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{{Short description|Mathematical models representing biological cells}}
'''Cell-based models''' are [[mathematical model]]s that represent biological [[cell (biology)|cells]] as discrete entities. Within the field of [[computational biology]] they are often simply called [[agent-based model]]s<ref name=":0" /> of which they are a specific application and they are used for simulating the [[biomechanics]] of multicellular structures such as [[Tissue (biology)|tissue]]s. to study the influence of these behaviors on how tissues are organised in time and space. Their main advantage is the easy integration of cell level processes such as [[cell division]], intracellular processes and [[single-cell variability]] within a cell population.<ref name=Liederkerke2015>{{cite journal | vauthors = Van Liedekerke P, Palm MM, Jagiella N, Drasdo D | title=Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results|journal=Computational Particle Mechanics|date=1 December 2015|volume=2|issue=4|pages=401–444|doi=10.1007/s40571-015-0082-3 | bibcode=2015CPM.....2..401V|doi-access=free}}</ref>
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=== On-lattice ===
On-lattice models such as [[Cellular automaton|cellular automata]] or [[Cellular Potts model|cellular potts]] restrict the spatial arrangement of the cells to a fixed grid. The mechanical interactions are then carried out according to literature-based rules (cellular automata)<ref>{{cite journal | vauthors = Peirce SM, Van Gieson EJ, Skalak TC | title = Multicellular simulation predicts microvascular patterning and in silico tissue assembly | journal = FASEB Journal | volume = 18 | issue = 6 | pages = 731–733 | date = April 2004 | pmid = 14766791 | doi = 10.1096/fj.03-0933fje | doi-access = free | s2cid = 11107214 }}</ref> or by minimizing the total energy of the system (cellular potts),<ref>{{cite journal | vauthors = Graner F, Glazier JA | title = Simulation of biological cell sorting using a two-dimensional extended Potts model | journal = Physical Review Letters | volume = 69 | issue = 13 | pages = 2013–2016 | date = September 1992 | pmid = 10046374 | doi = 10.1103/PhysRevLett.69.2013 | bibcode = 1992PhRvL..69.2013G }}</ref> resulting in cells being displaced from one grid point to another.
=== Off-lattice ===
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|ACAM<ref>{{cite journal | vauthors = Nestor-Bergmann A, Blanchard GB, Hervieux N, Fletcher AG, Étienne J, Sanson B | title = Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model | journal = PLOS Computational Biology | volume = 18 | issue = 1 | pages = e1009812 | date = January 2022 | pmid = 35089922 | doi = 10.1371/journal.pcbi.1009812 | pmc = 8887740 | s2cid = 246387965 | doi-access = free | bibcode = 2022PLSCB..18E9812N }}</ref>
|Off-lattice, ODE solvers
|2D
|<ref>{{cite journal | vauthors = Nestor-Bergmann A, Blanchard GB, Hervieux N, Fletcher AG, Étienne J, Sanson B | title = ACAM - Apposed Cortex Adhesion Model | year = 2021 | doi = 10.1101/2021.04.11.439313
| s2cid = 233246026 | url = https://zenodo.org/record/5838249 | via = Zenodo | doi-access = free }}</ref>
|Yes
|Yes
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|Center/agent-based, on-/off-lattice, cellular automata, vertex-based, immersed boundary
|2D, 3D
▲| url = https://github.com/Chaste/Chaste | via = GitHub }}</ref>
|Yes
|Yes
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|[[OpenMP]]
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|EdgeBased<ref>{{Cite journal | vauthors = Brown PJ, Green JE, Binder BJ, Osborne JM |title=A rigid body framework for multi-cellular modelling | journal = Nature Computational Science | date = November 2021 | volume = 1 | issue = 11 | pages = 754–766 |doi=
|Off-lattice, ODE solvers
|2D
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