Changes to bng.py: 1) Added a set_bng_path() method to allow the user to
specify where the BNG2.pl script is. 2) Added ‘verbose’ options to
generate_network() and generate_equations() that, if True, will print
the output from BNG2.pl to the screen. This is useful for monitoring the
progress of network generation, which can be lengthy for large models.
3) Added double underscores to the beginning of species names in
generate_equations() (e.g., __s1 instead of s1). This will minimize the
chance of conflicts with names of parameters in the model.