A framework for three-dimensional simulation of morphogenesis

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

doi:10.1109/TCBB.2005.46

A framework for three-dimensional simulation of morphogenesis

IEEE/ACM Trans Comput Biol Bioinform. 2005 Oct-Dec;2(4):273-88. doi: 10.1109/TCBB.2005.46.

Authors

Trevor M Cickovski¹, Chenbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H George E Hentschel, Mark S Alber, James A Glazier, Stuart A Newman, Jesús A Izaguirre

Affiliation

¹ Laboratory for Computational Life Sciences, Department of Computer Science and Engineering, University of Notre Dame, 325 Cushing Hall, Notre Dame, IN 46556, USA. tcickovs@nd.edu

PMID: 17044166
DOI: 10.1109/TCBB.2005.46

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Cell Physiological Phenomena
Chick Embryo
Chickens
Chondrogenesis
Computer Simulation*
Computing Methodologies
Database Management Systems
Energy Metabolism
Forelimb / cytology
Forelimb / embryology
Forelimb / physiology
Models, Biological*
Morphogenesis*
Programming Languages
User-Computer Interface