Welcome to the Johns Hopkins University Infectious Disease Dynamics COVID-19 Working Group's Flexible Epidemic Modeling Pipeline(“FlepiMoP”, formerly the COVID Scenario Pipeline, “CSP”), a flexible modeling framework that projects epidemic trajectories and healthcare impacts under different suites of interventions in order to aid in scenario planning. The model is generic enough to be applied to different spatial scales given shapefiles, population data, and COVID-19 confirmed case data. There are multiple components to the pipeline, which may be characterized as follows: 1) epidemic seeding; 2) disease transmission and non-pharmaceutical intervention scenarios; 3) calculation of health outcomes (hospital and ICU admissions and bed use, ventilator use, and deaths); and 4) summarization of model outputs.
We recommend that most new users use the code from the stable main branch. Please post questions to GitHub issues with the question tag. We are prioritizing direct support for individuals engaged in public health planning and emergency response.
For more details on the methods and features of our model, visit our preprint on medRxiv.
This open-source project is licensed under GPL v3.0.
A containerized environment is a packaged environment where all dependencies are bundled together. This means you're guaranteed to be using the same libraries and system configuration as everyone else and in any runtime environment. To learn more, Docker Curriculum is a good starting point.
A pre-built container can be pulled from Docker Hub via:
docker pull hopkinsidd/flepimop:latest-dev
To start the container:
docker run -it \
-v <dir1>\:/home/app/flepimop \
-v <dir2>:/home/app/drp \
hopkinsidd/flepimop:latest
In this command we run the docker image hopkinsidd/flepimop. The -v command is used to allocate space from Docker and mount it at the given location. This mounts the data folder to a path called drp within the docker environment, and the flepimop folder to flepimop.
You'll be dropped to the bash prompt where you can run the Python or R scripts (with dependencies already installed).
Run docker build -f build/docker/Dockerfile . if you ever need to rebuild the container after changing to the top directory of flepiMoP.
Note that the container build supports amd64 CPU architecture only, other architectures are unconfirmed. If you are using M1 MAC etc., please use the build kit to build an image with specifying the platform/architecture.