Monthly Archives: September 2020

Online Tools to fight the COVID-19 pandemic (updated 07-Sep-2020)

ToolLinkMain InstitutionNationArchitectureTagsProsCons
Epidemiology
JHU COVID-19 Dashboardhttp://coronavirus.jhu.edu/map.htmlJohns Hopkins UniversityUSAPythonDashboard, Interactive Map, Trend Assessment, WorldwideFrequently Updated, Quick Assessment, Worldwide Analysis 
DSCovRhttp://msph.shinyapps.io/dscovr_dashboardColumbia UniversityUSAShiny/RDashboard, Interactive Map, Trend AssessmentComparative Region Analysis, Demographics IncludedSlow to load, Focused on USA
WHO Dashboardhttp://covid19.who.intWHOWorldwideJavaScriptDashboard, Interactive Map, WorldwideComparative Region Analysis, Easy to Use, Frequently Updated, Quick Assessment, Worldwide Analysis 
Worldometershttp://worldometers.info/coronavirusWorldometers.infoUSAJavaScriptSpreadsheet, WorldwideEasy to Use, Frequently Updated, Quick Assessment, Worldwide Analysis 
COVID-19 Scenarioshttp://covid19-scenarios.orgUniversity of BaselSwitzerlandJavaScriptInteractive Simulator, WorldwideDemographics Included, High Number of ParametersNon-trivial to tailor the simulation for specific regions
Harvard COVID-19 Simulatorhttp://covid19sim.orgHarvard Medical SchoolUSARInteractive SimulatorFrequently UpdatedFocused on USA
CovidSIMhttp://covidsim.euExploSYS GmbHGermanyJavaScriptInteractive SimulatorHigh Number of ParametersNon-trivial to tailor the simulation for specific regions
COVID-19 Trajectory viewerhttp://apps.health-atlas.de/covid-19-grapher/University of LeipzigGermanyShiny/RInteractive SimulatorComparative Region Analysis 
COVID-19 Exit Strategieshttp://scienceversuscorona.shinyapps.io/covid-exit/Science versus Corona initiativeWorldwideShiny/RInteractive SimulatorComparison of Several Exit StrategiesTunable Parameters are Few
Greifswald COVID-19 Simulatorhttp://kaderali.org:3838/covidsimUniversity of GreifswaldGermanyShiny/RInteractive SimulatorPredict Effect of Social Contact ReductionFocused on specific countries and German regions
COVID19-Trackerhttp://ubidi.shinyapps.io/covid19Bellvitge Biomedical Research InstituteSpainShiny/RCase Number Visualizer and PredictorFrequently UpdatedFocused on Spain
Genomics
GISAIDhttp://gisaid.orgGISAIDWorldwideCMS TYPO3Data Repository, WorldwideDatabase Fully Downloadable, Frequently Updated, Precomputed Multiple Sequence Alignment 
Nextstrainhttp://nextstrain.org/ncov/globalUniversity of BaselSwitzerlandPythonDashboard, Nucleotide Mutation Analysis, Phylogenesis, WorldwideFrequently Updated, Simulation of Mutation Spread over Time, WorldwideDifficult to zoom into specific regions of the interactive phylogenetic tree
Covidexhttp://cacciabue.shinyapps.io/shiny2University of LujánArgentinaShiny/RPhylogenetic CategorizationAllows User-provided Data, Intuitive TutorialWorks exclusively with User-provided Data
Coronapphttp://giorgilab.dyndns.org/coronappUniversity of BolognaItalyShiny/RAmino Acid Mutation Analysis, Nucleotide Mutation Analysis, Frequency of Mutations over TimeAllows User-provided Data, Nucleotide and Protein Mutations, WorldwideSlow to load
COVID-19 Genotyping Toolhttp://covidgenotyper.appUniversity of TorontoCanadaShiny/RPhylogenetic Categorization via 2D clusteringAllows User-provided DataAnalysis is very slow, Maximum number of sequences is only 10
Pangolinhttp://pangolin.cog-uk.ioCentre for Genomic Pathogen SurveillanceUnited KingdomPythonPhylogenetic Categorization, Lineage AssignerAllows User-provided Data, Intuitive Assignment of LineageAnalysis is slow
SARS-CoV-2 Alignment Screenhttp://macman123.shinyapps.io/ugi-scov2-alignment-screenUniversity College LondonUnited KingdomShiny/RNucleotide Mutation AnalysisMutation Analysis can be Focused on specific Genomic Regions or GenesNot frequently updated
CoV-GLUEhttp://cov-glue.cvr.gla.ac.ukUniversity of GlasgowUnited KingdomJavaScriptAmino Acid Mutation Analysis, Nucleotide Mutation Analysis, SpreadsheetMutation Analysis can be Focused on specific Genomic Regions or Genes, Mutations Categorized as Replacements/Insertions/Deletions 
Coronavirus3Dhttp://coronavirus3d.orgUniversity of California RiversideUSAJavaScriptAmino Acid Mutation Analysis, 3D StructureAllows to project mutations on viral protein structures from PDB, Frequently Updated 
Interactomics
CoVexhttp://exbio.wzw.tum.de/covex/explorerTechnical University of MunichGermanyJavaScriptInteractome VisualizerAllows to identify Known Drugs for selected Target Proteins 
VirHostNet 2.0http://virhostnet.prabi.frUniversity of LyonFranceCytoscape webInteractome VisualizerPrediction of novel interactions on user-provided protein sequencesAnalysis is slow
P-HIPSTerhttp://phipster.orgColumbia UniversityUSAJavaScriptInteraction ListPrediction of novel interactions using sequence- and structure-based machine learningNot focused on SARS-CoV-2
Pharmacology
COVID-19 Gene/Drug Set Libraryhttp://amp.pharm.mssm.edu/covid19Icahn School of Medicine Mount SinaiUSAJavaScriptCurated Lists of Genes and DrugsLists can be Searched, New Sets can be ProposedNo link with external databases
canSARhttp://corona.cansar.icr.ac.ukCRUK Cancer Therapeutics UnitUnited KingdomJavaScriptDatabase of Clinical Trials, Drugs and Druggable TargetsIntuitive Visualization of Druggable Interactome, Drug Prediction 
CORDITEhttp://cordite.mathematik.uni-marburg.deUniversity of MarburgGermanyJavaScriptDatabase of Clinical Trials, Drugs and Druggable TargetsQuick SearchNot Frequently Updated
COVID-19 Disease Maphttp://covid19map.lcsb.uni.lu/MinervaUniversity of LuxemburgLuxemburgJavaScriptDatabase of Drugs and PathwaysSearch for relevant interactions between viral proteins and human pathwaysInteractome Labels are hard to read, Not Frequently Updated, No Examples provided, Not focused on SARS-CoV-2
CoV-Hipathiahttp://hipathia.babelomics.org/covid19Foundation for Progress and HealthSpainWeb ComponentsAnalysis of Druggable Pathways affected by Gene Expression ChangesAllows User-provided DataAnalysis is slow
Chemical Checkerhttp://sbnb.irbbarcelona.org/covid19Institute for Research in BiomedicineSpainJavaScriptDatabase of DrugsDrugs Ranked by Evidence Quality and Quantity, Frequently Updated 
Clinical Trialshttp://clinicaltrials.gov/ct2/who_tableWHO/NIHUnited StatesJavaScriptDatabase of Clinical TrialsFrequently Updated, Fully ComprehensiveNot categorized by Drugs