Convert Goldbeter 1991 Srn Model

[kwabenantim]

Summary
Fix code generation with lessons learned from Goldbeter 1991 sbml:

• Fix variable names. Names can have spaces so perhaps use ids instead, or do some name mangling.
• Fix generated number of ODE parameters (for Goldbeter, it was 5 rather than 3).
• Add methods to get state variables. Use variable names for clarity.
• Allow solver selection in command line e.g. RungeKutta4IvpOdeSolver or CVODE.
• Consider generating custom Srn model separately to replace template.
• Allow setting solver SetDt(0.1) in command line.
• Allow customizing timescale of results?

Related Issues

• Enable importing of SBML models into Chaste Chaste#134

[mirams]

For the solver selection, it is probably just "chaste solvers" or "CVODE", the only reason these need different generated code to specify an ODE system is that chaste solvers work with std::vector<double> and CVODE/SUNDIALS have their own N_Vector class. (copying what happens in cardiac code, which also generates for either, will be sensible here!)

Specifying what solver to use later on (RungeKutta/ForwardEuler etc.) should be fairly independent of the generated code apart from the CVODE special case.

[kwabenantim]

copying what happens in cardiac code, which also generates for either, will be sensible here!

Thanks @mirams! I think I've found the corresponding codegen:

• normal_chaste_model.py
• cvode_chaste_model.py