Cell-based models: Difference between revisions

Revision as of 03:45, 9 July 2023

Revision as of 22:11, 22 August 2023

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=== Off-lattice ===

Off-lattice models allow for continuous movement of cells in space and evolve the system in time according to [[force]] laws governing the mechanical interactions between the individual cells. Examples of off-lattice models are center-based models,<ref>{{cite journal | vauthors = Osborne JM, Fletcher AG, Pitt-Francis JM, Maini PK, Gavaghan DJ | title = Comparing individual-based approaches to modelling the self-organization of multicellular tissues | journal = PLOS Computational Biology | volume = 13 | issue = 2 | pages = e1005387 | date = February 2017 | pmid = 28192427 | pmc = 5330541 | doi = 10.1371/journal.pcbi.1005387 | veditors = Nie Q | bibcode = 2017PLSCB..13E5387O | doi-access = free }}</ref> vertex-based models,<ref name=":0" /> models

based on the [[immersed boundary method]]<ref>{{cite journal | vauthors = Rejniak KA | title = An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development | journal = Journal of Theoretical Biology | volume = 247 | issue = 1 | pages = 186–204 | date = July 2007 | pmid = 17416390 | doi = 10.1016/j.jtbi.2007.02.019 | bibcode = 2007JThBi.247..186R }}</ref> and the subcellular element

method.<ref>{{cite book | vauthors = Newman TJ | title = Modeling multicellular systems using subcellular elements | journal = Mathematical Biosciences and Engineering | volume = 2 | issue = 3 | pages = 613–24 | date = July 2005 | pmid = 20369943 | doi = 10.1007/978-3-7643-8123-3_10 | series = Mathematics and Biosciences in Interaction | isbn = 978-3-7643-8101-1 }}</ref> They differ mainly in the level of detail with which they represent the

cell shape. As a consequence they vary in their ability to capture different biological mechanisms, the effort needed to extend them from two- to three-dimensional models and also in their computational cost.<ref>{{cite journal | vauthors = Osborne JM, Fletcher AG, Pitt-Francis JM, Maini PK, Gavaghan DJ | title = Comparing individual-based approaches to modelling the self-organization of multicellular tissues | journal = PLOS Computational Biology | volume = 13 | issue = 2 | pages = e1005387 | date = February 2017 | pmid = 28192427 | pmc = 5330541 | doi = 10.1371/journal.pcbi.1005387 | bibcode = 2017PLSCB..13E5387O | doi-access = free }}</ref>

The simplest off-lattice model, the center-based model, depicts cells as spheres and models their mechanical interactions using pairwise potentials.<ref>{{cite journal | vauthors = Meineke FA, Potten CS, Loeffler M | title = Cell migration and organization in the intestinal crypt using a lattice-free model | journal = Cell Proliferation | volume = 34 | issue = 4 | pages = 253–266 | date = August 2001 | pmid = 11529883 | pmc = 6495866 | doi = 10.1046/j.0960-7722.2001.00216.x }}</ref><ref>{{cite journal | vauthors = Drasdo D, Höhme S | title = A single-cell-based model of tumor growth in vitro: monolayers and spheroids | journal = Physical Biology | volume = 2 | issue = 3 | pages = 133–147 | date = July 2005 | pmid = 16224119 | doi = 10.1088/1478-3975/2/3/001 | bibcode = 2005PhBio...2..133D | s2cid = 24191020 }}</ref> It is easily extended to a large number of cells in both 2D and 3D.<ref>{{cite journal | vauthors = Galle J, Aust G, Schaller G, Beyer T, Drasdo D | title = Individual cell-based models of the spatial-temporal organization of multicellular systems--achievements and limitations | journal = Cytometry. Part A | volume = 69 | issue = 7 | pages = 704–710 | date = July 2006 | pmid = 16807896 | doi = 10.1002/cyto.a.20287 | doi-access = free }}</ref>

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!Speedup

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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 }}</ref>

|Off-lattice, ODE solvers

|2D

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|[https://docs.julialang.org/en/v1/stdlib/Distributed/ Distributed.jl]

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|Artistoo<ref>{{Cite journal |last1=Wortel |first1=Inge MN |last2=Textor |first2=Johannes |date=2021-04-09 |editor-last=Walczak |editor-first=Aleksandra M |editor2-last=Buttenschoen |editor2-first=Andreas |editor3-last=Macklin |editor3-first=Paul |title=Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |url=https://doi.org/10.7554/eLife.61288 |journal=eLife |volume=10 |pages=e61288 |doi=10.7554/eLife.61288 |issn=2050-084X |pmc=8143789 |pmid=33835022 |doi-access=free }}</ref>

|Cellular Potts, Cellular Automaton

|2D, (3D)

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|CBMOS<ref>{{cite journal | vauthors = Mathias S, Coulier A, Hellander A | title = CBMOS: a GPU-enabled Python framework for the numerical study of center-based models | journal = BMC Bioinformatics | volume = 23 | issue = 1 | pages = 55 | date = January 2022 | pmid = 35100968 | pmc = 8805507 | doi = 10.1186/s12859-022-04575-4 | doi-access = free }}</ref>

|Center/agent-based

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|Chaste<ref>{{cite journal | vauthors = Pitt-Francis J, Bernabeu MO, Cooper J, Garny A, Momtahan L, Osborne J, Pathmanathan P, Rodriguez B, Whiteley JP, Gavaghan DJ | display-authors = 6 | title = Chaste: using agile programming techniques to develop computational biology software | journal = Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences | volume = 366 | issue = 1878 | pages = 3111–3136 | date = September 2008 | pmid = 18565813 | doi = 10.1016/j.cpc.2009.07.019 | url = http://eprints.maths.ox.ac.uk/846 | access-date = 2019-02-01 | author16-link = Sarah L. Waters | archive-url = https://web.archive.org/web/20151120234903/http://eprints.maths.ox.ac.uk/846/ | archive-date = 2015-11-20 }}</ref><ref>{{cite journal | vauthors = Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, Corrias A, Davit Y, Dunn SJ, Fletcher AG, Harvey DG, Marsh ME, Osborne JM, Pathmanathan P, Pitt-Francis J, Southern J, Zemzemi N, Gavaghan DJ | display-authors = 6 | title = Chaste: an open source C++ library for computational physiology and biology | journal = PLOS Computational Biology | volume = 9 | issue = 3 | pages = e1002970 | date = 14 March 2013 | pmid = 23516352 | pmc = 3597547 | doi = 10.1371/journal.pcbi.1002970 | bibcode = 2013PLSCB...9E2970M | doi-access = free }}</ref>

|Center/agent-based, on-/off-lattice, cellular automata, vertex-based, immersed boundary

|2D, 3D

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|PhysiCell<ref>{{cite journal | vauthors = Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P | title = PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems | journal = PLOS Computational Biology | volume = 14 | issue = 2 | pages = e1005991 | date = February 2018 | pmid = 29474446 | pmc = 5841829 | doi = 10.1371/journal.pcbi.1005991 | bibcode = 2018PLSCB..14E5991G | doi-access = free }}</ref>

|Center/agent-based, ODE

|3D