Competing_pathogens_Heterogenous_networks

Website

Introduction

In this project, we study the following:

• How sequential mutant strains of a virus, each mutnt more transmissible than its parent, compete in population
• How the heterogeneity in human contact patterns affect the competition dynamics and infection spread

Contributors

Team member name
Sudarshan Anand
Rohini Janivara
Alejandro Danies Lopez

Setup

We recommend using a Linux/Unix(Mac) environment. For windows users, we recommend using WSL2 to create a linux environment.

1. Install rye using the following command:

curl -sSf https://rye.astral.sh/get | bash
source "$HOME/.rye/env"

2. cd into the project directory and run the following command to create a virtual environment:

rye init .

3. Add dependencies as follows:

rye add jupyter networkx numpy matplotlib seaborn scipy tqdm sympy pyvis plotly 

4. Activate the virtual environment using the following command:

source .venv/bin/activate

Files

Synthetic networks generation

• Move into Network_generation
• Run the network_gen.py to generate the synthetic networks

cd Network_generation
python network_gen.py

Real world data calibration

• The folder Real_world_data contains all the data we have tried on for the calibration
• We finally calibrated on Influenza data (Real_world_data/calibration/Fludata_US_2016_2024.csv) and on the US High school contact network (Real_world_data/high_school_nw.txt)
• The calibration is done in calibration.ipynb

Simulations

• The simulations_and_analysis folder has all the notebooks and script files used for the simulation of the infection spread on various contact networks (synthetic and real-world), and the analysis part done for obtaining metrics for epidemic analysis and parameter sensitivity

• At the end of running the simulations, the results are stored in a results_final folder