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Everything about CompuCell3D

Biology software

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. {{Infobox connector Wikipedia →

🧭 Start here: a 6-step reading path

  1. Read the overview: CompuCell3DA 5-minute orientation
  2. Pick up a classic book: Systems biologyThe most-reprinted book on the subject
  3. Read the landmark paper: Integrating Intracellular Dynamics Using CompuCell3D and Bionetsolver: Applications to Multiscale Modelling of Cancer Cell Growth and InvasionCited 66 times
  4. Go sideways: Cellular Potts modelA closely related topic
  5. Go sideways: James A. GlazierA closely related topic

đź“– Definitions

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🗂️ The subject at a glance

  1. History of CompuCell3D
  2. Algorithms
  3. Model Definition and Scripting
  4. Model Execution Support
  5. Extensibility
  6. Applications
  7. Support for Learning CompuCell3D

🏆 Landmark papers (most cited)

đź“š Books worth reading

Ranked by number of editions on Open Library, a rough measure of how lasting a book is.

đź”— Related topics