README.md

Overview

This repository contains data and scripts for reproducing the results accompanying the manuscript

An inference model gives insights into innate immune adaptation and repertoire diversity

Yawei Qin¹, Emily M. Mace², and John P. Barton^1,3,#

¹ Department of Physics and Astronomy, University of California, Riverside, USA
² Department of Pediatrics, Columbia University Irving Medical Center, New York, USA
³ Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, USA
^# correspondence to jpbarton@pitt.edu

Contents

Scripts for solving the Fokker-Planck equation are contained in the FKE.py file. Scripts for generating data and figures contained in the manuscript are in the figures.ipynb notebook. Figures and analysis related to dynamic Bayesian networks are found in the DBN.ipynb notebook. Generated data is stored in the folder /data. Due to the large size of some files, the data has been stored in a compressed format. Final figues are saved in the folder /figures.

License

This repository is dual licensed as GPL-3.0 (source code) and CC0 1.0 (figures, documentation, and our presentation of the data).