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Bioinformatics Advance Access published online on February 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth050
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received March 12, 2003
Revised August 5, 2003
Accepted August 29, 2003

Article

COMPUCELL, a multi-model framework for simulation of morphogenesis

J. A. Izaguirre 1*, R. Chaturvedi 1, C. Huang 1, T. Cickovski 1, J. Coffland 1, G. Thomas 2, G. Forgacs 3, M. Alber 4, G. Hentschel 5, S. A. Newman 6, J. A. Glazier 7

1 Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
2 Department of Physics, University of Notre Dame, Notre Dame, IN 46556
3 Department of Physics and Biology, University of Missouri, Columbia, MO 65211
4 Department of Mathematics, University of Notre Dame, Notre Dame, IN 46556
5 Department of Physics, Emory University, Atlanta, GA 30332
6 Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595
7 Departments of Physics and Biology and Biocomplexity Institute, Indiana University, Bloomington, IN 47405

* To whom correspondence should be addressed. E-mail: izaguirr{at}cse.nd.edu.


  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.

Availability: Binaries and source code for Microsoft Windows, Linux, and Solaris are available for download from http://sourceforge.net/projects/compucell/


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