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SemBioProcess / SemGen

A tool for semantics-based annotation and composition of biosimulation models
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How to deal with merges that result in changes to conservation equations on entities? #219

Open maxneal opened 7 years ago

maxneal commented 7 years ago

If we take Herbert's HARMONY 2017 example where a reaction with product A is extracted from an SBML model and then inserted into another model where A is a reactant in a different reaction, the conservation equation for species A needs to be updated in the resulting simulation code.

If you export the resulting merged model as an SBML model, this isn't a problem b/c SBML models don't explicitly state the conservation equations. The simulation software (e.g. JSim) takes care of that.

But if we export to CellML, or directly to JSim, then we need to update the conservation equation.

maxneal commented 6 years ago

This is also an important issue for Dewan's work with the epithelial modeling platform, and is also important for performing the kind of electrophysiology modeling compositions envisioned by Jim Bassingthwaighte.