CompuCell, a multi-model framework for simulation of morphogenesis Article

Izaguirre, JA, Chaturvedi, R, Huang, C et al. (2004). CompuCell, a multi-model framework for simulation of morphogenesis . 20(7), 1129-1137. 10.1093/bioinformatics/bth050

cited authors

  • Izaguirre, JA; Chaturvedi, R; Huang, C; Cickovski, T; Coffland, J; Thomas, G; Forgacs, G; Alber, M; Hentschel, G; Newman, SA; Glazier, JA

fiu authors

abstract

  • Motivation: 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. © Oxford University Press 2004; all rights reserved.

publication date

  • May 1, 2004

Digital Object Identifier (DOI)

start page

  • 1129

end page

  • 1137

volume

  • 20

issue

  • 7