The accompanying code and data necessary to reproduce the figures from "Active degradation of MarA controls coordination of its downstream targets" by Nicholas A. Rossi, Thierry Mora, Aleksandra M. Walczak and Mary J. Dunlop
Figure 1: This figure contains: simulation, analytical solutions and illustrations. All analytical solutions and simulation results can be achieved by running Figure1_driver.py within the root layer of the codebase. This generates “static.pdf” as well as “ clouds.pdf” with the figures subfolder. These two figures were combined within adobe illustrator with a few illustrations. The growing microcolonies are taken from filmstrips of movies of wild-type E. coli containg the plasmid pVAI (see manuscript). Custom coloring was applied for visual presence in photoshop. Subfigure D is saved from Figure1_driver.py as clouds.pdf
Figure 2: To generate this figure, first run “crispr_driver.py” : this generates all experimental figures as well as the 2A simulation traces. This script generates the following figure components saved within the figures subfolder : crisp_ts.pdf, crisp_2dhist.pdf, crisp_hist.pdf as well as crispr_simulation_traces.pdf. Next, you can run analytical_driver.py which generates all the analytical solutions to variance over time for Gene X as well as the mutual information over time between gene Y and Z. The second row of “analytical_solutions.pdf” can be combined with the previous figure components in adobe illustrator. Figure 2D was created exclusively in Illustrator. For the microcolony snapshots, use the raw tiffs contained within the “raw_data” folder. Crispr_driver calls “image_finctions.py” which generates the snapshot images. It saves them independently as “WildType.png” and “CRISPRi.png” before combining them as “combined_images.png”
Figure 3: This figure is generated by running “modified_marA_driver.py”. This calls main which generates all of the experimental figures, and traces which generates the simulation examples. This script generates modified_marA_simulation_traces.pdf as well as modified_marA-TS.pdf. As in figure 2, analytical_driver.py generates the analytic solutions – here the first row shows the analytical solutions to this part. The schematic 3D was created in illustrator.
Figure 4: This figure is generated by running figur4_driver.py. It saves the output as figure4.pdf within the figures folder