[cellml-discussion] Prototype SBML to CellML converter

[Andrew Miller]

Hi all,

I have recently coded up a prototype designed to demonstrate how a 
program to convert from SBML to CellML might work. This prototype is 
written in Ruby using the REXML XPath parser, which was rapid to develop 
but makes it very slow to run - the intention is that once the 
algorithms to used are worked out, it could be re-written in a more 
efficient language.

The code has been pushed onto github - the project page is at 
http://github.com/A1kmm/sbml2cellml/tree/master

Features supported at present:
  * SBML parameters, compartments, species, rules, and reactions are 
translated into the equivalent component, variable and math elements in 
CellML (the reaction element in CellML is not used because this is 
considered informally deprecated).
  * Functions are substituted and expanded in the code invoking the 
function, since CellML doesn't allow them at present.
  * Units on constants (MathML cn elements) are automatically inferred 
from the context, where possible.
  * I have attempted to support all of SBML except events, time delays 
and other features which don't have a parallel in CellML yet.
  * The csymbol for time is replaced with a new variable introduced for 
time.

Feedback and comments on this code would be greatly appreciated.

Best wishes,
Andrew