CompuCell is a software framework for multimodel simulations of biocomplexity problems. It has been developed as an ongoing project for the Interdisciplinary Center for the study of Biocomplexity at the University of Notre Dame. By biocomplexity we mean the study of complex structures and behaviors that arise from the interaction of biological (biophysical!) entities (molecules, cells, organisms). The complex interplay of physical and chemical processes give rise to a great variety of spatial and temporal structures, resulting in rich complexity of even the simplest biological phenomena. CompuCell currently uses a combination of "extended Potts model" for cell sorting and clustering, and "Reaction Diffusion" equations to establish the underlying chemical field to which cells respond and form typical patterns found in such biological systems as a growing chicken limb. (from the Notre Dame CompuCell site)
Tissue Simulation Toolkit (TST)TST Homepage
Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.
“Polyworld is one of the earliest and one of the most sophisticated artificial worlds developed to study Artificial Life and Artificial Intelligence, using computational genetics, physiology, metabolism, neural networks, learning, vision, and behavior.” (from SourceForge.net PolyWorld site)