article

A Framework for Three-Dimensional Simulation of Morphogenesis

Authors:

Trevor M. Cickovski,

Chengbang Huang,

Rajiv Chaturvedi,

H. George E. Hentschel,

James A. Glazier,

Stuart A. Newman,

Jesus A. IzaguirreAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 2, Issue 4

Pages 273 - 288

https://doi.org/10.1109/TCBB.2005.46

Published: 01 October 2005 Publication History

Abstract

We present CompuCell3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. CompuCell3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. CompuCell3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have verified CompuCell3D by building a model of growth and skeletal pattern formation in the avian (chicken) limb bud. Binaries and source code are available, along with documentation and input files for sample simulations, at http://compucell.sourceforge.net.

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A Framework for Three-Dimensional Simulation of Morphogenesis

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cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 2, Issue 4

October 2005

112 pages

ISSN:1545-5963

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IEEE Computer Society Press

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Published: 01 October 2005

Published in TCBB Volume 2, Issue 4

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Ben Youssef B(2015)A parallel cellular automata algorithm for the deterministic simulation of 3-D multicellular tissue growthCluster Computing10.1007/s10586-015-0455-718:4(1561-1579)Online publication date: 1-Dec-2015
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Cickovski TAras KSwat MMerks RGlimm THentschel HAlber MGlazier JNewman SIzaguirre J(2007)From Genes to Organisms Via the CellComputing in Science and Engineering10.1109/MCSE.2007.749:4(50-60)Online publication date: 1-Jul-2007
https://dl.acm.org/doi/10.1109/MCSE.2007.74
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