https://github.com/andim/paper-bayesimmune
Source code accompanying the paper "How a well-adapting immune system remembers"
https://github.com/andim/paper-bayesimmune
biophysics openscience
Last synced: 10 days ago
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Source code accompanying the paper "How a well-adapting immune system remembers"
- Host: GitHub
- URL: https://github.com/andim/paper-bayesimmune
- Owner: andim
- Created: 2019-07-11T02:18:58.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-07-11T02:20:37.000Z (almost 7 years ago)
- Last Synced: 2025-12-26T06:54:33.813Z (5 months ago)
- Topics: biophysics, openscience
- Language: Python
- Size: 1.25 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# How a well-adapting immune system remembers
This repository contains the source code associated with the manuscript
Mayer, Balasubramanian, Walczak, Mora: [How a well-adapting immune system remembers](https://doi.org/10.1073/pnas.1812810116), PNAS 2019
It allows reproduction of all figures of the manuscript and also provides the simulation code.
## Installation requirements
The code uses Python 2.7+.
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 the following two packages:
- [projgrad](https://github.com/andim/projgrad)
- [palettable](https://github.com/jiffyclub/palettable)
## 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.
## 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).