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Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, and Akira Amano. A CellML Simulation Compiler and Code Generator Using ODE Solving Schemes. Source Code for Biology and Medicine, 7:11, 2012. Department of Bioinformatics, College of Life Sciences. A-amano(at)fc.ritsumei.ac.jp.

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TecML | tecml.org Reviews
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Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, and Akira Amano. A CellML Simulation Compiler and Code Generator Using ODE Solving Schemes. Source Code for Biology and Medicine, 7:11, 2012. Department of Bioinformatics, College of Life Sciences. A-amano(at)fc.ritsumei.ac.jp.
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1 overview
2 specification
3 tecml ode
4 tecml pde
5 tools
6 news
7 introduction
8 references
9 contributors
10 akira amano
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TecML | tecml.org Reviews

https://tecml.org

Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, and Akira Amano. A CellML Simulation Compiler and Code Generator Using ODE Solving Schemes. Source Code for Biology and Medicine, 7:11, 2012. Department of Bioinformatics, College of Life Sciences. A-amano(at)fc.ritsumei.ac.jp.

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1

TecML PDE | TecML

http://www.tecml.org/specification/tecml-pde

Different from the ODE TecML, PDE TecML can only describe single step discretization schemes. Consider you have a set of partial differential equation as follows. Dv/dt = a d 2v/dx 2;. In the FTCS (forward in time center in space) scheme of one dimensional case, we discretize above equation as follows. Dv/dt - (v(n 1, x) – v(n, x) / dt. D 2v/dx 2 - (v(n, x 1) v(n, x-1) – 2 v(n, x) /(dx) 2. We also have to add indices to each variable as follows. V - v(n, x). Description of each part. 8221; attribute defi...

2

news | TecML

http://www.tecml.org/news

Apologies, but no results were found for the requested archive. Perhaps searching will help find a related post.

3

tools | TecML

http://www.tecml.org/download

CellCompiler (formerly CellMLCompiler) is a tool which generates simulation program code from a CellML model file and a TecML calculation scheme. The correspondence between both files have to be provided by a relation file whose format is defined as RelML. Current version of the tool only supports TecML V2.0. Http:/ www.cellcompiler.org/.

4

specification | TecML

http://www.tecml.org/specification

There are two different formats for describing ODE (ordinary differential equation) schemes and PDE (partial differential equation).

5

TecML ODE | TecML

http://www.tecml.org/specification/tecml-ode

Consider you have a set of ordinary differential equation as follows. Dx/dt = x – r z;. You have to select a numerical method such as Euler method to calculate time evolution of x in the above equations. Euler method can be denoted as follows. X (n 1) = x (n) dx/dt * dt. However, there is no corresponding equation for r = x * x * x in Euler equation, therefore, we can provide two more equations to Euler method to have correspondence with the input ODE as follows. Y (n) = g(x (n), y (n). One TecML variabl...

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Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, and Akira Amano. A CellML Simulation Compiler and Code Generator Using ODE Solving Schemes. Source Code for Biology and Medicine, 7:11, 2012. Department of Bioinformatics, College of Life Sciences. A-amano(at)fc.ritsumei.ac.jp.

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