title: A framework for three-dimensional simulation of morphogenesis.
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.
authors.affiliation: 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
authors.forename: Trevor M
authors.initials: TM
authors.lastname: Cickovski
authors.forename: Chenbang
authors.initials: C
authors.lastname: Huang
authors.forename: Rajiv
authors.initials: R
authors.lastname: Chaturvedi
authors.forename: Tilmann
authors.initials: T
authors.lastname: Glimm
authors.forename: H George E
authors.initials: HG
authors.lastname: Hentschel
authors.forename: Mark S
authors.initials: MS
authors.lastname: Alber
authors.forename: James A
authors.initials: JA
authors.lastname: Glazier
authors.forename: Stuart A
authors.initials: SA
authors.lastname: Newman
authors.forename: Jesús A
authors.initials: JA
authors.lastname: Izaguirre
mesh_terms: 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