There is a newer version of this record available.

Software Open Access

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

Randy Heiland; Paul Macklin


DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
  <identifier identifierType="DOI">10.5281/zenodo.4283005</identifier>
  <creators>
    <creator>
      <creatorName>Randy Heiland</creatorName>
      <affiliation>Indiana University</affiliation>
    </creator>
    <creator>
      <creatorName>Paul Macklin</creatorName>
      <affiliation>Macklin cancer simulation lab</affiliation>
    </creator>
  </creators>
  <titles>
    <title>pc4covid19/pc4covid19: Version 4.0: Jupyter notebook (nanoHUB) COVID19 app</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <dates>
    <date dateType="Issued">2020-11-20</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4283005</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/pc4covid19/pc4covid19/tree/v4.0</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3750175</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/covid-19</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>v4.0</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <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;
Overview
&lt;p&gt;This repository contains code and data for the nanoHUB app &lt;a href="https://nanohub.org/tools/pc4covid19"&gt;https://nanohub.org/tools/pc4covid19&lt;/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="https://github.com/pc4covid19/COVID19"&gt;https://github.com/pc4covid19/COVID19&lt;/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;ul&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;/ul&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:
4.0:
&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;
3.2:
&lt;p&gt;Updates to the core model; nothing new in the GUI.&lt;/p&gt;
3.1:
&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;
3.0:
&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;
2.0:
&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;
1.0:
&lt;p&gt;Provides a "standard" PhysiCell-based Jupyter notebook GUI consisting of 5 tabs:&lt;/p&gt;
&lt;ul&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;
&lt;/ul&gt;</description>
  </descriptions>
</resource>
1,075
60
views
downloads
All versions This version
Views 1,075185
Downloads 6012
Data volume 24.6 MB6.3 MB
Unique views 862167
Unique downloads 4210

Share

Cite as