models.py: the implementation of models of the Master-Slave Flip-Flop, Johnson counter, etc.johnson_3bit.py: the implementation of the simulation-based analysis of a 3-bit Johnson counter.params.py: ranges of parameter values for the optimisation of the response of a circuit.hill_functions.py: Hill functions of different types of biological parts (e.g., activator, repressor, inducer, etc.). Used bymodels.py.