This directory contains a python implementation of the physiologically realistic model discussed near the end of the results section and in Figure 7.
Requirets numpy, scipy, matplotlib, and a recent python2 installation

The simulation parameters are specified by a series of configuration files read from the command line -- see the examples included with this directory for formatting. All sections present in the bundle of config files included here are required, and may be split across multiple files (or combined in the same one) in whatever way the user finds most convenient.

To run the simulation, simply call the tuning script with the config files included on the command line; for example,
python tuning_sim.py baseline.cfg  physiological_parameters_narrow.cfg  simulation_gen1_1genereal_production.cfg > tuning.log

python pickle objects containing the trajectories will be written to a series of .pkl files in the current working directory. One key parameter controlling the simulations to be performed is the 'methods' parameter of the [simulation] section, which lists the full set of simulated replicates that should be run. Thus, listing the same simulation type more than once is meaningful, as it will result in trajectories with the same parameters but different random number seeds.

Note well that all biological parameters (baseline and target transcription rates, protein stabilities, etc) are generated once for a single run of the program, and thus will be shared across all replicates of all simulation types. 


