Multi-Cell Modeling of Biological Development using the GGH Model and CompuCell3D—Applications, Technology and Open Problems

James A. Glazier, Biocomplexity Institute and Department of Physics
Indiana University
727 E 3rd Street, Swain Hall West 159
Bloomington, IN 47405-7105

While the bioinformatics of DNA sequences, the reaction kinetics of biomolecular networks and continuum pattern formation are all the targets of intensive research efforts, multi-cell modeling is still relatively undeveloped, even though the cell is a wonderful tool for hiding the complexity of biochemical networks. One of the key reasons for this neglect has been the lack of any widely accepted modeling approaches and of ways to describe models compactly. A growing community of modelers employs the GGH (aka CPM) Model to create sophisticated cell-level simulations of tissue development. The availability of new, open-source tools for building GGH models makes developing, validating and sharing such simulations much easier and makes model definition much more compact. I will introduce the GGH and the modeling environment CompuCell3D, which we have created to simplify writing developmental simulations (https://simtk.org/home/compucell3d). I will illustrate the application of the GGH to modeling somitogenesis in vivo, angiogenesis and vasculogenesis in vitro (see picture) and will also discuss modeling of other developmental phenomena including tumor growth, gastrulation, and biofilms. I will also discuss some of the key mathematical and computational issues which GGH models and modeling environments still need to address.