Academic Journal
A CellML simulation compiler and code generator using ODE solving schemes.
| Τίτλος: | A CellML simulation compiler and code generator using ODE solving schemes. |
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| Συγγραφείς: | Punzalan, Florencio Rusty, Yamashita, Yoshiharu, Soejima, Naoki, Kawabata, Masanari, Shimayoshi, Takao, Kuwabara, Hiroaki, Kunieda, Yoshitoshi, Amano, Akira |
| Πηγή: | Source Code for Biology & Medicine; 2012, Vol. 7 Issue 1, p1-11, 11p, 7 Black and White Photographs, 5 Charts, 2 Graphs |
| Θεματικοί όροι: | Language research, Boundary value problems, XML (Extensible Markup Language), Computer simulation, Mathematical models |
| Περίληψη: | Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. [ABSTRACT FROM AUTHOR] |
| Copyright of Source Code for Biology & Medicine is the property of BioMed Central and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Βάση Δεδομένων: | Complementary Index |
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| Items | – Name: Title Label: Title Group: Ti Data: A CellML simulation compiler and code generator using ODE solving schemes. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Punzalan%2C+Florencio+Rusty%22">Punzalan, Florencio Rusty</searchLink><br /><searchLink fieldCode="AR" term="%22Yamashita%2C+Yoshiharu%22">Yamashita, Yoshiharu</searchLink><br /><searchLink fieldCode="AR" term="%22Soejima%2C+Naoki%22">Soejima, Naoki</searchLink><br /><searchLink fieldCode="AR" term="%22Kawabata%2C+Masanari%22">Kawabata, Masanari</searchLink><br /><searchLink fieldCode="AR" term="%22Shimayoshi%2C+Takao%22">Shimayoshi, Takao</searchLink><br /><searchLink fieldCode="AR" term="%22Kuwabara%2C+Hiroaki%22">Kuwabara, Hiroaki</searchLink><br /><searchLink fieldCode="AR" term="%22Kunieda%2C+Yoshitoshi%22">Kunieda, Yoshitoshi</searchLink><br /><searchLink fieldCode="AR" term="%22Amano%2C+Akira%22">Amano, Akira</searchLink> – Name: TitleSource Label: Source Group: Src Data: Source Code for Biology & Medicine; 2012, Vol. 7 Issue 1, p1-11, 11p, 7 Black and White Photographs, 5 Charts, 2 Graphs – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Language+research%22">Language research</searchLink><br /><searchLink fieldCode="DE" term="%22Boundary+value+problems%22">Boundary value problems</searchLink><br /><searchLink fieldCode="DE" term="%22XML+%28Extensible+Markup+Language%29%22">XML (Extensible Markup Language)</searchLink><br /><searchLink fieldCode="DE" term="%22Computer+simulation%22">Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Mathematical+models%22">Mathematical models</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. [ABSTRACT FROM AUTHOR] – Name: Abstract Label: Group: Ab Data: <i>Copyright of Source Code for Biology & Medicine is the property of BioMed Central and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1186/1751-0473-7-11 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 1 Subjects: – SubjectFull: Language research Type: general – SubjectFull: Boundary value problems Type: general – SubjectFull: XML (Extensible Markup Language) Type: general – SubjectFull: Computer simulation Type: general – SubjectFull: Mathematical models Type: general Titles: – TitleFull: A CellML simulation compiler and code generator using ODE solving schemes. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Punzalan, Florencio Rusty – PersonEntity: Name: NameFull: Yamashita, Yoshiharu – PersonEntity: Name: NameFull: Soejima, Naoki – PersonEntity: Name: NameFull: Kawabata, Masanari – PersonEntity: Name: NameFull: Shimayoshi, Takao – PersonEntity: Name: NameFull: Kuwabara, Hiroaki – PersonEntity: Name: NameFull: Kunieda, Yoshitoshi – PersonEntity: Name: NameFull: Amano, Akira IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 05 Text: 2012 Type: published Y: 2012 Identifiers: – Type: issn-print Value: 17510473 Numbering: – Type: volume Value: 7 – Type: issue Value: 1 Titles: – TitleFull: Source Code for Biology & Medicine Type: main |
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