Title of host publication | 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012 |
| Pages | 6624-6627 |
| Number of pages | 4 |
| DOIs | |
| Publication status | Published - Dec 14 2012 |
| Event | 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2012 - San Diego, CA, United States Duration: Aug 28 2012 → Sep 1 2012 |
Publication series
| Name | Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS |
|---|---|
| ISSN (Print) | 1557-170X |
Other
| Other | 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2012 |
|---|---|
| Country | United States |
| City | San Diego, CA |
| Period | 8/28/12 → 9/1/12 |
Fingerprint
All Science Journal Classification (ASJC) codes
- Signal Processing
- Biomedical Engineering
- Computer Vision and Pattern Recognition
- Health Informatics
Cite this
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 proceeding › Conference contribution
}
TY - GEN
T1 - A program code generator for multiphysics biological simulation using markup languages
AU - Amano, Akira
AU - Kawabata, Masanari
AU - Yamashita, Yoshiharu
AU - Rusty Punzalan, Florencio
AU - Shimayoshi, Takao
AU - Kuwabara, Hiroaki
AU - Kunieda, Yoshitoshi
PY - 2012/12/14
Y1 - 2012/12/14
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84884178362&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84884178362&partnerID=8YFLogxK
U2 - 10.1109/EMBC.2012.6347513
DO - 10.1109/EMBC.2012.6347513
M3 - Conference contribution
C2 - 23367448
AN - SCOPUS:84884178362
SN - 9781424441198
T3 - Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
SP - 6624
EP - 6627
BT - 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012
ER -