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[cellml-discussion] CellML models in Antimony format


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  • From: c.lloyd at auckland.ac.nz (Catherine Lloyd)
  • Subject: [cellml-discussion] CellML models in Antimony format
  • Date: Mon, 26 Apr 2010 08:59:40 +1200
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
> 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.
>
> Other aspects that we didn't attempt to translate include units,
> compartments, and annotation. (And reactions, but there are zero
> reactions at cellml.org, so I think we're safe there.) We hope that
> future versions of the translator will include these aspects, at least
> insofar as cellml->antimony->SBML translators.
>
> If you have comments on how well or how poorly we managed to translate
> your favorite CellML model to Antimony, we would love to hear from
> you.
>
> Thank you!
>
> -Lucian
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