Welcome to IDM HIV 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.

Documentation structure

“Using the model” contains information for researchers who want to create simulations of disease dynamics using EMOD as developed by IDM.

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

IDM recently separated the EMOD documentation 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 HIV and other sexually transmitted infections.

Using the model

• What’s new
• Disease modeling with EMOD
  • 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
    • Geographic migration
  • Creating campaigns
    • Targeting interventions to nodes or individuals
    • Vaccination and herd immunity
    • Cascade of care
• EMOD installation
  • Install EMOD on Windows
  • Install EMOD on CentOS on Azure
• Overview of EMOD software
  • Input data files
    • Demographics file
    • Migration files
    • Climate files
    • Load-balancing file structure
  • Configuration file
    • Configuration overlay files
    • Example scripts to modify a configuration file
    • Parameter sweeps
  • Campaign file
    • Campaign overlay files
  • 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
• HIV disease overview
• HIV model overview
  • HIV model general information
  • Relationships and contact networks
  • Transmission
  • Intrahost dynamics and HIV biology
  • HIV intervention information
• HIV model tutorials and examples
• References
• 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)
• Troubleshooting EMOD simulations
• Glossary

Advancing the model

• EMOD source code installation
  • Install Windows prerequisites for EMOD source code
  • Install CentOS on Azure 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