Multi-Scale Modeling of Tissues Using CompuCell3D
By M. Swat, G. L. Thomas, J. Belmonte, A. Shirinifard, Dimitrij Hmeljak, James A. Glazier. Methods in Cell Biology, 2012
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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.
Subfields: Cell Biology, Modeling and Simulation, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/2a15d1ee8205ea3c4179f890fb567861d6e3c758
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Citations in the corpus
- A Review of Cell-Based Computational Modeling in Cancer Biology (2019, methodology): “35,36 VCell can simulate reacting fl ows of many proteins within a single detailed cell, 32,33 and many modeling packages (eg, Chaste, 37 CompuCell3D, 38 and EPISIM 39 ) support systems biology markup language (SBML) to include systems of ODEs that simulate molecular effects in individual cells.”
- PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems (2017, methodology): “CompuCell3D [7] and Morpheus [8] use Cellular Potts methods to simulate cells and their morphologies.”
- Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology (2014, background): “Currently available modeling environments typically require programming or scripting to account for dynamical feedback between submodels at different scales (Andasari et al. , 2012; Mirams et al. , 2013; Swat et al. , 2012).”