COMPUTER CODES RELATED TO  
 
Williams B, Lopez-Garcia M, Gillard JJ, Laws TR, Lythe G, Carruthers J, Finnie T and Molina-Paris C (2021) A Stochastic Intracellular Model of Anthrax Infection With 
Spore Germination Heterogeneity. Frontiers in Immunology 12:688257. DOI: 10.3389/fimmu.2021.688257

Author: Bevelynn Williams (Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK) 
Date: 15 July 2021 
Correspondence for questions: bevelynnw@gmail.com 
 
These computer codes can be used to reproduce results in "Williams B, Lopez-Garcia M, Gillard JJ, Laws TR, Lythe G, Carruthers J, Finnie T and Molina-Paris C 
(2021) A Stochastic Intracellular Model of Anthrax Infection With Spore Germination Heterogeneity. Frontiers in Immunology 12:688257. DOI: 10.3389/fimmu.2021.688257" 
 
Programming Language: Python 
Python version used: Python 3.7.0 
Operative system: Windows 10 

Description of .txt files: 
 
"posterior_norm.txt":  
Required for the file "predictions_norm.py". Contains lists of parameter values from the posterior distribution for the model with truncated normal distribution of 
germination rate, ordered from largest to smallest distance.  
Column 1: A list of values for log_{10}\mu_g.  
Column 2: A list of values for log_{10}\sigma_g.  
Column 3: A list of values for log_{10}\tilde\mu.  
Column 4: A list of values for log_{10}\lambda.  
Column 5: A list of values for log_{10}\mu.  
Column 6: A list of values for log_{10}\gamma.  

"posterior_2spore.txt":  
Required for the files "predictions_2spore.py", "results_plots_fig5.py", "results_plots_fig7.py", and "discussion_plots.py". Contains lists of parameter values from the posterior distribution for the model with two types of spores, ordered from largest to smallest distance.  
Column 1: A list of values for \epsilon.  
Column 2: A list of values for log_{10}g_A.  
Column 3: A list of values for log_{10}g_B.  
Column 4: A list of values for log_{10}\tilde\mu.  
Column 5: A list of values for log_{10}\lambda.  
Column 6: A list of values for log_{10}\mu.  
Column 7: A list of values for log_{10}\gamma.  
          
Description of .py files:

"predictions_norm.py":  
Uses the posterior distribution in "posterior_norm.txt" to calculate the prediction of the model with truncated normal distribution of the germination rate for the 
parameter set with the smallest distance, and the pointwise 95% credible intervals of the predictions using all posterior parameter sets. These are used to reproduce 
the top plot of Figure 4.

"predictions_2spore.py":  
Uses the posterior distribution in "posterior_2spore.txt" to calculate the prediction of the model with two types of spores for the parameter set with the smallest 
distance, and the pointwise 95% credible intervals of the predictions using all posterior parameter sets. These are used to reproduce the bottom plot of Figure 4.

"results_plots_fig5.py":  
Simulates realisations of the model with two types of spores for multiple infected cells, using the parameter set with the smallest distance from the data. The mean 
of the different populations in the model over time are also calculated. The mean population sizes and the output of a stochastic simulation is plotted for initial 
conditions of 30500 and 100 infected cells, creating Figure 5.

"results_plots_fig6.py":  
Simulates realisations of the model with two types of spores, using the parameter set with the smallest distance from the data. Calculates the probability density 
functions of time until rupture and recovery. Creates the plot in Figure 6.

"results_plots_fig7.py":  
Calculates the probability of rupture, conditional mean time until rupture, rupture size distribution, and average rupture size, for each parameter set in the 
posterior distribution in "posterior_2spore.txt". Reproduces Figure 7.

"discussion_plots.py":  
Reproduces Figures 8 and 10.