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Tommy Yu
Tommy Yu
CellML Discussion List
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- From: ak.miller at auckland.ac.nz (Andrew Miller)
- Subject: [cellml-discussion] About MatLab2CellML.
- Date: Tue, 11 Sep 2012 12:50:19 +1200
On 11/09/12 10:19, Jaekyoung Kim wrote:
> Hello.
>
> I have a question about how to use MatLab2CellML.
>
> Our model is generated with MatLab or Mathematica.
>
> I found that MatLab2CellML allows to convert Matlab code to CellML.
>
> However, I could not find any example or instruction about how to use it.
>
> Is there anyone who has an example or instructions for MatLab2CellML?
Hi Jae,
I would recommend using a tool other than Matlab2CellML.
Converting a model from Matlab to CellML is a manual process, because
MATLAB is an imperative language while CellML is declarative, so
converting to CellML will sometimes require judgement calls to be made
about the modelling intent.
Matlab2CellML does one part of the process, converting equations to
MathML. You will likely still need to edit the resulting MathML, and you
will definitely need to define things like the variables involved and
their units (CellML requires that all variables be declared, and have
physical units, and also requires that physical units be put on all
constants).
You might want to try a tool like OpenCOR (which is under development),
OpenCell (which is supposed to be eventually replaced by OpenCOR) or COR
(again, which OpenCOR is supposed to eventually replace). Alternatively,
you could try using the command line tools which come with the CellML API.
I have started creating this page as a tutorial:
http://cellml.wikia.com/wiki/Translating_from_MATLAB_to_CellML
I don't yet have a good Matlab example file to create the tutorial with,
but the page does have background, and might help point you in the right
direction. If anyone has a simple Matlab model they are willing to share
publicly on that wiki, I can try to develop the tutorial around
converting the model into CellML.
Best wishes,
Andrew
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- [cellml-discussion] About MatLab2CellML., Jaekyoung Kim, 09/11/2012
- [cellml-discussion] About MatLab2CellML., Andrew Miller, 09/11/2012
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