Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment

  • Maciej H. Swat
  • Susan D. Hester
  • Ariel I. Balter
  • Randy W. Heiland
  • Benjamin L. Zaitlen
  • James A. GlazierEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 500)


Mathematical modeling and computer simulation have become crucial to biological fields from genomics to ecology. However, multicell, tissue-level simulations of development and disease have lagged behind other areas because they are mathematically more complex and lack easy-to-use software tools that allow building and running in silico experiments without requiring in-depth knowledge of programming. This tutorial introduces Glazier—Graner—Hogeweg (GGH) multicell simulations and CompuCell3D, a simulation framework that allows users to build, test, and run GGH simulations.


Glazier—Graner—Hogeweg model GGH CompuCell3D Mitosis Cell growth Cell sorting Chemotaxis Multicell modeling Tissue-level modeling Developmental biology Computational biology 



We gratefully acknowledge support from the National Institutes of Health, National Institute of General Medical Sciences, grants 1R01 GM077138–01A1 and 1R01 GM076692-01, and the Office of Vice President for Research, the College of Arts and Sciences, the Pervasive Technologies Laboratories and the Biocomplexity Institute at Indiana University. Indiana University's University Information Technology Services provided time on their BigRed clusters for simulation execution. Early versions of CompuCell and CompuCell3D were developed at the University of Notre Dame by J.A.G., Dr. Mark Alber and Dr. Jesus Izaguirre and collaborators with the support of National Science Foundation, Division of Integrative Biology, grant IBN-00836563. Since the primary home of CompuCell3D moved to Indiana University in 2004, the Notre Dame team have continued to provide important support for its development.


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Copyright information

© Humana Press 2009

Authors and Affiliations

  • Maciej H. Swat
  • Susan D. Hester
  • Ariel I. Balter
  • Randy W. Heiland
  • Benjamin L. Zaitlen
  • James A. Glazier
    • 1
    Email author
  1. 1.Biocomplexity Institute and Department of PhysicsIndiana UniversityBloomingtonUSA

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