Commit a287908d authored by Vincent Noël's avatar Vincent Noël
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Updated about description

parent 9b25f0bb
<h2 id="about"><strong>COVID19 tissue simulator</strong></h2>
<h2 id="about"><strong>PhysiBoSS COVID19 tissue simulator</strong></h2>
<p>This model simulates viral dynamics of SARS-CoV-2 (coronavirus / COVID19) in a layer of epithelium
and an immune response. It is being rapidly prototyped and refined with community support
and an immune response. This particuliar version is an extension of the SARS-COV-2 tissue simulation coalition,
which integrates a mechanistic boolean model of invasion from the COVID19 Disease Maps initiative.
(<a href="#model_details">see below</a>). </p>
<p><b>Please note that this is a stochastic model: for some simulation runs, you may see the immune system fail to respond. Users are encouraged to try the simulation multiple times.</b></p>
......@@ -22,30 +23,44 @@ and an immune response. It is being rapidly prototyped and refined with communit
pharmacodynamics response (to assembled virions), infected cells can undergo apoptosis. Apoptosed cells release some or
all of their internal contents, notably including virions. </li>
<li><strong><span style="background-color: red; color: white; padding-left: 0.1in; padding-right: 0.1in">
<strong>Immune response (new in version 3)</strong></span>:</strong> </li>
<li><strong>
<strong>Immune response (new in version 3)</strong>:</strong> </li>
<ul>
<li><strong>Resident (and recruited) macrophages</strong> seek apoptotic cells. They phagocytose (ingest) dead cells
upon contact and activate. They also break down ("digest") ingested materials. </li>
<li><strong>Resident (and recruited) macrophages</strong> seek apoptotic cells. They phagocytose (ingest) dead cells
upon contact and activate. They also break down ("digest") ingested materials. </li>
<li><strong>Activated macrophages</strong> release a pro-inflammatory cytokine to recruit other immune cells, while
seeking both apoptotic and infected cells by chemotaxis. Activated macrophages can “wear out” and apoptose after phagocytosing
too much material.</li>
<li><strong>Activated macrophages</strong> release a pro-inflammatory cytokine to recruit other immune cells, while
seeking both apoptotic and infected cells by chemotaxis. Activated macrophages can “wear out” and apoptose after phagocytosing
too much material.</li>
<li><strong>Neutrophils</strong> are recruited by accumulated pro-inflammatory cytokine. They seek apoptotic cells,
phagocytose them, and activate. Activated neutrophils seek both apoptotic and infected cells. Neutrophils also capture
extracellular virions. </li>
<li><strong>Neutrophils</strong> are recruited by accumulated pro-inflammatory cytokine. They seek apoptotic cells,
phagocytose them, and activate. Activated neutrophils seek both apoptotic and infected cells. Neutrophils also capture
extracellular virions. </li>
<li><strong>CD8<sup>+</sup> T cells</strong> are recruited by accumulated pro-inflammatory cytokine.
They seek and adhere to infected cells. After sufficient contact time with one or more CD8<sup>+</sup> T cells, infected cells undergo apoptosis. </li>
</ul>
<li><strong>CD8<sup>+</sup> T cells</strong> are recruited by accumulated pro-inflammatory cytokine.
They seek and adhere to infected cells. After sufficient contact time with one or more CD8<sup>+</sup> T cells, infected cells undergo apoptosis.
</li>
</ul>
<li><strong><span style="background-color: red; color: white; padding-left: 0.1in; padding-right: 0.1in">
<strong>Apoptosis mechanistic model (new in this example)</strong></span>:</strong> </li>
<ul>
<li><strong>FADD KO proportion</strong> describes the proportion of the epithelial cells' population which inhibits FADD activity. </li>
<li><strong>M KO proportion</strong> describes the proportion of the epithelial cells' population which inhibits M activity. </li>
</ul>
</ul>
<p>
Please cite this project via the preprint:
Please cite this project via:
</p>
<p style="text-align: center;">
V. Noël et al., PhysiBoSS-COVID: the Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework allows for the uncovering of mechanistic insights.
<i>Zenodo</i> 10.5281/zenodo.4266778, 2020, <b>(Poster + Short talk)</b>.
doi: <a href="https://doi.org/10.5281/zenodo.4266778" target="_blank">10.5281/zenodo.4266778</a>.
</p>
<p style="text-align: center;">
......@@ -140,22 +155,13 @@ that will terminate (not pause) the simulation.
<h2 id="model_details"><strong>Model details</strong></h2>
<p>This model is being rapidly prototyped. Biological and mathematical detail can be found at:</p>
<ul>
<ul>
<li>
<b>Project website:</b> <a href="http://covid19.physicell.org" target="_blank">http://covid19.physicell.org</a> (opens in new tab)
<b>Poster/Short talk:</b> <a href="https://doi.org/10.5281/zenodo.4266778" target="_blank">Noel et al. (2020)</a> (opens in new tab)
</li>
<li>
<b>Model feedback:</b> <a href="https://forms.gle/12vmLR7aiMTHoD5YA" target="_blank">Google feedback form</a> (opens in new tab)
</li>
<li>
<b>Preprint:</b> <a href="https://dx.doi.org/10.1101/2020.04.02.019075" target="_blank">Wang et al. (2020)</a> (opens in new tab)
</li>
<li>
<b>GitHub codes:</b> <a href="https://github.com/pc4covid19" target="_blank">pc4covid19 GitHub organization</a> (opens in new tab)
<b>GitHub:</b> <a href="https://github.com/vincent-noel/pb4covid19" target="_blank">pb4covid19 GitHub repository</a> (opens in new tab)
</li>
</ul>
......@@ -189,6 +195,9 @@ This model and cloud-hosted demo are part of the education and outreach
<ol>
<li>
<a href="https://academic.oup.com/bioinformatics/article/35/7/1188/5087713">G. Letort, A. Montagud, G. Stoll, R. Heiland, E. Barillot, P. Macklin, A. Zinovyev, L. Calzone, PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling, Bioinformatics, Volume 35, Issue 7, 01 April 2019, Pages 1188–1196, https://doi.org/10.1093/bioinformatics/bty766</a> </li>
</li>
<li>
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005991">A. Ghaffarizadeh, R. Heiland, S.H. Friedman, S.M. Mumenthaler, and P. Macklin. PhysiCell: an open source physics-based cell simulator for 3-D multicellular systems. PLoS Comput. Biol. 14(2):e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991.</a> </li>
<li>
<a href="https://joss.theoj.org/papers/10.21105/joss.01408">R. Heiland, D. Mishler, T. Zhang, E. Bower, and P. Macklin. xml2jupyter: Mapping parameters between XML and Jupyter widgets. Journal of Open Source Software 4(39):1408, 2019. DOI: 10.21105/joss.01408.
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