This repository contains the source code associated with the manuscript
Mayer, Zhang, Perelson, Wingreen: Regulation of T cell expansion by antigen presentation dynamics, PNAS 2019
It allows reproduction of all numerical results reported in the manuscript.
The code uses Python 3.6+.
A number of standard scientific python packages are needed for the numerical simulations and visualizations. An easy way to install all of these is to install a Python distribution such as Anaconda.
Additionally the code also relies on this package:
Every folder contains a file plot.py which needs to be run to produce the figures. For a number of figures cosmetic changes were done in inkscape as a postprocessing step. In these cases the figures will not be reproduced precisely. To help reuse the final edited figures are provided in png/svg format.
If you run into any difficulties running the code, feel free to contact us at [email protected].
The source code is freely available under an MIT license. The plots are licensed under a Creative commons attributions license (CC-BY).