08/11/2024

Here, I will run TORCPhysics trying to find parametrisation that can reproduce and explain experimental results.

The *csv files in this folder correspond to the circuit files for the cases in which we have the minimum PleuWT and
full PleuWT, and their linearised versions *-linear.
The linear plasmid versions assume that the origin of replication is a barrier at each end. This is valid since
we are assuming a linear plasmid behaviour even if it's circular or in other words, we assume that the origin of
replication is always bound by an enzyme.

These is what each folder contains:

respones/ - contains the responses of each promoter calibrated with SIST. The other csv and python files there are just
needed for visualizating the responses.

test_lacI-repressor/ - tests the physical blocking of PleuWT by lacI binding upstream.

optimization/ - contains scripts to setup and run random search algorithm to find sets of parametrisation that
                approximate experimental behaviour.

single_sim/ - Scripts for running 1 simulation for 1 specific system.

analysis/ - Scripts for analysing results from optimization process.