Lucian Smith | 24 Apr 2010 02:04

CellML models in Antimony format

Thanks to the help of many of you on this list, I now have a working 
CellML-to-Antimony translator, and have used it to translate all the 
models at models.cellml.org into the Antimony format.  The results are at:

http://antimony.sourceforge.net/antimony-cellml.html

along with SBML versions of those files, as translated from Antimony.  
These SBML versions are probably not as good as those created with the 
existing cellml2sbml translators--various aspects of the CellML files have 
been lost.  They do, however, work for 1.1 models, which (I believe) some 
cellml2sbml translators are unable to do (thanks to the use of the CellML 
API).

The main advantage of this translator is that it preserves and translates 
the modularity from the CellML format to the Antimony format.  The 
Antimony format is very similar to the as-yet-hypothetical hierarchical 
modeling package for SBML, and thus should provide a good basis for 
future translations between CellML and that SBML package.  This modularity 
includes the 'encapsulation' concept in CellML--if one compartment 
'encapsulates' another in a CellML file, that corresponding parent module 
in Antimony will contain the submodule.

All of the math found in ~92% of the models was successfully translated; 
of the remaining 8%, most were due to Antimony's insistence that 
assignment rules not be defined circularly, and the remainder tended to be 
little-used CellML constructs such as partial differential equations or 
rates of change with respect to some non-time variable.  All elements like 
this that failed to translate are mentioned in a comment a the top of the 
file.

(Continue reading)

Catherine Lloyd | 25 Apr 2010 22:59
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Re: CellML models in Antimony format

A stellar effort Lucian - congratulations!

> little-used CellML constructs such as partial differential equations  
> or
> rates of change with respect to some non-time variable

Yes - these are a legacy of coding up models in a text editor without  
any way of testing them!  Partial diffs can be coded up in CellML but  
there are no existing tools which will recognise them.  There  
shouldn't be anymore PDE models added to the repository, I believe  
they fall under the FieldML domain.

But I am happy to be corrected if I am wrong!

Best wishes
Catherine

On 24/04/2010, at 12:04 PM, Lucian Smith wrote:

> Thanks to the help of many of you on this list, I now have a working
> CellML-to-Antimony translator, and have used it to translate all the
> models at models.cellml.org into the Antimony format.  The results  
> are at:
>
> http://antimony.sourceforge.net/antimony-cellml.html
>
> along with SBML versions of those files, as translated from Antimony.
> These SBML versions are probably not as good as those created with the
> existing cellml2sbml translators--various aspects of the CellML  
> files have
(Continue reading)

Alan Garny | 26 Apr 2010 10:13
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Re: CellML models in Antimony format

> > little-used CellML constructs such as partial differential equations
> > or rates of change with respect to some non-time variable
> 
> Yes - these are a legacy of coding up models in a text editor without any
way
> of testing them!  Partial diffs can be coded up in CellML but there are no
> existing tools which will recognise them.  There shouldn't be anymore PDE
> models added to the repository, I believe they fall under the FieldML
domain.

I believe PDE models fall under a standard (ModelML?) that has yet to be
specified, but like you I am happy to be corrected if I am wrong!

Alan

Gmane