Jump to content

List of COVID-19 simulation models: Difference between revisions

From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
Citation bot (talk | contribs)
Bots
5,221,215 edits
Add: doi. | Use this bot. Report bugs. | Suggested by Whoop whoop pull up | #UCB_webform 788/841
No edit summary
Line 39: Line 39:
* Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation<ref>[https://corona-lab.ch - Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation]''corona-lab.ch'', accessed 28 April 2021</ref><ref>{{Cite medRxiv |vauthors=Gorji H, Arnoldini M, Jenny DF, Hardt WD, Jenny P |date=2020-12-02 |title=Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation |language=en |medrxiv=10.1101/2020.11.30.20239566}}</ref>
* Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation<ref>[https://corona-lab.ch - Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation]''corona-lab.ch'', accessed 28 April 2021</ref><ref>{{Cite medRxiv |vauthors=Gorji H, Arnoldini M, Jenny DF, Hardt WD, Jenny P |date=2020-12-02 |title=Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation |language=en |medrxiv=10.1101/2020.11.30.20239566}}</ref>
* [[Youyang Gu COVID model]]
* [[Youyang Gu COVID model]]
* [[MechBayes COVID model]]


=== Genome databases ===
=== Genome databases ===

Revision as of 17:03, 2 November 2023

COVID-19 simulation models are mathematical infectious disease models for the spread of COVID-19.[1] The list should not be confused with COVID-19 apps used mainly for digital contact tracing.

Note that some of the applications listed are website-only models or simulators, and some of those rely on (or use) real-time data from other sources.

Models with the most scientific backing

The sub-list contains simulators that are based on theoretical models. Due to the high number of pre-print research created and driving by the COVID-19 pandemic,[2] especially newer models should only be considered with further scientific rigor.[3][4][5]

Simulations and models

Genome databases

Several of these models make use of genome databases, including the following:

Consortia, research clusters, other collections

  • CDC list of Forecast Inclusion and Assumptions[55] - large list with different models, etc.
  • CORSMA - EU consortium (COVID-19-Outbreak Response combining E-health, Serolomics, Modelling, Artificial Intelligence and Implementation Research)[56]
  • COVID-19 Forecast Hub[57] - Serves as a central repository of forecasts and predictions from over 50 international research groups.[58][59]
  • Nextstrain - Open-source project to harness the scientific and public health potential of pathogen genome data[60]
    • See also Nextstrain SARS-CoV-2 resources[61]
  • SIMID[62] - Simulation Models of Infectious Diseases - Belgium research consortium
  • RAMP - Rapid Assistance in Modelling the Pandemic[63] (UK)
  • UT Austin COVID-19 Modeling Consortium[64]
  • Computational Approaches to Foster Innovation in the Treatment and Diagnosis of Infectious Diseases by Frontiers

Vaccination monitors, models or dashboards

Note: The following (additional) resources are mostly based on actual data, not simulation. They might include predictive features, e. g. vaccination rate estimation, but in general are not based on theoretical or modeling grounds as the main list of this article. Nonetheless, forecasting remains important.[65] (See for example the COVID-19 Forecast Hub)[66]

Models with less scientific backing

The following models are purely for educational purposes only.

  • Cellular Defense Automata model
  • CoVariants - Overview of SARS-CoV-2 variants and mutations that are of interest
  • Covid-19 Simulator[76]
  • COVID19: Top 7 - A curated list[77] posted on Medium[78]
  • github.com/topics: covid-19[79]
  • ISEE Systems COVID-19 Simulator[80]
  • nCoV2019.live[81] - "Numbers you need at a quick glance" by Schiffmann/Conlon
    • cov19.cc- by Conlon[82]
  • Simul8 - COVID-19 Simulation Resources[83]
  • Simulating coronavirus with the SIR model[84]
  • Virus Spread Simulation[85]
  • (American Chemical Society) CAS COVID-19 BIOINDICATOR EXPLORER[86]
  • CDC's COVID Data Tracker[87]
  • Civil Society Partners in Solidarity against COVID-19 (CSPAC): Full, live, global, COVID-19 Status Report for 251 locales & 71 Ships[88]
  • Cornell Institute for Social & Economic Research (CISER): COVID-19 Data Sources[89]
  • Eulerian–Lagrangian multiphase modeling, e. g. for transmission of COVID-19 in elevators based on CFD[90]
  • Onset of Symptoms of COVID-19 simulation (Stochastic Progression Model) by Larsen et al.[91]
  • Our World in Data's Coronavirus Source Data[92]
  • The Atlantic's COVID 19 Tracking Project[93]
  • Vadere - Open Source Framework for Pedestrian and Crowd Simulation[94]
  • WHO Coronavirus (COVID-19) Dashboard[95]

Trainings and other resources

See also

References

  1. ^ Adam D (April 2020). "Special report: The simulations driving the world's response to COVID-19". Nature. 580 (7803): 316–318. Bibcode:2020Natur.580..316A. doi:10.1038/d41586-020-01003-6. PMID 32242115. S2CID 256820433.
  2. ^ Brierley L. "The role of research preprints in the academic response to the COVID-19 epidemic". Authorea Preprints. doi:10.22541/au.158516578.89167184.
  3. ^ "Another 178,000 deaths? Scientists' latest virus projection is a warning". NBC News. Retrieved 2021-02-22.
  4. ^ Tufekci Z (2020-04-02). "Don't Believe the COVID-19 Models". The Atlantic. Retrieved 2021-02-22.
  5. ^ Gonçalves B (2020-09-09). "Epidemic Modeling 102: All CoVID-19 models are wrong, but some are useful". Medium. Retrieved 2021-02-22.
  6. ^ Chen TM, Rui J, Wang QP, Zhao ZY, Cui JA, Yin L (February 2020). "A mathematical model for simulating the phase-based transmissibility of a novel coronavirus". Infectious Diseases of Poverty. 9 (1): 24. doi:10.1186/s40249-020-00640-3. PMC 7047374. PMID 32111262.
  7. ^ CoSim19 shiny.covid-simulator.com
  8. ^ COVID-19 MOBILITY MODELING covid-mobility.stanford.edu
  9. ^ Chang S, Pierson E, Koh PW, Gerardin J, Redbird B, Grusky D, Leskovec J (January 2021). "Mobility network models of COVID-19 explain inequities and inform reopening". Nature. 589 (7840): 82–87. Bibcode:2021Natur.589...82C. doi:10.1038/s41586-020-2923-3. PMID 33171481.
  10. ^ COVID-19 Simulator covid19sim.org
  11. ^ "Policy Simulator Methodology". COVID-19 Simulator. Retrieved 2021-02-21.
  12. ^ COVID-19 Surge www.cdc.gov
  13. ^ CDC (2020-02-11). "Healthcare Workers". Centers for Disease Control and Prevention. Retrieved 2021-02-22.
  14. ^ COVIDSIM www.markusng.com
  15. ^ CovidSim www.hm.edu
  16. ^ COVIDSim github.com/nkymark
  17. ^ Ng M (2020-12-23), nkymark/COVIDSim, retrieved 2021-03-09
  18. ^ Ng KY, Gui MM (October 2020). "COVID-19: Development of a robust mathematical model and simulation package with consideration for ageing population and time delay for control action and resusceptibility". Physica D: Nonlinear Phenomena. 411: 132599. arXiv:2004.01974. Bibcode:2020PhyD..41132599N. doi:10.1016/j.physd.2020.132599. PMC 7282799. PMID 32536738.
  19. ^ CovidSIM.eu covidsim.eu
  20. ^ "CovidSIM". covidsim.eu. Retrieved 2021-03-13.
  21. ^ Schneider KA, Ngwa GA, Schwehm M, Eichner L, Eichner M (November 2020). "The COVID-19 pandemic preparedness simulation tool: CovidSIM". BMC Infectious Diseases. 20 (1): 859. doi:10.1186/s12879-020-05566-7. PMC 7675392. PMID 33213360.
  22. ^ CovRadar covradar.net
  23. ^ Wittig A, Miranda F, Hölzer M, Altenburg T, Bartoszewicz JM, Dieckmann MA, et al. (2021-04-06). "CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance". bioRxiv 10.1101/2021.02.03.429146v2.
  24. ^ "Molecular surveillance of SARS-CoV-2 spike protein mutations using CovRadar". News-Medical.net. 2021-02-07. Retrieved 2021-04-25.
  25. ^ De-Leon H, Pederiva F (August 2020). "Particle modeling of the spreading of coronavirus disease (COVID-19)". Physics of Fluids. 32 (8): 087113. arXiv:2005.10357. Bibcode:2020PhFl...32h7113D. doi:10.1063/5.0020565. PMC 7441410. PMID 32848352.
  26. ^ De-Leon H, Pederiva F (July 2021). "Statistical mechanics study of the introduction of a vaccine against COVID-19 disease". Physical Review E. 104 (1): 014132. arXiv:2012.07306. Bibcode:2021PhRvE.104a4132D. doi:10.1103/PhysRevE.104.014132. PMID 34412259. S2CID 229155979.
  27. ^ "Dr. Ghaffarzadegan's model - Simulate your university's covid-19 cases". forio.com. Retrieved 2 May 2021.
  28. ^ Ghaffarzadegan N (2021-02-01). "Simulation-based what-if analysis for controlling the spread of Covid-19 in universities". PLOS ONE. 16 (2): e0246323. Bibcode:2021PLoSO..1646323G. doi:10.1371/journal.pone.0246323. PMC 7850497. PMID 33524045.
  29. ^ "COVID-19 simulation model creates scenarios". www.vtnews.vt.edu. Archived from the original on 2021-03-06. Retrieved 2021-02-21.
  30. ^ Event Horizon - COVID-19 rocs.hu-berlin.de
  31. ^ Maier BF, Brockmann D (May 2020). "Effective containment explains subexponential growth in recent confirmed COVID-19 cases in China". Science. 368 (6492): 742–746. arXiv:2002.07572. Bibcode:2020Sci...368..742M. doi:10.1126/science.abb4557. PMC 7164388. PMID 32269067.
  32. ^ Evolutionary AI evolution.ml
  33. ^ "Evolutionary AI". evolution.ml. Retrieved 2021-04-26.
  34. ^ Miikkulainen R, Francon O, Meyerson E, Qiu X, Sargent D, Canzani E, Hodjat B (2020-08-01). "From Prediction to Prescription: Evolutionary Optimization of Non-Pharmaceutical Interventions in the COVID-19 Pandemic". arXiv:2005.13766 [cs.NE].
  35. ^ a b "Can Computer Models Select the Best Public Health Interventions for COVID-19?". IEEE Spectrum: Technology, Engineering, and Science News. 5 January 2021. Retrieved 2021-04-26.
  36. ^ Abele D, Kühn MJ, Koslow W, Rack K, Siggel M, Kleinert J, et al. (2022-01-01). "MEmilio - a high performance Modular EpideMIcs simuLatIOn software". GitHub.
  37. ^ Kühn MJ, Abele D, Mitra T, Koslow W, Abedi M, Rack K, et al. (September 2021). "Assessment of effective mitigation and prediction of the spread of SARS-CoV-2 in Germany using demographic information and spatial resolution". Mathematical Biosciences. 339: 108648. doi:10.1016/j.mbs.2021.108648. PMC 8243656. PMID 34216635.
  38. ^ Kühn MJ, Abele D, Binder S, Rack K, Klitz M, Kleinert J, et al. (2021-04-28). "Regional opening strategies with commuter testing and containment of new SARS-CoV-2 variants". medRxiv 10.1101/2021.04.23.21255995.
  39. ^ Koslow W, Kühn MJ, Binder S, Klitz M, Abele D, Basermann A, et al. (2021-11-29). "Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant". medRxiv 10.1101/2021.07.09.21260257.
  40. ^ Shattock AJ, Le Rutte EA, Dünner RP, Sen S, Kelly SL, Chitnis N, Penny MA (March 2022). "Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland". Epidemics. 38 (7): 100535. Bibcode:2021PLSCB..17E9146H. doi:10.1016/j.epidem.2021.100535. PMC 8669952. PMID 34923396.
  41. ^ "Git-repository with open access source-code for OpenCOVID". GitHub. Swiss TPH. 2022-01-31. Retrieved 2022-02-15.
  42. ^ OxCGRT www.bsg.ox.ac.uk
  43. ^ "COVID-19 Government Response Tracker". www.bsg.ox.ac.uk. Retrieved 2021-04-26.
  44. ^ SC-COSMO www.sc-cosmo.org
  45. ^ SDL-PAND maps global pand.sdlps.com, accessed 2023-05-20
  46. ^ Khailaie S, Mitra T, Bandyopadhyay A, Schips M, Mascheroni P, Vanella P, et al. (2020-04-07). "Estimate of the development of the epidemic reproduction number Rt from Coronavirus SARS-CoV-2 case data and implications for political measures based on prognostics". medRxiv 10.1101/2020.04.04.20053637v1.
  47. ^ "simm / covid19 / SECIR". GitLab. Retrieved 2021-07-05.
  48. ^ "Report · Wiki · simm / covid19 / SECIR". GitLab. Retrieved 2021-07-05.
  49. ^ "Our research". Helmholtz Centre for Infection Research. Retrieved 2021-07-05.
  50. ^ Syga S, David-Rus D, Schälte Y, Hatzikirou H, Deutsch A (November 2021). "Inferring the effect of interventions on COVID-19 transmission networks". Scientific Reports. 11 (1): 21913. arXiv:2012.03846. Bibcode:2021NatSR..1121913S. doi:10.1038/s41598-021-01407-y. PMC 8578219. PMID 34754025.
  51. ^ Epidemiology Collection epubs.siam.org
  52. ^ Kastalskiy IA, Pankratova EV, Mirkes EM, Kazantsev VB, Gorban AN (November 2021). "Social stress drives the multi-wave dynamics of COVID-19 outbreaks". Scientific Reports. 11 (1): 22497. arXiv:2106.08966. Bibcode:2021NatSR..1122497K. doi:10.1038/s41598-021-01317-z. PMC 8602246. PMID 34795311.
  53. ^ - Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigationcorona-lab.ch, accessed 28 April 2021
  54. ^ Gorji H, Arnoldini M, Jenny DF, Hardt WD, Jenny P (2020-12-02). "Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation". medRxiv 10.1101/2020.11.30.20239566.
  55. ^ CDC list of Forecast Inclusion and Assumptions www.cdc.gov
  56. ^ "CORESMA". CORESMA. Retrieved 2021-07-05.
  57. ^ COVID-19 Forecast Hub
  58. ^ Best R, Boice J (2020-05-01). "Where The Latest COVID-19 Models Think We're Headed — And Why They Disagree". FiveThirtyEight. Retrieved 2021-02-21.
  59. ^ "Home - COVID 19 forecast hub". covid19forecasthub.org. Retrieved 2021-02-21.
  60. ^ "Nextstrain". nextstrain.org. Retrieved 2021-04-26.
  61. ^ Nextstrain SARS-CoV-2 resources nextstrain.org/sars-cov-2
  62. ^ SIMID www.simid.be
  63. ^ "Rapid Assistance in Modelling the Pandemic: RAMP | Royal Society". royalsociety.org. Retrieved 2021-03-09.
  64. ^ UT Austin COVID-19 Modeling Consortium covid-19.tacc.utexas.edu
  65. ^ CDC (2020-02-11). "Coronavirus Disease 2019 (COVID-19) - COVID-19 Forecasting: Background Information". Centers for Disease Control and Prevention. Retrieved 2021-10-03.
  66. ^ "About the Hub - COVID 19 forecast hub". covid19forecasthub.org. Retrieved 2021-10-03.
  67. ^ COVID-19 Dashboard coronavirus.jhu.edu
  68. ^ "COVID-19 Map". Johns Hopkins Coronavirus Resource Center. Retrieved 2021-04-26.
  69. ^ Dong E, Du H, Gardner L (May 2020). "An interactive web-based dashboard to track COVID-19 in real time". The Lancet. Infectious Diseases. 20 (5): 533–534. doi:10.1016/S1473-3099(20)30120-1. PMC 7159018. PMID 32087114.
  70. ^ "COVIDVaxView | CDC". www.cdc.gov. 2021-09-23. Retrieved 2021-10-03.
  71. ^ Datopian; Open Knowledge International. "Novel Coronavirus 2019". DataHub.io. Retrieved 2021-05-02.
  72. ^ datasets/covid-19, Data Packaged Core Datasets at GitHub, 2021-05-02, retrieved 2021-05-02
  73. ^ Bundesministerium für Gesundheit. "Das offizielle Dashboard zur Impfkampagne der Bundesrepublik Deutschland". impfdashboard.de (in German). Retrieved 2021-06-07.
  74. ^ Simulation der COVID19-Impfkampagne
  75. ^ COVID-19 Projections covid19.healthdata.org
  76. ^ Covid-19 Simulator www.coronasimulator.com, accessed 28 April 2021
  77. ^ COVID19: Top 7 - A curated list towardsdatascience.com
  78. ^ Prabowo A (2020-05-03). "COVID19: Top 7 online interactive simulations, curated". Medium. Retrieved 2021-02-21.
  79. ^ covid-19 github.com/topics
  80. ^ COVID-19 Simulator exchange.iseesystems.com
  81. ^ nCoV2019.live ncov2019.live
  82. ^ "cov19.cc". Retrieved 18 August 2023.
  83. ^ "COVID-19 Simulation Resources". Retrieved 2020-02-21.
  84. ^ "Simulating coronavirus with the SIR model". fatiherikli.github.io. Archived from the original on 2021-04-19. Retrieved 2021-02-21.
  85. ^ Virus Spread Simulation c19model.com
  86. ^ "CAS COVID-19 Resources". CAS. Retrieved 2021-06-02.
  87. ^ COVID Data Tracker covid.cdc.gov
  88. ^ "Full, live, global, COVID-19 Status Report for 251 locales & 71 Ships". civilsocietysolidarityagainstcovid19.com. Retrieved 2021-07-01.
  89. ^ COVID-19 Data Sources guides.library.cornell.edu
  90. ^ Dbouk T, Drikakis D (January 2021). "On airborne virus transmission in elevators and confined spaces". Physics of Fluids. 33 (1): 011905. Bibcode:2021PhFl...33a1905D. doi:10.1063/5.0038180. PMC 7984422. PMID 33790526.
  91. ^ Larsen JR, Martin MR, Martin JD, Kuhn P, Hicks JB (2020). "Modeling the Onset of Symptoms of COVID-19". Frontiers in Public Health. 8: 473. doi:10.3389/fpubh.2020.00473. PMC 7438535. PMID 32903584.
  92. ^ Coronavirus Source Data ourworldindata.org
  93. ^ COVID 19 Tracking Project covidtracking.com
  94. ^ Vadere - Open Source Framework for Pedestrian and Crowd Simulation www.vadere.org
  95. ^ "WHO Coronavirus (COVID-19) Dashboard". covid19.who.int. Retrieved 2021-07-01.

Further reading

Articles

Books

Retrieved from "https://en.wikipedia.org/w/index.php?title=List_of_COVID-19_simulation_models&oldid=1183175027"