Antibiotics

Scripts to process data from antibiotics experiments.

Manuscript:

Lukas Geyrhofer, Philip Ruelens, Andrew D. Farr, Diego Pesce, J. Arjan G. M. de Visser, Naama Brenner
Minimal Surviving Inoculum in Collective Antibiotic Resistance
mBio, Volume 14 Issue 2 e02456-22, 2023
https://doi.org/10.1128/mbio.02456-22

Contents

• ExperimentalData

  All experimental data from plates for the MSI curve measurements (ChangeRHO, ChangeEPS), and for kill curve measurements (KillCurves) in Fig1.

• MeasureKillCurves

  Additional Code to analyze KillCurves, used in Fig1.

• MeasureMSP

  Wrapper for experimental data (platereaderclass.py) and rendering a figure for plates (plateimageclass.py), together with main fitting code for MSI curves (plates_EstimateMSP.py)

• Plots

  Notebook to generate all figures in manuscript.

• SimulationDynamics

  Code to numerically solve model equations (PopulationDynamicsClasses.py)