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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>
{{Orphan|date=August 2017}}
 
Continuum-based models (PDE-based) models have also been developed – in particular, for cardiomyocytes and neurons. These represent the cells through explicit geometries and take into account spatial distributions of both intracellular and extracellular processes. They capture, depending on the research question and areas, ranges from a few to many thousand cells. In particular, the framework for electrophysiological models of cardiac cells is well-developed and made highly efficient using [[high-performance computing]].<ref>{{cite book | url=https://link.springer.com/book/10.1007/978-3-030-61157-6 | title=Modeling Excitable Tissue | series=Simula SpringerBriefs on Computing |editor=Aslak Tveito |editor2=Kent-Andre Mardal |editor3=Marie E. Rognes | year=2021 | volume=7 | publisher=Springer| doi=10.1007/978-3-030-61157-6 | isbn=978-3-030-61156-9 | s2cid=228872673 }}</ref>
'''Cell-based models''' are [[mathematical model]]s that represent biological [[cell (biology)|cells]] as a discrete entities. Within the field of [[computational biology]] they are often simply called [[Agent-based model|agent-based models]]<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>
 
Continuum-based models (PDE-based) models have also been developed – in particular, for cardiomyocytes and neurons. These represent the cells through explicit geometries and take into account spatial distributions of both intracellular and extracellular processes. They capture, depending on the research question and areas, ranges from a few to many thousand cells. In particular, the framework for electrophysiological models of cardiac cells is well-developed and made highly efficient using [[high-performance computing]].<ref>{{cite book | url=https://link.springer.com/book/10.1007/978-3-030-61157-6 | title=Modeling Excitable Tissue |editor=Aslak Tveito |editor2=Kent-Andre Mardal |editor3=Marie E. Rognes | year=2021 | publisher=Springer}}</ref>
 
== Model types ==
 
Cell-based models can be divided into on- and off-lattice models.
 
=== 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 = 731–3731–733 | date = April 2004 | pmid = 14766791 | doi = 10.1096/fj.03-0933fje | s2ciddoi-access = 11107214free | urls2cid = http://www.fasebj.org/content/18/6/731.short11107214 }}</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 ===
 
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 | veditorsdoi-access = Nie Qfree }}</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 = Single-Cell-Based Models in Biology and Medicine | chapter = Modeling multicellularMulticellular Structures Using systemsthe usingSubcellular subcellularElement elementsModel | 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 = 253–66253–266 | date = August 2001 | pmid = 11529883 | pmc = 6495866 | doi = 10.1046/j.0960-7722.2001.00216.x | pmc = 6495866 }}</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 = 133–47133–147 | 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 = 704–10704–710 | date = July 2006 | pmid = 16807896 | doi = 10.1002/cyto.a.20287 | doi-access = free }}</ref>
 
==== Vertex ====
Line 29 ⟶ 27:
 
Since they account for individual behavior at the cell level such as [[cell proliferation]], [[cell migration]] or [[apoptosis]], cell-based models are a useful tool to study the influence of these behaviors on how tissues are organised in time and space.<ref name=Liederkerke2015 />
Due in part to the increase in computational power, they have arisen as an alternative to [[continuum mechanics]] models<ref>{{cite journal | vauthors = Rodriguez EK, Hoger A, McCulloch AD | title = Stress-dependent finite growth in soft elastic tissues | journal = Journal of Biomechanics | volume = 27 | issue = 4 | pages = 455–67455–467 | date = April 1994 | pmid = 8188726 | doi = 10.1016/0021-9290(94)90021-3 }}</ref> which treat tissues as viscoelastic materials by averaging over single cells.
 
Cell-based mechanics models are often coupled to models describing intracellular dynamics, such as an [[ordinary differential equation|ODE]] representation of a relevant [[gene regulatory network]]. It is also common to connect them to a [[partial differential equation|PDE]] describing the diffusion of a chemical [[cell signaling|signaling molecule]] through the [[extracellular matrix]], in order to account for [[cellular communication|cell-cell communication]]. As such, cell-based models have been used to study processes ranging from [[embryogenesis]]<ref>{{cite journal | vauthors = Tosenberger A, Gonze D, Bessonnard S, Cohen-Tannoudji M, Chazaud C, Dupont G | title = A multiscale model of early cell lineage specification including cell division | journal = NPJnpj Systems Biology and Applications | volume = 3 | issue = 1 | pages = 16 | date = 9 June 2017 | pmid = 28649443 | pmc = 5466652 | doi = 10.1038/s41540-017-0017-0 }}</ref> over [[Epithelium|epithelial]] [[morphogenesis]]<ref>{{cite journal | vauthors = Fletcher AG, Cooper F, Baker RE | title = Mechanocellular models of epithelial morphogenesis | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 372 | issue = 1720 | pages = 20150519 | date = May 2017 | pmid = 28348253 | pmc = 5379025 | doi = 10.1098/rstb.2015.0519 }}</ref> to tumour growth<ref>{{cite book | vauthors = Drasdo D, Dormann S, Hoehme S, Deutsch A |chapter=Cell-Based Models of Avascular Tumor Growth |veditors=Deutsch A, Howard J, Falcke M, Zimmermann W|title=Function and Regulation of Cellular Systems|date=2004|pages=367–378|doi=10.1007/978-3-0348-7895-1_37|isbn=978-3-0348-9614-6 }}</ref> and intestinal crypt dynamics<ref>{{cite journal | vauthors = De Matteis G, Graudenzi A, Antoniotti M | title = A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development | journal = Journal of Mathematical Biology | volume = 66 | issue = 7 | pages = 1409–1462 | date = June 2013 | pmid = 22565629 | doi = 10.1007/s00285-012-0539-4 | s2cid = 32661526 }}</ref>
 
== Simulation frameworks ==
There exist several software packages implementing cell-based models, e.g.
{| class="wikitable sortable"
|+
!Name
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!Speedup
|-
|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>
|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 |date=September 2008 |title=Chaste: using agile programming techniques to develop computational biology software |url=http://eprints.maths.ox.ac.uk/846 |journal=Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences |volume=366 |issue=1878 |pages=3111–36 |doi=10.1016/j.cpc.2009.07.019 |pmid=18565813 |archive-url=https://web.archive.org/web/20151120234903/http://eprints.maths.ox.ac.uk/846/ |archive-date=2015-11-20 |access-date=2019-02-01 |author16-link=Sarah L. Waters}}</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 |date=14 March 2013 |title=Chaste: an open source C++ library for computational physiology and biology |journal=PLOS Computational Biology |volume=9 |issue=3 |pages=e1002970 |bibcode=2013PLSCB...9E2970M |doi=10.1371/journal.pcbi.1002970 |pmc=3597547 |pmid=23516352}}</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
|[[Python (programming language)|Python]]
|
|-
|Agents.jl<ref>{{Cite journal | vauthors = Datseris G, Vahdati AR, DuBois TC |date=2022-01-05 |title=Agents.jl: a performant and feature-full agent-based modeling software of minimal code complexity |url=http://journals.sagepub.com/doi/10.1177/00375497211068820 |journal=Simulation |language=en |pages=003754972110688 |doi=10.1177/00375497211068820 |arxiv=2101.10072 |s2cid=231698977 |issn=0037-5497}}</ref>
|Center/agent-based
|2D,3D
|<ref>{{cite web | title = JuliaDynamics
| url = https://github.com/JuliaDynamics/Agents.jl | via = GitHub }}</ref>
|Yes
|Yes
|[[Julia (programming language)|Julia]]
|[https://docs.julialang.org/en/v1/stdlib/Distributed/ Distributed.jl]
|-
|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 |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)
|https://github.com/ingewortel/artistoo
|Yes
|Yes
|[[JavaScript]]
|
|-
|Biocellion<ref>{{cite journal | vauthors = Kang S, Kahan S, McDermott J, Flann N, Shmulevich I | title = Biocellion: accelerating computer simulation of multicellular biological system models | journal = Bioinformatics | volume = 30 | issue = 21 | pages = 3101–3108 | date = November 2014 | pmid = 25064572 | pmc = 4609016 | doi = 10.1093/bioinformatics/btu498 }}</ref><ref>{{Cite web |title=biocellion |url=https://biocellion.com/ |access-date=2022-04-05 |website=biocellion |language=en-US}}</ref>
|Center/agent-based
|
|No
|Yes
|Yes
|[[C++]]
|
|-
| cellular_raza
|Off-lattice, Allows for Generic Implementations
| 1D, 2D, 3D
| [https://github.com/jonaspleyer/cellular_raza github.com/jonaspleyer/cellular_raza]
| Yes
| [https://docs.rs/cellular_raza Yes]
| [[Rust_(programming_language)|Rust]]
|
|-
|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
|
|<ref>{{cite web | title = JuliaDynamics
| url = https://github.com/somathias/cbmos | via = GitHub }}</ref>
|
|
|[[Python (programming language)|Python]]
|GPU
|-
|CellularPotts.jl
|Cellular Potts, agent-based
|2D,3D
|https://github.com/RobertGregg/CellularPotts.jl
|
|not ready for usage
|[[Julia (programming language)|Julia]]
|
|-
|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 = https://ora.ox.ac.uk/objects/uuid:61d9bb9f-95c6-4054-8118-294f6ca94d54/files/m680698b55b2efad4aabc9cdd27c24a09 | access-date = 2019-02-01 | author16-link = Sarah L. Waters | archive-url = | archive-date = }}</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
|[https://github.com/Chaste/Chaste https://github.com/Chaste/Chaste]
|Yes
|Yes
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|
|-
|[[CompuCell3D]]<ref>{{cite book |title=Computational Methods in Cell Biology |vauthors=Swat MH, Thomas GL, Belmonte JM, Shirinifard A, Hmeljak D, Glazier JA |datetitle=1Computational January 2012 |journal=Methods in Cell Biology |chapter=Multi-Scale Modeling of Tissues Using CompuCell3D |date=1 January 2012 |isbn=9780123884039 |volume=110 |pages=325–66 |chapter=Multi-scale modeling of tissues using CompuCell3D |doi=10.1016/B978-0-12-388403-9.00013-8 |pmc=3612985 |pmid=22482955}}</ref>
|Cellular Potts, PDE solvers, cell type automata
|3D
Line 64 ⟶ 128:
|[[OpenMP]]
|-
|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=10.1038/s43588-021-00154-4|biorxiv=10.1101/2021.02.10.430170|pmid=38217146 |s2cid=231939320}}</ref>
|[https://www.hoehme.com/software/tisim TiSim] (formerly CellSys)
|Center/agent-based, offOff-lattice, ODE solvers
|2D, 3D
|https://github.com/luckyphill/EdgeBased
|in preparation
|
|
|
|
|-
|Morpheus<ref>{{cite journal |vauthors=Starruß J, de Back W, Brusch L, Deutsch A |date=May 2014 |title=Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology |journal=Bioinformatics |volume=30 |issue=9 |pages=1331–2 |doi=10.1093/bioinformatics/btt772 |pmc=3998129 |pmid=24443380}}</ref>
|Cellular Potts, ODE solvers, PDE solvers
|2D, 3D
|https://morpheus.gitlab.io/
|Yes
|Yes
|[[C++MATLAB|Matlab]]
|
|-
|VirtualLeafEPISIM<ref>{{cite journal | vauthors =Merks RMSütterlin T, GuravageHuber MS, InzéDickhaus DH, BeemsterGrabe GTN |date=February 2011 |title =VirtualLeaf: anModeling openmulti-sourcecellular frameworkbehavior forin cell-basedepidermal modelingtissue ofhomeostasis plantvia tissuefinite growthstate andmachines developmentin multi-agent systems | journal =Plant PhysiologyBioinformatics | volume =155 25 | issue =2 16 | pages =656–66 2057–2063 | date = August 2009 | pmid = 19535533 | doi = 10.11041093/pp.110.167619bioinformatics/btp361 |pmc=3032457 |pmiddoi-access =21148415 free }}</ref>
|Center/agent-based
|2D, 3D
|<s>http://tigacenter.bioquant.uni-heidelberg.de/downloads.html</s>
|
|2D
|https://github.com/rmerks/VirtualLeaf2021
|
|[[Java (programming language)|Java]]
|
|-
|IAS (Interacting Active Surfaces)<ref>{{Cite journal | vauthors = Torres-Sánchez A, Winter MK, Salbreux G |date=2022-03-22 |title=Interacting active surfaces: a model for three-dimensional cell aggregates | journal = bioRxiv |volume=18 |issue=12 |pages=2022.03.21.484343 |doi=10.1101/2022.03.21.484343|pmid=36525467 |pmc=9803321 |s2cid=247631653 }}</ref>
|[[Finite element method|FEM]], ODE solvers
|3D
|https://github.com/torressancheza/ias
|Yes
|No
|[[C++]]
|[[Message Passing Interface|MPI]], [[OpenMP]]
|
|-
|IBCell
Line 100 ⟶ 164:
|
|-
|LBIBCell<ref>{{cite journal | vauthors = Tanaka S, Sichau D, Iber D |date=July 2015 |title = LBIBCell: a cell-based simulation environment for morphogenetic problems | journal = Bioinformatics | volume = 31 | issue = 14 | pages =2340–7 2340–2347 |arxiv date =1503.06726 July 2015 | pmid = 25770313 | doi = 10.1093/bioinformatics/btv147 |pmid arxiv =25770313 1503.06726 | s2cid = 16749503 }}</ref>
|Lattice-Boltzmann, Immersed Boundary
|2D
Line 109 ⟶ 173:
|[[OpenMP]]
|-
|MecaGen<ref>{{cite journal | vauthors = Delile J, Herrmann M, Peyriéras N, Doursat R |date=January 2017title |title= A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation | journal = Nature Communications | volume = 8 | pages = 13929 |bibcode date =2017NatCo...813929D January 2017 | pmid = 28112150 | pmc = 5264012 | doi = 10.1038/ncomms13929 |pmc=5264012 |pmidbibcode =28112150 2017NatCo...813929D }}</ref>
|Center/agent-based
|3D
Line 118 ⟶ 182:
|[[CUDA]], [[Graphics processing unit|GPU]]
|-
|PhysiCellMinimal Cell<ref>{{cite journal | vauthors =Ghaffarizadeh AThornburg ZR, HeilandBianchi RDM, FriedmanBrier SHTA, MumenthalerGilbert SMBR, MacklinEarnest PTM, |date=FebruaryMelo 23MC, 2018Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z | display-authors = 6 | title =PhysiCell: anFundamental Openbehaviors Sourceemerge Physics-Basedfrom Cellsimulations Simulatorof fora 3-Dliving Multicellularminimal Systemscell |journal language =PLOS ComputationalEnglish Biology| journal = Cell | volume =14 185 | issue = 2 | pages =e1005991 345–360.e28 |bibcode date =2018PLSCB..14E5991G January 2022 | pmid = 35063075 | doi = 10.13711016/journalj.pcbicell.10059912021.12.025 | pmc =5841829 9985924 |pmid s2cid =29474446 246065847 | doi-access = free }}</ref>
|ODE solvers, stochastic PDE solvers
|Center/agent-based, ODE
|3D
|https://github.com/Luthey-Schulten-Lab/Lattice_Microbes<nowiki/>https://github.com/Luthey-Schulten-Lab/Minimal_Cell
|https://github.com/MathCancer/PhysiCell
|Yes
|Yes
|[[Python (programming language)|Python]]
|[[C++]]
|[[CUDA]], [[Graphics processing unit|GPU]]
|[[OpenMP]]
|-
|BiocellionMorpheus<ref>{{cite journal | vauthors =Kang S,Starruß Kahan SJ, McDermottde JBack W, FlannBrusch NL, ShmulevichDeutsch IA |date=November 2014title |title=Biocellion Morpheus: acceleratinga computeruser-friendly simulationmodeling ofenvironment for multiscale and multicellular biologicalsystems systembiology models| |journal = Bioinformatics | volume = 30 | issue =21 9 | pages =3101–3108 1331–1332 |doi date =10.1093/bioinformatics/btu498 May 2014 |pmc=4609016 |pmid =25064572}}</ref><ref>{{Cite web24443380 |title pmc =biocellion 3998129 |url doi =https: 10.1093/bioinformatics/biocellion.com/btt772 |access-date=2022-04-05 |website=biocellion |language=en-US}}</ref>
|Cellular Potts, ODE solvers, PDE solvers
|Center/agent-based
|2D, 3D
|
|https://morpheus.gitlab.io/
|No
|Yes
|Yes
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|
|-
|[https://ccl.northwestern.edu/netlogo/ NetLogo]
|Timothy
|Lattice gas cellular automata
|Center/agent-based
|2D, (3D)
|https://github.com/NetLogo/NetLogo
|<s>http://timothy.icm.edu.pl/downloads.html</s>
|No
|No
|[[C (programming language)|C]]
|[[Message Passing Interface|MPI]], [[OpenMP]]
|-
|yalla
|Center/agent/spheroid-based
|3D
|https://github.com/germannp/yalla
|
|
|[[Scala (programming language)|Scala]], [[Java (programming language)|Java]]
|
|[[CUDA]], [[Graphics processing unit|GPU]]
|-
|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>
|EPISIM
|Center/agent-based, ODE
|Cellular Potts
|3D
|https://github.com/MathCancer/PhysiCell
|No
|Yes
|Yes
|[[C++]]
|[[OpenMP]]
|-
|[https://www.hoehme.com/software/tisim TiSim] (formerly CellSys)
|Center/agent-based, off-lattice, ODE solvers
|2D, 3D
|in preparation
|
|
Line 163 ⟶ 227:
|
|-
|Timothy<ref>{{Cite journal | vauthors = Cytowski M, Szymanska Z |date=September 2014 |title=Large-Scale Parallel Simulations of 3D Cell Colony Dynamics |journal=Computing in Science & Engineering |volume=16 |issue=5 |pages=86–95 |doi=10.1109/MCSE.2014.2 |bibcode=2014CSE....16e..86C |s2cid=427712 |issn=1558-366X}}</ref>
|CBMOS
|Center/agent-based
|3D
|<s>http://timothy.icm.edu.pl/downloads.html</s>
|https://github.com/somathias/cbmos
|No
|No
|[[PythonC (programming language)|PythonC]]
|[[Message Passing Interface|MPI]], [[OpenMP]]
|GPU
|-
|URDME - DLCM workflow<ref>{{cite journal | vauthors = Engblom S, Wilson DB, Baker RE |date=August 2018title |title= Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time | journal = Royal Society Open Science | volume = 5 | issue = 8 | pages = 180379 |arxiv date =1706.03375 August 2018 |bibcode pmid =2018RSOS....580379E 30225024 | pmc = 6124129 | doi = 10.1098/rsos.180379 |pmc bibcode =6124129 2018RSOS....580379E |pmid arxiv =30225024 1706.03375 }}</ref><ref>{{Cite web |title=URDME |url=http://urdme.github.io/urdme/ |access-date=2022-04-05 |website=URDME |language=en-US}}</ref>
|[[Finite element method|FEM]], [[Finite volume method|FVM]]
|2D,3D
Line 181 ⟶ 245:
|
|-
|VirtualLeaf<ref>{{cite book | vauthors = Antonovici CC, Peerdeman GY, Wolff HB, Merks RM | title = Plant Systems Biology | chapter = Modeling Plant Tissue Development Using VirtualLeaf | series = Methods in Molecular Biology | volume = 2395 | pages = 165–198 | date = 2022 | pmid = 34822154 | doi = 10.1007/978-1-0716-1816-5_9 | publisher = Springer | isbn = 978-1-0716-1816-5 | hdl = 1887/3479570 | s2cid = 244668621 | place = New York, NY | veditors = Lucas M }}</ref> (2021)
|[https://github.com/torressancheza/ias Interacting Active Surfaces]
|Off-lattice
|[[Finite element method|FEM]], ODE solvers
|3D2D
|https://github.com/torressanchezarmerks/iasVirtualLeaf2021
|Yes
|Yes
|No
|[[C++]]
|
|[[Message Passing Interface|MPI]], [[OpenMP]]
|-
|yalla<ref>{{cite journal | vauthors = Germann P, Marin-Riera M, Sharpe J | title = ya&#124;&#124;a: GPU-Powered Spheroid Models for Mesenchyme and Epithelium | language = English | journal = Cell Systems | volume = 8 | issue = 3 | pages = 261–266.e3 | date = March 2019 | pmid = 30904379 | doi = 10.1016/j.cels.2019.02.007 | s2cid = 85497718 | doi-access = free | hdl = 10230/42284 | hdl-access = free }}</ref>
|[https://github.com/Luthey-Schulten-Lab/Minimal_Cell Minimal Cell]
|Center/agent-based
|ODE solvers, stochastic PDE solvers
|3D
|https://github.com/germannp/yalla
|https://github.com/Luthey-Schulten-Lab/Lattice_Microbes<nowiki/>https://github.com/Luthey-Schulten-Lab/Minimal_Cell
|Yes
|Yes
|
|[[Python (programming language)|Python]]
|[[CUDA]], [[Graphics processing unit|GPU]]
|-
Line 208 ⟶ 272:
|
|-
|Tyssue<ref>{{Cite journal | vauthors = Theis S, Suzanne M, Gay G |date=2021-06-07 |title=Tyssue: an epithelium simulation library |journal=Journal of Open Source Software |language=en |volume=6 |issue=62 |pages=2973 |doi=10.21105/joss.02973 |bibcode=2021JOSS....6.2973T |s2cid=235965728 |issn=2475-9066|doi-access=free }}</ref>
|Tyssue
|Vertex-based
|2D, 3D
Line 215 ⟶ 279:
|Yes
|[[Python (programming language)|Python]]
|
|-
|[https://ccl.northwestern.edu/netlogo/ NetLogo]
|Lattice gas cellular automata
|2D, (3D)
|https://github.com/NetLogo/NetLogo
|
|
|[[Scala (programming language)|Scala]], [[Java (programming language)|Java]]
|
|-
|EdgeBased
|Off-lattice
|
|https://github.com/luckyphill/EdgeBased
|Yes
|Yes
|[[MATLAB|Matlab]]
|
|-
Line 243 ⟶ 289:
|[[MATLAB|Matlab]], [[C (programming language)|C]], [[Python (programming language)|Python]]
|
|-
|Agents.jl
|Center/agent-based
|2D,3D
|https://github.com/JuliaDynamics/Agents.jl
|Yes
|Yes
|[[Julia (programming language)|Julia]]
|[https://docs.julialang.org/en/v1/stdlib/Distributed/ Distributed.jl]
|}
 
 
== References ==
Line 259 ⟶ 295:
 
[[Category:Cells]]
[[Category:Simulation software]]
[[Category:Numerical analysis]]
[[Category:Biophysics]]
[[Category:Computational biology]]
[[Category:Tissues (biology)]]
Retrieved from "https://en.wikipedia.org/wiki/Cell-based_models"