Whole cell model with plasmid loss experiments

Python 3.6+, see requirements.txt for python libraries used

Run main.py with arguments stating the plasmid copy number (PCN) and number of passages (n_passsages)

python3 main.py --PCN 5 --n_passages 30

python3 main.py --help to see other arguments

Configuration files are used to define the bioreactor environment and each strain (See example config files).

Each parameter definition take two values for uniform sampling, [lower_bound, upper_bound] .
Make lower_bound == upper_bound if the parameter is fixed

The prefix set in each config file is used to define the membership of paramters and species.

bioreactor_config.yaml defines the bioreactor environment. For batch cultures efflux and influx are zerro,
k_in = d_s = 0

Chemostat simulations can be made by setting efflux and influx to constant values,
k_in = d_s > 0

Q_strain_config.yaml defines a wild-type strain with no heterologous expression. All parameters and species here present are essential to the model, their values can be changed

P_strain_config.yaml defines an engineered strain, expressing a heterologous protein, h. We declare the necessary species to the priors, the prefixes define the species type.
g_h (protein),
m_h (mRNA),
c_h (mRNA-ribosome complex).

We also declare the necessary parameters for the heterologous expression.
w_h (transcription rate),
n_h (transcript length) and
theta_h (non-ribosome transcription threshold)