In this tutorial, we will implement a program that simulates the spread of the COVID-19 epidemic. We will work on a particle-based SEIR simulator where SEIR is the abbreviation of the four main epidemic states of a particle: susceptible, exposed, infected, and recovered.
git-clone or download the package. The scripts and folders should be saved in the same directory.
SEIR_simulator_material.pdf contains the material on particle model, simulator structure, and programming tasks. The metadata folder contains four pickle files that are provided to you to check your code after you complete the tasks.
We recommend to watch the videos below before diving into the tutorial.
- Anaconda3 (with Jupyter included): https://docs.anaconda.com/anaconda/install/
- Spyder IDE: https://www.spyder-ide.org
Download the sim_env.yaml file and create a new environment in the Anaconda terminal:
conda-env create -n sim_env -f \path\to\sim_env.yaml
Activate sim_env:
conda activate sim_env
Run the Spyder IDE from the sim_env environment.
Step 1. The following video provides the overview of the simulator, the particle model and the epidemic state transitions.
Click on the image below to watch the video.
Click on the image below to watch the video.
Click on the image below to watch the video.
B. Kuzdeuov, A. Karabay, D. Baimukashev, B. Ibragimov, and H. A. Varol, “A Particle-based covid-19 simulator with contact tracing and testing,” medRxiv, 2020. [Online]. Available: https: https://ieeexplore.ieee.org/document/9372866
A.Karabay, A. Kuzdeuov, M. Lewis and H.A. Varol, “A Vaccination Simulator for COVID-19: Effective and Sterilizing immunization cases”, medRxiv, 2021. [Online]. Available: https://ieeexplore.ieee.org/document/9542855
Link to the Github repository for the original Matlab source code files: