CompuCell3D
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| Stable release | 4.2.4.3
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| Repository | |
| Written in | C++ and Python |
| Website | https://compucell3d.org/ |
CompuCell3D[1] (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) (originally developed by James A. Glazier, François Graner and Paulien Hogeweg) of the dynamic reorganization of generalized cells (clusters of cells, volumes of extracellular matrix, 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 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.
Model Definition and Scripting
[edit]Users can rapidly define highly complex simulations using the CompuCell3D Markup [XML] language, CC3DML and Python scripts called steppables. CompuCell3D provides high-level Python classes and functions based on common biological processes to simplify the development of modular, reusable and compact model specifications. Users can also write C++ steppables to improve execution speed.
CompuCell3D includes a GUI model editor, Twedit++ which provides a model specification Wizard for rapid definition of model architectures as well as customized editors for CC3DML, Python and C++ which contains code-snippet templates for most commonly used functions.
Model Execution Support
[edit]CompuCell3D supports exploration and testing of 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 desktop GUI built upon Qt threads which execute in parallel with the computational back end. Player provides functionality such as playing and pausing simulations, changing parameter values during execution (steering) and the on-the-fly creation of two-dimensional and three-dimensional rendering windows showing cell configurations and chemical fields. Users can interactively zoom, rotate and change the color and cross-sections for rendered images, define movie exports and save screenshots and rotation of rendered images of the simulation geometry, set colors and viewing cross sections. A sample screenshot is shown below.
CompuCell3D also can be run in batch mode on clusters and as a callable Python library in Jupyter Notebook, Colab or other Python environments.
Extensibility
[edit]Extending the back end is possible with C++ extensions in the form of steppables and plugins. The back end uses object-oriented design patterns 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.
As a Python library, CompuCell3D can call and be called by other modeling tools and frameworks.
Applications
[edit]CompuCell3D is used extensively across a broad range of biological and biomedical research fields, including developmental biology, developmental toxicity, cancer biology, toxicology, immunology, and tissue engineering. Its applications include modeling tumor growth and metastasis, angiogenesis and vasculogenesis, liver toxicity[2] and metabolism,[3] immune cell dynamics, and developmental processes such as limb morphogenesis and tissue patterning, encompassing mechanisms and phenomena such as somitogenesis,[4] gastrulation, neurulation, branching morphogenesis (e.g., lung, kidney, salivary glands), chondrogenesis, cell sorting, vascular network formation, stem cell differentiation, collective cell migration, morphogen gradient establishment, and regeneration processes. CompuCell3D integrates multicellular simulations with intracellular signaling, biomechanical interactions, and reaction-diffusion models, enabling researchers to explore complex biological phenomena across multiple scales. The software's flexibility and Python-based scripting facilitate integration with experimental data, driving insights into disease mechanisms, including the prediction of adverse outcomes and applications in risk science to evaluate disease progression, drug dosimetry and therapeutic responses.
For a list of more than 150 publications that used CompuCell3D please visit the CompuCell3D Publications page.
See also
[edit]References
[edit]- ^ Swat, Maciej H.; Thomas, Gilberto L.; Belmonte, Julio M.; Shirinifard, Abbas; Hmeljak, Dimitrij; Glazier, James A. (2012). Multi-Scale Modeling of Tissues Using CompuCell3D. Methods in Cell Biology. Vol. 110. pp. 325–366. doi:10.1016/B978-0-12-388403-9.00013-8. ISBN 9780123884039. PMC 3612985. PMID 22482955.
- ^ Sluka, James P.; Fu, Xiao; Swat, Maciej; Belmonte, Julio M.; Cosmanescu, Alin; Clendenon, Sherry G.; Wambaugh, John F.; Glazier, James A. (16 September 2016). "A Liver-Centric Multiscale Modeling Framework for Xenobiotics". PLOS ONE. 11 (9): e0162428. Bibcode:2016PLoSO..1162428S. doi:10.1371/journal.pone.0162428. PMC 5026379. PMID 27636091.
- ^ Yang, Yongliang; Filipovic, David; Bhattacharya, Sudin (April 2022). "A Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8-Tetrachlorodibenzo-p-Dioxin in the Mouse Liver". Hepatology Communications. 6 (4): 750–764. doi:10.1002/hep4.1848. PMC 8948569. PMID 34726355.
- ^ Hester, Susan D.; Belmonte, Julio M.; Gens, J. Scott; Clendenon, Sherry G.; Glazier, James A. (6 October 2011). "A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation". PLOS Computational Biology. 7 (10): e1002155. Bibcode:2011PLSCB...7E2155H. doi:10.1371/journal.pcbi.1002155. PMC 3188485. PMID 21998560.