Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment

Swat, Maciej; Hester, Susan D.; Balter, Ariel; Heiland, Randy; Zaitlen, Benjamin; Glazier, James A.

doi:10.1007/978-1-59745-525-1_13

Cited by 58 publications

(54 citation statements)

References 91 publications

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“…CompuCell3D is an open-source software package that simulates multi-cell interactions and behaviours according to the Glazier-Graner-Hogeweg (GGH) model of cell behaviours 56,57 . For a more complete introduction to GGH modelling with CompuCell3D, see Swat et al 57 See Supplementary Note 1 for additional details of the modelling.…”

Section: Methodsmentioning

confidence: 99%

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Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Nakamoto

Hester²,

Constantinou

et al. 2015

Nat Commun

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Segmented animals are found in major clades as phylogenetically distant as vertebrates and arthropods. Typically, segments form sequentially in what has been thought to be a regular process, relying on a segmentation clock to pattern budding segments and posterior mitosis to generate axial elongation. Here we show that segmentation in Tribolium has phases of variable periodicity during which segments are added at different rates. Furthermore, elongation during a period of rapid posterior segment addition is driven by high rates of cell rearrangement, demonstrated by differential fates of marked anterior and posterior blastoderm cells. A computational model of this period successfully reproduces elongation through cell rearrangement in the absence of cell division. Unlike current models of steady-state sequential segmentation and elongation from a proliferative growth zone, our results indicate that cell behaviours are dynamic and variable, corresponding to differences in segmentation rate and giving rise to morphologically distinct regions of the embryo.

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Section: Methodsmentioning

confidence: 99%

“…For a more complete introduction to GGH modelling with CompuCell3D, see Swat et al 57 See Supplementary Note 1 for additional details of the modelling.…”

Section: Methodsmentioning

confidence: 99%

Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Nakamoto

Hester²,

Constantinou

et al. 2015

Nat Commun

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“…As the focus of CPM is cell rearrangement, they have been used mainly for modelling developmental mechanisms. Compucell3D [3] is the most widely used modelling environment for implementation of CPMs. It is an open source resource and extensible, enabling the sharing of results.…”

Section: Methodsmentioning

confidence: 99%

Computational modelling of epithelial to mesenchymal transition

Abdulla

Imms

Dillenseger

et al. 2011

IRBM

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International audienceCell behaviour during epithelial to mesenchymal transition (EMT) was simulated using the cellular Potts formalism in Compucell3D. A recent in vitro study revealed that the mechanism of endocardial scattering can be induced independently of invasion into the extracellular matrix (ECM). This suggests that loss of endocardial cohesion alone is not sufficient for full EMT. The 3D simulations, which take account of changes in adhesion, match this conclusion. The principle by which the rate of mitosis regulates the endocardial monolayer was demonstrated; suggesting a route by which VEGF might regulate EMT

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“…In this type of model a lattice-based computational modelling method is used to simulate the collective behaviour of cellular structures [54,55]. Each lattice site represents a single cell and during each timestep transport equations for IL-8, Growth Factor 2, VEGF and oxygen were solved for each cell (Figure 4).…”

Section: Cellular Modelsmentioning

confidence: 99%

Modelling drug transport during intraperitoneal chemotherapy

Steuperaert

Debbaut

Segers

et al. 2017

Pleura and Peritoneum

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Despite a strong rationale for intraperitoneal (IP) chemotherapy, the actual use of the procedure is limited by the poor penetration depth of the drug into the tissue. Drug penetration into solid tumours is a complex mass transport process that involves multiple parameters not only related to the used cytotoxic agent but also to the tumour tissue properties and even the therapeutic setup. Mathematical modelling can provide unique insights into the different transport barriers that occur during IP chemotherapy as well as offer the possibility to test different protocols or drugs without the need for in vivo experiments. In this work, a distinction is made between three different types of model: the lumped parameter model, the distributed model and the cell-based model. For each model, we discuss which steps of the transport process are included and where assumptions are made. Finally, we focus on the advantages and main limitations of each category and discuss some future perspectives for the modelling of IP chemotherapy.

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Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment

Cited by 58 publications

References 91 publications

Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Computational modelling of epithelial to mesenchymal transition

Modelling drug transport during intraperitoneal chemotherapy

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