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

Randy Heiland; Paul Macklin

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  <identifier identifierType="DOI">10.5281/zenodo.4283005</identifier>
      <creatorName>Randy Heiland</creatorName>
      <affiliation>Indiana University</affiliation>
      <creatorName>Paul Macklin</creatorName>
      <affiliation>Macklin cancer simulation lab</affiliation>
    <title>pc4covid19/pc4covid19: Version 4.0: Jupyter notebook (nanoHUB) COVID19 app</title>
    <date dateType="Issued">2020-11-20</date>
  <resourceType resourceTypeGeneral="Software"/>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3750175</relatedIdentifier>
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    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">pc4covid19 - COVID19 (SARS-CoV-2) tissue simulator nanoHUB app
&lt;p&gt;&lt;strong&gt;Version:&lt;/strong&gt; 4.0&lt;/p&gt;
&lt;p&gt;&lt;strong&gt;Release date:&lt;/strong&gt; 20 November 2020&lt;/p&gt;
&lt;p&gt;This repository contains code and data for the nanoHUB app &lt;a href=""&gt;;/a&gt;.
Here, we primarily report on changes to the app's GUI.&lt;/p&gt;
&lt;p&gt;It is based on the model at &lt;a href=""&gt;;/a&gt;. Refer to that repository
for a summary of changes to the model.&lt;/p&gt;
Caveats and disclaimers:
&lt;p&gt;&lt;strong&gt;This model is under active development using rapid prototyping:&lt;/strong&gt;&lt;/p&gt;
&lt;li&gt;It has not been peer reviewed. &lt;/li&gt;
&lt;li&gt;It is intended to drive basic scientific research and public education at this stage. &lt;/li&gt;
&lt;li&gt;&lt;strong&gt;It cannot be used for public policy decisions.&lt;/strong&gt;&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;It cannot be used for individual medical decisions.&lt;/strong&gt;&lt;/li&gt;
&lt;p&gt;&lt;strong&gt;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.&lt;/strong&gt;&lt;/p&gt;
Release summary:
&lt;p&gt;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.&lt;/p&gt;
&lt;p&gt;Updates to the core model; nothing new in the GUI.&lt;/p&gt;
&lt;p&gt;Minor updates to &lt;code&gt;About&lt;/code&gt; text, e.g., explaining nature of stochastic results. Edits to &lt;code&gt;immune_submodels.cpp&lt;/code&gt; (see details in the core model repository).&lt;/p&gt;
&lt;p&gt;The major change to the GUI in this release is the addition of a 'Cell Types' tab.
This allows editing parameters associated with &lt;code&gt;&amp;lt;cell_definitions&amp;gt;&lt;/code&gt; in the configuration file.&lt;/p&gt;
&lt;p&gt;This version also includes a &lt;code&gt;&amp;lt;style&amp;gt;&lt;/code&gt; block in the Jupyter notebook that fixed an unwanted scrollbar in the lengthy &lt;code&gt;About&lt;/code&gt; tab.&lt;/p&gt;
&lt;p&gt;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.&lt;/p&gt;
&lt;p&gt;Provides a "standard" PhysiCell-based Jupyter notebook GUI consisting of 5 tabs:&lt;/p&gt;
&lt;li&gt;About: a description of the model and the app&lt;/li&gt;
&lt;li&gt;Config Basics: input parameters common to all models (e.g., domain grid, simulation time, choice/frequency of outputs)&lt;/li&gt;
&lt;li&gt;Microenvironment: microenvironment parameters that are model-specific&lt;/li&gt;
&lt;li&gt;User Params: user parameters that are model-specific&lt;/li&gt;
&lt;li&gt;Out: Plots:  output display of cells and substrates&lt;/li&gt;
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