Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,516
datasets available to search
ShareScore release 0.9.0
Dataset results
2,516 results for “Seri”
DeepOrchidSeries: A Sentinel-2 Dataset to inform convolutional SDMs with twelve-month Sentinel-2 image time-series, Orchid family
<p><strong>Deep Species Distribution Modelling from Sentinel-2 Image Time-series: a Global Scale Analysis on the Orchid Family</strong> </p> <ul> <li><strong><em>DeepOrchidSeries</em></strong> dataset gathers Sentinel-2 image time-series around geolocated orchid occurrences. Seasonal evolutions of the habitats are captured in the twelve-month RGB/IR time-series with 640x640m spatial resolution. It allows novel Species Distribution Models (SDMs) coupled with convolutional networks to take advantage of both spatial and temporal information.</li> <li>Our <strong>associated article</strong> is describing the modeling choices made to shape this ambitious dataset. It is submitted to <a href="https://www.frontiersin.org/research-topics/18336/plant-biodiversity-science-in-the-era-of-artificial-intelligence">https://www.frontiersin.org/research-topics/18336/plant-biodiversity-science-in-the-era-of-artificial-intelligence</a>. We believe such global data, methods and scripts are valuable to the conservation ecology community and especially deep-SDMs users. To our knowledge, no similar ready-to-use dataset is available. In the article, the dataset's temporal dimension is proven to significantly improve SDMs performances.</li> <li><strong><em>sen2patch</em></strong> is the gitlab project gathering the code to create such dataset. It is available at <a href="https://gitlab.inria.fr/jestopin/sen2patch">https://gitlab.inria.fr/jestopin/sen2patch</a>.</li> <li><strong><em>DeepOrchidSeries.csv</em></strong> contains all occurrences-level information. <ul> <li>We advice to load it with: <pre><code class="language-python">import pandas as pd df = pd.read_csv("path/to/DeepOrchidSeries.csv", sep=';') df.columns ['gbifid', 'canonical_name', 'decimallatitude', 'decimallongitude', 'speciesKey', 'cell_index', 'bot_country', 'bot_code', 'lvl2_code', 'continent_code']</code></pre> <ul> <li>'gbifid' is the occurrences GBIF ID</li> <li>'canonical_name', is the species canonical name</li> <li>'decimallatitude', 'decimallongitude' are the species coordinates in decimal degrees</li> <li>'speciesKey' is the species GBIF unique identifier</li> <li>'cell_index' is a unique cell ID in a 0.0025° lon/lat grid partitioning the Earth (used to stratify train/val/test set by geographic blocks)</li> <li>'bot_country', 'bot_code', 'lvl2_code', 'continent_code' are geographic subdivisions defined in <a href="https://github.com/tdwg/wgsrpd">https://github.com/tdwg/wgsrpd</a> (code and string for WGSRPD level 1, the botanical countries)</li> </ul> </li> </ul> </li> <li> <p>Initial <a href="https://www.gbif.org/">GBIF</a> query DOI is <a href="http://https://doi.org/10.15468/dl.4bijtu">https://doi.org/10.15468/dl.4bijtu</a> (26 August 2019).</p> </li> <li><strong><em>DeepOrchidSeries.tar</em></strong> file contains the satellite image time-series and is available at <a href="https://lab.plantnet.org/deeporchidseries/">https://lab.plantnet.org/deeporchidseries/</a> <ul> <li><em>.tar</em> archive measure 286 GB and extends to 432 GB once decompressed.</li> <li>Image time-series relative tree paths are constructed from the occurrences unique GBIF IDs.</li> <li>For a given occurence <em>gbifid</em>, matching patches are located in: <em>final_dataset_by_gbifid/gbifid[-2:]/gbifid[-4:-2]</em>, <em>i.e.</em> in a first folder named with the <em>gbifid</em> last two numbers and a subfolder with the previous two ones. Example: the time-series files matching occurrence 2236837714 are located at <em>final_dataset_by_gbifid/14/77/</em>. </li> <li>Image time-series are composed of twelve 16 bits RGB <em>.png</em> and twelve 16 bits IR <em>.png</em> files containing data identical to the original L1C products, no lossy compression was made. There are one RGB and one IR .png file per month.</li> <li>Patches from month MM/YYYY of occurrence <em>gbifid</em> are named<em> </em><em>RGB_YYYY_MM_gbifid_.png</em> and <em>IR0_YYYY_MM_gbifid_.png</em>.</li> </ul> </li> <li><em><strong>models.zip</strong></em> is the archive containing the four PyTorch models weights described in our article and<strong><em> </em></strong><em><strong>inception_env.py</strong></em> the used Inception V3 architecture. <em><strong>index.json</strong></em> contains the dictionnary linking the models class indexes from 0 to 14128 with our labels <em>speciesKey</em>: {"class_index":speciesKey}.</li> </ul> <p> </p> <ul> <li><strong>ACKNOWLEDGMENTS</strong>: We warmly thank Alexander Zizka et al. for providing us the geographically and taxonomically curated set of Orchids occurrences. This dataset contains modified Copernicus Sentinel data and Copernicus Service information (2018). Sentinel-2 MSI data used were available at no cost from ESA Sentinels Scientific Data Hub.</li> </ul>
Global GFED-based monthly burned area time series (1996-2016) at 1 km and ESA CCI MODIS-based long-term monthly P90 burned area occurrence at 500 m
<p>Contains two separate datasets:</p> <ol> <li>Global <a href="https://www.globalfiredata.org/data.html">GFED-based monthly burned area</a> (in ha) <a href="https://youtu.be/kBJcP8mL2Qs">time series (1996-2016)</a> at 1 km (downscaled using cubic-splines from 25 km);</li> <li>Global burned area long term (2000-2012) P90 (quantile probability = 0.9) based on the <a href="http://maps.elie.ucl.ac.be/CCI/viewer/index.php">ESA CCI burned area accumulated weekly product</a>;</li> </ol> <p>Original GFED monthly data is provided as HDF4 files (ftp.fuoco.geog.umd.edu/data/GFED/GFED4). Dataset is described in detail in <a href="https://doi.org/10.1002/jgrg.20042">Giglio et al. (2013)</a>. Processing steps are available <a href="https://gitlab.com/openlandmap/global-layers/tree/master/input_layers/GFED"><strong>here</strong></a>. Antarctica is not included.</p> <p>To access and visualize global datasets use: <a href="https://openlandmap.org"><strong>https://openlandmap.org</strong></a> or watch <a href="https://youtu.be/kBJcP8mL2Qs"><strong>this video</strong></a>.</p> <p>If you discover a bug, artifact or inconsistency in the maps, or if you have a question please use some of the following channels:</p> <ul> <li>Technical issues and questions about the code: <a href="https://gitlab.com/openlandmap/global-layers/issues">https://gitlab.com/openlandmap/global-layers/issues</a> </li> </ul> <p>All files provided as Cloud-Optimized GeoTIFFs / internally compressed using "COMPRESS=DEFLATE" creation option in GDAL. File naming convention:</p> <ul> <li>nhz = theme: natural hazards,</li> <li>monthly.burned.ha = variable: estimated monthly burned area in ha,</li> <li>gfed = data source GFED data,</li> <li>m = mean value,</li> <li>1km = spatial resolution / block support: 1 km,</li> <li>s0..0cm = vertical reference: land surface,</li> <li>2000.02 = time reference aggregated: month Feb of year 2000,</li> <li>v4 = version number: GFEDv4,</li> </ul>
Portobello Marine Laboratory sea surface temperature time series
<p>This table contains the daily sea surface temperature observations taken at the Portobello Marine Laboratory wharf (LAT: -45.8160, LON: 170.6500). The first column is time in MATLAB datenum format. The second column is daily sea surface temperature recorded at 9am local time. Measurements are recorded to an accuracy of <span class="math-tex">\(\pm\)</span>0.1°C. Missing observations have been assigned the value -999. Additional station details and sampling information can be found in <a href="https://environment.govt.nz/publications/new-zealand-coastal-sea-surface-temperature/">Chiswell and Grant (2018)</a>.</p> <p>We acknowledge the foresight and dedication of the founders of this <em>in situ</em> dataset in the 1950s. We are grateful for all the people involved in the data collection. Notably these include</p> <ul> <li>Doug Mackie (data acquisition and record maintenance)</li> <li>Elizabeth (Betty) Batham who championed the long term climate sampling</li> <li>All the researchers who have assisted with sampling</li> </ul>
Arctic vegetation cover fractions derived from Landsat time series (1984-2020) for the greater Mackenzie Delta Region (Western Canadian Arctic)
<p>Data to the publication by Nill et al. (2022) "<em>Arctic shrub expansion revealed by Landsat-derived multitemporal<br> vegetation cover fractions in the Western Canadian Arctic"</em></p> <p>The dataset features Landsat-derived fractional cover estimates of Arctic plant functional types (shrub, evergreen trees, herbaceous, lichen) and other land cover (barren, water) in the greater Mackenzie Delta Region, Canada.<br> We utilized regression-based unmixing based on synthetic training data in order to build multitemporal Kernel Ridge Regression (KRR) models for estimating fractional cover and validated our predictions based on independent very-high-resolution imagery (please be referred to publication for details).<br> <br> <strong>Dataset information</strong><br> The fraction cover predictions ("krr-avg") are provided separately for each epoch (1984-1990, 1991-1996, ..., 2015-2020) and class/cover type. The decadal change images ("dec-cng") between 1984 and 2020 are provided separately for each class/cover type. The naming convention of the files is as follows:</p> <p>XXXX-XXXX_YYY-YYY_int16-10e3_class-Z-Z</p> <ul> <li>XXXX-XXXX = epoch, e.g. 2015-2020</li> <li>YYY-YYY = dataset ("krr-avg" = fraction cover, "dec-cng" = decadal fraction cover change)</li> <li>Z-Z = class ID and associated class name (sh = shrub, cf = coniferous, hb = herbaceous, lc = lichen, wt = water, br = barren)</li> </ul> <p>The fraction cover values are % scaled by 10,000. For instance, a value of 1234 refers to 12.34%. Further image metadata:</p> <ul> <li><strong>Datatype:</strong> Signed 16-bit integer (Int16) </li> <li><strong>Data format: </strong>GeoTiff (.tif)</li> <li><strong>No data value:</strong> -9999</li> <li><strong>Projection:</strong> EPSG:3573 with custom central meridian; WKT string: 'PROJCS["WGS 84 / North Pole LAEA Canada",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Lambert_Azimuthal_Equal_Area"],PARAMETER["latitude_of_center",90],PARAMETER["longitude_of_center",-135],PARAMETER["false_easting",0],PARAMETER["false_northing",0],UNIT["metre",1],AXIS["Easting",EAST],AXIS["Northing",NORTH]]'</li> </ul> <p><strong>Publication</strong><br> Nill, L., Grünberg, I., Ullmann, T., Gessner, M., Boike, J. & Hostert, P. (2022): Arctic shrub expansion revealed by Landsat-derived multitemporal vegetation cover fractions in the Western Canadian Arctic. Remote Sensing of Environment, 2022, 281. https://doi.org/10.1016/j.rse.2022.113228</p> <p><strong>Further information</strong><br> For further information, please see the publication or contact Leon Nill (leon.nill@geo.hu-berlin.de).<br> A web-visualization of this dataset is available <a href="https://ows.geo.hu-berlin.de/webviewer/arctic-shrub/">here</a>.</p>
Wikipedia time-series graph
<p>Wikipedia temporal graph.</p> <p>The dataset is based on two Wikipedia SQL dumps: (1) English language articles and (2) user visit counts per page per hour (aka pagecounts). The original datasets are publicly available on the Wikimedia website.</p> <p>Static graph structure is extracted from English language Wikipedia articles. Redirects are removed. Before building the Wikipedia graph we introduce thresholds on the minimum number of visits per hour and maximum in-degree. We remove the pages that have less than 500 visits per hour at least once during the specified period. Besides, we remove the nodes (pages) with in-degree higher than 8 000 to build a more meaningful initial graph. After cleaning, the graph contains 116 016 nodes (out of total 4 856 639 pages), 6 573 475 edges. The graph can be imported in two ways: (1) using edges.csv and vertices.csv or (2) using enwiki-20150403-graph.gt file that can be opened with open source Python library Graph-Tool.</p> <p>Time-series data contains users' visit counts from 02:00, 23 September 2014 until 23:00, 30 April 2015. The total number of hours is 5278. The data is stored in two formats: CSV and H5. CSV file contains data in the following format [page_id :: count_views :: layer], where layer represents an hour. In H5 file, each layer corresponds to an hour as well.</p>
Training Datasets for Epilepsy Analysis: Preprocessing and Feature Extraction from EEG Time Series
<h2>The files include the 20 training datasets, in csv format, from 20 epileptic patients. Each set of data is described by 1080 features extracted using the sliding window technique.</h2>
Merged SCIAMACHY-OMPS limb ozone time series
<p>This data set contains the time series of merged monthly mean ozone profiles retrieved at the University of Bremen from SCIAMACHY and OMPS-LP limb observations. The merging is performed on deseasonalized anomalies, but the data set contains also the reconstructed number density time series. The data set is longitudinally resolved, with a 5° latitude and 20° longitude resolution, and a vertical grid with 3.3 km spacing. </p>
Nighttime Lights PC1-4 based on the Version 4 DMSP-OLS Nighttime Lights Time Series 1997–2014
<p>Nighttime Lights PC1-4 based on the Version 4 <a href="https://ngdc.noaa.gov/eog/dmsp/downloadV4composites.html">DMSP-OLS Nighttime Lights Time Series</a> 1997–2014. Derived using SAGA GIS Principal Component analysis. Image and data processing by NOAA's National Geophysical Data Center. DMSP data collected by US Air Force Weather Agency.</p> <p>To access and visualize maps use: <a href="http://www.openlandmap.org/">OpenLandMap.org</a></p> <p>If you discover a bug, artifact or inconsistency in the maps, or if you have a question please use some of the following channels:</p> <ul> <li>Technical issues and questions about the code: <a href="https://gitlab.com/openlandmap/global-layers/issues">https://gitlab.com/openlandmap/global-layers/issues</a> </li> <li>General questions and comments: <a href="https://disqus.com/home/forums/landgis/">https://disqus.com/home/forums/landgis/</a></li> </ul>
Soil organic carbon stock (0–30 cm) in kg/m2 time-series 2001–2015 based on the land cover changes
<p>Estimated SOC loss based on the European Space Agency (ESA) Climate Change Initiative (ESACCI-LC) land cover maps 2001–2015. This only shows estimated SOC loss (in kg/m2) as a result of change in land use / land cover (assuming standard change factors based on the literature and IPCC reports). Methodology produced for the purpose of the Land Degradation Neutrality (UNCCD) project. Processing steps are described in detail <strong><a href="https://gitlab.com/openlandmap/global-layers/tree/master/soil/LDN">here</a></strong>. Antartica is not included.</p> <p>To access and visualize maps use: <a href="http://www.openlandmap.org/">OpenLandMap.org</a></p> <p>If you discover a bug, artifact or inconsistency in the maps, or if you have a question please use some of the following channels:</p> <ul> <li>Technical issues and questions about the code: <a href="https://gitlab.com/openlandmap/global-layers/issues">https://gitlab.com/openlandmap/global-layers/issues</a> </li> <li>General questions and comments: <a href="https://disqus.com/home/forums/landgis/">https://disqus.com/home/forums/landgis/</a></li> </ul> <p>All files internally compressed using "COMPRESS=DEFLATE" creation option in GDAL. File naming convention:</p> <ul> <li>sol = theme: soil,</li> <li>organic.carbon.stock = variable: soil organic carbon stock in kg/m2,</li> <li>msa.kgm2 = determination method: derived from carbon content, bulk density and coarse fragments,</li> <li>m = mean value,</li> <li>250m = spatial resolution / block support: 250 m,</li> <li>b0..30cm = vertical reference: standard layer 0-30 cm below surface,</li> <li>2014 = time reference: year 2014,</li> <li>v0.2 = version number: 0.2,</li> </ul>
Outdoor monitoring data of an Insolight B-series module - CPV sub-module
<p>Dataset from the outdoor characterization of a B Series module from Insolight at the rooftop of the Instituto de Energía Solar - Universidad Politécnica de Madrid. It was the basis of its power rating at CSTC and has informed several scientific and technical articles like the oral presentation by Gaël Nardin et al. "Towards Industrialization of Planar Microtracking Photovoltaic Panels" at the 15th International Conference on Concentrator Photovoltaics (CPV-15), held between 25 and 27 March of 2019 in Fes, Morocco. </p> <p><strong>Monitoring campaign:</strong></p> <ul> <li>Location: 40.453°N, -3.727°E. <a href="https://www.google.com/maps/place/40%C2%B027'11.6%22N+3%C2%B043'37.3%22W/@40.453215,-3.7275722,142m/data=!3m2!1e3!4b1!4m13!1m6!3m5!1s0x0:0xc636231f90c3bbeb!2sInstituto+de+Energ%C3%ADa+Solar!8m2!3d40.4531766!4d-3.7269107!3m5!1s0x0:0x0!7e2!8m2!3d40.4532142!4d-3.7270248">Instituto de Energía Solar</a>, Universidad Politécnica de Madrid. 28040 Madrid, Spain.</li> <li>Starting date: 21 November 2018</li> <li>End date: 14 December 2018</li> </ul> <p><strong>Description of data files:</strong></p> <ul> <li><strong>Data files format:</strong> tab-separated text file; headers in first row.</li> <li><strong>I-V parameters</strong>: single file "Insolight Preseries outdoor monitoring - IES rooftop - UPM.txt". Headers: <ul> <li>Date (DD/MM/YYYY) </li> <li>Time (HH:MM:SS): time in CET / UTC+1</li> <li>Pmp (W): peak power</li> <li>Vmp (V): voltage at maximum power point</li> <li>Imp (A): current at maximum power point</li> <li>Isc (A): short-circuit current</li> <li>Voc (V): open-circuit voltage</li> <li>FF: fill factor</li> <li>Tair (°C): ambient temperature </li> <li>Tlens (°C): temperature at the aperture plane</li> <li>GNI (W/m<sup>2</sup>): global normal irradiance at the aperture plane as measured with a pyranometer. Spectral range: 305 – 2800 nm.</li> </ul> </li> <li><strong>Weather data</strong>: daily files "geonica2018_**_**.txt". Headers: <ul> <li>yyyy/mm/dd: date</li> <li>hh:mm: time in GMT/UTC</li> <li>V_Viento (m/s): wind speed</li> <li>D_Viento (°N): wind direction</li> <li>Temp_Air(°C): ambient temperature</li> <li>Rad_Dir(W/m<sup>2</sup>): direct normal irradiance as measured by a Normal Incidence Pyrheliometer from Eppley. Spectral Range: 250-3000 nm. Field of view: 5°</li> <li>Ele_Sol (°): solar tilt</li> <li>Ori_Sol (°N): solar position azimuth</li> <li>Top (W/m<sup>2</sup>): direct normal irradiance as measured by a top component cell of a lattice-matched III-V triple-junction cell in the <a href="http://solaraddedvalue.com/en/category/products/spectro-heliometer/">ICU-3J35</a> spectroheliometer from Solar Added Value. Spectral range: 300 - 680 nm. Field of view: 5.7º</li> <li>Mid (W/m<sup>2</sup>): direct normal irradiance as measured by a middle component cell of a lattice-matched III-V triple-junction cell in the <a href="http://solaraddedvalue.com/en/category/products/spectro-heliometer/">ICU-3J35</a> spectroheliometer from Solar Added Value. Spectral range: 680 - 900 nm. Field of view: 5.7º</li> <li>Bot (W/m<sup>2</sup>): direct normal irradiance as measured by a bottom component cell of a lattice-matched III-V triple-junction cell in the <a href="http://solaraddedvalue.com/en/category/products/spectro-heliometer/">ICU-3J35</a> spectroheliometer from Solar Added Value. Spectral range: 900 - 1800 nm. Field of view: 5.7º</li> <li>Cal_Top: n/a</li> <li>Cal_Mid: n/a</li> <li>Cal_Bot: n/a</li> <li>Pres_Aire: n/a</li> </ul> </li> </ul>
Mars Odyssey Neutron Spectrometer Time Series of Corrected Cateogry 1 Counting Rates, 2002-2017
<p>Ubinned time series of derived neutron data from the Mars Odyssey Neutron Spectrometer (MONS) Category 1 data, from 200 - 2017.</p>
A Novel Framework to Harmonise Satellite Data Series for Climate Applications: Matchups, Calibration Parameters and Residuals
<p>The datasets included with this archive supplement the journal article:</p> <p>Giering, R.; Quast, R.; Mittaz, J.P.D.; Hunt, S.E.; Harris, P.M.; Woolliams, E.R.; Merchant, C.J. A Novel Framework to Harmonise Satellite Data Series for Climate Applications. <em>Remote Sens. 2019</em>, <strong>11</strong>, 1002. doi:<a href="https://doi.org/10.3390/rs11091002">10.3390/rs11091002</a>.</p> <p>The archive includes a README file with further explanations.</p>
A new method for approximating fractional derivatives/ integrals as a series of higher-integer-order derivatives - examples and results of applying the method to initial/boundary value problems
<p>The posted research data includes examples of the application of the author's fractional derivative/integral approximation method using the sum of higher integer derivatives. The attached text files contain the numerical solutions of the presented examples, recorded as a set of numerical values obtained from the performed computations.</p> <ul> <li>Example 4.1 <br> \(\begin{cases}<br> \displaystyle<br> ^{C}D^{\alpha}_{a+}\sin (x), \\<br> x \in \langle a, 3\pi \rangle \quad \hbox{and} \quad<br> \alpha = \{1.0,\ 0.8,\ 0.6,\ 0.4,\ 0.2\},<br> \end{cases}\)<br><br></li> <li>Example 4.2 <br>\( \begin{cases}<br> \displaystyle<br> I^{\alpha}_{0+} e^{-x}\cos 7x, \\<br> x \in \langle 0,1\rangle \quad \hbox{and} \quad<br> \alpha =\{1.0,\ 1.2,\ 1.4,\ 1.6,\ 1.8,\ 2.0 \},<br> \end{cases} \)<br><br></li> <li>Example 5.1 <br>\(\begin{cases}<br> ^{C} D_{0+}y(x)+2y(x)=x+ \frac{2x^{\alpha+1}}{\Gamma(\alpha+2)},\\<br> x\in\langle0,1\rangle, \\<br> y(0) = 0; \quad y(1) = \frac{1}{\Gamma(\alpha+2)}, \\<br> \alpha = \{1.2,\ 1.4,\ 1.6,\ 1.8,\ 2.0\}. <br>\end{cases}\)<br><br></li> <li>Example 5.2 <br>\(\begin{cases}<br> ^{C}D_{0+}^{\alpha}y(x)+1.8 y(x)=0,\\<br> x\in \langle 0,2\rangle \quad \hbox{and} \quad \alpha=\{1.0,\ 0.8,\ 0.6,\ 0.4,\ 0.2\},\\<br> y(0)=1.<br>\end{cases}\)</li> </ul>
18S V4 rDNA sequences organized at the OTU level for the SOMLIT-Astan time-series (2009-2016)
<p>The present file includes metadata for each 18S V4<strong> rDNA OTU</strong> from the SOMLIT-Astan time series (2009-2016) including the following fields: <strong>amplicon</strong> = identifier of the representative (most abundant) sequence; <strong>total</strong> = total number of reads; <strong>spread </strong>= number of samples in which the OTU has been found; <strong>cloud </strong>= number of unique sequences constituting the OTU; <strong>sequence</strong> = nucleic acid sequence of the representative sequence; <strong>length</strong> = length of the representative sequence; <strong>quality </strong>= minimum expected error observed for the representative sequence, divided by sequence length; <strong> taxonomy</strong> = taxonomic path assigned to the representative sequence; <strong>identity</strong> = percentage of identity of the representative sequence to the closest reference sequence from PR2; <strong>references</strong> = best hit reference sequence(s) ; <strong>RA090107_02:RA161222_3 </strong>= 375 samples from January 2009 to December 2016, the first two number are the year followed by the month and the day (sampling twice a month during 8 years). Values after “_” indicate the size of the filter used for the filtration: 02 for 0.2 µm and 3 for 3 µm.</p> <p>Generation of 18S V4 rDNA Operational Taxonomic Units (OTUs) from the raw sequencing reads and their assembly into a OTUtable was obtained according to the following pipeline (https://doi.org/10.5281/zenodo.5791089). The V4 region was extracted from the 18S rDNA reference sequences from PR2 v4.12 (Guillou et al., 2013) with Cutadapt. The representative sequences of each OTU were compared to these V4 reference sequences by pairwise global alignment (usearch_global VSEARCH’s command). Each OTU inherits the taxonomy of the best hit or the last common ancestor in case of ties. OTUs with a score below 80% similarity were considered as unassigned (Mahé et al., 2017; Stoeck et al., 2010).</p> <p>The final dataset (filtered OTU table) contains 375 samples (sampled twice per month from 2009 to 2016) with a total of ~30 million sequence reads and 21,418 OTUs.</p>
CAMISIM hybrid time series data
<p>CAMISIM was used to simulate Illumina and Nanopore reads for a time series based on the genome sources from the “CAMI II challenge toy mouse gut dataset” (Meyer et al., 2021), containing 791 genomes. For this, the most recent development version of CAMISIM at the time of preparing this data was used (available at <a href="https://doi.org/10.5281/zenodo.5137751">https://doi.org/10.5281/zenodo.5137751</a>). Two groups of samples were generated by using different CAMISIM seeds, each comprising a time series of four samples.</p> <p>The sample sheet file (samplesheet.CAMISIM_hybrid.csv) can be used as direct input for the nf-core/mag pipeline, e.g. with the command:</p> <p>> nextflow run nf-core/mag -r 2.1.0 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input https://zenodo.org/record/5155395/files/samplesheet.CAMISIM_hybrid.csv --coassemble_group</p> <p>Note, in case of download problems, restarting the pipeline run with `-resume` or downloading the files beforehand and adjusting the paths in the sample sheet file should help.</p> <p>See <a href="https://nf-co.re/mag">https://nf-co.re/mag</a> for a comprehensive usage documentation.</p> <p> </p>
Preprocessed rat brain voxel time series
<p>Preprocessed version of voxel time-series for three rats, originally described in Becq et al., Functional connectivity is preserved but reorganized across several anesthetic regimes, NeuroImage, 2020. Used in Achard et al., Inter-regional correlation estimators for functional magnetic resonance imaging, arXiv, 2022, arXiv:2011.08269.</p> <p>The files named "coord_ROI_x.txt" contain the coordinates of the voxels inside region x (each line corresponds to one voxel).</p> <p>The files named "ts_ROI_x.txt" contain the BOLD signal time series of the voxels inside region x (each line corresponds to one voxel, each column to one timepoint). The voxels with time series equal to zero have been removed</p> <p>The files named "weight_ROI_x.txt" contain the weights associated with the voxels inside region x (each line corresponds to one voxel). Indeed, when assigning voxels to regions, some voxels end up at the border of several regions. These weights characterize the proportion of a given voxel present inside a given region. Hence, some voxels are included in several different regions. So when we compute the voxel-to-voxel inter-correlation between two regions we sometimes end up with inter-correlations equal to 1. In the current dataset this issue has been resolved and each voxel has been assigned to a single region.</p>
High-frequency, year-round time series of the carbonate chemistry in a high-Arctic fjord (Svalbard)
<p>The Arctic Ocean is subject to high rates of ocean warming and acidification, with critical implications for marine organisms as well as ecosystems and the services they provide. Carbonate system data in the Arctic realm are spotty in space and time and, until recently, there was no time-series station measuring the carbonate chemistry at high frequency in this region, particularly in coastal waters. We report here on the first high-frequency (1 h), multi-year (6 years) dataset of salinity, temperature, dissolved inorganic carbon, total alkalinity, CO2 partial pressure (pCO2) and pH at a coastal site (12 m) in Kongsfjorden, Svalbard. We show that the choice of formulations for calculating the dissociation constants of the carbonic acid remains unsettled, (2) the water column is generally somewhat stratified despite the shallow depth, (3) the saturation state of calcium carbonate is subject to large seasonal changes but never reaches undersaturation (Oa ranges between 1.4 and 3.0) and (4) pCO2 is lower than atmospheric CO2 at all seasons, making this site a sink for atmospheric CO2.</p> <p>In addition to the sources of funding findable within the Zenodo interface, this work has been supported by the Coastal Observing System for Northern and Arctic Seas (COSYNA), the two Helmholtz large-scale infrastructure projects ACROSS and MOSES, the French Polar Institute (IPEV) as well as the European Union's Horizon 2020 research and innovation programme Jericho-Next (No 871153 and 951799). <br> <br> ------ <br> <br> Column descriptions are as follows: <br> <br> date/time [UTC+0]: The date and time of sampling at UTC <br> pressure [dbar]: hydrostatic pressure (profiler) <br> s_insitu [unit]: salinity in situ (profiler) <br> s_fb [unit], salinity (FerryBox) <br> t_11m [°C]: temperature in situ (static at 11 m) <br> t_ctd [°C]: temperature in situ (profiler) <br> t_fb [°C]: temperature (FerryBox) <br> t_sf [°C]: temperature SeaFET (profiler) <br> pco2 [uatm]: Partial pressure of CO2 (FerryBox) <br> pH_sensor [total scale]: pH in situ at in situ temperature (profiler) <br> at [umol kg-1] at, total alkalinity in situ(discrete) <br> ct [umol kg-1]: dissolved inorganic carbon in situ (discrete) <br> pH_discrete [total scale]: spectrophotometric pH in situ (total scale) at in situ temperature (discrete)</p>
UDP Synthetic Dataset for training ML time series models
<p>The dataset available has been produced by the "Next-Generation IoT solutions for the universal supply chain" (iNGENIOUS) project’s consortium under EC grant agreement 957216, made publicly available as part of the Horizon 2020 Open Research Data Pilot (<a href="https://www.openaire.eu/what-is-the-open-research-data-pilot">ORD pilot</a>).<br> The European Commission is not liable for any use that may be made of the information contained herein.</p> <p>The available dataset is in csv format and contains synthetic data of UDP packets received and sent by a single User Plane Function (UPF) covering a span of 6 weeks. The format of the datafile is:</p> <ul> <li>index</li> <li>timestamp </li> <li>UDP packets_rcvd - Total number of UDP packets received</li> <li>UDP packets sent - Total number of UDP packets sent</li> </ul> <p>The simulation was performed based on behavior of UPF and 5GC Network functions inferred from stress tests performed in the iNGENIOUS project's Automated Robots with Heterogeneous Networks Use Case, as well as patterns in urban mobility taken from available UE datasets [NCS+19].</p> <p>More information on the iNGENIOUS project can be found on the project’s website: <a href="https://ingenious-iot.eu/">https://ingenious-iot.eu/</a></p> <p>[NCS+19] Noussan M, Carioni G, Sanvito FD, Colombo E. Urban Mobility Demand Profiles:<br> Time Series for Cars and Bike-Sharing Use as a Resource for Transport and Energy<br> Modeling. Data. 2019; 4(3):108. https://doi.org/10.3390/data4030108</p>
Raw data to "Series expansions in closed and open quantum many-body systems with multiple quasiparticle types"
<p>This collection of data is complementary to the publication "Series expansions in closed and open quantum many-body systems with multiple quasiparticle types", Lea Lenke, Andreas Schellenberger, Kai Phillip Schmidt, <a href="https://arxiv.org/abs/2302.01000">arXiv:2302.01000</a> (<a href="https://arxiv.org/abs/2302.01000">https://arxiv.org/abs/2302.01000</a>).</p> <p>It contains all data used for Figure 2 given in the file `Figure_2_complementary_data.yaml` and all needed data to recalculate the energies of the visualized modes in the files `Figure_2_coefficients_expectation_values.yaml` and `Figure_2_broad_signum_coefficients_expectation_values.yaml`.</p> <p>For the last two files, we used a program to calculate the coefficients. The source code for coefficient calculation is openly available under GitHub (<a href="https://github.com/FAU-kpslab/pcstpp_CoefficientGenerator">https://github.com/FAU-kpslab/pcstpp_CoefficientGenerator</a>) including configuration files to reproduce the coefficients given here.</p> <p>All files are self-consistent, for further information we recommend the comments directly in the files.</p> <p>For further details on the used method pcst<sup>++ </sup>and discussion of the results we refer to the linked publication.</p> <p>If any question may arise, you are highly welcome to contact us (see e.g. contact information on the publication).</p>
Multivariate Time Series data of Fatigued and Non-Fatigued Running from Inertial Measurement Units
<p>The data captured came from mounting a single Shimmer3 IMU on the lumbar of 19 recreational runners. The participants were all regular runners and injury free. The study protocol was reviewed and approved by the human research ethics committee at University College Dublin.<br><br>The data was collected in three segments; in the first, the participant completed a 400m run at a comfortable pace; the second segment consisted of a beep test which acted as the fatiguing protocol for this study; and the last segment where the runner was required to complete the 400m run at their comfortable pace, this time in their fatigued state. The beep test requires the runner to continuously run between two points 20m apart following an audio which produces `beeps' indicating when the person should begin running from one end to the other. The test eventually requires the runner to increase their pace as the interval between the `beeps' reduces as the test progresses. The fatiguing protocol ends when the runner is unable to keep up the increase in pace. The runs were all done on an outdoor running track. The sensor captured acceleration, angular velocity and magnetometer data throughout the three stages of the trials at a sampling rate of 256Hz. The data included here are segmented strides from the two 400m runs of each of the 19 participants. The labels on the data represent the participant number and whether it was a fatigued stride ('F') or a not fatigued stride ('NF').<br>The data used from the sensors includes data from the accelerometer in three directions (X, Y, Z) and the gyroscope in three directions (X, Y, Z). The direction of each of the axis is relative to the sensor. Two extra signals, magnitude acceleration and magnitude gyroscope were derived from the component signals and included in the analysis.</p><p>Kindly cite one of the following papers when using this data:</p><p>B. Kathirgamanathan, B. Caulfield and P. Cunningham, "Towards Globalised Models for Exercise Classification using Inertial Measurement Units," 2023 IEEE 19th International Conference on Body Sensor Networks (BSN), Boston, MA, USA, 2023, pp. 1–4, doi: 10.1109/BSN58485.2023.10331612</p><p>B. Kathirgamanathan, T. Nguyen, G. Ifrim, B. Caulfield, P. Cunningham. Explaining Fatigue in Runners using Time Series Analysis on Wearable Sensor Data, XKDD 2023: 5th International Workshop on eXplainable Knowledge Discovery in Data Mining, ECML PKDD, 2023, <a href="http://xkdd2023.isti.cnr.it/papers/223.pdf">http://xkdd2023.isti.cnr.it/papers/223.pdf</a></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.