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

Randy Heiland; Paul Macklin

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  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.4283005", 
  "title": "pc4covid19/pc4covid19: Version 4.0: Jupyter notebook (nanoHUB) COVID19 app", 
  "issued": {
    "date-parts": [
  "abstract": "pc4covid19 - COVID19 (SARS-CoV-2) tissue simulator nanoHUB app\n<p><strong>Version:</strong> 4.0</p>\n<p><strong>Release date:</strong> 20 November 2020</p>\nOverview\n<p>This repository contains code and data for the nanoHUB app <a href=\"\"></a>.\nHere, we primarily report on changes to the app's GUI.</p>\n<p>It is based on the model at <a href=\"\"></a>. Refer to that repository\nfor a summary of changes to the model.</p>\nCaveats and disclaimers:\n<p><strong>This model is under active development using rapid prototyping:</strong></p>\n<ul>\n<li>It has not been peer reviewed. </li>\n<li>It is intended to drive basic scientific research and public education at this stage. </li>\n<li><strong>It cannot be used for public policy decisions.</strong></li>\n<li><strong>It cannot be used for individual medical decisions.</strong></li>\n</ul>\n<p><strong>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.</strong></p>\nRelease summary:\n4.0:\n<p>Updates to the core model. The Cell Types tab now shows \"flattened\" versions of the cell types, instead of \nthe hierarchical version in v3. The Out:Plots tab now has an additional \"Extra analysis\" plot and provides \na dropdown menu of options. The widgets have been rearranged to accommodate. The Animate tab has been removed.</p>\n3.2:\n<p>Updates to the core model; nothing new in the GUI.</p>\n3.1:\n<p>Minor updates to <code>About</code> text, e.g., explaining nature of stochastic results. Edits to <code>immune_submodels.cpp</code> (see details in the core model repository).</p>\n3.0:\n<p>The major change to the GUI in this release is the addition of a 'Cell Types' tab.\nThis allows editing parameters associated with <code>&lt;cell_definitions&gt;</code> in the configuration file.</p>\n<p>This version also includes a <code>&lt;style&gt;</code> block in the Jupyter notebook that fixed an unwanted scrollbar in the lengthy <code>About</code> tab.</p>\n2.0:\n<p>The major change to the GUI in this release is the addition of an 'Animate' tab.\nThis allows animation of cells (not substrates) in the tab and the generation of a .mp4\nvideo that can be downloaded. The animation uses the cells' SVG files.</p>\n1.0:\n<p>Provides a \"standard\" PhysiCell-based Jupyter notebook GUI consisting of 5 tabs:</p>\n<ul>\n<li>About: a description of the model and the app</li>\n<li>Config Basics: input parameters common to all models (e.g., domain grid, simulation time, choice/frequency of outputs)</li>\n<li>Microenvironment: microenvironment parameters that are model-specific</li>\n<li>User Params: user parameters that are model-specific</li>\n<li>Out: Plots:  output display of cells and substrates</li>\n</ul>", 
  "author": [
      "family": "Randy Heiland"
      "family": "Paul Macklin"
  "version": "v4.0", 
  "type": "article", 
  "id": "4283005"
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