08/11/2024

calibrate_TORC-plasmid.py - Builds systems and runs the optimization process to find set of parameters that best
                            reproduce experimental results.
create_oparams.py - Uses results from the optimization process to build the parametrization file for each
                    circuit component (promoters and lacI).

reproduce_TORC-plasmid.py - Runs simulations for all systems considered (same as optimization process) to produce
                            data for analyses. It outputs a pickle file (check the script for the output name)
                            with data for analysis


disp-sites* are sites in which lac1 was displaced by -16bp. This is to simulate the lacI blocking of the
minimal PleuWT but not in the complete system.