Cell-based models: Difference between revisions

Revision as of 06:49, 24 January 2023

Revision as of 20:30, 29 January 2023

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|EPISIM<ref>{{cite journal | vauthors = Sütterlin T, Huber S, Dickhaus H, Grabe N | title = Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems | journal = Bioinformatics | volume = 25 | issue = 16 | pages = 2057–2063 | date = August 2009 | pmid = 19535533 | doi = 10.1093/bioinformatics/btp361 | doi-access = free }}</ref>

|Center/agent-based

|2D, 3D

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|[[CUDA]], [[Graphics processing unit|GPU]]

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|Minimal Cell<ref>{{cite journal | vauthors = Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest TM, Melo MC, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z | display-authors = 6 | title = Fundamental behaviors emerge from simulations of a living minimal cell | language = English | journal = Cell | volume = 185 | issue = 2 | pages = 345–360.e28 | date = January 2022 | pmid = 35063075 | doi = 10.1016/j.cell.2021.12.025 | s2cid = 246065847 | doi-access = free }}</ref>

|ODE solvers, stochastic PDE solvers

|3D

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|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 }}</ref>

|Center/agent-based

|3D

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|Tyssue<ref>{{Cite journal | vauthors = Theis S, Suzanne M, Gay G |date=2021-06-07 |title=Tyssue: an epithelium simulation library |url=https://joss.theoj.org/papers/10.21105/joss.02973 |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>

|Vertex-based

|2D, 3D