A framework for three-dimensional simulation of morphogenesis

Author

Cickovski, Trevor M. ; Huang, Chengbang ; Chaturvedi, Rajiv ; Glimm, Tilmann ; Hentschel, H.George E. ; Alber, Mark S. ; Glazier, James A. ; Newman, Stuart A. ; Izaguirre, Jesús A.

Author_Institution

Dept. of Comput. Sci., Notre Dame Univ., IN, USA

Volume

2

Issue

4

fYear

2005

Firstpage

273

Lastpage

288

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.

Keywords

biology computing; cellular biophysics; physiological models; source coding; COMPUCELL3D; avian limb bud; binaries; cell clustering; cell growth; chemical fields; documentation; source code; three-dimensional morphogenesis simulation; Biological information theory; Biological system modeling; Biology computing; Cells (biology); Chemicals; Computational modeling; Mathematical model; Organisms; Shape; XML; Cellular Potts Model (CPM); Extensible Markup Language (XML).; biological development; cellular automata; morphogenesis; reaction-diffusion; Animals; Cell Physiology; Chick Embryo; Chickens; Chondrogenesis; Computer Simulation; Computing Methodologies; Database Management Systems; Energy Metabolism; Forelimb; Models, Biological; Morphogenesis; Programming Languages; User-Computer Interface;

fLanguage

English

Journal_Title

Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Publisher

ieee

ISSN

1545-5963

Type

jour

DOI

10.1109/TCBB.2005.46

Filename

1541981