November 20, 2020 Software Open Access

pc4covid19/pc4covid19: Version 4.0: Jupyter notebook (nanoHUB) COVID19 app

Randy Heiland; Paul Macklin

pc4covid19 - COVID19 (SARS-CoV-2) tissue simulator nanoHUB app

Version: 4.0

Release date: 20 November 2020

This repository contains code and data for the nanoHUB app https://nanohub.org/tools/pc4covid19. Here, we primarily report on changes to the app's GUI.

It is based on the model at https://github.com/pc4covid19/COVID19. Refer to that repository for a summary of changes to the model.

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• It has not been peer reviewed.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.

Updates to the core model. The Cell Types tab now shows "flattened" versions of the cell types, instead of the hierarchical version in v3. The Out:Plots tab now has an additional "Extra analysis" plot and provides a dropdown menu of options. The widgets have been rearranged to accommodate. The Animate tab has been removed.

Updates to the core model; nothing new in the GUI.

Minor updates to About text, e.g., explaining nature of stochastic results. Edits to immune_submodels.cpp (see details in the core model repository).

The major change to the GUI in this release is the addition of a 'Cell Types' tab. This allows editing parameters associated with <cell_definitions> in the configuration file.

This version also includes a <style> block in the Jupyter notebook that fixed an unwanted scrollbar in the lengthy About tab.

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