This repository contains the code and data required to reproduce the results in the manuscript “Using bacterial population dynamics to count phages and their lysogens”.
Each folder is named according to the figure(s) it contains. Inside each folder, you will find the following subfolders:
data(optional): Contains the raw data used to generate the plots.script: Contains the Python/MATLAB scripts used to generate the plots.tmp(optional): Stores intermediate files generated during code execution, such as ensembles of model parameters.
Each script is named according to the figure panel(s) it corresponds to. The scripts are either MATLAB files (for Fig. 4, Figs. 5b-e, and Sfig. 17) or Jupyter notebooks (for other figures).
The scripts were developed using Python 3.8.5. To run the Jupyter notebooks, you need the following packages:
- numpy
- scipy
- matplotlib
- pandas
- emcee
- lmfit
To store the output figures, you need to create a output subfolder, inside the main folder of the figure.
For scripts involving MCMC (Fig. 3c, Fig. 5f, Sfig. 7, Sfig. 12, Sfig. 17, Sfig. 19, and Sfig. 20), we have provided the sampled parameters from previous runs in .csv in the tmp folder, which can be directly loaded into the notebooks using pd.read_csv.
The scripts were developed using MATLAB versions 2020a–2023b (64-bit). To run the MATLAB scripts:
- Set the folder containing the
.mfiles as the working directory for the current MATLAB session. - Add the relevant folders and subfolders to the search path of the current MATLAB session.
- Modify the paths in the MATLAB scripts to correctly load the data files.
- The sections of the code must be run from top to bottom (in the order in the script file).
Please cite the following paper: Geng, Yuncong, et al. "Using population dynamics to count bacteriophages and their lysogens." bioRxiv (2023): 2023-10.
- Yuncong Geng ([email protected])
- Thu Vu Phuc Nguyen ([email protected])
- Ido Golding ([email protected])