BioLogo, a Domain-Specific Language for Morphogenesis

Morphogenesis governs the clustering and pattern formation of embryonic cells into bone and organs. Many of the patterning instabilities that result from cell interaction with membrane bound chemicals can be described by mathematical models. One such known model is the Cellular Potts Model, which has been incorporated into the three-dimensional C++ framework CompuCell3D. CompuCell3D uses various design patterns to address the issues of speed, flexibility and memory consumption, and allow for extensibility of the framework through dynamically loaded plugin libraries. BioLogo is a domain-specific language (DSL) which we use to provide a higher level of abstraction to the framework with understandable syntax for morphogenesis researchers, further improving extensibility of the software. Finally, we validate BioLogo and CompuCell3D using three simulations representative of morphogenesis modeling.