CompuCell is a software framework for multimodel simulations of biocomplexity problems. It has been developed as an ongoing project for the Interdisciplinary Center for the study of Biocomplexity at the university of Notre Dame (http://www.nd.edu/~icsb/). By biocomplexity we mean the study of complex structures and behaviors that arise from the interaction of biological (biophysical!) entities (molecules, cells, organisms). The complex interplay of physical and chemical processes give rise to a great variety of spatial and temporal structures, resulting in rich complexity of even the simplest biological phenomena.
CompuCell currently uses a combination of "extended Potts model" for cell sorting and clustering, and "Schnakenberg Reaction Diffusion" equations to establish the underlying chemical field to which cells respond and form typical patterns found in such biological systems as a growing chicken limb. All the examples shown have been computed and displayed using CompuCell and/or the external CompuCell3D visualization engine.
(Written: July 2, 2002, by Rajiv Chaturvedi: rchaturv@nd.edu)
Download
Solaris (.tar file)
Windows (.msi file)
Example Input Files (.zip format)
Documentation
Below are some helpful resources related to CompuCell.
- Overview of the Actual Keywords, Default Values and Types (TEXT) (Trevor M. Cickovski)
- User Guide 1.6 Beta : CompuCell: A Software Framework For Multimodel Simulations Of Biocomplexity Problems (PS) (PDF) (HTML) (Jesus A. Izaguirre, Rajiv Chaturvedi, Trevor M. Cickovski and Chengbang Huang)
- A Front End Design For Simulation Engines (PS) (PDF) (HTML) (Jesus A. Izaguirre with Trevor M. Cickovski)
- Design Document For CompuCell and BioLogo (PS) (PDF) (HTML) (Jesus A. Izaguirre with Trevor M. Cickovski)
2D Examples
Gamma:
2 steps |
Gamma:
3 steps |
Gamma:
linear |
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Fibronectin
Simulations |
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Moving
Potts Simulations |
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| CompuCell1.5
100 Cells |
CompuCell1.6
100 Cells |
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Configuration |
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2-D
Simulation with Fibronectin and Mitosis |
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2D Movies
Fibronectin Movie #1
Fibronectin Movie #2
Moving potts with Boundary - 100 cells
2-D simulation with Fribronectin and mitosis (initial height: one 6th of total)
Questions? Please Contact Us!
CompuCell Team
Laboratory for Computational Life Sciences
Department of Computer Science and Engineering
University of Notre Dame
325 Fitzpatrick Hall of Engineering
Notre Dame, Indiana 46556 USA
compucell@cse.nd.edu
Acknowledgments
This research is supported in part by
a National Science Foundation Biocomplexity
grant PHY-0083653
a National Science Foundation ACI CAREER
award ACI 01-35195
an Arthur J. Schmitt Fellowship
and the Center For Applied Mathematics at
the University of Notre Dame
This page is maintained by Trevor Cickovski
Last update: 6/29/2004