antigen-prime

antigen-prime is an epidemiological simulation framework written in Java that models virus evolution and population dynamics. It simulates SIR (Susceptible-Infected-Recovered) models with genetic/phenotypic evolution of pathogens.

Quick Start

# Clone and build
git clone https://github.com/matsengrp/antigen-prime.git
cd antigen-prime
mvn clean package

# Run simulation
java -jar target/antigen-prime.jar -XX:+UseSerialGC -Xmx8G

Documentation

• Requirements - System requirements and dependencies
• Compilation - Build instructions
• Mutation Model - K80 mutation and antigenic evolution
• Immunity Centroids - Host population immunity sampling
• Parameters Reference - Configuration options
• Output Analysis - Understanding simulation output

Key Features

• SIR Epidemiology: Full susceptible-infected-recovered dynamics with demographics
• Metapopulation Structure: Multiple demes with migration and seasonal forcing
• Phenotype Evolution: Multiple evolution models (geometric, sequence-based, DMS-informed)
• Phylogenetic Tracking: Complete genealogy of virus lineages
• Flexible Sampling: Configurable sampling schemes for downstream analysis

Building Documentation

pip install -r docs/requirements.txt
mkdocs serve  # preview at http://127.0.0.1:8000
mkdocs build  # build static site to site/