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pc4covid19/pc4covid19: v2.1 - COVID19 tissue simulator nanoHUB app

Randy Heiland; Paul Macklin

pc4covid19 - COVID19 tissue simulator nanoHUB app

Version: 2.1 - uses the core model at

Release date: 26 April 2020


This repository contains code and data for the nanoHUB app Here, we primarily report on changes to the app's GUI.

It is based on the model at Refer to that repository for a summary of changes to the model.

Caveats and disclaimers:

This model is under active development using rapid prototyping:

  • It has not been peer reviewed.
  • It is intended to drive basic scientific research and public education at this stage.
  • It cannot be used for public policy decisions.
  • It cannot be used for individual medical decisions.

This model will be continually refined with input from the community, particularly experts in infectious diseases. The validation state will be updated as this progresses.

Release summary: 2.1:

Sync up with the version number of the published app,, and include a reference to the version of the core model in this README.


The major change to the GUI in this release is the addition of an 'Animate' tab. This allows animation of cells (not substrates) in the tab and the generation of a .mp4 video that can be downloaded. The animation uses the cells' SVG files.


Provides a "standard" PhysiCell-based Jupyter notebook GUI consisting of 5 tabs:

  • About: a description of the model and the app
  • Config Basics: input parameters common to all models (e.g., domain grid, simulation time, choice/frequency of outputs)
  • Microenvironment: microenvironment parameters that are model-specific
  • User Params: user parameters that are model-specific
  • Out: Plots: output display of cells and substrates

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