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EpiRust

An agent-based epidemiology simulation framework built in Rust

This is a monorepo containing code for the EpiRust framework -

  1. engine - The main EpiRust engine, which can be run as a CLI app
  2. server - The API server that talks to the engine and serves the frontend
  3. web - The Web UI for EpiRust

Quickstart

The quickest way to run the application is using the CLI interface on the engine.

Prerequisites:

  • Install Rust and Cargo (version 1.40.0 or above). Refer to https://rustup.rs/ for rust installation
  • Install cmake (version 3.16.4 or later). Installation instructions will depend on your platform. On MacOS you can install it using brew install cmake. Refer to https://cmake.org/download/
  • Python 3 (for visualization and charting). We also need the pandas and plotly libraries which can be installed using pip or conda.
    • pip install pandas plotly

Running:

  • Go to the engine directory: cd engine/
  • Run cargo run --release
  • To modify the settings, or run with custom settings, use cargo run --release -- -c config/[your-config].json. Refer to default.json for the available settings.

Visualization:

  • After the simulation is run, it will generate a CSV file. We can plot this using a simple script included in the engine/plot directory
    • Ensure you're in the engine directory
    • Run python plot/plot.py - this will plot all the CSVs in the current directory.

Sample output: Epicurves plot

License

EpiRust is an open source project licensed under AGPL v3

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