23 datasets found
  1. n

    Coronavirus (Covid-19) Data in the United States

    • nytimes.com
    • openicpsr.org
    • +2more
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    New York Times, Coronavirus (Covid-19) Data in the United States [Dataset]. https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
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    Dataset provided by
    New York Times
    Description

    The New York Times is releasing a series of data files with cumulative counts of coronavirus cases in the United States, at the state and county level, over time. We are compiling this time series data from state and local governments and health departments in an attempt to provide a complete record of the ongoing outbreak.

    Since late January, The Times has tracked cases of coronavirus in real time as they were identified after testing. Because of the widespread shortage of testing, however, the data is necessarily limited in the picture it presents of the outbreak.

    We have used this data to power our maps and reporting tracking the outbreak, and it is now being made available to the public in response to requests from researchers, scientists and government officials who would like access to the data to better understand the outbreak.

    The data begins with the first reported coronavirus case in Washington State on Jan. 21, 2020. We will publish regular updates to the data in this repository.

  2. j

    Coronavirus COVID-19 Global Cases by the Center for Systems Science and...

    • systems.jhu.edu
    • github.com
    • +1more
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    Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE), Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU) [Dataset]. https://systems.jhu.edu/research/public-health/ncov/
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    Dataset provided by
    Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE)
    Area covered
    Global
    Description

    2019 Novel Coronavirus COVID-19 (2019-nCoV) Visual Dashboard and Map:
    https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

    • Confirmed Cases by Country/Region/Sovereignty
    • Confirmed Cases by Province/State/Dependency
    • Deaths
    • Recovered

    Downloadable data:
    https://github.com/CSSEGISandData/COVID-19

    Additional Information about the Visual Dashboard:
    https://systems.jhu.edu/research/public-health/ncov

  3. covid visualization with leaflet heatmap - Dataset - HiDALGO CKAN portal

    • ckan.hidalgo-project.eu
    Updated Apr 27, 2020
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    ckan.hidalgo-project.eu (2020). covid visualization with leaflet heatmap - Dataset - HiDALGO CKAN portal [Dataset]. https://ckan.hidalgo-project.eu/dataset/jquery-csv-min-js
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    Dataset updated
    Apr 27, 2020
    Dataset provided by
    CKANhttps://ckan.org/
    Description

    Includes a staic and dynamic visualization of sample data of Covid Infections in London. Open: - static visualization of covid infections - dynamicCovidVisualization

  4. a

    Heat Charts

    • coronavirus-response-moco.hub.arcgis.com
    Updated May 30, 2020
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    Montgomery County, Texas IT-GIS (2020). Heat Charts [Dataset]. https://coronavirus-response-moco.hub.arcgis.com/app/heat-charts
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    Dataset updated
    May 30, 2020
    Dataset authored and provided by
    Montgomery County, Texas IT-GIS
    Description

    A story map featuring heat charts relating to coronavirus cases in Montgomery County, Texas.

  5. a

    Region Hot Spot WebMap

    • resources-covid19canada.hub.arcgis.com
    Updated Sep 9, 2020
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    COVID-19 Canada (2020). Region Hot Spot WebMap [Dataset]. https://resources-covid19canada.hub.arcgis.com/maps/ac7ec85ca2be4f01aa522f00c8051264
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    Dataset updated
    Sep 9, 2020
    Dataset authored and provided by
    COVID-19 Canada
    Area covered
    Description

    How to Read the map.This map allows you to visualize the trends over time and cases, recoveries, deaths and testing at the regional health unit. The Map shows the relative state of the COVID-19 outbreak in each region. Colour (red to green) shows the time since a new reported case.

    7 Day Hot Spots

    The map highlights regions with an active outbreak with a "glowing ball". The size of the ball reflects the average number of new cases in the past 7 days as a rate per 100K population.

    High

    Low

    Important InformationNot all data is reported for all regional health units. Data sources are consulted every 24 hours, however not all organizations report on a daily bases. As this data is cumulative, values carry-forward if updates are not provided. Values can go down due to corrected errors as reported. Data SourcesThe source of the data for each regional health unit is listed in the "SourceURL" field.

    Looking for the raw data? You can find it here.

  6. a

    Transmission Heatmap of COVID-19 India & Kerala (Viswaprabha)

    • hub.arcgis.com
    Updated Mar 13, 2020
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    viswaprabha (2020). Transmission Heatmap of COVID-19 India & Kerala (Viswaprabha) [Dataset]. https://hub.arcgis.com/maps/4665d945ad8e425482a2990bde73c8cd
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    Dataset updated
    Mar 13, 2020
    Dataset authored and provided by
    viswaprabha
    Area covered
    Description

    City-wise confirmed Covid-19 cases within India and specifically within KeralaFor discussions, please visit and follow the Facebook profile: https://www.facebook.com/viswaprabhaTo see the underlying live data, please visit this Google Sheet

  7. o

    FAIR raw data and heat maps of ARAP deposition modeling

    • explore.openaire.eu
    • data.niaid.nih.gov
    • +1more
    Updated Dec 2, 2020
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    Sabine Hofer; Norbert Hofstätter; Martin Himly (2020). FAIR raw data and heat maps of ARAP deposition modeling [Dataset]. http://doi.org/10.5281/zenodo.6641215
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    Dataset updated
    Dec 2, 2020
    Authors
    Sabine Hofer; Norbert Hofstätter; Martin Himly
    Description

    FAIR Supplementary Information and Raw Data for Hofer S. et al., 2021, SARS-CoV-2-Laden Respiratory Aerosol Deposition in the Lung Alveolar-Interstitial Region Is a Potential Risk Factor for Severe Disease: A Modeling Study, Journal of Personalized Medicine 11(5):431, DOI: https://doi.org/10.3390/jpm11050431 1. pdf/A of deposition heat maps (incl probability values) for 5 different ARAP modes 2. xls-formatted file of MPPD v3.04-derived deposition raw data sets for 5 different ARAP modes 3.-7. rpt-formatted MPPD v3.04 files of deposition raw data sets for 5 different ARAP modes 8.-12. csv-formatted files of MPPD v3.04-derived deposition raw data sets for 5 different ARAP modes 13. pdf/A of deposition heat maps (incl probability values) for 5 different ERAP modes (upon rehydration of ARAPs) 14. txt-formatted README file for Hofer et al 2021

  8. f

    DataSheet_1_Case report: Bilateral panuveitis resembling...

    • frontiersin.figshare.com
    docx
    Updated Jun 3, 2023
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    Tomohito Sato; Ryotaro Nihei; Daisuke Sora; Yoshiaki Nishio; Masaru Takeuchi (2023). DataSheet_1_Case report: Bilateral panuveitis resembling Vogt-Koyanagi-Harada disease after second dose of BNT162b2 mRNA COVID-19 vaccine.docx [Dataset]. http://doi.org/10.3389/fimmu.2022.967972.s001
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    docxAvailable download formats
    Dataset updated
    Jun 3, 2023
    Dataset provided by
    Frontiers
    Authors
    Tomohito Sato; Ryotaro Nihei; Daisuke Sora; Yoshiaki Nishio; Masaru Takeuchi
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a serious pandemic. COVID-19 vaccination is urgent needed for limiting SARS-CoV-2 outbreaks by herd immunity. Simultaneously, post-marketing surveillance to assess vaccine safety is important, and collection of vaccine-related adverse events has been in progress. Vision-threatening ophthalmic adverse events of COVID-19 vaccines are rare but are a matter of concern. We report a 45-year-old Japanese male with positive for HLA-DR4/HLA-DRB1*0405, who developed bilateral panuveitis resembling Vogt-Koyanagi-Harada (VKH) disease after the second dose of Pfizer-BioNTech COVID-19 mRNA (BNT162b2) vaccine. Glucocorticosteroid (GC) therapy combined with cyclosporine A (CsA) readily improved the panuveitis. The immune profile at the time of onset was analyzed using CyTOF technology, which revealed activations of innate immunity mainly consisting of natural killer cells, and acquired immunity predominantly composed of B cells and CD8+ T cells. On the other hand, the immune profile in the remission phase was altered by GC therapy with CsA to a profile composed primarily of CD4+ cells, which was considerably similar to that of the healthy control before the vaccination. Our results indicate that BNT162b2 vaccine may trigger an accidental immune cross-reactivity to melanocyte epitopes in the choroid, resulting in the onset of panuveitis resembling VKH disease.

  9. Geostatistical Analysis of SARS-CoV-2 Positive Cases in the United States

    • zenodo.org
    • data.niaid.nih.gov
    Updated Sep 17, 2020
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    Peter K. Rogan; Peter K. Rogan (2020). Geostatistical Analysis of SARS-CoV-2 Positive Cases in the United States [Dataset]. http://doi.org/10.5281/zenodo.4032708
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    Dataset updated
    Sep 17, 2020
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Peter K. Rogan; Peter K. Rogan
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Area covered
    United States
    Description

    Geostatistics analyzes and predicts the values associated with spatial or spatial-temporal phenomena. It incorporates the spatial (and in some cases temporal) coordinates of the data within the analyses. It is a practical means of describing spatial patterns and interpolating values for locations where samples were not taken (and measures the uncertainty of those values, which is critical to informed decision making). This archive contains results of geostatistical analysis of COVID-19 case counts for all available US counties. Test results were obtained with ArcGIS Pro (ESRI). Sources are state health departments, which are scraped and aggregated by the Johns Hopkins Coronavirus Resource Center and then pre-processed by MappingSupport.com.

    This update of the Zenodo dataset (version 6) consists of three compressed archives containing geostatistical analyses of SARS-CoV-2 testing data. This dataset utilizes many of the geostatistical techniques used in previous versions of this Zenodo archive, but has been significantly expanded to include analyses of up-to-date U.S. COVID-19 case data (from March 24th to September 8th, 2020):

    Archive #1: “1.Geostat. Space-Time analysis of SARS-CoV-2 in the US (Mar24-Sept6).zip” – results of a geostatistical analysis of COVID-19 cases incorporating spatially-weighted hotspots that are conserved over one-week timespans. Results are reported starting from when U.S. COVID-19 case data first became available (March 24th, 2020) for 25 consecutive 1-week intervals (March 24th through to September 6th, 2020). Hotspots, where found, are reported in each individual state, rather than the entire continental United States.

    Archive #2: "2.Geostat. Spatial analysis of SARS-CoV-2 in the US (Mar24-Sept8).zip" – the results from geostatistical spatial analyses only of corrected COVID-19 case data for the continental United States, spanning the period from March 24th through September 8th, 2020. The geostatistical techniques utilized in this archive includes ‘Hot Spot’ analysis and ‘Cluster and Outlier’ analysis.

    Archive #3: "3.Kriging and Densification of SARS-CoV-2 in LA and MA.zip" – this dataset provides preliminary kriging and densification analysis of COVID-19 case data for certain dates within the U.S. states of Louisiana and Massachusetts.

    These archives consist of map files (as both static images and as animations) and data files (including text files which contain the underlying data of said map files [where applicable]) which were generated when performing the following Geostatistical analyses: Hot Spot analysis (Getis-Ord Gi*) [‘Archive #1’: consecutive weeklong Space-Time Hot Spot analysis; ‘Archive #2’: daily Hot Spot Analysis], Cluster and Outlier analysis (Anselin Local Moran's I) [‘Archive #2’], Spatial Autocorrelation (Global Moran's I) [‘Archive #2’], and point-to-point comparisons with Kriging and Densification analysis [‘Archive #3’].

    The Word document provided ("Description-of-Archive.Updated-Geostatistical-Analysis-of-SARS-CoV-2 (version 6).docx") details the contents of each file and folder within these three archives and gives general interpretations of these results.

  10. r

    NSW Covid 19 Vaccination data

    • researchdata.edu.au
    Updated Sep 16, 2021
    + more versions
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    data.nsw.gov.au (2021). NSW Covid 19 Vaccination data [Dataset]. https://researchdata.edu.au/nsw-covid-19-vaccination/1769823
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    Dataset updated
    Sep 16, 2021
    Dataset provided by
    data.nsw.gov.au
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Area covered
    New South Wales
    Description

    The data displayed on the NSW vaccination map on nsw.gov.au is an important tool to help encourage the community to see the value of getting vaccinated to keep themselves and their loved ones safe. The Department of Customer Service has presented the data in a way that is easy to read and understand, but the data sources belong to the federal and state health agencies.\r \r This map is updated every Tuesdays and Fridays.

  11. f

    CpG Signature Profiling and Heatmap Visualization of SARS-CoV Genomes:...

    • figshare.com
    txt
    Updated Apr 5, 2025
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    Tahir Hussain Bhatti (2025). CpG Signature Profiling and Heatmap Visualization of SARS-CoV Genomes: Tracing the Genomic Divergence From SARS-CoV (2003) to SARS-CoV-2 (2019) [Dataset]. http://doi.org/10.6084/m9.figshare.28736501.v1
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    txtAvailable download formats
    Dataset updated
    Apr 5, 2025
    Dataset provided by
    figshare
    Authors
    Tahir Hussain Bhatti
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    ObjectiveThe primary objective of this study was to analyze CpG dinucleotide dynamics in coronaviruses by comparing Wuhan-Hu-1 with its closest and most distant relatives. Heatmaps were generated to visualize CpG counts and O/E ratios across intergenic regions, providing a clear depiction of conserved and divergent CpG patterns.Methods1. Data CollectionSource : The dataset includes CpG counts and O/E ratios for various coronaviruses, extracted from publicly available genomic sequences.Format : Data was compiled into a CSV file containing columns for intergenic regions, CpG counts, and O/E ratios for each virus.2. PreprocessingData Cleaning :Missing values (NaN), infinite values (inf, -inf), and blank entries were handled using Python's pandas library.Missing values were replaced with column means, and infinite values were capped at a large finite value (1e9).Reshaping :The data was reshaped into matrices for CpG counts and O/E ratios using meltpandas[] and pivot[] functions.3. Distance CalculationEuclidean Distance :Pairwise Euclidean distances were calculated between Wuhan-Hu-1 and other viruses using the scipy.spatial.distance.euclidean function.Distances were computed separately for CpG counts and O/E ratios, and the total distance was derived as the sum of both metrics.4. Identification of Closest and Distant RelativesThe virus with the smallest total distance was identified as the closest relative .The virus with the largest total distance was identified as the most distant relative .5. Heatmap GenerationTools :Heatmaps were generated using Python's seaborn library (sns.heatmap) and matplotlib for visualization.Parameters :Heatmaps were annotated with numerical values for clarity.A color gradient (coolwarm) was used to represent varying CpG counts and O/E ratios.Titles and axis labels were added to describe the comparison between Wuhan-Hu-1 and its relatives.ResultsClosest Relative :The closest relative to Wuhan-Hu-1 was identified based on the smallest Euclidean distance.Heatmaps for CpG counts and O/E ratios show high similarity in specific intergenic regions.Most Distant Relative :The most distant relative was identified based on the largest Euclidean distance.Heatmaps reveal significant differences in CpG dynamics compared to Wuhan-Hu-1 .Tools and LibrariesThe following tools and libraries were used in this analysis:Programming Language :Python 3.13Libraries :pandas: For data manipulation and cleaning.numpy: For numerical operations and handling missing/infinite values.scipy.spatial.distance: For calculating Euclidean distances.seaborn: For generating heatmaps.matplotlib: For additional visualization enhancements.File Formats :Input: CSV files containing CpG counts and O/E ratios.Output: PNG images of heatmaps.Files IncludedCSV File :Contains the raw data of CpG counts and O/E ratios for all viruses.Heatmap Images :Heatmaps for CpG counts and O/E ratios comparing Wuhan-Hu-1 with its closest and most distant relatives.Python Script :Full Python code used for data processing, distance calculation, and heatmap generation.Usage NotesResearchers can use this dataset to further explore the evolutionary dynamics of CpG dinucleotides in coronaviruses.The Python script can be adapted to analyze other viral genomes or datasets.Heatmaps provide a visual summary of CpG dynamics, aiding in hypothesis generation and experimental design.AcknowledgmentsSpecial thanks to the open-source community for developing tools like pandas, numpy, seaborn, and matplotlib.This work was conducted as part of an independent research project in molecular biology and bioinformatics.LicenseThis dataset is shared under the CC BY 4.0 License , allowing others to share and adapt the material as long as proper attribution is given.DOI: 10.6084/m9.figshare.28736501

  12. f

    Gene disruptive variants heatmap plots

    • figshare.com
    txt
    Updated Sep 15, 2022
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    Daniele Traversa (2022). Gene disruptive variants heatmap plots [Dataset]. http://doi.org/10.6084/m9.figshare.21118690.v3
    Explore at:
    txtAvailable download formats
    Dataset updated
    Sep 15, 2022
    Dataset provided by
    figshare
    Authors
    Daniele Traversa
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The folder contains the heatmap plots obtained from the gene burden analysis considering gene disruptive variants. The plots are provided in a static format (.jpeg) and in a more interactive one (.html). Additionally, tables generating the heatmaps are provided in a .txt file format.

  13. All atom simulations snapshots and contact maps analysis scripts for...

    • zenodo.org
    • data.niaid.nih.gov
    application/gzip, xz
    Updated May 13, 2020
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    Rodrigo A. Moreira; Rodrigo A. Moreira; Mateusz Chwastyk; Joseph L. Baker; Joseph L. Baker; Horacio V Guzman; Horacio V Guzman; Adolfo B. Poma; Adolfo B. Poma; Mateusz Chwastyk (2020). All atom simulations snapshots and contact maps analysis scripts for SARS-CoV-2002 and SARS-CoV-2 spike proteins with and without ACE2 enzyme [Dataset]. http://doi.org/10.5281/zenodo.3817447
    Explore at:
    application/gzip, xzAvailable download formats
    Dataset updated
    May 13, 2020
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Rodrigo A. Moreira; Rodrigo A. Moreira; Mateusz Chwastyk; Joseph L. Baker; Joseph L. Baker; Horacio V Guzman; Horacio V Guzman; Adolfo B. Poma; Adolfo B. Poma; Mateusz Chwastyk
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The dataset contains a total of 40 snapshots of the four trajectories (10 snapshots each system = two per replica x 5 replicas/system):

    1. SARS-CoV-2002 spike protein without ACE2
    2. SARS-CoV-2 spike protein without ACE2
    3. SARS-CoV-2002 spike protein with ACE2
    4. SARS-CoV-2 spike protein with ACE2

    Molecular dynamics simulation trajectories (320ns each) have been performed using the Amber ff14SB force field running with the Amber18 package at the the NSF-funded (OAC-1826915, OAC-1828163) ELSA high performance computing cluster at The College of New Jersey. Under the following simulation methodology:

    All-atom simulations were carried out with Amber18 (ambermd.org), and system components (protein, ions, water) were modeled with the included FF14SB and TIP3P parameter sets. Energy minimization used CPU pmemd, while later simulation stages used GPU pmemd. CoV2 and CoV1 systems with one RBD up (with/without ACE2) were solvated in 12 angstrom water shells. Cysteine residues identified in the initial models as having a disulfide bond (DB) were bonded using tLeap. All simulations used 0.150 M NaCl. Hydrogen mass repartitioning was applied only to the protein to enable a 4 fs timestep (https://pubs.acs.org/doi/abs/10.1021/ct5010406). The SHAKE algorithm was applied to hydrogens, and a real-space cutoff of 8 angstroms was used. Periodic boundary conditions were applied and PME was used for long-range electrostatics. Minimization was by steepest descent (2000 steps) followed by conjugate gradient (3000 steps). Heating used two stages: (1) NVT heating from 0 K to 100 K (50 ps), and (2) NPT heating from 100 K to 300 K (100 ps). Restraints of 10 kcal mol-1 angstrom-2 were applied during minimization and heating to C-alpha atoms. During 6 ns of equilibration at 300 K C-alpha restraints were gradually reduced from 10 kcal mol-1 angstrom-2 to 0.1 kcal mol-1 angstrom-2. Finally, restraints were released and 320 ns unrestrained production simulations were carried out for CoV2 and CoV1 systems. Production simulations began from the final equilibrated snapshots, and five copies of each system were simulated. As unrestrained systems can freely rotate we monitored simulations for any close contacts and found that in one copy of the CoV1 simulation without ACE2 and one RBD up that a few contacts close to 8 angstrom occur near the end of the 320 ns between the RBD and a different subdomain of the spike complex in a periodic image. However this did not influence analyzed structural properties which is verified by comparing results across simulations. The Monte Carlo barostat was used to maintain pressure (1 atm), and the Langevin thermostat was used to maintain 300 K temperature (collision frequency 1 ps-1), as implemented in Amber18. In aggregate, nearly 7 microseconds of simulation of systems ranging from 396,147 to 879,100 atoms was carried out for this work.
    For further details on the trajectories, please contact Joseph Baker (bakerj@tcnj.edu).

    Regarding the contact map analysis scripts (contactMaps_Analysis.tar.gz), they contain the following workflow:

    contactmap --> source files from contact_map executable
    process_nc.sh --> convert raw data from all-atom simulation to numbered PDB files and get the contact maps
    frequency.lua --> read a set of PDB files and output the frequency count for each contact
    consensus.fasta --> align sequence of Covid19 and SARS from Chimera
    consensus.lua --> read data previously generated and compute the frequency per residue, among other things.
    consensus.sh --> input information to consensus.lua
    consensus.gp --> gnuplot script to plot figures

    This dataset and the code is part of tripartite collaboration between:

    • The Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland (supported by the National Science Centre, Poland, under grant No. 2017/26/D/NZ1/0046)
    • Department of Chemistry, The College of New Jersey, New Jersey, United States (supported by National Science Foundation under grant numbers OAC-1826915 and OAC-1828163).
    • Jozef Stefan Institute, Ljubljana, Slovenia (supported by the Slovenian Research Agency (Funding No. P1-0055)).
  14. f

    Non-coding heatmap plots

    • figshare.com
    txt
    Updated Sep 15, 2022
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    Daniele Traversa (2022). Non-coding heatmap plots [Dataset]. http://doi.org/10.6084/m9.figshare.21118759.v1
    Explore at:
    txtAvailable download formats
    Dataset updated
    Sep 15, 2022
    Dataset provided by
    figshare
    Authors
    Daniele Traversa
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The folder contains the heatmap plots obtained from the gene burden analysis considering non-coding variants. The plots are provided in a static format (.jpeg) and in a more interactive one (.html). Additionally, tables generating the heatmaps are provided in a .txt file format.

  15. a

    Visualize A Space Time Cube in 3D

    • hub.arcgis.com
    • gemelo-digital-en-arcgis-gemelodigital.hub.arcgis.com
    Updated Dec 3, 2020
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    Society for Conservation GIS (2020). Visualize A Space Time Cube in 3D [Dataset]. https://hub.arcgis.com/maps/acddde8dae114381889b436fa0ff4b2f
    Explore at:
    Dataset updated
    Dec 3, 2020
    Dataset authored and provided by
    Society for Conservation GIS
    Description

    Stamp Out COVID-19An apple a day keeps the doctor away.Linda Angulo LopezDecember 3, 2020https://theconversation.com/coronavirus-where-do-new-viruses-come-from-136105SNAP Participation Rates, was explored and analysed on ArcGIS Pro, the results of which can help decision makers set up further SNAP-D initiatives.In the USA foods are stored in every State and U.S. territory and may be used by state agencies or local disaster relief organizations to provide food to shelters or people who are in need.US Food Stamp Program has been ExtendedThe Supplemental Nutrition Assistance Program, SNAP, is a State Organized Food Stamp Program in the USA and was put in place to help individuals and families during this exceptional time. State agencies may request to operate a Disaster Supplemental Nutrition Assistance Program (D-SNAP) .D-SNAP Interactive DashboardAlmost all States have set up Food Relief Programs, in response to COVID-19.Scroll Down to Learn more about the SNAP Participation Analysis & ResultsSNAP Participation AnalysisInitial results of yearly participation rates to geography show statistically significant trends, to get acquainted with the results, explore the following 3D Time Cube Map:Visualize A Space Time Cube in 3Dhttps://arcg.is/1q8LLPnetCDF ResultsWORKFLOW: a space-time cube was generated as a netCDF structure with the ArcGIS Pro Space-Time Mining Tool : Create a Space Time Cube from Defined Locations, other tools were then used to incorporate the spatial and temporal aspects of the SNAP County Participation Rate Feature to reveal and render statistically significant trends about Nutrition Assistance in the USA.Hot Spot Analysis Explore the results in 2D or 3D.2D Hot Spotshttps://arcg.is/1Pu5WH02D Hot Spot ResultsWORKFLOW: Hot Spot Analysis, with the Hot Spot Analysis Tool shows that there are various trends across the USA for instance the Southeastern States have a mixture of consecutive, intensifying, and oscillating hot spots.3D Hot Spotshttps://arcg.is/1b41T43D Hot Spot ResultsThese trends over time are expanded in the above 3D Map, by inspecting the stacked columns you can see the trends over time which give result to the overall Hot Spot Results.Not all counties have significant trends, symbolized as Never Significant in the Space Time Cubes.Space-Time Pattern Mining AnalysisThe North-central areas of the USA, have mostly diminishing cold spots.2D Space-Time Mininghttps://arcg.is/1PKPj02D Space Time Mining ResultsWORKFLOW: Analysis, with the Emerging Hot Spot Analysis Tool shows that there are various trends across the USA for instance the South-Eastern States have a mixture of consecutive, intensifying, and oscillating hot spots.Results ShowThe USA has counties with persistent malnourished populations, they depend on Food Aide.3D Space-Time Mininghttps://arcg.is/01fTWf3D Space Time Mining ResultsIn addition to obvious planning for consistent Hot-Hot Spot Areas, areas oscillating Hot-Cold and/or Cold-Hot Spots can be identified for further analysis to mitigate the upward trend in food insecurity in the USA, since 2009 which has become even worse since the outbreak of the COVID-19 pandemic.After Notes:(i) The Johns Hopkins University has an Interactive Dashboard of the Evolution of the COVID-19 Pandemic.Coronavirus COVID-19 (2019-nCoV)(ii) Since March 2020 in a Response to COVID-19, SNAP has had to extend its benefits to help people in need. The Food Relief is coordinated within States and by local and voluntary organizations to provide nutrition assistance to those most affected by a disaster or emergency.Visit SNAPs Interactive DashboardFood Relief has been extended, reach out to your state SNAP office, if you are in need.(iii) Follow these Steps to build an ArcGIS Pro StoryMap:Step 1: [Get Data][Open An ArcGIS Pro Project][Run a Hot Spot Analysis][Review analysis parameters][Interpret the results][Run an Outlier Analysis][Interpret the results]Step 2: [Open the Space-Time Pattern Mining 2 Map][Create a space-time cube][Visualize a space-time cube in 2D][Visualize a space-time cube in 3D][Run a Local Outlier Analysis][Visualize a Local Outlier Analysis in 3DStep 3: [Communicate Analysis][Identify your Audience & Takeaways][Create an Outline][Find Images][Prepare Maps & Scenes][Create a New Story][Add Story Elements][Add Maps & Scenes] [Review the Story][Publish & Share]A submission for the Esri MOOCSpatial Data Science: The New Frontier in AnalyticsLinda Angulo LopezLauren Bennett . Shannon Kalisky . Flora Vale . Alberto Nieto . Atma Mani . Kevin Johnston . Orhun Aydin . Ankita Bakshi . Vinay Viswambharan . Jennifer Bell & Nick Giner

  16. f

    Non-synonymous heatmap plots

    • figshare.com
    txt
    Updated Sep 15, 2022
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    Daniele Traversa (2022). Non-synonymous heatmap plots [Dataset]. http://doi.org/10.6084/m9.figshare.21118729.v1
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    txtAvailable download formats
    Dataset updated
    Sep 15, 2022
    Dataset provided by
    figshare
    Authors
    Daniele Traversa
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The folder contains the heatmap plots obtained from the gene burden analysis considering non-synonymous variants. The plots are provided in a static format (.jpeg) and in a more interactive one (.html). Additionally, tables generating the heatmaps are provided in a .txt file format.

  17. f

    Variant prioritisation heatmap plots

    • figshare.com
    html
    Updated Sep 15, 2022
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    Daniele Traversa (2022). Variant prioritisation heatmap plots [Dataset]. http://doi.org/10.6084/m9.figshare.21118594.v1
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    htmlAvailable download formats
    Dataset updated
    Sep 15, 2022
    Dataset provided by
    figshare
    Authors
    Daniele Traversa
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    The folder contains the different heatmaps originating from the variant prioritization analysis in both .jpeg and .html file. The latter are interactive. Moreover, the individuals genotype table originating the heatmaps is provided in .txt format.

  18. f

    Statistical analysis of the SUS.

    • plos.figshare.com
    xls
    Updated Aug 1, 2024
    + more versions
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    Ardvin Kester S. Ong; Yogi Tri Prasetyo; Regina Pia Krizzia M. Tapiceria; Reny Nadlifatin; Ma. Janice J. Gumasing (2024). Statistical analysis of the SUS. [Dataset]. http://doi.org/10.1371/journal.pone.0306701.t004
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    xlsAvailable download formats
    Dataset updated
    Aug 1, 2024
    Dataset provided by
    PLOS ONE
    Authors
    Ardvin Kester S. Ong; Yogi Tri Prasetyo; Regina Pia Krizzia M. Tapiceria; Reny Nadlifatin; Ma. Janice J. Gumasing
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    PurposeStaySafe PH is the Philippines’ official contact tracing software for controlling the propagation of COVID-19 and promoting a uniform contact tracing strategy. The StaySafe PH has various features such as a social distancing system, LGU heat map and response system, real-time monitoring, graphs, infographics, and the primary purpose, which is a contact tracing system. This application is mandatory in establishments such as fast-food restaurants, banks, and malls.Objective and methodologyThe purpose of this research was to determine the country’s willingness to utilize StaySafe PH. Specifically, this study utilized 12 latent variables from the integrated Protection Motivation Theory (PMT), Unified Theory of Acceptance and Use of Technology (UTAUT2), and System Usability Scale (SUS). Data from 646 respondents in the Philippines were employed through Structural Equation Modelling (SEM), Deep Learning Neural Network (DLNN), and SUS.ResultsUtilizing the SEM, it is found that understanding the COVID-19 vaccine, understanding the COVID-19 Delta variant, perceived vulnerability, perceived severity, performance expectancy, social influence, hedonic motivation, behavioral intention, actual use, and the system usability scale are major determinants of intent to utilize the application. Understanding of the COVID-19 Delta Variant was found to be the most important factor by DLNN, which is congruent with the results of SEM. The SUS score of the application is "D", which implies that the application has poor usability.ImplicationsIt could be implicated that large concerns stem from the trust issues on privacy, data security, and overall consent in the information needed. This is one area that should be promoted. That is, how the data is stored and kept, utilized, and covered by the system, how the assurance could be provided among consumers, and how the government would manage the information obtained. Building the trust is crucial on the development and deployment of these types of technology. The results in this study can also suggest that individuals in the Philippines expected and were certain that vaccination would help them not contract the virus and thus not be vulnerable, leading to a positive actual use of the application.NoveltyThe current study considered encompassing health-related behaviors using the PMT, integrating with the technology acceptance model, UTAUT2; as well as usability perspective using the SUS. This study was the first one to evaluate and assess a contact tracing application in the Philippines, as well as integrate the frameworks to provide a holistic measurement.

  19. f

    Composite reliability and validity.

    • plos.figshare.com
    xls
    Updated Aug 1, 2024
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    Ardvin Kester S. Ong; Yogi Tri Prasetyo; Regina Pia Krizzia M. Tapiceria; Reny Nadlifatin; Ma. Janice J. Gumasing (2024). Composite reliability and validity. [Dataset]. http://doi.org/10.1371/journal.pone.0306701.t002
    Explore at:
    xlsAvailable download formats
    Dataset updated
    Aug 1, 2024
    Dataset provided by
    PLOS ONE
    Authors
    Ardvin Kester S. Ong; Yogi Tri Prasetyo; Regina Pia Krizzia M. Tapiceria; Reny Nadlifatin; Ma. Janice J. Gumasing
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    PurposeStaySafe PH is the Philippines’ official contact tracing software for controlling the propagation of COVID-19 and promoting a uniform contact tracing strategy. The StaySafe PH has various features such as a social distancing system, LGU heat map and response system, real-time monitoring, graphs, infographics, and the primary purpose, which is a contact tracing system. This application is mandatory in establishments such as fast-food restaurants, banks, and malls.Objective and methodologyThe purpose of this research was to determine the country’s willingness to utilize StaySafe PH. Specifically, this study utilized 12 latent variables from the integrated Protection Motivation Theory (PMT), Unified Theory of Acceptance and Use of Technology (UTAUT2), and System Usability Scale (SUS). Data from 646 respondents in the Philippines were employed through Structural Equation Modelling (SEM), Deep Learning Neural Network (DLNN), and SUS.ResultsUtilizing the SEM, it is found that understanding the COVID-19 vaccine, understanding the COVID-19 Delta variant, perceived vulnerability, perceived severity, performance expectancy, social influence, hedonic motivation, behavioral intention, actual use, and the system usability scale are major determinants of intent to utilize the application. Understanding of the COVID-19 Delta Variant was found to be the most important factor by DLNN, which is congruent with the results of SEM. The SUS score of the application is "D", which implies that the application has poor usability.ImplicationsIt could be implicated that large concerns stem from the trust issues on privacy, data security, and overall consent in the information needed. This is one area that should be promoted. That is, how the data is stored and kept, utilized, and covered by the system, how the assurance could be provided among consumers, and how the government would manage the information obtained. Building the trust is crucial on the development and deployment of these types of technology. The results in this study can also suggest that individuals in the Philippines expected and were certain that vaccination would help them not contract the virus and thus not be vulnerable, leading to a positive actual use of the application.NoveltyThe current study considered encompassing health-related behaviors using the PMT, integrating with the technology acceptance model, UTAUT2; as well as usability perspective using the SUS. This study was the first one to evaluate and assess a contact tracing application in the Philippines, as well as integrate the frameworks to provide a holistic measurement.

  20. f

    (PART 1 OF 5) 9 molecular dynamics simulations (500ps 3 x 3 replicates) of...

    • figshare.com
    png
    Updated Feb 12, 2020
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    Marco Cespugli; Vedat Durmaz; Georg Steinkellner; Christian C. Gruber (2020). (PART 1 OF 5) 9 molecular dynamics simulations (500ps 3 x 3 replicates) of coronavirus 2019-nCoV protease unrefined crystal structure in complex with 3 different conformations of lopinavir. [Dataset]. http://doi.org/10.6084/m9.figshare.11808396.v1
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    pngAvailable download formats
    Dataset updated
    Feb 12, 2020
    Dataset provided by
    figshare
    Authors
    Marco Cespugli; Vedat Durmaz; Georg Steinkellner; Christian C. Gruber
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Description

    Molecular dynamics simulations (500 ps MD at 310 K) of the unrefined crystal structure by Prof. Yang group from ShanghaiTech of novel coronavirus 2019-nCoV protease Mpro in complex with the ligand lopinavir (see note below). The starting positions of the ligand (LP1, LP2, LP3) derive from docking experiments.The suffixes (a, b, c) on the filenames represent the replicates of the same MD simulation using random initial velocities.The archives contain also an heatmap representing the protein-ligand contact frequencies. Green-boxed occurrences in the heatmap represent hydrogen bond occurrences during the simulation.Note: The refined crystal structure of the protease of our partner Prof. Yang group from ShanghaiTech is oficially released: https://www.rcsb.org/structure/6LU7Part 1 of 5:XHD_LC1aXHD_LC1b+ images of the 3 docked starting positions

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New York Times, Coronavirus (Covid-19) Data in the United States [Dataset]. https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html

Coronavirus (Covid-19) Data in the United States

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Dataset provided by
New York Times
Description

The New York Times is releasing a series of data files with cumulative counts of coronavirus cases in the United States, at the state and county level, over time. We are compiling this time series data from state and local governments and health departments in an attempt to provide a complete record of the ongoing outbreak.

Since late January, The Times has tracked cases of coronavirus in real time as they were identified after testing. Because of the widespread shortage of testing, however, the data is necessarily limited in the picture it presents of the outbreak.

We have used this data to power our maps and reporting tracking the outbreak, and it is now being made available to the public in response to requests from researchers, scientists and government officials who would like access to the data to better understand the outbreak.

The data begins with the first reported coronavirus case in Washington State on Jan. 21, 2020. We will publish regular updates to the data in this repository.

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