Software Open Access
Randy Heiland; Paul Macklin
pc4covid19 - COVID19 (SARS-CoV-2) tissue simulator nanoHUB app
Release date: 20 November 2020Overview
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:
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: 4.0:
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.3.2:
Updates to the core model; nothing new in the GUI.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).
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
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: