CompuCell3D

<p>CompuCell3D (CC3D) is an <a href="/facts/Open_source/7X9rCdz4">open source</a> software <a href="/facts/Problem_solving_environment/26VDzFAt">problem solving environment</a> for constructing two- and three-dimensional multiscale <a href="/facts/Agent-based_model/C3C1vR8s">agent-based models</a> of multicellular biology, including <a href="/facts/Morphogenesis/zHJh8Eae">morphogenesis</a>, <a href="/facts/Homeostasis/rloTGAHa">homeostasis</a>, 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 <a href="/facts/C%252B%252B/Et0F2qn9">C++</a> and <a href="/facts/Python_(programming_language)/YbuGqofa">Python</a>. CC3D supports a number of different object classes and modeling methodologies including the <a href="/facts/Cellular_Potts_model/HymsL8za">Cellular Potts model</a> (CPM) or Glazier-Graner-Hogeweg model (GGH) (originally developed by <a href="/facts/James_A._Glazier/4LCRvpFv">James A. Glazier</a>,  François Graner and <a href="/facts/Paulien_Hogeweg/foW6mKqA">Paulien Hogeweg</a>) of the dynamic reorganization of generalized cells (clusters of cells, volumes of <a href="/facts/Extracellular_matrix/kaHC5Ez8">extracellular matrix</a> (ECM), cells and their subregions) 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 <a href="/facts/Diffusion_equation/l3CUuLqF">diffusion equation</a> and <a href="/facts/Reaction%25E2%2580%2593diffusion/deqI4VAP">reaction–diffusion</a> of chemical fields, and biochemical transport, signaling, regulatory and metabolic networks solved with <a href="/facts/Chemical_kinetics/D8vyX4aE">chemical kinetics</a> <a href="/facts/Rate_equation/VK18zUhN">rate equations</a> or stochastic <a href="/facts/Boolean_network/JzhgfKvm">Boolean network</a> approaches. By integrating these submodels CompuCell3D enables modeling of cellular reactions to external chemical fields such as <a href="/facts/Secretion/VHk9eLAV">secretion</a> or <a href="/facts/Resorption/PsQIN5TA">resorption</a>, and responses such as <a href="/facts/Chemotaxis/hYPRdPTk">chemotaxis</a> and <a href="/facts/Haptotaxis/BREVThUX">haptotaxis</a>, <a href="/facts/Differentiation/bj0KjhDe">differentiation</a> in response to external signals, cell polarization and motility and other basic biological mechanisms.
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CompuCell3D open-in-new

CompuCell3D