A framework for three-dimensional simulation of morphogenesis.
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.
Cickovski
Trevor M
TM
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
Huang
Chenbang
C
Chaturvedi
Rajiv
R
Glimm
Tilmann
T
Hentschel
H George E
HG
Alber
Mark S
MS
Glazier
James A
JA
Newman
Stuart A
SA
Izaguirre
Jesús A
JA
D000818:Animals; D002468:Cell Physiological Phenomena; D002642:Chick Embryo; D002645:Chickens; D020219:Chondrogenesis; D003198:Computer Simulation; D003205:Computing Methodologies; D003628:Database Management Systems; D004734:Energy Metabolism; D005552:Forelimb / Q000166:cytology / Q000196:embryology / Q000502:physiology; D008954:Models, Biological; D009024:Morphogenesis; D011381:Programming Languages; D014584:User-Computer Interface