Understanding the temporal and spatial spread of gene drive alleles through modeling

Introduction

Artificial gene drive is a genetic engineering technology that could be used for the control of natural populations. Gene drive alleles bias their own transmission and can therefore spread in a population within a relatively small number of generations, even if they are deleterious. Understanding the potential outcomes of this technology, including the modification and/or the eradication of a natural population, is essential before real-world applications are considered. Here is the code we used to simulate the spatial and temporal spread of gene drive alleles in the population.

Authors

This code was written by Léna Kläy. The project was carried out in collaboration with Vincent Calvez, Florence Débarre and Léo Girardin.

Contents

This repository contains the pdf of my first article, my PhD final presentation and two main folders:

Determinist to simulate the deterministic models (PDE, reaction-diffusion),

Stochastic to simulate the stochastic models (birth–death process with migration).

They always follow the same organisation inside:

1. Functions contains the code to run the simulations (.py), as well as a README.rmd file detailing each function,

2. Outputs stores the results of the simulations,

3. Illustrations contains the important figures, sometimes improved with Inkscape.

4. Migale contains the code to run the heaviest simulations on the cluster Migale (INRAE, doi: 10.15454/1.5572390655343293E12) as well as some outputs of previous simulations.

(only in the Determinist folder:)

5. Mathematica contains the mathematica files used in preliminary mathematical analyses.

6. Poster contains some posters I presented during my PhD.