Conversion from SBML to CellML

CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.

Quick Setup

To generate a CellML file from an SBML model, run:

Xalan MyModel_SBML.xml sbml_to_cellml.xsl > MyModel_CellML.xml

Download

1. sbml_to_cellml.xsl
2. cellml_template.xsl
3. cellml_variable.xsl
4. cellml_connection.xsl

Documentation

The conversion is performed in one XSLT pass, but using four stylesheets.

Know Issues/Improvements

• Only one argument for plus (the MathML element) seems to be a problem. This occurs in all models were species are only product or reactant in one and only one reaction.
• The csymbols delay and time in SBML are not converted to variables in CellML
• e notation is not converted correctly.
• Connections for modifiers in reactions are doubled.
• If a species is a product and a reactant in the one and same reaction a delta variable gets assigned to two roles for this species. This could be easily evaded by adding one delta variable for each product or substrate, even if that means adding more than one for each species. Maybe one should add _r or _p for reactant and product to the delta vars.
• We should be able to support model with user-defined units

Development

We are planning, in collaboration with the CellML team, to create a new converter not using the reaction element and with a better support for unit for example.

Getting Help and Support

Please send any help requests or bug reports to :