Computational Modeling of Biological Development

The patterns of gene expression are only part of the complex set of processes that govern the formation of tissue structures during embryonic development. Cells need to differentiate and to migrate long distances through tissues. How do they know what to become and where to go? Cells secrete and follow gradients of diffusible chemicals (chemotaxis) and secrete non-diffusing extracellular matrix. In addition, variable adhesion molecules expressed on cells' surfaces help them to form coherent structures by differential adhesion. CompuCell is a public domain modeling environment which implements a simple, energy minimization framework to describe these and related morphogenetic processes. One attractive feature of this approach is that it can interface at small length scales with increasingly sophisticated models for genetic regulation and biochemistry inside individual cells and at large length scales with continuum Partial Differential Equation and Finite Element models. We provide examples of how this method applies to problems including the development of the bone structure in the avian wing, the life cycle of the simple organism, \textit{Dictyostelium discoideum} and to vascular development and show how it ``postdicts'' the results of VE-cadherin knock-out experiments on \textit{in vitro }vasculogenesis experiments.