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

James A. Glazier

Biocomplexity Institute and Department of Physics

While the bioinformatics
of DNA sequences, the reaction kinetics of biomolecular networks and
continuum pattern formation are all the targets of intensive research
efforts, cell-level modeling is still relatively undeveloped, even
though the cell is a wonderful tool for hiding biological complexity.
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 the *Dictyostelium discoideum* life cycle. I will also
discuss some of the key mathematical and computational issues which
GGH models and modeling environments still need to address.