Glossary#
- agent-based model
A type of simulation that models the actions and interactions of autonomous agents (both individual and collective entities such as organizations or groups).
- Boost
Free, peer-reviewed, portable C++ source libraries aimed at a wide range of uses including parallel processing applications (Boost.MPI). For more information, please see the Boost website, http://www.boost.org.
- boxcar function
A mathematical function that is equal to zero over the entire real line except for a single interval where it is equal to a constant.
- campaign
A collection of events that use interventions to modify a simulation.
- campaign event
A JSON object that determines when and where an intervention is distributed during a campaign.
- campaign file
A JSON (JavaScript Object Notation) formatted file that contains the parameters that specify the distribution instructions for all interventions used in a campaign, such as diagnostic tests, the target demographic, and the timing and cost of interventions. The location of this file is specified in the configuration file with the Campaign_Filename parameter. Typically, the file name is campaign.json.
- channel
A property of the simulation (for example, “Parasite Prevalence”) that is accumulated once per simulated time step and written to file, typically as an array of the accumulated values.
- class factory
A function that instantiate objects at run-time and use information from JSON-based configuration information in the creation of these objects.
- configuration file
A JSON (JavaScript Object Notation) formatted file that contains the parameters sufficient for initiating a simulation. It controls many different aspects of the simulation, such as population size, disease dynamics, and length of the simulation. Typically, the file name is config.json.
- core
In computing, a core refers to an independent central processing unit (CPU) in the computer. Multi-core computers have more than one CPU. However, through technologies such as Hyper- Threading Technology (HTT or HT), a single physical core can actually act like two virtual or logical cores, and appear to the operating system as two processors.
- demographics file
A JSON (JavaScript Object Notation) formatted file that contains the parameters that specify the demographics of a population, such as age distribution, risk, birthrate, and more. IDM provides demographics files for many geographic regions. This file is typically named <region>_demographics.json.
- disease-specific build
A build of the EMOD executable (Eradication.exe) built using SCons without any dynamic link libraries (DLLs).
- dynamic link library (DLL)
Microsoft’s implementation of a shared library, separate from the EMOD executable (Eradication.exe), that can be dynamically loaded (and unloaded when unneeded) at runtime. This loading can be explicit or implicit.
- EMODule
A modular component of EMOD that are consumed and used by the EMOD executable (Eradication.exe). Under Windows, a EMODule is implemented as a dynamic link library (DLL) and, under CentOS, EMODules are currently not supported. EMODules are primarily custom reporters.
- Epidemiological MODeling software (EMOD)
The modeling software from the Institute for Disease Modeling (IDM) for disease researchers and developers to investigate disease dynamics, and to assist in combating a host of infectious diseases. You may see this referred to as Disease Transmission Kernel (DTK) in the source code.
- Eradication.exe
Typical (default) name for the EMOD executable (Eradication.exe), whether built using monolithic build or modular (EMODule-enabled) build.
- event coordinator
A JSON object that determines who will receive a particular intervention during a campaign.
- flattened file
A single campaign or configuration file created by combining a default file with one or more overlay files. Multiple files must be flattened prior to running a simulation. Configuration files are flattened to a single-depth JSON file without nesting, the format required for consumption by the EMOD executable (Eradication.exe). Separating the parameters into multiple files is primarily used for testing and experimentation.
- Heterogeneous Intra-Node Transmission (HINT)
A feature for modeling person-to-person transmission of diseases in heterogeneous population segments within a node for generic simulations.
- high-performance computing (HPC)
The use of parallel processing for running advanced applications efficiently, reliably, and quickly.
- individual properties
Labels that can be applied to individuals within a simulation and used to configure heterogeneous transmission, target interventions, and move individuals through a health care cascade.
- input files
The JSON and binary files used as inputs to an EMOD simulation. The primary input files are the JSON-formatted configuration, demographics, and campaign files. They may also include the binary files for migration, climate, population serialization, or load- balancing.
- inset chart
The default JSON output report for EMOD that includes multiple channels that contain data at each time step of the simulation. These channels include number of new infections, prevalence, number of recovered, and more.
- intervention
An object aimed at reducing the spread of a disease that is distributed either to an individual; such as a vaccine, drug, or bednet; or to a node; such as a larvicide. Additionally, initial disease outbreaks and intermediate interventions that schedule another intervention are implemented as interventions in the campaign file.
- JSON (JavaScript Object Notation)
A human-readable, open standard, text-based file format for data interchange. It is typically used to represent simple data structures and associative arrays, and is language-independent. For more information, see https://www.json.org.
- JSON
See JavaSCript Object Notation.
- Keyhole Markup Language (KML)
A file format used to display geographic data in an Earth browser, for example, Google Maps. The format uses an XML-based structure (tag-based structure with nested elements and attributes). Tags are case-sensitive.
- Link-Time Code Generation (LTCG)
A method for the linker to optimize code (for size and/or speed) after compilation has occurred. The compiled code is turned not into actual code, but instead into an intermediate language form (IL, but not to be confused with .NET IL which has a different purpose). The LTCG then, unlike the compiler, can see the whole body of code in all object files and be able to optimize the result more effectively.
- Message Passing Interface (MPI)
An interface used to pass information between computing cores in parallel simulations. One example is the migration of individuals from one geographic location to another within EMOD simulations.
- microsolver
A type of “miniature model” that operates within the framework of EMOD to compute a particular set of parameters. Each microsolver, in effect, is creating a microsimulation in order to accurately capture the dynamics of that particular aspect of the model.
- Monte Carlo method
A class of algorithms using repeated random sampling to obtain numerical results. Monte Carlo simulations create probability distributions for possible outcomes, which provides a more realistic way of describing uncertainty.
- monolithic build
A single EMOD executable (Eradication.exe) with no DLLs that includes all components as part of Eradication.exe itself. You can still use EMODules with the monolithic build; for example, a custom reporter is a common type of EMODule. View the documentation on EMODules and emodules_map.json for more information about creation and use of EMODules.
- node
A grid size that is used for modeling geographies. Within EMOD, a node is a geographic region containing simulated individuals. Individuals migrate between nodes either temporarily or permanently using mobility patterns driven by local, regional, and long- distance transportation.
- node properties
Labels that can be applied to nodes within a simulation and used to target interventions based on geography.
- node-targeted intervention
An intervention that is distributed to a geographical node rather than to a single individual. One example is larvicides, which affect all mosquitoes living and feeding within a given node.
- nodes
See node.
- output report
A file that is the output from an EMOD simulation. Output reports are in JSON, CSV, or binary file format. You must pass the data from an output report to graphing software if you want to visualize the output of a simulation.
- overlay file
An additional configuration, campaign, or demographic file that overrides the default parameter values in the primary file. Separating the parameters into multiple files is primarily used for testing a nd experimentation. In the case of configuration and campaign files, the files can use an arbitrary hierarchical structure to organize parameters into logical groups. Configuration and campaign files must be flattened into a single file before running a simulation.
- preview
Software that undergoes a shorter testing cycle in order to make it available more quickly. Previews may contain software defects that could result in unexpected behavior. Use EMOD previews at your own discretion.
- regression test
A test to verify that existing EMOD functionality works with new updates, located in the Regression subdirectory of the EMOD source code repository. Directory names of each subdirectory in Regression describe the main regression attributes, for example, “1_Generic_Seattle_MultiNode”. Also can refer to the process of regression testing of software.
- release
Software that includes new functionality, scientific tutorials leveraging new or existing functionality, and/or bug fixes that have been thoroughly tested so that any defects have been fixed before release. EMOD releases undergo full regression testing.
- reporter
Functionality that extracts simulation data, aggregates it, and saves it as an output report. EMOD provides several built-in reporters for outputting data from simulations and you also have the ability to create a custom reporter.
- scenario
A collection of input files that describes a real-world example of a disease outbreak and interventions. Many scenarios are included with EMOD source installations or are available to download at EMOD scenarios to learn more about epidemiology and disease modeling.
- schema
A text or JSON file that can be generated from the EMOD executable (Eradication.exe) that defines all configuration and campaign parameters.
- simulation
An execution of the EMOD software using an associated set of input files.
- simulation type
The disease or disease class to model.
EMOD supports the following simulation types for modeling a variety of diseases:
Generic disease (GENERIC_SIM), which can be used for modeling a variety of diseases such as influenza or measles
Vector-borne diseases (VECTOR_SIM), which can be used for modeling vector-borne diseases such as dengue
Malaria (MALARIA_SIM), which adds features specific to malaria biology and treatment
Sexually transmitted infections (STI_SIM), which adds features for sexual relationship networks
HIV (HIV_SIM), which adds features specific to HIV biology and treatment
- solvers
Solvers are used to find computational solutions to problems. In simulations, they can be used, for example, to determine the time of the next simulation step, or to compute the states of a model at particular time steps.
- Standard Template Library (STL)
A library that contains a set of common C++ classes (including generic algorithms and data structures) that are independent of container and implemented as templates, which enables compile-time polymorphism (often more efficient than run-time polymorphism). For more information and discussion of STL, see Wikipedia - Standard Template Library for more information.
- state transition event
A change in state (e.g. healthy to infected, undiagnosed to positive diagnosis, or birth) that may trigger a subsequent action, often an intervention. “Campaign events” should not be confused with state transition events.
- time step
A discrete number of hours or days in which the “simulation states” of all “simulation objects” (interventions, infections, immune systems, or individuals) are updated in a simulation. Each time step will complete processing before launching the next one. For example, a time step would process the migration data for populations moving between nodes via rail, airline, and road. The migration of individuals between nodes is the last step of the time step after updating states.
- tutorial
A set of instructions in the documentation to learn more about epidemiology and disease modeling. Tutorials are based on real-world scenarios and demonstrate the mechanics of the the model. Each tutorial consists of one or more scenarios.
- working directory
The directory that contains the configuration and campaign files for a simulation. You must be in this directory when you invoke Eradication.exe at the command line to run a simulation.