title: Multi-scale modeling of tissues using CompuCell3D.
abstract: The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. This tutorial introduces the lattice-based Glazier-Graner-Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi-cellular behaviors in the context of tissue formation and subsequent dynamics. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D.
authors.affiliation: Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, Indiana, USA.
authors.forename: Maciej H
authors.initials: MH
authors.lastname: Swat
authors.forename: Gilberto L
authors.initials: GL
authors.lastname: Thomas
authors.forename: Julio M
authors.initials: JM
authors.lastname: Belmonte
authors.forename: Abbas
authors.initials: A
authors.lastname: Shirinifard
authors.forename: Dimitrij
authors.initials: D
authors.lastname: Hmeljak
authors.forename: James A
authors.initials: JA
authors.lastname: Glazier
mesh_terms: D000465:Algorithms; D002448:Cell Adhesion; D016923:Cell Death; D002465:Cell Movement; D049109:Cell Proliferation; D002633:Chemotaxis; D003198:Computer Simulation; D061307:Human Umbilical Vein Endothelial Cells / Q000166:cytology / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D009010:Monte Carlo Method; D009383:Neoplasms, Vascular Tissue / Q000098:blood supply* / Q000473:pathology; D009389:Neovascularization, Pathologic; D012984:Software; D013816:Thermodynamics; D023822:Tissue Engineering; D042461:Vascular Endothelial Growth Factor A / Q000378:metabolism
chemical_list: D042461:Vascular Endothelial Growth Factor A