Tutorial

We recently released a tutorial on PhysiBoSS.
You can find it at Briefing in Bioinformatics: https://academic.oup.com/bib/article/25/6/bbae509/7826460
A step-by-step tutorial is provided as a Supplementary Material.
You can find it, together with all models at: https://physiboss.github.io/tutorial

Ruscone, Marco, Checcoli, Andrea, Heiland, Randy, Barillot, Emmanuel, Macklin, Paul, Calzone, Laurence, Noël, Vincent, "Building multiscale models with PhysiBoSS, an agent-based modeling tool", Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae509 DOI : 10.1093/bib/bbae509

References

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." Bioinformatics 35, no. 7 (2019): 1188-1196.
DOI : 10.1093/bioinformatics/bty766

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." npj Systems Biology and Applications 9, no. 1 (2023): 54.
DOI : 10.1038/s41540-023-00314-4

GitHub repo

PhysiBoSS is open-source, under the BSD-3 clause license, and is available on GitHub: https://github.com/PhysiBoSS/PhysiBoSS

Sponsors

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).