Table 1.

An overview of (I) articles that present computational models of organoid systems and (II) access information of software frameworks mentioned for agent-based models.

I. Overview of in silico organoid models
Model type	Basis of the model	Author/references	Simulated cell types	Software	Space	Model outcome	Figure ref.
Agent-based model	Intestinal organoid	Buske et al., 2012	Undifferentiated, Paneth, enterocyte, goblet cells	CGAL	3D	Provides an analysis of the biomechanical impact alongside with Wnt and Notch signaling dynamics in the spatiotemporal organization of intestinal organoids	Figure 1A
		Langlands et al., 2016	Stem cells and Paneth cells	CHASTE	2D	Presents a biomechanical analysis of the Paneth cells’ role in the production of crypt fission	Figure 1B
		Almet el al., 2018	Hard and soft cells	CHASTE	2D	Analyzes the biomechanical properties of hard cells and soft cells and the required population proportions to produce crypt fission	Figure 1B
		Thalheim et al., 2018	Stem, Paneth, goblet, and enterocyte cells	CGAL	3D	Explores the growth pattern of intestinal organoids produced by Wnt and Notch signaling dynamics and attempts to simulate a cyst-like growth pattern	Figure 1A
	Optic-cup organoid	Okuda et al., 2018a	Embryonic stem cells (ESCs)	Custom C++ software	3D	Describes the effect that individual-cell mechanical forces have in the formation of the optic cup by performing in vitro and in silico experimentation	Figure 1C
Equation-based model	Intestinal organoid	Yan et al., 2018	Stem, committed progenitor, terminally differentiated and dead cells	MATLAB	3D	Investigates the growth patterns and spatial distributions of cell populations in the presence of exogenous substances such as Wnt, BMP, and HGF	Figure 1D
	Cerebral organoid	McMurtrey, 2016	Metabolic active brain cells	MATLAB	3D	Examines diverse diffusion models to test and predict growth patterns of cerebral organoids	Figure 1E
		Berger et al., 2018	Human neuroepithelial stem cells (NESCs)	COMSOL Multiphysics 4.3	3D	Introduces a computational model of oxygen transport and consumption in midbrain-specific organoids	Figure 1F
	Gastruloids	Etoc et al., 2016	Human ESCs (hESCs)	MATLAB	2D	Presents a model based on the dynamics of BMP4, pSMAD1, NOGGIN, and receptor re-localization to determine the micropatterns produced in gastruloids	Figure 1G
		Tewary et al., 2017	Human pluripotent stem cells (hPSCs)	MATLAB	2D	Develops a reaction-diffusion model of BMP4 and NOGGIN dynamics and complements it with a positional information system to study the fate patterning of gastruloids	Figure 1H
II. Agent-based software frameworks
Framework		Author/reference				Access
CGAL		Fabri et al., 2000				https://www.cgal.org/
CellSys		Hoehme and Drasdo, 2010				http://msysbio.com/software/cellsys
CHASTE		Mirams et al., 2013; Pitt-Francis et al., 2009				http://www.cs.ox.ac.uk/chaste
CompuCell3D		Swat et al., 2012				http://www.compucell3d.org
MecaGen		Delile et al., 2014				https://github.com/juliendelile/MECAGEN
EmbryoMaker		Marin-Riera et al., 2016				http://www.biocenter.helsinki.fi/salazar/software.html
PhysiCell		Ghaffarizadeh et al., 2018				http://PhysiCell.MathCancer.org
PhisiBoSS		Letort et al., 2018				https://github.com/sysbio-curie/PhysiBoSS
ya||a		Germann et al., 2019				https://github.com/germannp/yalla