EMULSION

EMULSION implements a framework for building, simulating, and refining mechanistic stochastic epidemiological models across scales to assess pathogen emergence and spread.

Key Features:

• Domain-Specific Language: A structured text-based domain-specific language explicitly defines model components such as structure, processes, and parameters.
• Knowledge Representation: Incorporates knowledge representation methods to formalize model assumptions and components.
• Multi-level Agent-Based Simulation: Employs multi-level agent-based simulation to represent dynamics from compartmental to individual-based models and up to metapopulation scales.
• Multi-paradigm Modelling: Supports multiple modelling paradigms, including compartmental and individual-based approaches, within the same framework.
• Iterative Model Revision: Enables late revisions of core assumptions and iterative development while maintaining model consistency.
• Model Checking and Diagram Production: Provides capabilities for model checking and automatic diagram production to represent model structure and processes.
• Simulation Execution and Output Plotting: Includes simulation execution and output plotting functionalities for analyzing stochastic model runs.

Scientific Applications:

• Pathogen emergence and spread assessment: Simulates pathogen emergence and spread across scales from within-host dynamics to transnational metapopulation levels.
• Cross-pathosystem epidemiology: Applies to human, animal, and plant epidemiology for modelling disease dynamics in diverse pathosystems.
• Control strategy evaluation: Evaluates impacts of control strategies within complex, multi-scale stochastic epidemiological models.

Methodology:

Models are specified in a structured text domain-specific language; the engine uses knowledge representation and a multi-level agent-based simulation framework to implement compartmental and individual-based models up to metapopulation scales, with facilities for model checking, diagram generation, simulation execution, and output plotting.