is a collection of Python scripts and utilities created to streamline user interactions with disease models. This framework provides the user with tools necessary to complete projects, starting from the creation of input files (if required), to calibration of the model to data, to commissioning and running simulations, through the analysis of results. Modelers can use to run models locally or send suites of simulations to an HPC or other computing source. This framework is free, open-source, and model agnostic: it can be used to interact with a variety of models, such as custom models written in R or Python, or IDM's own . Additional functionality for interacting with is provided in the emod_api:emod_api and emodpy:emodpy.
includes a variety of options for each step of the modeling process. Because of this, the tool suite was developed in a modular fashion, so that users can select the utilities they wish to use. In order to simplify the desired workflow, facilitate the modeling process, and make the model (and its results) reusable and sharable, allows the user to create assets. Assets can be added at any level of the process, from running a specific task, through creating a simulation, to creating a experiment. This allows the user to create inputs based on their specific needs: they can be transient, or sharable across multiple simulations.
The diagram below shows how and each of the related packages are used in an end-to-end workflow using as the disease transmission model.
hide stereotype skinparam component { BackgroundColor<<emodpy-disease>> F9BA9D BackgroundColor<<idmtools>> 006CA6 BackgroundColor<<calibration>> gray BackgroundColor<<emodpy-core>> F18153 BackgroundColor<<COMPS>> lightgray BackgroundColor<<EMOD>> 47C8F5 }
[emodpy-generic] <<emodpy-disease>> [emodpy-generic] --> [emodpy]
[emodpy-hiv] <<emodpy-disease>> [emodpy-hiv] --> [emodpy]
[emodpy-malaria] <<emodpy-disease>> [emodpy-malaria] --> [emodpy]
[emodpy-measles] <<emodpy-disease>> [emodpy-measles] --> [emodpy]
[emodpy-tbhiv] <<emodpy-disease>> [emodpy-tbhiv] --> [emodpy]
[emodpy] <<emodpy-core>> [emod-api] <<emodpy-core>> [emodpy] --> [emod-api]
[emodpy] <-> [idmtools]
[idmtools] <<idmtools>> [COMPS] <<COMPS>> [idmtools] <-> [COMPS] : Commission and status
[idmtools-calibra] <<calibration>> [idmtools-calibra] <--> [idmtools] : Commission and analysis [idmtools-calibra] <--> [emodpy] : Calibration
[emodpy-calibra] <<calibration>> [emodpy-calibra] <--> [emodpy]: EMOD-specific calibration utils [emodpy-calibra] <--> [idmtools-calibra] [Input files] <<EMOD>> [emod-api] --> [Input files] : Create
[Input files] ..> [emod-api] : Inspect
[EMOD Eradication.exe] <<EMOD>> [Input files] -> [EMOD Eradication.exe]
[Output files] <<EMOD>> [EMOD Eradication.exe] -> [Output files] [Output files] --> [emod-api]
Exact workflows for using is user-dependent, and can include any of the tasks listed below.
installation configuration platforms/platforms create-sims containers/containers parameter-sweeps reports analyzers/analyzers plots reference plugin_documentation/index recipes_index cli/cli_index dtkt-convert faq glossary changelog/changelog