Codebase of Rossi et. al. 2017 : Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA

Here is the rawdata and code necessary to produce all figures from the above paper.

_Note: all code below was generated with python 2.7, python 3 should work but is untested

Figure 1: To generate this figure you need only run Experimental_analysis.py within the experimental analysis subfolder of the codebase. This generates the same figures for all 6 promoters used – within the paper we only visualize the examples of SFK and SIK (micF and inaA reporters). The example snapshots were taken from the tiffs at 0uM IPTG and 100uM IPTG. Figures are exported to the output_graphs subfolder.

Figure 2: This figure is generated by running two separate scripts and combining them in illustrator. The first half is generated by running stochastic_simulation.py followed by stochastic_simulation_graphing.py within the stochastic_simulation subfolder. You will need to run both twice to generate the first two columns: first edit stochastic_simulation.py to looping to Kd for the first column, then the hill coefficient for the second column (see comments where this is highlighted). Graphs are saved to the simulation_graphs folder as “combined.pdf”. The third column is generated by running experimental_analysis.py within the experimental_analysis subfolder. It is saved as “trajectories.pdf” within the output_graphs subfolder

Figure 3: As above this figure is generated from experimental_analysis.py and combining the figures “heatmap.pdf”, “wt_mapped_dist” and “mv_mapped_dist” saved within the output_graphs subfolder

Figure 4: As within figure 4 we run experimental_analysis.py to generate the figures and combine “chimera_heat_map” with “chimera_trajectories.pdf” within adobe illustrator.