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On 25/10/11 09:14, David Nickerson wrote:
> Hi Maxwell,
>
> If you wrap the MathML into a CellML model/component, COR does a good
> job generating Matlab. OpenCell should work as well. Actually, I think
> OpenCell might be able to generate all the variables for you from the
> equation, whereas in COR you might also have to create the variables
> before it will let you export to Matlab.

To add to what David said, the CellML API includes a general facility
for translating CellML into imperative languages, and a specific
description of how to do this for MATLAB, and this was exposed in OpenCell.

There are a few problems with the generated MATLAB that have been found
since the final release of OpenCell (which is no longer maintained in
Auckland) that have been fixed in the API.

There is a program that comes with the API (and which exists purely for
testing the API, rather than as a user friendly program) - if you build
the CellML API from source code, you can run it as follows:

cd cellml-api
./testCeLEDS urlToModelHere ./CeLEDS/languages/MATLAB.xml

Hopefully OpenCOR, which is based on the CellML API, and being developed
in Oxford, will expose this functionality in a user friendly way.

Best wishes,
Andrew

>
> Cheers,
> David.
>
> On Tue, Oct 25, 2011 at 7:58 AM, Maxwell Neal<mneal at u.washington.edu>
> wrote:
>> Hi all,
>>
>> Does anyone know of a good java package for translating MathML into MATLAB?
>> Many thanks,
>>
>> M
>>
>> ---------------------------------
>> Maxwell Neal
>>
>> Post-doctoral researcher
>> University of Washington
>> mneal at uw.edu
>> (206) 543-8769
>> ---------------------------------
>>
>>
>>
>>
>> On Oct 23, 2011, at 4:00 PM, cellml-discussion-request at cellml.org wrote:
>>
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>>> Today's Topics:
>>>
>>> 1. Re: cellml-discussion Digest, Vol 87, Issue 9 (Maxwell Neal)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Sat, 22 Oct 2011 19:02:16 -0700
>>> From: Maxwell Neal<mneal at u.washington.edu>
>>> Subject: Re: [cellml-discussion] cellml-discussion Digest, Vol 87,
>>> Issue 9
>>> To: cellml-discussion at cellml.org
>>> Message-ID:<28198366-57CF-471F-8882-34E73FC05C35 at u.washington.edu>
>>> Content-Type: text/plain; charset=us-ascii
>>>
>>> Great. Thanks, Lucian and David.
>>>
>>> M
>>>
>>> ---------------------------------
>>> Maxwell Neal
>>>
>>> Post-doctoral researcher
>>> University of Washington
>>> mneal at uw.edu
>>> (206) 543-8769
>>> ---------------------------------
>>>
>>>
>>>
>>>
>>> On Oct 22, 2011, at 4:00 PM, cellml-discussion-request at cellml.org
>>> wrote:
>>>
>>>> Send cellml-discussion mailing list submissions to
>>>> cellml-discussion at cellml.org
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>> http://lists.cellml.org/mailman/listinfo/cellml-discussion
>>>> or, via email, send a message with subject or body 'help' to
>>>> cellml-discussion-request at cellml.org
>>>>
>>>> You can reach the person managing the list at
>>>> cellml-discussion-owner at cellml.org
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of cellml-discussion digest..."
>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. Re: nested components in CellML (David Nickerson)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Sat, 22 Oct 2011 14:30:37 +1300
>>>> From: David Nickerson<david.nickerson at gmail.com>
>>>> Subject: Re: [cellml-discussion] nested components in CellML
>>>> To: CellML Discussion List<cellml-discussion at cellml.org>
>>>> Message-ID:
>>>> <CADizRjhqHMOpDDm=8xoZLAD=BCOGNSm0XdLFma6Yeox20K-R4Q at
>>>> mail.gmail.com>
>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>>
>>>> On Sat, Oct 22, 2011 at 10:10 AM, Lucian Smith<lpsmith at
>>>> spod-central.org> wrote:
>>>>> * Maxwell Neal<mneal at u.washington.edu> [2011-10-21 22:03] writes:
>>>>>> Hi all,
>>>>>>
>>>>>> I was wondering - can CellML models have nested components? ?That is,
>>>>>> are there instances where some model component is a component in
>>>>>> another model component?
>>>>>> Thanks,
>>>>>
>>>>> Yes--this is covered by the concept of encapsulation. ?See
>>>>> http://www.cellml.org/getting-started/tutorials/tutorial/best_practice/#grouping
>>>>> for more detail, but basically you set up a whole tree of nested
>>>>> components, and this nesting determines the rules for how you can
>>>>> connect
>>>>> the variables in those components.
>>>>>
>>>>> Also, an imported component from another file that encapsulates other
>>>>> components brings those components (and corresponding connections) with
>>>>> it in the import.
>>>>>
>>>>> Is that a reasonable summary, list denizens?
>>>>
>>>> yep, I think that summarises it nicely. Importing along with
>>>> encapsulation allows the definition of models where some components
>>>> are components from another model.
>>>>
>>>>
>>>> Cheers,
>>>> Andre.
>>>>
>>>>
>>>> ------------------------------
>>>>
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>>>>
>>>> End of cellml-discussion Digest, Vol 87, Issue 9
>>>> ************************************************
>>>
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>>
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• [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10, Maxwell Neal, 10/25/2011
  • [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10, David Nickerson, 10/25/2011
    • [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10, Andrew Miller, 10/25/2011

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