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Building multiscale models with PhysiBoSS, an agent-based modeling tool.

Marco Ruscone^1,2,3, Andrea Checcoli^4,5, Randy Heiland⁶

¹Institut Curie, Université PSL, 26 rue d'Ulm, 75005, Paris, France.

Briefings in Bioinformatics

|October 19, 2024

Summary

This summary is machine-generated.

Multiscale models simulate biological processes across scales. The PhysiBoSS framework, integrated with PhysiCell Studio, simplifies creating these complex computational models for broader scientific accessibility.

Keywords:

Boolean modeling agent-based modeling multiscale modeling

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Area of Science:

Computational Biology
Systems Biology
Biophysics

Background:

Multiscale models analyze complex biological processes across spatial and temporal scales.
These models simulate intracellular (e.g., signaling) and extracellular (e.g., cell communication) events.
Applications include understanding complex diseases, tissue-immune interactions, and therapeutic strategies.

Purpose of the Study:

To simplify the construction of complex multiscale biological models.
To introduce the PhysiBoSS framework, an extension of PhysiCell.
To demonstrate the use of PhysiCell Studio for easier model development.

Main Methods:

Utilized the PhysiBoSS framework, integrating continuous time Boolean models for intracellular processes with agent-based modeling.
Employed PhysiCell Studio, a graphical user interface for PhysiCell, to streamline model construction.
Developed three example multiscale models using this integrated approach.

Main Results:

Demonstrated a simplified workflow for building multiscale biological models.
Showcased the integration of intracellular Boolean models with agent-based simulations via PhysiBoSS.
Provided accessible tutorials and model repositories for users.

Conclusions:

PhysiBoSS and PhysiCell Studio significantly lower the barrier to entry for creating sophisticated multiscale biological models.
This approach enhances accessibility for non-experts and efficiency for advanced users.
Facilitates broader application of multiscale modeling in biological research and disease study.