CompuCell3D (CC3D) is a three-dimensional C++ and Python software

problem solving environment A problem solving environment (PSE) is a completed, integrated and specialised computer software for solving one class of problems, combining automated problem-solving methods with human-oriented tools for guiding the problem resolution. A PSE may a ...

for simulations of biocomplexity problems, integrating multiple mathematical orphogenesismodels. These include the

cellular Potts model In computational biology, a Cellular Potts model (CPM, also known as the Glazier-Graner-Hogeweg model) is a computational model of cells and tissues. It is used to simulate individual and collective cell behavior, tissue morphogenesis and cancer de ...

(CPM) which can model cell clustering, growth, division, death, adhesion, and volume and surface area constraints; as well as partial differential equation solvers for modeling reaction–diffusion of external chemical fields and cell type automata for differentiation. By integrating these models CompuCell3D enables modeling of cellular reactions to external chemical fields such as

secretion 440px Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classical ...

resorption Resorption is the absorption of cells or tissue into the circulatory system, usually by osteoclasts. Types of resorption include: * Bone resorption * Herniated Disc Resorption * Tooth resorption * Fetal resorption * Blood resorption See also ...

, and responses such as

chemotaxis Chemotaxis (from '' chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemica ...

and

haptotaxis Haptotaxis (from Greek ἅπτω (hapto, "touch, fasten") and τάξις (taxis, "arrangement, order")) is the directional motility or outgrowth of cells, e.g. in the case of axonal outgrowth, usually up a gradient of cellular adhesion sites or sub ...

. CompuCell3D is conducive for experimentation and testing biological models by providing a flexible and extensible package, with many different levels of control. High-level steering is possible through CompuCell Player, an interactive GUI built upon Qt threads which execute in parallel with the computational back end. Functionality such as zooming, rotation, playing and pausing simulations, setting colors and viewing cross sections is available through the player, with a sample screenshot shown below. Extending the back end is possible through an XML-based

domain-specific language A domain-specific language (DSL) is a computer language specialized to a particular application domain. This is in contrast to a general-purpose language (GPL), which is broadly applicable across domains. There are a wide variety of DSLs, ranging f ...

Biologo, which after lexical analysis and generation transparently converts to C++ extensions which can be compiled and dynamically loaded at runtime. The back end uses object-oriented

design pattern A design pattern is the re-usable form of a solution to a design problem. The idea was introduced by the architect Christopher Alexander and has been adapted for various other disciplines, particularly software engineering. The " Gang of Four" b ...

s which contribute to extensibility, reducing coupling between independently operating modules. Optional functionality can be encapsulated through plugins, which are dynamically loaded at runtime through an XML configuration file reference. CompuCell3D can model several different phenomena, including avian limb development, ''in vitro'' capillary development, adhesion-driven cell sorting,

Dictyostelium discoideum ''Dictyostelium discoideum'' is a species of soil-dwelling amoeba belonging to the phylum Amoebozoa, infraphylum Mycetozoa. Commonly referred to as slime mold, ''D. discoideum'' is a eukaryote that transitions from a collection of unicellular ...

, and fluid flows. The binaries and source code, as well as documentation and examples, are available at th
CompuCell3D Website
For a list of more than 150 publications that used CompuCell3D please visit th
CompuCell3D Publications page

References

{{reflist Systems biology Scientific simulation software