List of COVID-19 simulation models
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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[]
- Chen et al. simulation based on Bats-Hosts-Reservoir-People (BHRP) model (simplified to RP only)[6]
- CoSim19[7] - Prof Lehr, based on SEIRD model
- COVID-19 MOBILITY MODELING[8] - Stanford based on SEIR model[9]
- COVID-19 Simulator[10] - Harvard Medical School based on a validated system dynamics (compartment) model[11]
- COVID-19 Surge[12] - CDC[13]
- COVIDSIM[14] - by Mark Kok Yew Ng et al.
- CovidSim - Imperial College London, MRC Centre for Global Infectious Disease Analysis, Neil Ferguson et al.
- CovidSim[15] - Research project by Munich University of Applied Sciences, Prof Köster
- COVIDSim[16] - written in MATLAB[17] by Ng and Gui[18]
- CovidSIM.eu[19] - Martin Eichner, Markus Schwehm supported by University of Tübingen and sponsored by the German Federal Ministry of Education and Research.[20]
- CovidSIM[21] - Schneider et al.
- CovRadar[22] - for molecular surveillance of the Corona spike protein[23][24]
- Dr. Ghaffarzadegan’s model[25][26][27]
- Event Horizon - COVID-19[28] - HU Berlin based on SIR-X model[29]
- Evolutionary AI[30] - "Non-pharmaceutical interventions (NPIs) that the AI generates for different countries and regions over time, their predicted effect."[31][32][33]
- IHME model - Institute for Health Metrics and Evaluation COVID model
- OxCGRT[34] - The Oxford COVID-19 Government Response Tracker[35][33]
- SC-COSMO[36] - Stanford-CIDE Coronavirus Simulation Model
- SECIR[37][38][39][40] - Model by Helmholtz Centre for Infection Research
- Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation[41][42]
- SIAM's Epidemiology Collection[43]
- Youyang Gu COVID model
Genome databases[]
Several of these models make use of genome databases, including the following:
- DNA Data Bank of Japan
- European Nucleotide Archive
- GISAID
- Phylogenetic Assignment of Named Global Outbreak Lineages
Consortia, research clusters, other collections[]
- CDC list of Forecast Inclusion and Assumptions[44] - large list with different models, etc.
- CORSMA - EU consortium (COVID-19-Outbreak Response combining E-health, Serolomics, Modelling, Artificial Intelligence and Implementation Research)[45]
- COVID-19 Forecast Hub[46] - Serves as a central repository of forecasts and predictions from over 50 international research groups.[47][48]
- Nextstrain - Open-source project to harness the scientific and public health potential of pathogen genome data[49]
- See also Nextstrain SARS-CoV-2 resources[50]
- SIMID[51] - Simulation Models of Infectious Diseases - Belgium research consortium
- RAMP - Rapid Assistance in Modelling the Pandemic[52] (UK)
- UT Austin COVID-19 Modeling Consortium[53]
- 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.[54] (See for example the: The COVID-19 Forecast Hub)[55]
- COVID-19 Dashboard[56] - Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)[57][58]
- COVIDVaxView by the CDC[59]
- Datahub Novel Coronavirus 2019 dataset[60][61] - COVID-19 dataset Coronavirus disease 2019 (COVID-19) time series listing confirmed cases, reported deaths and reported recoveries.
- Impfdashboard.de - Germany's vaccination monitor[62]
- Simulation der COVID19-Impfkampagne[63] - Monitor for vaccination-campaign in Germany by Zi Data Science Lab
- The Institute for Health Metrics and Evaluation (IHME) COVID-19 Projections[64]
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[65]
- COVID19: Top 7 - A curated list[66] posted on Medium[67]
- github.com/topics: covid-19[68]
- ISEE Systems COVID-19 Simulator[69]
- nCoV2019.live[70] - "Numbers you need at a quick glance" by Schiffmann/Conlon
- cov19.cc- by Conlon[71]
- Simul8 - COVID-19 Simulation Resources[72]
- Simulating coronavirus with the SIR model[73]
- Virus Spread Simulation[74]
[]
- (American Chemical Society) CAS COVID-19 BIOINDICATOR EXPLORER[75]
- CDC's COVID Data Tracker[76]
- Civil Society Partners in Solidarity against COVID-19 (CSPAC): Full, live, global, COVID-19 Status Report for 251 locales & 71 Ships[77]
- Cornell Institute for Social & Economic Research (CISER): COVID-19 Data Sources[78]
- Eulerian–Lagrangian multiphase modeling, e. g. for transmission of COVID-19 in elevators based on CFD[79]
- Onset of Symptoms of COVID-19 simulation (Stochastic Progression Model) by Larsen et al.[80]
- Our World in Data's Coronavirus Source Data[81]
- The Atlantic's COVID 19 Tracking Project[82]
- Vadere - Open Source Framework for Pedestrian and Crowd Simulation[83]
- WHO Coronavirus (COVID-19) Dashboard[84]
Trainings and other resources[]
- Infectious Disease Modelling Specialization - provided on Coursera by Imperial College London
- Introducing the COVID-19 Simulator and Machine Learning Toolkit for Predicting COVID-19 Spread - AWS Machine Learning Blog
See also[]
- SIR Model
- Computer simulation
- Mathematical modelling of infectious disease
- Computational biology
- Bioinformatics
References[]
- ^ 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.
- ^ Brierley L. "The role of research preprints in the academic response to the COVID-19 epidemic". doi:10.22541/au.158516578.89167184. Cite journal requires
|journal=(help) - ^ "Another 178,000 deaths? Scientists' latest virus projection is a warning". NBC News. Retrieved 2021-02-22.
- ^ Tufekci Z (2020-04-02). "Don't Believe the COVID-19 Models". The Atlantic. Retrieved 2021-02-22.
- ^ Gonçalves B (2020-09-09). "Epidemic Modeling 102: All CoVID-19 models are wrong, but some are useful". Medium. Retrieved 2021-02-22.
- ^ 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.
- ^ CoSim19 shiny.covid-simulator.com
- ^ COVID-19 MOBILITY MODELING covid-mobility.stanford.edu
- ^ 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.
- ^ COVID-19 Simulator covid19sim.org
- ^ "Policy Simulator Methodology". COVID-19 Simulator. Retrieved 2021-02-21.
- ^ COVID-19 Surge www.cdc.gov
- ^ CDC (2020-02-11). "Healthcare Workers". Centers for Disease Control and Prevention. Retrieved 2021-02-22.
- ^ COVIDSIM www.markusng.com
- ^ CovidSim www.hm.edu
- ^ COVIDSim github.com/nkymark
- ^ Ng M (2020-12-23), nkymark/COVIDSim, retrieved 2021-03-09
- ^ 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.
- ^ CovidSIM.eu covidsim.eu
- ^ "CovidSIM". covidsim.eu. Retrieved 2021-03-13.
- ^ 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.
- ^ CovRadar covradar.net
- ^ 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.
- ^ "Molecular surveillance of SARS-CoV-2 spike protein mutations using CovRadar". News-Medical.net. 2021-02-07. Retrieved 2021-04-25.
- ^ "Dr. Ghaffarzadegan's model - Simulate your university's covid-19 cases". forio.com. Retrieved 2 May 2021.
- ^ 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.
- ^ "COVID-19 simulation model creates scenarios". www.vtnews.vt.edu. Retrieved 2021-02-21.
- ^ Event Horizon - COVID-19 rocs.hu-berlin.de
- ^ 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.
- ^ Evolutionary AI evolution.ml
- ^ "Evolutionary AI". evolution.ml. Retrieved 2021-04-26.
- ^ 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].
- ^ 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.
- ^ OxCGRT www.bsg.ox.ac.uk
- ^ "COVID-19 Government Response Tracker". www.bsg.ox.ac.uk. Retrieved 2021-04-26.
- ^ SC-COSMO www.sc-cosmo.org
- ^ 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: 2020.04.04.20053637. doi:10.1101/2020.04.04.20053637. hdl:10033/622727. S2CID 215782202.
- ^ "simm / covid19 / SECIR". GitLab. Retrieved 2021-07-05.
- ^ "Report · Wiki · simm / covid19 / SECIR". GitLab. Retrieved 2021-07-05.
- ^ "Our research". Helmholtz Centre for Infection Research. Retrieved 2021-07-05.
- ^ - Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigationcorona-lab.ch, accessed 28 April 2021
- ^ 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. doi:10.1101/2020.11.30.20239566. S2CID 227247293.
- ^ Epidemiology Collection epubs.siam.org
- ^ CDC list of Forecast Inclusion and Assumptions www.cdc.gov
- ^ "CORESMA". CORESMA. Retrieved 2021-07-05.
- ^ COVID-19 Forecast Hub
- ^ 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.
- ^ "Home - COVID 19 forecast hub". covid19forecasthub.org. Retrieved 2021-02-21.
- ^ "Nextstrain". nextstrain.org. Retrieved 2021-04-26.
- ^ Nextstrain SARS-CoV-2 resources nextstrain.org/sars-cov-2
- ^ SIMID www.simid.be
- ^ "Rapid Assistance in Modelling the Pandemic: RAMP | Royal Society". royalsociety.org. Retrieved 2021-03-09.
- ^ UT Austin COVID-19 Modeling Consortium covid-19.tacc.utexas.edu
- ^ CDC (2020-02-11). "Coronavirus Disease 2019 (COVID-19) - COVID-19 Forecasting: Background Information". Centers for Disease Control and Prevention. Retrieved 2021-10-03.
- ^ "About the Hub - COVID 19 forecast hub". covid19forecasthub.org. Retrieved 2021-10-03.
- ^ COVID-19 Dashboard coronavirus.jhu.edu
- ^ "COVID-19 Map". Johns Hopkins Coronavirus Resource Center. Retrieved 2021-04-26.
- ^ 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.
- ^ "COVIDVaxView | CDC". www.cdc.gov. 2021-09-23. Retrieved 2021-10-03.
- ^ Datopian; Open Knowledge International. "Novel Coronavirus 2019". DataHub.io. Retrieved 2021-05-02.
- ^ datasets/covid-19, Data Packaged Core Datasets at GitHub, 2021-05-02, retrieved 2021-05-02
- ^ Bundesministerium für Gesundheit. "Das offizielle Dashboard zur Impfkampagne der Bundesrepublik Deutschland". impfdashboard.de (in German). Retrieved 2021-06-07.
- ^ Simulation der COVID19-Impfkampagne
- ^ COVID-19 Projections covid19.healthdata.org
- ^ Covid-19 Simulator www.coronasimulator.com, accessed 28 April 2021
- ^ COVID19: Top 7 - A curated list towardsdatascience.com
- ^ Prabowo A (2020-05-03). "COVID19: Top 7 online interactive simulations, curated". Medium. Retrieved 2021-02-21.
- ^ covid-19 github.com/topics
- ^ COVID-19 Simulator exchange.iseesystems.com
- ^ nCoV2019.live ncov2019.live
- ^ cov19.cc
- ^ "COVID-19 Simulation Resources". Retrieved 2020-02-21.
- ^ Simulating coronavirus with the SIR model fatiherikli.github.io
- ^ Virus Spread Simulation c19model.com
- ^ "CAS COVID-19 Resources". CAS. Retrieved 2021-06-02.
- ^ COVID Data Tracker covid.cdc.gov
- ^ "Full, live, global, COVID-19 Status Report for 251 locales & 71 Ships". civilsocietysolidarityagainstcovid19.com. Retrieved 2021-07-01.
- ^ COVID-19 Data Sources guides.library.cornell.edu
- ^ 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.
- ^ 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.
- ^ Coronavirus Source Data ourworldindata.org
- ^ COVID 19 Tracking Project covidtracking.com
- ^ Vadere - Open Source Framework for Pedestrian and Crowd Simulation www.vadere.org
- ^ "WHO Coronavirus (COVID-19) Dashboard". covid19.who.int. Retrieved 2021-07-01.
Further reading[]
- 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 214771531.
- Alper J. "WXML 2020 covid-modeling learning guide". Department of Mathematics. Seattle, Washington: University of Washington.
- Fuller J (March 2021). "What are the COVID-19 models modeling (philosophically speaking)?". History and Philosophy of the Life Sciences. 43 (2): 47. doi:10.1007/s40656-021-00407-5. PMC 7994354. PMID 33770267.
- Prabha S, Karthikeyan P, Kamalanand K, Selvaganesan N (July 2021). Prabha S, Karthikeyan P, Kamalanand K, Selvaganesan N (eds.). Computational Modelling and Imaging for SARS-CoV-2 and COVID-19 (1 ed.). Boca Raton: CRC Press. doi:10.1201/9781003142584. ISBN 978-1-003-14258-4. S2CID 237802484.
- Roberts M, Driggs D, Selby I, Sala E, Schönlieb CB (1 June 2021). "Fighting a Pandemic with Medical Imaging and Machine Learning: Lessons Learned from COVID-19". SIAM News.
Categories:
- COVID-19 models