This repository contains the code implementation of the Stochastic Simulation Algorithm (SSA, aka Gillespie algorithm) with delayed reactions and weighted-ensemble resampling. The code was written primarily in January-May 2014 for my undergraduate thesis.

The current implementation is in Python; see the python directory and Python readme for details.

The results directory contains some of the plots and data used in the thesis and accompanying presentation. The literature directory contains citation data for most of the references used.

The thesis and presentation directories contain preliminary work on the thesis and accompanying presentation, although that work has been moved to separate branches. It may be added to this repository at some point.

You may contact me at <maxdveit+wessa at gmail dot com> if you would like help using the software. If you discover an error or would like to add a feature, please open an issue on the Github repository.