Modified pysb.bng.run_ssa to fill in the model elements 'species',
'reactions', 'observables', and 'odes' by parsing the NET file generated
by BNG. To accomplish this, pysb.bng.generate_equations had to be
refactored. Specifically, the majority of the code was moved into a new
function named '_parse_netfile'. This allows this function to be called
at the end of pysb.bng.run_ssa.