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CompuCell3D specifications


Unique identifier OMICS_08775
Name CompuCell3D
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Version 3.7.4
Stability Stable
Maintained Yes


No version available


  • person_outline James A. Glazier

Publications for CompuCell3D

CompuCell3D citations


High Performance Agent Based Modeling Applied to Vocal Fold Inflammation and Repair

Front Physiol
PMCID: 5906585
PMID: 29706894
DOI: 10.3389/fphys.2018.00304

[…] provides support for running multiple non-interacting single-cell instances concurrently on massively parallel computers. more examples include hpc abm frameworks for multi-core cpus such as compucell3d (swat et al., ,), cellsys (hoehme and drasdo, ), and morpheus (starruß et al., ). these frameworks target multi-core cpu acceleration on a single compute node using openmp. in addition, […]


A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self‐renewal

Mol Syst Biol
PMCID: 5408779
PMID: 28455349
DOI: 10.15252/msb.20167324

[…] turnovers. however, they could be important during regeneration when cell divisions and migration perturb the pattern. we therefore constructed a multiscale, agent‐based stochastic model using compucell3d (swat et al, ). the model takes into consideration the three‐dimensional structure, cell growth, division, migration, and cell–cell physical contact (fig e, see ). notch signaling […]


Comparing individual based approaches to modelling the self organization of multicellular tissues

PLoS Comput Biol
PMCID: 5330541
PMID: 28192427
DOI: 10.1371/journal.pcbi.1005387

[…] which to compare different classes of cell-based model. a longer-term challenge is to extend such comparison studies across simulation tools, of which there is an increasing ecosystem, including compucell3d [], morpheus [], episim [], cellsys [], virtualleaf [], biocellion [], biofvm [], lbibcell [] and embryomaker []. we emphasize here the lack of ‘benchmarks’ on which to make […]


A cell based computational model of early embryogenesis coupling mechanical behaviour and gene regulation

Nat Commun
PMCID: 5264012
PMID: 28112150
DOI: 10.1038/ncomms13929

[…] a polygonal mesh of elastic compartments, the latter also allowing the specification of complex chemical networks, but only for plant growth in 2d and without coupling between grn and biomechanics; compucell3d (ref. ), an on-lattice voxel-based model without freely moving components, provides a simulation environment merging the cellular potts model with chemical fields and diffusion equations. […]


Simulating Heterogeneous Tumor Cell Populations

PLoS One
PMCID: 5193460
PMID: 28030620
DOI: 10.1371/journal.pone.0168984

[…] potts model to study tumor growth, invasion, and evolution [], angiogenesis [], and to create multiscale models of tumor cell growth and invasion that use biophysics simulation frameworks like compucell3d and bionetsolver []. despite the longterm degenerate behavior of the cellular potts model and the modeling limitations imposed by the central role of surface fluctuations [], efforts […]


Spatiotemporal Dynamics of Insulitis in Human Type 1 Diabetes

Front Physiol
PMCID: 5186767
PMID: 28082906
DOI: 10.3389/fphys.2016.00633

[…] of the lattice comes an associated computational cost. it should be noted that there are several actively maintained packages for agent-based modeling, such as chaste (mirams et al., ) and compucell3d (swat et al., )., one approach that combines the flexibility of lattice-free approaches together whilst allowing for cells to change shape is to treat points on the cell membrane […]

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CompuCell3D institution(s)
Biocomplexity Institute and Department of Physics, Indiana University, Bloomington, IN, USA

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