CellML models in Antimony format
Lucian Smith <lpsmith <at> u.washington.edu>
2010-04-24 00:04:35 GMT
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:
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
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
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.