Workflow and calibration toolsΒΆ

IDM also makes several tools available to simplify user interactions with disease models. These tools help with configuration of the model, commissioning and running simulations, calibration, and analysis of modeling results. Several of these tools are specific to the EMOD model.

Model

Code repository

Tool documentation

Description

Model agnostic

https://github.com/InstituteforDiseaseModeling/idmtools

idmtools docs

idmtools is a collection of Python scripts and utilities created to streamline user interactions with disease models, from the creation of input files (if required), to commissioning and running simulations, through the analysis of results. It can be used to interact with a variety of models, such as custom models written in R or Python, Starsim, or EMOD.

Model agnostic

https://github.com/InstituteforDiseaseModeling/idmtools-calibra

idmtools_calibra docs

idmtools_calibra is a collection of Python scripts and utilities to aid in model calibration.

EMOD

https://github.com/InstituteforDiseaseModeling/emod-api

emod-api docs

emod-api is a Python library for interacting with EMOD input and output files.

EMOD

https://github.com/InstituteforDiseaseModeling/emodpy

emodpy docs

emodpy is a collection of Python scripts and utilities created to streamline user interactions with EMOD and idmtools, agnostic of the disease being simulated.

EMOD generic

https://github.com/InstituteforDiseaseModeling/emodpy-covid

emodpy-covid docs

emodpy-covid is a Python library with scripts and tooling to model COVID transmission using the EMOD generic model.

EMOD generic

https://github.com/InstituteforDiseaseModeling/emodpy-generic

emodpy-generic docs

emodpy-generic is a Python library with scripts and tooling to use the EMOD generic model.

EMOD generic

https://github.com/InstituteforDiseaseModeling/emodpy-measles

emodpy-measles docs

emodpy-measles is a Python library with scripts and tooling to model measles with the EMOD generic model.

EMOD HIV

https://github.com/InstituteforDiseaseModeling/emodpy-hiv

emodpy-hiv docs

emodpy-hiv is a Python library with scripts and tooling to use the EMOD HIV model.

EMOD HIV

https://github.com/InstituteforDiseaseModeling/hiv_workflow

hiv_workflow docs

hiv_workflow is a collection of Python scripts and libraries utilizing idmtools, idmtools-calibra, and emodpy-hiv for calibration and running of the EMOD HIV model.

EMOD malaria

https://github.com/InstituteforDiseaseModeling/emodpy-malaria

emopdy-malaria docs

emodpy-malaria is a Python library with scripts and tooling to use the EMOD malaria model.

EMOD tuberculosis (TBHIV)

https://github.com/InstituteforDiseaseModeling/emodpy-tbhiv

emodpy-tbhiv docs

emodpy-tbhiv is a Python library with scripts adn tooling to use the EMOD tuberculosis (TBHIV) model.

Examples of workflows that use the idmtools and emodpy packages are available in the Jupyter notebooks for emodpy documentation.