Coronavirus Disease Research Community - COVID-19

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Published July 4, 2020 | Version v3.1
Software Open

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

Creators

  • 1. Indiana University
  • 2. Macklin cancer simulation lab

Description

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

Version: 3.1

Release date: 3 July 2020

Overview

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.

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  • It has not been peer reviewed.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: 3.1:

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

3.0:

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.

2.0:

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.

1.0:

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

Files

pc4covid19/pc4covid19-v3.1.zip

Files (409.8 kB)

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Additional details

Related works

Is supplement to
https://github.com/pc4covid19/pc4covid19/tree/v3.1 (URL)