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https://github.com/andim/paper-tcellexp

Source code accompanying the paper "Regulation of T cell expansion by antigen presentation dynamics "

https://github.com/andim/paper-tcellexp

Science Score: 13.0%

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biophysics openscience
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Source code accompanying the paper "Regulation of T cell expansion by antigen presentation dynamics "

Basic Info
  • Host: GitHub
  • Owner: andim
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 916 KB
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  • Watchers: 3
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Topics
biophysics openscience
Created almost 7 years ago · Last pushed almost 7 years ago

https://github.com/andim/paper-tcellexp/blob/master/ 

# Regulation of T cell expansion by antigen presentation dynamics

Figure 1

This repository contains the source code associated with the manuscript

Mayer, Zhang, Perelson, Wingreen: [Regulation of T cell expansion by antigen presentation dynamics](https://doi.org/10.1073/pnas.1812800116), PNAS 2019

It allows reproduction of all numerical results reported in the manuscript.

## Installation requirements

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](https://www.continuum.io/downloads). 

- [numpy](http://github.com/numpy/numpy/)
- [scipy](https://github.com/scipy/scipy)
- [pandas](http://github.com/pydata/pandas)
- [matplotlib](http://github.com/matplotlib/matplotlib)

Additionally the code also relies on this package:

- [projgrad](https://github.com/andim/projgrad)

## Structure/running the code

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.

## Contact

If you run into any difficulties running the code, feel free to contact us at `andimscience@gmail.com`.

## License

The source code is freely available under an MIT license. The plots are licensed under a Creative commons attributions license (CC-BY).

Owner

  • Name: Andreas Tiffeau-Mayer
  • Login: andim
  • Kind: user
  • Location: London
  • Company: University College London

Quantitative Immunology, Biological Physics

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