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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta name="description" content="PhysiBoSS" />
<meta name="keywords" content="PhysiBoSS, PhysiCell, agent-based, Boolean, boolean, intracellular, multiscale, framework" />
<meta name="author" content="Vincent Noël" />
<title>PhysiBoSS</title>
</head>
<body>
<div align="center">
<img src="images/PhysiBoSS_logo.png" alt="PhysiBoSS" width="300" height="300">
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<h3>
PhysiBoSS is a multiscale modeling framework integrating Boolean intracellular models into the PhysiCell agent-based framework.<br/>
PhysiBoSS project is a collaboration between the Computational Systems Biology of Cancer team at Institut Curie and the Computational Biology group at BSC.
</h3>
<br/><br/>
<img src="images/curie.jpg" alt="Institut Curie" height="50">
<img src="images/bsc.jpg" alt="Barcelona Supercomputing Center" height="50">
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<div style="width: 1000px; text-align: center;">
<h1>Tutorial</h1>
<h4>
We recently released a tutorial on PhysiBoSS. <br/>
You can find it at Briefing in Bioinformatics: <a href="https://academic.oup.com/bib/article/25/6/bbae509/7826460">https://academic.oup.com/bib/article/25/6/bbae509/7826460</a><br/>
A step-by-step tutorial is provided as a Supplementary Material. <br/>
You can find it, together with all models at: <a href="https://physiboss.github.io/tutorial">https://physiboss.github.io/tutorial</a>
</h4>
Ruscone, Marco, Checcoli, Andrea, Heiland, Randy, Barillot, Emmanuel, Macklin, Paul, Calzone, Laurence, Noël, Vincent, "Building multiscale models with PhysiBoSS, an agent-based modeling tool", <i>Briefings in Bioinformatics</i>, Volume 25, Issue 6, November 2024, bbae509
DOI : <a href="https://doi.org/10.1093/bib/bbae509">10.1093/bib/bbae509</a><br/>
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<h1>References</h1>
Letort, Gaelle, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev, and Laurence Calzone. "PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling." <i>Bioinformatics</i> 35, no. 7 (2019): 1188-1196.<br/>
DOI : <a href="https://doi.org/10.1093/bioinformatics/bty766">10.1093/bioinformatics/bty766</a><br/>
<br/>
Ponce-de-Leon, Miguel, Arnau Montagud, Vincent Noël, Annika Meert, Gerard Pradas, Emmanuel Barillot, Laurence Calzone, and Alfonso Valencia. "PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks." <i>npj Systems Biology and Applications</i> 9, no. 1 (2023): 54.<br/>
DOI : <a href="https://doi.org/10.1038/s41540-023-00314-4">10.1038/s41540-023-00314-4</a><br/>
<br/><br/><br/><br/>
<h1>GitHub repo</h1>
PhysiBoSS is open-source, under the BSD-3 clause license, and is available on GitHub: <a href="https://github.com/PhysiBoSS/PhysiBoSS">https://github.com/PhysiBoSS/PhysiBoSS</a>
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<h1>Sponsors</h1>
This work has received funding from the Horizon 2020 projects INFORE (ID: 825070) and PerMedCoE (ID: 951773) and from the Horizon Europe project CREXDATA (ID: 101092749). This work was funded in part by the French government under the management of Agence Nationale de la Recherche as part of the “Investissements d’avenir” programme, reference ANR-19-P3IA-0001 (PRAIRIE 3IA Institute).
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<img src="images/Flag_of_Europe.png" alt="EU" height="50">
<img src="images/Investissements_davenir.jpeg" alt="Investissements d'avenir" height="50">
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</body>
</html>