Modelling the Spread of COVID-19 using an SEIR Model

Instructions to deploy this project on an EC2 instance

1. Launch a new instance

2. Select a ubuntu 18.04 VM and a t2 microinstance

3. Configure a security group that allows you to SSH into the instance and set up port 80 to enable HTTP requests

4. Launch the instance and SSH into the instance

5. Install nodejs 10.x from Nodesource

   curl -sL https://deb.nodesource.com/setup_10.x | sudo -E bash -
   sudo apt-get install -y nodejs
   

6. Install python's package manager, pip

   sudo apt-get install -y python3-pip

7. Install the nodejs production process manager

   sudo npm install -g pm2
   sudo pm2 startup systemd
   

8. Install nginx sudo apt-get install -y nginx

9. Clone this repository sudo git clone https://github.com/CheranMahalingam/COVID-19_Projections_SEIR_Model.git

10. Install the flask backend dependencies

    cd COVID-19_Projections_SEIR_Model/api
    sudo pip3 install --user -r requirements.txt
    

11. Manually install scrapy sudo pip3 uninstall scrapy && sudo pip3 install scrapy

12. Start the production process manager sudo pm2 start application.py --interpreter=python3

13. Install the react frontend dependencies and run the frontend build

 cd ../covid-projections
 sudo npm install
 sudo npm run build

14. Create a custom Nginx configuration sudo rm /etc/nginx/sites-available/default sudo nano /etc/nginx/sites-available/default Copy the following into the text editor

    server {
      listen 80;
      server_name _;
      
      location / {
        root /home/ubuntu/COVID-19_Projections_SEIR_Model/covid-projections/build;
        try_files $uri $uri/ /index.html;
      }
      
      location http://localhost:5000 {
        proxy_pass http://localhost:5000;
      }
    }
    

15. Restart Nginx sudo systemctl restart nginx

16. Copy the IPv4 or DNS address into the browser to run the fullstack application

Instructions to run locally

1. Open the terminal and cd into the covid-projections directory

   cd *****/COVID-19_Projections_SEIR_Model/covid-projections

2. Install dependencies using npm

   npm install

3. Install dependencies using pip

   cd ../api
   pip3 install -r requirements.txt
   

4. To run the flask backend use,

   flask run

5. Open a new terminal and cd into the covid-projections directory

   cd *****/COVID-19_Projections_SEIR_Model/covid-projections

6. To run the web application use,

   npm start

7. The program will open on port 3000 and is available at http://localhost:3000

SEIR Model

The model splits the population into four groups. Susceptible (people who are not immune to infection), Exposed (people who have been infected but are yet to become infectious), Infected (people who can spread the disease), Recovered (people who are immune). The population of each group can be approximated using the following differential equations: