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 _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
