MATLAB: Do I get error messages when an SBML file created by exporting a SimBiology model is imported into a third-party tool

SimBiology

I have a SimBiology project in which I define some reactions in MATLAB functions. If I export the model as .sbml file and test this file in the sbml validator (<http://sbml.org/Facilities/Validator/index.jsp)>, I get the error messages with ids 10214 and 21121.

Best Answer

You may see errors when using third-party tools to import SBML files created by SimBiology when your model uses functionality that is not supported for SBML export. In particular, SimBiology does not export function definitions for MATLAB functions referenced in a SimBiology model. To maintain compatibility with SBML, your SimBiology model should only reference the MATLAB equivalent of functions that are predefined in MathML (for example, cos and abs). Alternatively, you can manually edit an SBML file created by SimBiology to include MathML function definitions for any referenced functions. Also note that the export functionality of SimBiology (i.e. "sbmlexport") only exports the SimBiology model object but nothing else that is contained within a SimBiology project (such as data or results). Unsupported modeling elements and any other SBML limitations are described in the documentation:  <http://www.mathworks.com/help/simbio/gs/simbiology-and-sbml.html> . Some of these limitations are inherent to the limitations of SBML itself. For example, SBML cannot describe the data that are stored in SimBiology projects.
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