CompuCell3D (CC3D) is an open source software problem solving environment for constructing two- and three-dimensional multiscale agent-based models of multicellular biology, including morphogenesis, homeostasis, disease, therapy and tissue engineering. CompuCell3D was designed to make the development, execution and analysis of complex biological models accessible to non-experts. CompuCell3D is written in C++ and Python. CC3D supports a number of different object classes and modeling methodologies including the Cellular Potts model (CPM) or Glazier-Graner-Hogeweg model (GGH) of the dynamic reorganization of generalized cells which can model cell clustering, growth, division, death, adhesion, and volume and surface area constraints; as well as partial differential equation solvers for modeling the diffusion equation and reaction–diffusion of chemical fields, and biochemical transport, signaling, regulatory and metabolic networks solved with chemical kinetics rate equations or stochastic Boolean network approaches. By integrating these submodels CompuCell3D enables modeling of cellular reactions to external chemical fields such as secretion or resorption, and responses such as chemotaxis and haptotaxis, differentiation in response to external signals, cell polarization and motility and other basic biological mechanisms.
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