Introduction

Broadwick is a framework for developing sophisticated epidemiological based mathematical models, and consists of several Java libraries and bespoke packages. The components of Broadwick are written in such a way that a scientist may combine them in order to rapidly prototype a model for a new specific scenario.

Features

• Supports single (e.g. within herd) or structured populations (e.g. multi-species or locations)
• Inclusion of movement over network data (e.g. Cattle movement Tracing System)
• Stochastic Individual Based simulations (including fast approximate options)
• Approximate Bayesian Computation inference for estimating model parameters from data via simulations
• Monte Carol Markov Chain inference for estimating model parameters from data

Tutorial

The manual that accompanies Broadwick includes a step-by-step guide to install the framework and use it in your project. As with all manuals for open source projects, it is a work in progress and will be updated with each update to the framework.

We have produced several videos (EPIC Scotland YouTube Channel) to help you install and use the Broadwick Framework.

• Download Broadwick (video 1)
• Download and install Netbeans (video 2)
• Create a simple SIR Model with Broadwick (video 3)
• Create a Stochastic SIR model (Video 4-7)
• Download Stochastic SIR model code (Video 4a)
• Stochastic flow part 1 - Background to implementation (Video 4)
• Stochastic flow part 2 - Theta events, reading data (Video 5)
• Stochastic flow part 3 - Handling fired events (Video 6)
• Stochastic flow part 4 - Build, run and plot output (video 7)
• Use Multithreading with Broadwick (Video 8)
• Use ABC with Broadwick (Video 9)

All the code for these tutorials are available at https://github.com/EPICScotland/BroadwickTutorial

Examples

BroadwickExamples contains some simple stochastic compartmental models written within the Broadwick framework.
To run these you will need the built jar file BroadwickExamples-1.0-SNAPSHOT.one-jar.jar and the xml configuration files: Broadwick_with_(XXX).xml

Instructions for running the examples, and an outline of how to write your own (but see the tutorial above for detailed instructions) can be found in the BroadwickExamples/doc directory:

• HowTo_RunBroadwickExamples_QuickStart.pdf (19 June 2014)
• HowTo_WriteBroadwickModel_QuickStart.pdf (19 June 2014)

Get the code from https://github.com/EPICScotland/BroadwickExamples

MovementSimulations

The MovementSimulations repository is for movement simulation code and test data, and contains the AnimalMovementSimulations java project.

The AnimalMovementSimulations project generates simulated animal movement data for use with Broadwick, particularly for the BroadwickTutorial. Since the examples are based upon the implemented Soho model (which uses Broadwick), this project focuses on simulating cattle movements and CTS data, although different livestock scenarios might be added later.

Please see the AnimalMovementSimulations.pdf document in the AnimalMovementSimulations/doc folder for more information on the source code and how to run the RandomMovementSimulator.jar command line java application.

Example simulated cattle movement data can be found in the AnimalMovementSimulations/simulations folder.

Get the code from: https://github.com/EPICScotland/MovementSimulations