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1,079 results for “source data”
Source data for gamete binning for an autotetraploid potato cultivar Otava
<p>Here we provide the source data for analyzing a highly heterozygous autotetraploid potato cultivar 'Otava'.</p>
Research data and code for Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants
<p># Research data repository</p> <p>## Introduction</p> <p>This repository contains the research data, scripts and codes to process the simulation and generate the figures in research article: <br> <em>"Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants"</em></p> <p>This work uses the discrete 3D mesh of the thorax of a newborn that is available at: http://doi.org/10.5281/zenodo.4916863</p> <p>This article has been submitted and publied in Journal of Biophotonics:<br> - DOI: 10.1002/jbio.202200041<br> - Link: <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202200041">https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202200041</a></p> <p>## Article status</p> <p> [X] Submitted <br> [X] Under review <br> [X] Corrections <br> [X] Published<br> <br> ## Content</p> <p>- Folder "data": This folder needs to be unzipped and contains the raw data from the simulation, as well as some processed data needed to generate the figures. This folder contains all the data necessary to generate the figures. However some intermediate data files (the Photon Hitting Density values interpolated on the elements of the mesh) are not given here because the files are too big. These can be created using the convertPHD2element script.<br> - Folder "function": This folder needs to be unzipped and contains some functions that are used by the scripts to process data or generate the figures<br> - Matlab .m files: The .m files are scripts that are used to generate the figures (generateFigX.m) or to process the data computeYYY.m. The description of each script and function is given in the comment section at the beginning of each file.</p> <p>## Licence<br> This data is published under the creative common CC-BY licence. You are free to use this data as long as you cite this dataset and the article (when DOI available)</p> <p>## Digital Object Identifier<br> DOI: 10.5281/zenodo.5996855</p> <p>## Authors<br> Simulation: Andrea Pacheco<br> Article writing: Andrea Pacheco<br> Data processing and figure generation: Andrea Pacheco and Baptiste Jayet<br> Conceptualisation, investigation, review and editing: Emilie Krite Svanberg, Hamid Dehghani and Eugene Dempsey<br> Project supervision: Stefan Andersson-Engels</p> <p>## Funding<br> The research leading to these results was funded by Science Fundation Ireland project no. SFI/15/RP/2828</p>
Data supplement to: Quality control of image sensors using gaseous tritium light sources
<p>In the article "Quality Control of Image Sensors using Gaseous Tritium Light Sources" (<a href="https://doi.org/10.1098/rsta.2021.0130)">https://doi.org/10.1098/rsta.2021.0130)</a> we propose a practical method for radiometrically calibrating cameras using widely available gaseous tritium light sources (<em>betalights</em>). This dataset includes all the recorded data along with the scripts necessary to reproduce the results and figures.</p>
Source data to publication "Benchmarking of Analysis Strategies for Data-Independent Acquisition Proteomics Using a Large-Scale Dataset Comprising Inter-Patient Heterogeneity"
<p>Source data to publication "Benchmarking of Analysis Strategies for Data-Independent Acquisition Proteomics Using a Large-Scale Dataset Comprising Inter-Patient Heterogeneity".</p> <p>Data and further information at GitHub repository https://github.com/kreutz-lab/dia-benchmarking (DOI: 10.5281/zenodo.6371925)</p>
Development and evaluation of a method to identify potential release areas of snow avalanches based on watershed delineation - source data
<p>Full data files for the paper:</p> <p>Duvillier, C., Eckert, N., Evin, G., and Deschâtres, M.: Development and evaluation of a method to identify potential release areas of snow avalanches based on watershed delineation, Nat. Hazards Earth Syst. Sci., 23, 1383–1408, https://doi.org/10.5194/nhess-23-1383-2023, 2023.</p> <p>Can be used to reproduce all the results of the paper and for further benchmarking of snow avalanche potential release area detection methods.</p>
Supporting data for "Modeling the albedo neutron decay source of radiation belt electrons and protons"
<p>Data sets are provided in support of the publication to appear in JGR-Space Physics. They include tabulated values of computed albedo neutron flux above the atmosphere, and of resulting radiation belt electron and proton source functions. Data format is described in the README files.</p>
Source data and code for: Existing fossil fuel extraction would warm the world beyond 1.5°C
<p>Source data and code for the study, "Existing fossil fuel extraction would warm the world beyond 1.5°C." Datasets 1-4 include mine-level data collected for China (Dataset 1), India (Dataset 2), and five other countries (Dataset 3) that are among the world's top nine coal producers - the United States, Indonesia, Australia, South Africa, and Poland. Dataset 4 includes global and country-level output data from the 1,000-run Monte Carlo simulation. <Committed_Reserves_Monte_Carlo_Input_Data.zip> includes data and code to replicate the Monte Carlo simulation.</p>
Source data belonged to "Geometric flow control in lateral flow assays: Macroscopic single-phase modeling"
<p>This record contains all the necessary data to obtain the results of the study "Geometric flow control in lateral flow assays: Macroscopic single-phase modeling" (<a href="https://doi.org/10.1063/5.0093316">https://doi.org/10.1063/5.0093316</a>).</p>
Growth and metabolome data of Saccharomyces uvarum grown in synthetic wine must with different nitrogen sources
<p><em>Raw data: Metabolome of S. uvarum (Su) and S. cerevisiae (Sc) in wine fermentations in 13 different nitrogen conditions. Concentrations of compounds expressed in mg/L at 60 g/L CO2 sampling point and at the end of fermentation. The volatile compounds are grouped according to the chemical functional group (ethyl esters, acetate esters, higher alcohols, medium chain fatty acids (MCFA) and branched-chain fatty acids (BCFA)). The central carbon metabolites (CCM) and sugars conform the last group. Each value is the mean of three biological replicates. The raw data is reported in a processed form in the manuscript entitled “The growth and metabolome of Saccharomyces uvarum in wine fermentations is strongly influenced by the route of nitrogen assimilation” </em></p>
Transcriptome data of Saccharomyces uvarum grown in synthetic wine must with different nitrogen sources Created Jun 9, 2022 12:06:22 PM, modified Jun 9, 2022 12:07:57 PM
<p>Transcriptome analysis of S. uvarum grown on synthetic wine must with different nitrogen sources: Ammonium, Phenylalanine, Asparagine, or Methionine. This is a dataset for the thesis of Angela Coral (Autumn 2022) , which can be accessed at www.ucc.ie. The work will also be submitted for publication and this will be a supplementary data file.</p>
Data from: Evolved differences in thermal plasticity of mosquitofish mating behavior are unrelated to source temperature
<p>Phenotypic plasticity in response to temperature is expected to play a key role in how organisms cope with climate change. Evolved differences in plastic responses are often linked to historical differences in average temperatures, yet we know little about how behavioral plasticity is affected by prevailing thermal environments. In this study, we used a common-garden design to test whether historical differences in average temperatures caused evolutionary divergence in the plasticity of mating behavior of Western mosquitofish (<em>Gambusia affinis</em>) inhabiting geothermal springs with average source temperatures spanning from 18.8 to 33.3 C. We found population differences in the thermal plasticity of courtship displays, copulation attempts, copulations, and mating efficiency, but these differences could not be explained by average source temperatures. We also tested for differences in thermal optima and maximum performance in mating behavior among populations. We found that only the maximum number of displays differed among populations, although these differences were also unrelated to source temperature. While temperature may have predictable evolutionary consequences for some thermally sensitive traits, our findings are inconsistent with theoretical predictions of evolutionary responses to divergent average temperatures, highlighting the need for greater synergy between empirical and theoretical work to understand thermal adaptation.</p>
Image data for bioRxiv article named: mtFociCounter - Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci
<p>Raw imaging data to reproduce and test the findings of the bioRxiv article: <strong>mtFociCounter </strong>- Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci. It contains data from three imaging days and 2 or three technical replicates on each day.</p> <p> </p>
Mapping 10-m global impervious surface area (GISA-10m) using multi-source geospatial data
<p>Artificial impervious surface area (ISA) documents human footprints. Accurate, timely, and detailed ISA datasets are therefore essential for global climate change and urban planning. However, due to the lack of sufficient training samples and operational mapping methods, global ISA mapping at 10-m resolution is still lacking. To this end, we proposed a global ISA mapping method leveraging multi-source geospatial data. Based on the existing satellite-derived ISA maps and the crowdsourcing OpenStreetMap (OSM), 58 million training samples were extracted via a series of temporal, spatial, spectral, and geometric rules. Combined with over 2.7 million Sentinel optical and radar images on the Google Earth Engine, we produced the 10 m global ISA dataset (GISA-10m). Based on the test samples that are independent to the training set, GISA-10m embraced an overall accuracy greater than 86%. In addition, the GISA-10m was comprehensively compared with the existing global ISA datasets, and the superiority of GISA-10m was demonstrated. </p>
Interrogating genomic data in the phylogenetic placement of treeshrews reveals potential sources of conflict
<p>The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In this study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. The results suggest that the data has statistical support for two hypotheses for the placements of treeshrews, sister to Primatomorpha and to Primatomorpha + Glires. While we observe differences in properties of loci of different types (e.g., CDS, intron, etc.) with respect to the strength of the signal, the support for any particular topology is not dependent on the properties of the data. Rather, we show that the method of phylogenetic signal assessment, as well as whether the signal is measured using the full dataset or only loci with the strongest signal, impacts the results much more.</p>
Source code and data from: Foraging personalities modify effects of habitat fragmentation on biodiversity
<p><span>Habitat loss undeniably poses a substantial threat to biodiversity, but whether fragmentation per se drives the loss of species is still widely debated. While negative consequences from fragmentation are often anticipated, many empirical studies report positive effects. However, the intrinsic mechanisms governing species' persistence in fragmented landscapes are not yet understood. In this study, we investigated consistent personality-dependent differences in foraging behavior among individuals as a possible mechanism underlying the discrepancy of reported fragmentation effects. </span><span>We </span><span>devised a mechanistic individual-based model simulating the home range behavior of a competitive small mammal community based on the availability of a shared resource. Thereby, an individual's risk-taking behavior dictates its foraging decisions at risky habitat edges, an inherent property of fragmentation per se. Our simulations show that differences in risk-taking while foraging are potentially a further mechanism contributing to reconciling the fragmentation debate. The first scenario considering risk-seeking communities showed a neutral response towards fragmentation, while the second scenario featuring risk-avoiding communities confirmed the negative effects of fragmentation. Notably, the third scenario, simulating behaviorally diverse communities including risk-avoiding and risk-seeking individuals, demonstrated a positive influence of fragmentation on biodiversity. Intraspecific differences in behavior could also enhance the temporal species coexistence (coviability) of communities threatened by an ongoing habitat loss. Our study highlights the importance of recognizing the behavioral composition of populations and communities for estimating fragmentation effects, because differences in risk-taking can influence the coping abilities of animal communities in light of fragmentation.</span></p>
Data for FEgrow: An Open-Source Molecular Builder and Free Energy Preparation Workflow
<p>Data illustrating the use of de novo design in building and scoring protein-ligand complexes.</p> <p>This is relationship to the FEgrow publication with the intiial preprint here: <br> https://chemrxiv.org/engage/chemrxiv/article-details/6287bb98a42e9c78d34769f6<br> </p> <p>The FEgrow software snapshot used can be found here: https://zenodo.org/record/7105647#.YzFwINLMIUE</p>
Network Theme: Can blood sampling become a new data source in the role of self-monitoring and self-management of health? - Dr Mark Elliott (University of Warwick)
<p>This video is the fourth talk from our Future Blood Testing Network Plus Launch that took place on the 23/11/2021.</p> <p>Network Theme: Can blood sampling become a new data source in the role of self-monitoring and self-management of health? - Dr Mark Elliott (University of Warwick)</p> <p>Bio: <strong><a href="https://warwick.ac.uk/fac/sci/wmg/people/profile/?wmgid=1147">Dr Mark Elliott</a> </strong>Mark is an Associate Professor at the Institute of Digital Healthcare, WMG, University of Warwick (UoW). Mark’s core research focuses on human movement and physiology analytics. His research uses signal processing and data science approaches to monitor, measure and model human movement and physiology to infer health status. He is the PI of the WMG Motion Capture Laboratory. His work further extends into the broader area of using wearable and on-the- body sensing devices to make objective measures of human behaviour and behaviour change. Much of Dr Elliott’s research is highly applied and involves collaborating with commercial and NHS partners. He has received funding from EPSRC, Innovate UK and SBRI Healthcare, as well as direct industrial funding. He is currently Data Analytics Theme Lead for the EPSRC funded OATech+ Network and on the steering committee for the EPSRC funded VSimulators facilities at Bath and Exeter.</p> <p>Further details on this event can be found at: https://futurebloodtesting.org/event/23-11-21-future-blood-testing-network-launch/</p> <p>This video is an output from the Future Blood Testing Network which is funded by EPSRC under Grant Number EP/W000652/1</p> <p>YouTube Link: https://youtu.be/ChdbggScUgo</p>
Data and Source codes: Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behavior
<p>This repository provides access to the tracking data and analysis code used for the manuscript:</p> <p>Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behavior</p> <p>by Nobuaki Mizumoto<sup>1</sup>, Thomas Bourguignon<sup>1</sup>, and Nathan W. Bailey<sup>2</sup></p> <p><sup>1</sup> Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan <br /><br> <sup>2</sup> School of Biology, University of St Andrews, St Andrews, U.K. <br /></p> <p>published in the Proceedings of the National Academy of Sciences of the United States of America.</p>
Open source measurement data of the ground water physio-chemical parameters in the Peshawar District, Pakistan
<p>This excel file provides the measurement data of the physio-chemical parameters in the Peshawar district, Pakistan. The physio-chemical parameters include pH, electrical conductivity, total dissolved solids, Ca hardness, Mg hardness, Total hardness, Turbidity, Nitrate and Chloride. The data also include the latitude and longitude and location and depth to groundwater level (water table). The data was collected and sample were analyzed in June-August 2012.</p> <p>The full data collection and case studies are described in Adnan and Iqbal 2014, Adnan et al. 2018 and Adnan et al. 2019.</p>
Final data of the adjoint-state full waveform tsunami source inversion, applied to Chile-Iquique tsunami event
<p>We develop an adjoint-state full waveform inversion procedure to recover the initial water elevation of a tsunami event. Traditional finite-fault tsunami source inversion methods suffer from the uncertainty of fault parameters or crustal rigidity. Moreover, the heavy computational burden of calculating Green’s functions results in limited spatial resolution and hinders the real-time applicability of the traditional methods to tsunami early warning. In this work, we apply the adjoint-state full waveform inversion method to the tsunami source inversion. The benefits of the adjoint inversion are two folds: 1) independence of fault parameters, and 2) high computational efficiency, especially for dense tsunami arrays and high resolution grids. We valid this approach with synthetic tsunami sources, and apply it to the 2014 Chile-Iquique tsunami event. Both synthetic and real-data preliminary results show that the adjoint-state method is of high efficiency and high resolution, outperforming the traditional tsunami source inversions. </p> <p>The data is in three comma-separated ascii files. We shared the three inversion results with different starting models. The source region is 70.3~71.5W, 18.5~21S on uniform grids. The src_TRIstart.txt is the inversion result with TRI image starting model, src_USGS_unistart.txt is the inversion result with USGS uniform slip model (https://earthquake.usgs.gov/earthquakes/eventpage/usc000nzvd/finite-fault). The src_zerostart.txt is the inversion result with zero starting model. The text file has longitude (in degrees), latitude (in degrees) and water elevation (in meters) of each column.</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.