EMOD model documentation
EMOD (Epidemiological MODeling software) is a stochastic, agent-based modeling framework that simulates the simultaneous interactions of agents in an effort to recreate the complex phenomena of disease transmission. Built in C++, the models are feature-rich and designed to track the movement, development, health, and other traits of interest for individuals over a course of lifetimes.
Project status
EMOD-Hub projects are provided as open source software under the MIT License for community use, research, and development.
Unless otherwise noted, these projects are no longer actively maintained or supported by IDM or the Gates Foundation.
Community contributions are welcome, and trusted collaborators may review and merge pull requests, but no guarantees are made regarding support, pull request review, security response, maintenance, or release timelines.
Getting started
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emodpy-hiv
Tutorials for emodpy-hiv.
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emodpy-malaria
Tutorials for emodpy-malaria.
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emodpy-workflow
Workflow examples with emodpy-hiv.
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EMOD-Generic-Scripts
Example models for the Generic branch of EMOD.
Available models and utilities
EMOD is the disease model framework, offering disease-specific models for malaria and HIV alongside Python packages for configuring and running simulations. The idmtools package is a model-agnostic framework that handles the surrounding infrastructure: job commissioning, HPC integration, calibration, and more. While each can be used independently, we recommend using them together for a seamless, integrated workflow.
EMOD
The EMOD framework is powerful and flexible, and can be customized to examine a variety of epidemiological problems. Source code is available for those interested in modifying code to create custom models, and various transmission modes are available to investigate specific disease-oriented questions.
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EMOD { #emod }
The source files for building EMOD.
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EMOD-Generic
Modeling framework best suited for low-complexity disease transmission, such as measles.
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emod-api
The Python API used for editing EMOD files.
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emodpy
Shared Python workflow infrastructure used to configure and run EMOD simulations.
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emodpy-malaria
The malaria-specific model and Python code used to configure and run malaria-based EMOD. It includes vector transmission, within-host parasite dynamics, and malaria-specific interventions.
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emodpy-hiv
The HIV-specific model and Python code used to configure and run HIV-based EMOD. It includes within-host viral dynamics, HIV virology parameters, and HIV-specific interventions.
idmtools
The idmtools package is a collection of Python scripts and utilities that streamlines the full modeling workflow: input file creation, model calibration, commissioning simulations (both locally and on an HPC), and analyzing results. While idmtools is model-agnostic and compatible with custom R or Python models, it is purpose-built to work seamlessly with EMOD.
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idmtools
Framework of Python scripts and utilities to streamline modeling workflows.
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idmtools container
The local runner enabling the execution of tasks in a docker container.
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idmtools calibra
Python scripts and utilities to aid in model calibration.