BharatSim Documentation

Welcome to this BharatSim Tutorial!

BharatSim is a collaborative project between Ashoka University and Thoughtworks, funded by the Bill & Melinda Gates Foundation. Its vision is to build a simulation framework that is distributed, multi-scale, and agent-based for use by the scientific community. It was originally designed to run decision-critical scenarios for India during the COVID-19 pandemic. Real-world systems involve interactions between individuals with different attributes (age, weight, etc.) and geographies. These interactions lead to emergent phenomena, while events like pandemics affect individuals according to their attributes. Existing simple models are ill-suited for prediction and analysis of such complex real-world phenomena. Agent-based modeling accounts for individual differences and allows us to simulate scenarios of varying complexity. These simulations can guide policy level interventions (eg. lockdowns). The framework has two components:

• Simulation engine: Given a Synthetic Population, simulation engine can support India-wide simulations with multi-million agents, incorporating daily behaviours and policy-level interventions. It structures this information by treating agents, locations, and their relations like nodes and edges on a network. This way modellers can analyse how population structure affects the spread of the disease. The simulation engine is written in Scala.

• Visualization engine: A key feature of BharatSim is the dashboard visualisation that allows you to view multiple types of results at the same time. The simulation engine can generate customizable outputs, which the visualisation engine allows you to plot and arrange for viewing and presentation. This customizable dashboard system is flexible in order to suit the user’s analytical and insight formation process.

In this tutorial documentation, we look be looking at BharatSim in detail, introducing the novice programmer to both components. The tutorial assumes a familiarity with (or at least an eagerness to learn) Object-oriented Programming. Prior familiarity with Scala or Java is desirable, but by no means a prerequisite.

Contents

• Introduction
• Synthetic Population

Epidemiology

• A Basic Introduction to Epidemic Modelling
  • The SIR Model
    • Mean-field or “Well-mixed” solution to this model
    • Stochastic solutions to this model
  • Introducing a network structure
  • Residence times in different compartments
  • Other Compartmental Models
    • The SEIR Model
    • The SAIR Model
    • The SIRS Model
  • Exercises

The Simulation Engine

• Getting Started
  • Setup Requirements
  • Setting up Scala
    • Installing JDK
    • Installing Scala with Coursier
  • Setting up an IDE and First Run
    • IntelliJ Idea
    • Visual Studio Code
  • Running Scala on Command Line
• Framework Basics
  • Inputs and Outputs in BharatSim
    • Inputs
      • Using the framework-defined functions
      • Using the User-Defined function
    • Outputs
      • Saving your output to a CSV file
        • Output at a single instant of time
        • Output at every time step
  • Interventions in BharatSim
    • 1. Intervention
      • Example using the Intervention object:
    • 2.IntervalBasedIntervention
      • Example using the IntervalBasedIntervention object:
    • 3.OffsetBasedIntervention
      • Example suing the OffsetBasedIntervention object:
    • 4.SingleInvocationIntervention
      • Example using the SingleInvocationIntervention object:
• Writing your First Program
  • Single Location SIR
    • Creating an Empty Class
    • The Required Classes
    • Inputting a File
  • Introduction of Disease Dynamics
    • The Required Classes
    • Outputting a File
  • Expanding the Network
    • The Required Classes
    • Implementation
  • Introduction of Social Interventions
    • Quarantine
• Miscellaneous
  • Assembling an Executable Jar file
  • Importing a Jar file as a Library
  • Using args in main method
  • Saving location-level information from the simulation
• Optimisation
  • PerTickCache
    • Example for PerTickCache implementation:
  • Outputting data to a csv
    • The target to be optimized
    • A (naive) approach to help
    • The fastest solution
• Other examples
  • Houses on a lattice
• Known Issues
  • java.util.NoSuchElementException on fetchActiveState