Code related to a project investigating the evolution of antibiotic resistance conducted at Edinburgh University, 2016, with Bartek Waclaw and Rosalind Allen.
C++ agent based simulations originally written by Bartek and developed by me.
Java/Python simulations and data analysis scripts written by me.
Directory layout:
"Notes" contains various notes and working reports. The "Notes on code" subdirectory contains information regarding each program/script along with specific instructions on how to run them.
"Agent based simulation" contains the main C++ program. This is an agent based simulation of bacteria swimming and reproducing in a series of 24 3-dimensional wells connected by channels as in the experiments conducted by Bartek.
"Data analysis scripts" contains all the python scripts for data analysis and visualization.
"SampleData" contains an example of the data generated in the main agent based simulation. Follow the instructions in "Notes on code" to run the data analysis scripts on this data.
"TauLeaping" contains simplified simulations using the tau leaping algorithm to investigate the population wavefronts observed in the experiments.
"_images_gifs" contains a selection of results with no explanation, just pretty pictures/gifs.