**Our research tools**

This is a collection of programs, scripts and descriptions to produce results in various publications. You can get the publications from the publication section of this webpage. Some of the code is relatively well documented, some isn’t. Feel free to use and modify the programs any way you want. If you need help understanding certain programs, I will try to help. But my time is limited, and for a lot of the old programs, I might not even remember anymore what exactly I did. That’s especially true for anything Matlab or Fortran since I haven’t used either in years.

TB-MAC UGA Model - A file containing the R code and description of the model that was used by us to produce the results described in a multi-model project on TB intervention analysis (under review).”

TB Persistence - A collection of R scripts to run the simulations described in our 2014 PLoS One publication “Modeling the potential impact of host population survival on the evolution of M. tuberculosis latency.”

script1.r, script2.r, script3.r, script4.r, script5.r, decaydata.csv, duckdata.csv - A collection of R scripts and accompanying data to do the various analyses described in Handel et al. (2013) PLoS Comp Bio.

resimmcode.m - A short Matlab program that simulates the dynamics of bacteria and drugs during emergence of resistance. A version of this code was used in Handel et al. (2009) JTB.

gapjunction.nlogo - An agent-based simulation, written for the freely available Netlogo platform. The code simulates gap junction mediated antigen transport during the local spread of virus and clearance by CTL. The simulation is described and used in Handel et al. 2009 JRSI.

populationmodel.m - A Matlab program that simulates the evolution of a bacterial population in repeated exponential growth and serial dilution cycles. A version of this code was used in Handel and Rozen 2009 BMC Evo Bio. Note that to run the program, you will need to also install the freely available lightspeed collection of Matlab functions.

compensatorymutation.m, SIS3strainsteady_prob.f90, SIS3strainsteady_time.f90 - (sparsely documented) Matlab and Fortran programs to simulate the evolution and spread of drug resistance through compensatory mutations. Details about the mathematical model can be found in Handel et al (2006) PLoS Comp Bio.