InstituteforDiseaseModeling/GWSpatialGenetics

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InstituteforDiseaseModeling/GWSpatialGenetics

InstituteforDiseaseModeling

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The Institute of Disease Modeling interdisciplinary collaboration with Elizabeth Thiele (Vassar) and James Cotton (Wellcome Sanger Institute) to maximize the value of epidemiological and genetics data to understand Guinea worm transmission in Chad.

covasim

COVID-19 Agent-based Simulator (Covasim): a model for exploring coronavirus dynamics and interventions

EMOD

Source files for building the IDM EMOD disease transmission model.

synthpops

Create synthetic populations for COVID-19 epidemic analyses.

vis-tools

Visualization Toolkit

COVID-public

Repo to share open work on the COVID-19 outbreak

covid-health-systems

Simulate various COVID-19 health system capacity scenarios

IDM-CMS

IDM compartmental modeling software (CMS)

kingcounty_rainier

RAINIER applied to COVID-19 data in King County, WA from the Washington Disease Reporting System

hpvsim

Human papillomavirus simulator (HPVsim)

covid-mobility-and-behavior

Jupyter Notebook

idmtools

PACE-HRH

PACE-HRH (Population-Aware Capacity Estimator for Human Resources for Health)

cookiecutter-dash-ui

cookiecutter project for a dash UI

Climate

IDM climate files for Senegal 2013

SeasonalityStudyOfGEMSdata

Data and code associated with "The seasonality of diarrheal pathogens: A retrospective study of seven sites over three years"

docs-emod-scenarios

Tutorial materials as referenced in IDM's documentation for EMOD, an agent-based disease dynamics model.

laser

Light Agent Spatial modeling for ERadication

EMOD-InputData

Full set of input data files for use with the EMOD disease transmission model

PACE-HRH-UI

PACE-HRH-UI is a health capacity estimation tool built using R and Shinyapps

stepping-back-to-school

Code used for IDM's school reopening analysis presented in the Stepping Back to School modeling report

malaria-model_validation

SFS-coinfection-interactions

EMOD-Typhoid

IDM typhoid model source code for ASTMH November 2016

EMOD-Generic-Scripts

Demonstration simulations using Generic-Ongoing branch of EMOD

genepi_science

a space for genepi research collaboration

HIV-MetaAnalysis-Shiny

EVD

Data, analysis, visualization of 2014-2015 West African Ebola outbreak

archetypes-intervention-impact

covasim_webapp

Webapp for Covasim

testing-the-waters

Supporting code for "Testing the waters: time to go back to school?"

SAEDashboard

TransmissionSankey

Look at flows of where infections come from and go to, cross-referencing EMOD log files

EMOD-Generic

Source files for building IDM's EMOD computational epidemiology software.

winogrande-mmlu-clinical-za

Expanding Reasoning Benchmarks in Low-Resourced African Languages: Winogrande and Clinical MMLU in Afrikaans, Xhosa, and Zulu

Jupyter Notebook

abm-software-comparison

ABM software comparison for spatial disease modeling