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Polo Oceano (talk | contribs) m →Simulation frameworks: added info |
Polo Oceano (talk | contribs) m →Simulation frameworks: sorted, added citations |
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!Language
!Speedup
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|Agents.jl<ref>{{Cite journal |last=Datseris |first=George |last2=Vahdati |first2=Ali R. |last3=DuBois |first3=Timothy C. |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 |issn=0037-5497}}</ref>
|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]
|-
|Biocellion<ref>{{cite journal |vauthors=Kang S, Kahan S, McDermott J, Flann N, Shmulevich I |date=November 2014 |title=Biocellion: accelerating computer simulation of multicellular biological system models |journal=Bioinformatics |volume=30 |issue=21 |pages=3101–3108 |doi=10.1093/bioinformatics/btu498 |pmc=4609016 |pmid=25064572}}</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++]]
|
|-
|CBMOS<ref>{{Cite journal |last=Mathias |first=Sonja |last2=Coulier |first2=Adrien |last3=Hellander |first3=Andreas |date=2022-01-31 |title=CBMOS: a GPU-enabled Python framework for the numerical study of center-based models |url=https://doi.org/10.1186/s12859-022-04575-4 |journal=BMC Bioinformatics |volume=23 |issue=1 |pages=55 |doi=10.1186/s12859-022-04575-4 |issn=1471-2105 |pmc=PMC8805507 |pmid=35100968}}</ref>
|Center/agent-based
|
|https://github.com/somathias/cbmos
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|[[Python (programming language)|Python]]
|GPU
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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 |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>
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|[[OpenMP]]
|-
|EdgeBased<ref>{{Cite journal |last=Brown |first=Phillip J. |last2=Green |first2=J. Edward F. |last3=Binder |first3=Benjamin J. |last4=Osborne |first4=James M. |date=2021-02-10 |title=A rigid body framework for multi-cellular modelling |url=https://www.biorxiv.org/content/10.1101/2021.02.10.430170v1 |language=en |pages=2021.02.10.430170 |doi=10.1101/2021.02.10.430170v1.full}}</ref>
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|2D
|https://github.com/luckyphill/EdgeBased
|Yes
|Yes
|[[MATLAB|Matlab]]
|
|-
|EPISIM<ref>{{Cite web |url=https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp361 |access-date=2022-11-08 |website=academic.oup.com |doi=10.1093/bioinformatics/btp361}}</ref>
|Center/agent-based
|2D, 3D
|<s>http://tigacenter.bioquant.uni-heidelberg.de/downloads.html</s>
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|[[Java (programming language)|Java]]
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|-
|IAS (Interacting Active Surfaces)<ref>{{Cite journal |last=Torres-Sánchez |first=Alejandro |last2=Winter |first2=Max Kerr |last3=Salbreux |first3=Guillaume |date=2022-03-22 |title=Interacting active surfaces: a model for three-dimensional cell aggregates |url=https://www.biorxiv.org/content/10.1101/2022.03.21.484343v1 |language=en |pages=2022.03.21.484343 |doi=10.1101/2022.03.21.484343}}</ref>
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|https://
|Yes
|No
|[[C++]]
|[[Message Passing Interface|MPI]], [[OpenMP]]
|-
|IBCell
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|[[C++]]
|[[CUDA]], [[Graphics processing unit|GPU]]
|-
|Minimal Cell<ref>{{Cite journal |last=Thornburg |first=Zane R. |last2=Bianchi |first2=David M. |last3=Brier |first3=Troy A. |last4=Gilbert |first4=Benjamin R. |last5=Earnest |first5=Tyler M. |last6=Melo |first6=Marcelo C. R. |last7=Safronova |first7=Nataliya |last8=Sáenz |first8=James P. |last9=Cook |first9=András T. |last10=Wise |first10=Kim S. |last11=Hutchison |first11=Clyde A. |last12=Smith |first12=Hamilton O. |last13=Glass |first13=John I. |last14=Luthey-Schulten |first14=Zaida |date=2022-01-20 |title=Fundamental behaviors emerge from simulations of a living minimal cell |url=https://www.cell.com/cell/abstract/S0092-8674(21)01488-4 |journal=Cell |language=English |volume=185 |issue=2 |pages=345–360.e28 |doi=10.1016/j.cell.2021.12.025 |issn=0092-8674 |pmid=35063075}}</ref>
|ODE solvers, stochastic PDE solvers
|3D
|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]]
|-
|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++]]
|
|-
|[https://ccl.northwestern.edu/netlogo/ NetLogo]
|Lattice gas cellular automata
|2D, (3D)
|https://github.com/NetLogo/NetLogo
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|
|[[Scala (programming language)|Scala]], [[Java (programming language)|Java]]
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|PhysiCell<ref>{{cite journal |vauthors=Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P |date=February 23, 2018 |title=PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems |journal=PLOS Computational Biology |volume=14 |issue=2 |pages=e1005991 |bibcode=2018PLSCB..14E5991G |doi=10.1371/journal.pcbi.1005991 |pmc=5841829 |pmid=29474446}}</ref>
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|[[OpenMP]]
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|[https://www.hoehme.com/software/tisim TiSim] (formerly CellSys)
|Center/agent-based, off-lattice, ODE solvers
|2D, 3D
|in preparation
|
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|Timothy<ref>{{Cite journal |last=Cytowski |first=Maciej |last2=Szymanska |first2=Zuzanna |date=2014-09 |title=Large-Scale Parallel Simulations of 3D Cell Colony Dynamics |url=https://ieeexplore.ieee.org/document/6728930 |journal=Computing in Science & Engineering |volume=16 |issue=5 |pages=86–95 |doi=10.1109/MCSE.2014.2 |issn=1558-366X}}</ref>
|Center/agent-based
|3D
Line 144 ⟶ 198:
|[[C (programming language)|C]]
|[[Message Passing Interface|MPI]], [[OpenMP]]
|-
|URDME - DLCM workflow<ref>{{cite journal |vauthors=Engblom S, Wilson DB, Baker RE |date=August 2018 |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=1706.03375 |bibcode=2018RSOS....580379E |doi=10.1098/rsos.180379 |pmc=6124129 |pmid=30225024}}</ref><ref>{{Cite web |title=URDME |url=http://urdme.github.io/urdme/ |access-date=2022-04-05 |website=URDME |language=en-US}}</ref>
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|VirtualLeaf<ref>{{Citation |last=Antonovici |first=Claudiu-Cristi |title=Modeling Plant Tissue Development Using VirtualLeaf |date=2022 |url=https://doi.org/10.1007/978-1-0716-1816-5_9 |work=Plant Systems Biology: Methods and Protocols |pages=165–198 |editor-last=Lucas |editor-first=Mikaël |place=New York, NY |publisher=Springer |language=en |doi=10.1007/978-1-0716-1816-5_9 |isbn=978-1-0716-1816-5 |access-date=2022-11-08 |last2=Peerdeman |first2=Guacimo Y. |last3=Wolff |first3=Harold B. |last4=Merks |first4=Roeland M. H.}}</ref> (2021)
|Off-lattice
|
|https://github.com/
|Yes
|Yes
|[[C++]]
|
|-
|yalla<ref>{{Cite journal |last=Germann |first=Philipp |last2=Marin-Riera |first2=Miquel |last3=Sharpe |first3=James |date=2019-03-27 |title=ya{{!}}{{!}}a: GPU-Powered Spheroid Models for Mesenchyme and Epithelium |url=https://www.cell.com/cell-systems/abstract/S2405-4712(19)30068-7 |journal=Cell Systems |language=English |volume=8 |issue=3 |pages=261–266.e3 |doi=10.1016/j.cels.2019.02.007 |issn=2405-4712 |pmid=30904379}}</ref>
|Center/agent-based
|3D
|https://github.com/germannp/yalla
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|
|
|[[CUDA]], [[Graphics processing unit|GPU]]
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|Tyssue<ref>{{Cite journal |last=Theis |first=Sophie |last2=Suzanne |first2=Magali |last3=Gay |first3=Guillaume |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 |issn=2475-9066}}</ref>
|Vertex-based
|2D, 3D
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|Yes
|[[Python (programming language)|Python]]
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|-
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|[[MATLAB|Matlab]], [[C (programming language)|C]], [[Python (programming language)|Python]]
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