Welcome to EMOD malaria modeling

The Institute for Disease Modeling (IDM) develops disease modeling software that is thoroughly tested and shared with the research community to advance the understanding of disease dynamics. This software helps determine the combination of health policies and intervention strategies that can lead to disease eradication. If you encounter any issues while using the software, please contact support@idmod.org.

The primary software, EMOD, is an agent-based model (ABM) that simulates the simultaneous interactions of agents in an effort to recreate complex phenomena. Each agent (such as a human or vector) can be assigned a variety of “properties” (for example, age, gender, etc.), and their behavior and interactions with one another are determined by using decision rules. These models have strong predictive power and are able to leverage spatial and temporal dynamics.

EMOD is also stochastic, meaning that there is randomness built into the model. Infection and recovery processes are represented as probabilistic Bernoulli random draws. In other words, when a susceptible person comes into contact with a pathogen, they are not guaranteed to become infected. Instead, you can imagine flipping a coin that has a λ chance of coming up tails S(t) times, and for every person who gets a “head” you say they are infected. This randomness better approximates what happens in reality. It also means that you must run many simulations to determine the probability of particular outcomes.

Documentation structure

Using the model contains information that will help you get started with EMOD, including installation instructions, a basic overview of the software, and some example simulations you can run on your computer.

Understanding the model contains more detailed information about the disease biology, workings of the EMOD model, complete parameter reference, and a glossary.

Advancing the model contains information for researchers and developers who want to modify the EMOD source code to add more functionality to the model.

The EMOD documentation is broken up into disease-specific sets that provide guidance for researchers modeling particular diseases. The documentation contains only the parameters, output reports, and other components of the model that are available to use with this disease model.

For example, this documentation set includes general installation and usage instructions that are common in all simulation types in addition to content specific to modeling malaria and other vector-borne diseases.

Using the model

• What’s new
• EMOD installation
  • Install EMOD on Windows
  • Install EMOD on Linux
• Overview of EMOD software
  • Input files
    • Demographics file
    • Configuration file
    • Campaign file
    • Migration files
    • Climate files
    • Load-balancing files
    • Serialized population file
  • Running a simulation
    • Run a simulation using the command line
    • Run a simulation using mpiexec
    • Run a simulation using Python
    • Run a simulation using MATLAB
    • Speed up EMOD simulations
  • Output files
    • Inset chart output report
    • Binned output report
    • Demographic summary output report
    • Property output report
    • Spatial output report
    • Custom reporters
    • Error and logging files
    • Vector species output report
• Tutorials and simulation examples
  • Generic model scenarios
  • Malaria model scenarios
• Troubleshooting EMOD simulations

Understanding the model

• Generic model overview
  • Compartmental models and EMOD
    • SIR and SIRS models
    • SEIR and SEIRS models
    • SI and SIS models
  • Disease outbreaks and animal reservoirs
  • Adding heterogeneity
    • Population density and transmission scaling
    • Individual and node properties
    • Property-based heterogeneous disease transmission
    • Multi-route HINT
    • Geographic migration
  • Creating campaigns
    • Targeting interventions to nodes or individuals
    • Vaccination and herd immunity
    • Cascade of care
• Malaria disease overview
• Malaria model overview
  • Malaria model general information
  • Malaria model structure and framework
    • Climate and demographics spatial data
    • Larval habitat
    • Vector transmission model
    • Malaria infection and immune model
    • Malaria symptoms and diagnostics
    • Antimalarial drugs
• EMOD parameter reference
  • Demographics parameters
  • Configuration parameters
  • Campaign parameters
    • Events and event coordinators
    • Node-level interventions
    • Individual-level interventions
    • Waning effect classes
    • Event list
  • Generate a list of all available parameters (a schema)
• Frequently asked questions
• Glossary

Advancing the model

• EMOD source code installation
  • Install Windows prerequisites for EMOD source code
  • Install CentOS prerequisites for EMOD source code
  • Download the EMOD source code
  • Build EMOD from source code
• EMOD architecture
  • Environment subsystem
  • Simulation controller subsystem
    • Simulation core components
    • Campaign management
    • Reporter component
• Debugging and testing
  • Set log levels
  • Run debug simulations in Visual Studio
  • Troubleshooting EMOD builds
  • Regression testing
    • Run regression tests
    • Create a new regression test
  • Scientific feature testing