COMPUTER CODES RELATED TO  
 
Carruthers J, Lopez-Garcia M, Gillard JJ, Laws TR, Lythe G, Molina-Paris C (2018) A Novel Stochastic Multi-Scale Model of Francisella tularensis Infection to Predict Risk of Infection in a Laboratory. Frontiers in Microbiology 9:1165. DOI: 10.3389/fmicb.2018.01165 
 
Author: Jonathan Carruthers (Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK) 
Date: 4 June 2018 
Correspondence for questions: jonty.carruthers@btinternet.com 
 
These computer codes can be used to reproduce all the results in "Carruthers J, Lopez-Garcia M, Gillard JJ, Laws TR, Lythe G, Molina-Paris C (2018) A Novel Stochastic Multi-Scale Model of Francisella tularensis Infection to Predict Risk of Infection in a Laboratory. Frontiers in Microbiology 9:1165. DOI: 10.3389/fmicb.2018.01165" 
 
Programming Language: Python 
Python version used: Python 3.6.0 
Operative system: Windows 10 
 
 
Description of .txt files: 
 
"Figure5_Data.txt": Required for the files "Figure5_Left.py" and "Figure5_Right.py" 
					Column 1: A list of parameter values for lambda from the posterior distribution for the within-phagocyte model. 
					Column 2: A list of parameter values for C from the posterior distribution for the within-phagocyte model. 
 
					 
"Figure6_Data.txt": Required for the file "Figure6.py" 
					Column 1: A list of distances between model predictions found using the posterior sample and experimental data (Eigelsbach et al. 1962, White et al. 1964) for the within-host model 
					Column 2: A list of parameter values for alpha from the posterior distribution for the within-host model 
					Column 3: A list of parameter values for mu from the posterior distribution for the within-host model 
 
"Figure7_Data.txt": Required for the file "Figure7.py" 
					Row 1: Predictions of the number of extracellular bacteria for the within-host model using posterior median estimates of alpha and mu to compare with data from Eigelsbach et al. (1962) 
					Row 2: Predictions of the number of extracellular bacteria for the within-host model using posterior median estimates of alpha and mu to compare with data from White et al. (1964) 
					 
					 
All of the following .txt files are required for the file "Figure11_Left.py". Each file contains a list of the times until response of the within-host model for different realisations.  
The initial dose of bacteria is indicated in the respective file name and posterior median values are used for all remaining parameters. 
"dose_1_response_times.txt" 
"dose_10_response_times.txt" 
"dose_100_response_times.txt" 
"dose_1000_response_times.txt" 
"dose_10000_response_times.txt" 
"dose_100000_response_times.txt"