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Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment

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Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 500))

Summary

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.

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Notes

  1. 1.

    Because of lattice discretization and the option of defining long-range neighborhoods, the surface area of a cell scales in a non-Euclidian, lattice-dependent manner with cell volume, i.e., (see ref. 61 on bubble growth).

  2. 2.

    In the text, we denote XML, CC3DML, and Python code using the Courier font. In listings presenting syntax, user-supplied variables are given in italics. Broken-out listings are boxed. Punctuation at the end of boxes is implicit.

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Acknowledgments

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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Swat, M., Hester, S., Balter, A., Heiland, R., Zaitlen, B., Glazier, J. (2009). Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment. In: Maly, I. (eds) Systems Biology. Methods in Molecular Biology, vol 500. Humana Press. https://doi.org/10.1007/978-1-59745-525-1_13

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