Modeling Complexity of Biological Systems approaches, challenges and partial answers. Multi-cell modeling with CompuCell3D

Maciej Swat (mswat@indiana.edu), Biocomplexity Institute, Indiana University

Mathematical modeling and computer simulation have become crucial to biological fields from genomics to ecology. However, multi-cell, 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. Biologically relevant simulations should capture key cell-level behaviors, providing a phenomenological description of cell interactions without requiring prohibitively detailed molecular-level simulations of the internal state of each cell. While an understanding of cell biology, biochemistry, genetics, etc. is essential for building useful, predictive simulations, the hardest part of simulation building is identifying and quantitatively describing appropriate subsets of this knowledge. In the excitement of discovery, scientists often forget that modeling and simulation, by definition, require simplification of reality. In this talk I will present Glazier Graner Hogeweg (GGH) model and its applications to study and model multi-cell biological phenomena ranging from developmental biology (gastrulation, somitogenesis) to entire life cycle of simple organisms (Dictyostelium discoideum). I will also present CompuCell3D a modeling framework for building and running GGH simulations.