title: CompuCell, a multi-model framework for simulation of morphogenesis.
abstract: BACKGROUND
  CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning.
  
  
  RESULTS
  We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud.
  
  
  BACKGROUND
  Binaries and source code for Microsoft Windows, Linux and Solaris are available for download from http://sourceforge.net/projects/compucell/
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. compucell@cse.nd.edu
authors.forename: J A
authors.initials: JA
authors.lastname: Izaguirre
authors.forename: R
authors.initials: R
authors.lastname: Chaturvedi
authors.forename: C
authors.initials: C
authors.lastname: Huang
authors.forename: T
authors.initials: T
authors.lastname: Cickovski
authors.forename: J
authors.initials: J
authors.lastname: Coffland
authors.forename: G
authors.initials: G
authors.lastname: Thomas
authors.forename: G
authors.initials: G
authors.lastname: Forgacs
authors.forename: M
authors.initials: M
authors.lastname: Alber
authors.forename: G
authors.initials: G
authors.lastname: Hentschel
authors.forename: S A
authors.initials: SA
authors.lastname: Newman
authors.forename: J A
authors.initials: JA
authors.lastname: Glazier
mesh_terms: D000818:Animals; D001842:Bone and Bones / Q000196:embryology; D002450:Cell Communication / Q000502:physiology; D002455:Cell Division / Q000502:physiology; D002465:Cell Movement / Q000502:physiology*; D002468:Cell Physiological Phenomena; D002642:Chick Embryo; D002645:Chickens; D003198:Computer Simulation; D005552:Forelimb / Q000196:embryology / Q000502:physiology; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D009024:Morphogenesis / Q000502:physiology*; D012984:Software; D018511:Systems Integration