Data for Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response

Data from simulations used to generate the figures in the paper <em>Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response</em>. To reproduce analyses, extract <em>colony_data.zip</em> in the <em>data</em> folder after cloning the <em>vivarium-ecoli</em> repository. The extracted folder contains the following items: <em>sim_dfs</em>: a folder containing the CSV files that represent a subset of the raw simulation data used for downstream analyses. <em>glc_10000_fluxome.csv</em>: Each row represents a reaction in central carbon metabolism (in same order as listed in <em>validation/ecoli/flat/toya_2010_central_carbon_fluxes.tsv</em>). Each column represents a single time point for a single cell in a baseline glucose simulation (seed 10000). Each value is a flux (mmol/L/hr). Provided as input to <em>ecoli/analysis/centralCarbonMetabolism.py </em>script to reproduce fluxome validation plot. <em>glc_10000_proteome_avgs.csv</em>: Each row represents a protein monomer (in same order as <em>sim_data.translation.monomer_data["id"]</em> where <em>sim_data</em> is <em>reconstruction/sim_data/kb/validationData.cPickle</em>). Each column represents a cell in a baseline glucose simulation (seed 10000). Each row represents a protein monomer. Each value represents the average count of a given protein monomer for a given cell. Provided as input to <em>ecoli/analysis/proteinCountsValidation.py</em> script to reproduce proteome validation plot. <em>glc_10000_expressome.csv</em>: Each column represents a gene (with the exception of the final two metadata columns: "Time" and "Agent ID"). Each row represents a specific cell (agent) at a specific time in a baseline glucose simulation (seed 10000). Each value represents the number of new RNA transcripts for a given gene in a given cell at a given time. Provided as input to <em>ecoli/analysis/antibiotics_colony/subgen_gene_plots/count_subgen.py</em> script to calculate number of sub-generational genes among all genes and antibiotic response genes. <em>glc_10000_total_mrna.json</em>: Mapping of agent IDs for all cells in a baseline glucose simulation (seed 10000) to their average total mRNA count. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 2C,D. <em>jenner_2013.csv</em>: Data extracted from Fig. 2C of 10.1073/pnas.1216691110. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A. <em>olson_2006.csv</em>: Data extracted from Fig. 2D of 10.1128/AAC.01499-05. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A. <em>lysis_ratios.csv</em>: Data extracted from Fig. 2 of 10.1099/00221287-31-3-339. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 4N.