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COVID-19 Scenarios

Models of COVID-19 outbreak trajectories and hospital demand

๐ŸŒ covid19-scenarios.org

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๐Ÿ‘€ Overview

This tool is based on the SIR model (see about page for details) that simulates a COVID19 outbreak. The population is initially mostly susceptible (other than for initial cases). Individuals that recover from COVID19 are subsequently immune. Currently, the parameters of the model are not fit to data but are simply defaults. These might fit better for some localities than others. In particular the initial cases counts are often only rough estimates.

The primary purpose of the tool is to explore the dynamics of COVID19 cases and the associated strain on the health care system in the near future. The outbreak is influenced by infection control measures such as school closures, lock-down etc. The effect of such measures can be included in the simulation by adjusting the mitigation parameters. Analogously, you can explore the effect of isolation on specific age groups in the column "Isolated" in the table on severity assumptions and age specific isolation.

Most parameters can be adjusted in the tool and for many of them we provide presets (scenarios).

Input data for the tool and the basic parameters of the populations are collected in the /data directory. Please add data on populations and parsers of publicly available case count data there.

๐Ÿ“• User's Guide

The online application provides a friendly user interface with drop downs to choose model parameters, run the model, and export results in CSV format. A detailed process is below.

Parameters: population

Select the population drop down and select a country/region to auto-populate the model's parameters with respective UN population data. These parameters can be individually updated manually if necessary.

Parameters: epidemiology

The epidemiology parameters are a combination of speed and region - specifying growth rate, seasonal variation, and duration of hospital stay. To choose a preset distribution, select one of the options from the epidemiology drop down to auto-populate the model's parameters with the selected parameters.

Parameters: mitigation

Mitigation parameters represent the reduction of transmission through mitigation (infection control) measures over time. To select a preset, click on the mitigation dropdown and select one of the options. Otherwise, the points on the graph can be dragged and moved with the mouse. The parameter ranges from one (no infection control) to zero (complete prevention of all transmission).

Running the Model

Once the correct parameters are inputted, select the run button located in the Results section of the application. The model output will be displayed in 2 graphs: Cases through time and Distribution across groups and 2 tables: Populations and Totals/Peak.

Exporting Results

The model's results can be exported in CSV format by clicking the "export" button in the right hand corner.

๐Ÿ–ฅ๏ธ Developer's guide

Quick Start

Run natively

Install the requirements:

  • git >= 2.0
  • node.js >= 10 (we recommend installation through nvm or nvm-windows)
  • 1.0 < yarn < 2.0

Then in your terminal type:

git clone --recursive https://github.com/neherlab/covid19_scenarios
cd covid19_scenarios/
cp .env.example .env
yarn install
yarn dev

(on Windows, substitute cp with copy)

This will trigger the development server and build process. Wait for the build to finish, then navigate to http://localhost:3000 in a browser (last 5 versions of Chrome or Firefox are supported in development mode).

โ„น๏ธ Hint: type "rs" in terminal to restart the build

โ„น๏ธ Hit Ctrl+C in to shutdown the server

Run in docker container

Install the requirements:

  • Docker > 19.0
  • docker-compose >= 1.25

Run docker-compose with docker/docker-compose.dev.yml file:

UID=$(id -u) docker-compose -f docker/docker-compose.dev.yml up --build

Variable UID should be set to your Unix user ID. On single-user setups these are usually 1000 on Linux and 523 on Mac.

Directory Structure

As a developer you are most likely interested in the actual source code in src/ directory.

File or directory Contents
๐Ÿ“algorithims/ Algorithm's implementation
โ”œ๐Ÿ“„model.ts/ Model's implementation
โ”œ๐Ÿ“„run.ts/ Algorithm's entry point
๐Ÿ“assets/ Input data, images, and text assets
๐Ÿ“components/ React components
โ”œ๐Ÿ“Form/ Form components
โ”œ๐Ÿ“Main/ Simulator's UI main component implementation
| โ”œ๐Ÿ“Containment/ Containment widget
| โ”œ๐Ÿ“Results/ Results panel
| โ”œ๐Ÿ“Scenario/ Scenario panel
| โ”œ๐Ÿ“state/ Main component's state management (hooks)
| โ”œ๐Ÿ“validation/ Form validation
| โ”œ๐Ÿ“„Main.scss/
| โ”œ๐Ÿ“„Main.tsx/ Simulator's UI main component entry point
โ”œ๐Ÿ“„App.tsx/ App main component
๐Ÿ“locales/ Locales for translation
๐Ÿ“pages/ Application's pages
๐Ÿ“server/ Server that serves production build artifacts
๐Ÿ“state/ App state management (Redux and sagas)
๐Ÿ“styles/ Stylesheets
๐Ÿ“types/ Typescript typings
๐Ÿ“„index.ejs HTML template
๐Ÿ“„index.polyfilled.ts Entry point wrapper with polyfills
๐Ÿ“„index.tsx Real entry point
๐Ÿ“„links.ts Navbar links
๐Ÿ“„routes.ts Routes (URL-to-page mapping)

Production build

In order to replicate the production build locally, use this command:

yarn prod:watch

This should build the application in production mode and to start static server that will serve the app on http://localhost:8080 (by default)

Translations

The translation JSON files are in src/i18n/resources You can edit them directly or using GitLocalize. Here are the direct links to GitLocalize for each language that has translations currently:

Schemas

The directory schemas/ contains JSON schemas which serve as a base for type checking, validation and serialization.

In particular, some of the types:

  • are generated from schemas for both Python (as classes) and Typescript (as interfaces)
  • are validated on runtime using corresponding libraries in these languages
  • are (when appropriate) serialized and deserialized using generated serialization/deserialized functions

We make emphasis on types that are shared across languages (e.g. Python to Typescript) as well as on types that participate in input-output (e.g. URLs, Local Storage, File I/O) and require particularly careful validation and serialization.

If you are planning to change one of the types that happens to be generated, you need to modify the corresponding schema first and them re-run the type generation.

See also:

Release cycle, continuous integration and deployment

TODO

Getting Started

For new contributers, follow the guide below to learn how to install required software, fork & clone, and submit changes using a pull request.

โœจ Installing Required Software

  1. Install Git by following GitHub's instructions here

  2. Node.js can be installed using nvm on Mac/Linux and nvm-windows on Windows.

  3. Yarn can be globally installed following these steps

๐Ÿด Forking the Repo

Click the Fork button on the upper right-hand side of the repositoryโ€™s page.

๐Ÿ‘ฏ Clone Forked Repository

Clone this repository to your local machine. You can use the URL of your repo inside git command, for example:

git clone https://github.com/<YOUR_GITHUB_USERNAME>/covid19_scenarios

๐Ÿ”จ Start coding!

๐Ÿ’ป Updating the Forked Repository

To ensure that the forked code stays updated, youโ€™ll need to add a Git remote pointing back to the original repository and create a local branch.

git remote add upstream https://github.com/neherlab/covid19_scenarios

To create and checkout a branch,

  1. Create and checkout a branch
git checkout -b <new branch name>
  1. Make changes to the files
  2. Commit your changes to the branch using git add and then git commit

๐Ÿ’ช Submitting changes using a Pull Request

To submit your code to the repository, you can submit a pull request.

๐Ÿ™ Acknowledgements

Initial development

Initially, the development was started in the Research group of Richard Neher at the Biozentrum, University of Basel (Basel, Switzerland) by Richard Neher (@rneher), Ivan Aksamentov (@ivan-aksamentov) and Nicholas Noll (@nnoll).

Jan Albert from Karolinska Institute (Stockholm, Sweden) had the initial idea to develop this tool and suggested features and parameters, and Robert Dyrdak provided initial parameter estimates.


Richard Neher
@rneher

Ivan Aksamentov
@ivan-aksamentov

Nicholas Noll
@nnoll

Jan Albert

Robert Dyrdak

Contributors โœจ

We are thankful to all our contributors, no matter how they contribute: in ideas, science, code, documentation or otherwise. Thanks goes to these wonderful people (emoji key):


Aditya Sharad

๐Ÿ’ป ๐Ÿ”ง

Agon Hasani

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Alexis Iglauer

๐Ÿ’ป ๐Ÿ”ฃ ๐Ÿšง

Andrew McKeever

๐Ÿ’ป ๐Ÿ’ฌ

Anson Chong

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Arkadiusz Goralski

๐Ÿ’ป ๐ŸŒ

Arnaud

๐Ÿ’ป ๐Ÿ‘€

Ashwin Gokhale

๐Ÿ’ป

Bradley Betts

๐Ÿ’ป ๐Ÿ”ง

Bruno RZN

๐Ÿ’ป ๐Ÿ’ฌ ๐Ÿ‘€

Christian Wienbruch

๐Ÿ’ป ๐Ÿ”ฃ

Christian-G-UT

๐Ÿ’ป ๐Ÿ”ฃ

Danko Kozar

๐Ÿ’ป ๐ŸŽจ

Danny Sepler

๐Ÿ’ป ๐Ÿ’ฌ ๐Ÿ‘€

Darรญo Hereรฑรบ

๐Ÿ“– ๐ŸŒ ๐Ÿ’ป ๐Ÿ”ฃ

David Hansen

๐Ÿ’ป

Di Guan

๐Ÿ’ป

Emmanuel Murillo Sรกnchez

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Evan Krell

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Fabio Zanini

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Gabriel Homsi

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Gavin Jefferies

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Gustavo Ribeiro

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Hannes Granstrรถm

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Hui Xiang Chua

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Igor Savin

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Ivan Aksamentov

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Ivรกn Yepes

๐Ÿ’ป ๐Ÿ’ฌ

Jacob Smith

๐Ÿ’ป ๐Ÿ’ฌ ๐Ÿ‘€

Jill Adona

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John Yani

๐Ÿ’ป ๐Ÿ”ฃ

Joram van den Boezem

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Jose Eduardo Kimura

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Joรซl

๐Ÿ’ป ๐Ÿ’ฌ ๐Ÿšง

Juha

๐Ÿ–‹ ๐ŸŒ

Kamil Bobrowski

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Kartik

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Manuel Blechschmidt

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Maoz Gelbart

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Martin Vejmelka

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Max Tarsis

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Mickey Pearce

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Miguel Serrano

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Mika Laaksonen

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MikaMaracuja

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Nataliya Karatkova

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Nathan Springman

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Nicholas Noll

๐Ÿ’ป ๐Ÿ“– ๐Ÿ”ฃ ๐Ÿšง ๐Ÿ‘€

Nils Ole Tippenhauer

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Patrick Assaf

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Patrik Varga

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Pete Bacon Darwin

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Rachel Harvill

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Rebecca Mullin

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Rich Evans

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Richard Neher

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Rizky Maulana Nugraha

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Rui Lima

๐Ÿ’ป ๐Ÿ’ฌ ๐ŸŒ

Rui Saraiva

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Sam

๐Ÿ“– ๐Ÿ–‹

Sebastian Gierth

๐Ÿ’ป ๐Ÿ’ฌ ๐Ÿ‘€ ๐ŸŒ

TIAGO ANDRES VAZ

๐Ÿ’ป ๐Ÿ”ฃ ๐Ÿค”

TeepaBlue

๐Ÿ’ป

Thomas Eckert

๐Ÿ’ป ๐Ÿ“–

Tryggvi Gylfason

๐Ÿ’ป ๐ŸŽจ

Valentin Druelle

๐Ÿ’ป ๐Ÿ”ฃ ๐Ÿค” ๐Ÿ“ข

Victor Cordova

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William Hiver

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abrie

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alebrand

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arieltonglet

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aschelch

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bharath6365

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btoo

๐Ÿ’ป ๐Ÿ“– ๐Ÿšง

ceporche

๐ŸŒ

joaopn

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kmid5280

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kupad95

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nono

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pvillamartin

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r-s-rai

๐Ÿ’ป ๐ŸŽจ

thoo1

๐Ÿ’ป ๐ŸŽจ

This project follows the all-contributors specification. Contributions of any kind welcome!

License

MIT License

Copyright (c) 2020 neherlab


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