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.
6,467
datasets available to search
ShareScore release 0.9.0
Dataset results
6,467 results for “process”
Codes and datasets associated with the paper "Day-ahead Wind Power Predictions at Regional Scales: Post-processing Operational Weather Forecasts with a Hybrid Neural Network"
<p>The jupyter notebooks and datasets associated with the EEM20 forecasts are available here. More details will be provided shortly. </p> <p>Please check the EEM20 website (<a href="https://eem20.eu/forecasting-competition/">https://eem20.eu/forecasting-competition/</a>) for the details of the forecasting competition. </p>
PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci – processed datasets
<p>Processed datasets from PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci. Raw data are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658511. </p> <p>Available datasets: </p> <p>- reference file for regions selected for amplicon sequencing: <em>Phaeodactylum_tricornutum_amplicon_sequencing_loci.fa</em></p> <p>- final .bam files containing processed PacBio sequencing reads aligned to the reference:</p> <p><em>PacBio_amplicon_seq_T1.bam</em> and <em>PacBio_amplicon_seq_T6.bam</em> </p> <p>- . table files with the position, reference and alternative allele for reliable biallelic SNPs selected in ILLUMINA sequencing of the culture at T1: </p> <p><em>P_tricornutum_PacBio_amplicon_sequencing_T1_SNPs.table</em> and <em>P_tricornutum_PacBio_amplicon_sequencing_T6_SNPs.table</em></p> <p>Re-sequencing of 62 endogenous P. tricornutum loci selected in a genome-wide analysis of haplotype diversity. The goal was to determine the number of haplotypes per locus and the appearance of new haplotypes over time. The length of the sequenced loci was 2kb (+/- 5%). Loci were amplified by emulsion PCR on the same culture harvested in two time points: five loci were amplified one month (T1) and all loci were amplified 6 months (T6) after the start of the culture from a single cell. Plasmids containing cloned GFP or YFP were amplified separately as a control for random errors. Control reactions for artificial haplotypes detection consisted of mixed CFP with YFP or CFP with GFP. Amplicons were pooled together into two samples. Sample PacBio_AS_T1 contained five P. tricornutum endogenous amplicons from DNA harvested at T1 time point, GFP amplified separately and CFP+YFP amplified in one reaction. Sample PacBio_AS_T6 contained 63 P. tricornutum endogenous amplicons from DNA harvested at T6 time point, YFP amplified separately and CFP+GFP amplified in one reaction. Samples were mixed in 1:9 PacBio_AS_T1: PacBio_AS_T6 ratio before sequencing on one PacBio Sequel SMRT cell.</p>
Genome sequencing of P. tricornutum mother and daughter cultures derived from single cell and separated by 30 days of proliferation - processed datasets
<p><strong>Genome sequencing of <em>P. tricornutum</em> mother and daughter cultures derived from single cell and separated by 30 days of proliferation - processed datasets.</strong></p> <p>Raw data for this experiment are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658224.</p> <p> </p> <p><strong>Please note that the naming of files differs from the general description on /www.ncbi.nlm.nih.gov/bioproject website and in related publication:</strong></p> <p>Instead of MC1-3, the processed datasets are labelled Sc1-3</p> <p>Instead of DC1.1; DC1.2 and DC1.3, the processed datasets are labelled Sc11, Sc12 and Sc14 respectively</p> <p>Instead of DC2.1; DC2.2 and DC2.3, the processed datasets are labelled Sc21, Sc22 and Sc24 respectively</p> <p>Instead of DC3.1; DC3.2 and DC3.3, the processed datasets are labelled Sc31, Sc32 and Sc33 respectively</p> <p><strong>Available datasets: </strong></p> <p><em>.bam</em> files with ILLUMINA reads aligned to the reference P. tricornutum v2 genome used for SNP calling </p> <p><em>.vcf</em> files for individual samples with SNPs called using GATK3.7.0</p> <p><em>joint_genotyping_cohort.vcf</em> file with SNPs called jointly for all samples using GATK4.2.1 </p> <p> </p> <p><strong>Description of the experiment:</strong> </p> <p>Whole-genome Illumina sequencing of mother and daughter cultures derived from single cell to reveal genomic changes occurring within 30 day time frame. Three independent single cells were isolated from CCAP 1055/1 culture (sample label: Pt1) to start mother cultures (MC1; MC2; MC3 . On day 30 after mother culture isolation (T1 time point), three daughter cells were isolated from each mother culture forming cultures DC11-DC33. Part of mother cultures and CCAP 1055/1 culture were harvested at T1 (Samples: Pt1T1; MC1T1; MC2T1; MC3T1) . After another 30 days (T2 time point), all cultures were harvested (Samples: Pt1T2; mother culture MC1T2 and respective daughter cultures DC11, DC12 and DC13 ; mother culture MC2T2 and respective daughter cultures DC21, DC22 and DC23; mother culture MC3T1 and respective daughter cultures DC31, DC32, DC33).</p>
Pre-processed data for kmspd
<p>This is the pre-processed SAR data used for the paper <a href="https://arxiv.org/pdf/2008.03454.pdf">k-means on Positive Definite Matrices, and an Application to Clustering in Radar Image Sequences </a></p> <p>Code for reproducing results in the paper is available at <a href="https://github.com/frycast/kmspd">github.com/frycast/kmspd</a></p> <p>Any use of this data should attribute the author Pascal Catellazzi for his work in pre-processing.</p>
Dataset of Paper "Mechanistic modelling of wastewater disinfection by the photo-Fenton process at circumneutral pH"
<p>Datasets of Paper “Mechanistic modelling of wastewater disinfection by the photo-Fenton process at circumneutral pH”:</p> <ul> <li>Optical properties of the Simulated Wastewater at different iron concentrations</li> <li>Optical parameters of dispersed iron in the simulated wastewater</li> <li>Modelled and experimental data of <em>E. coli </em>solar disinfection</li> <li>Experimental data of <em>E. coli</em> photo-Fenton disinfection</li> <li>Modelled data of <em>E. coli</em> photo-Fenton disinfection</li> </ul> <p>.</p>
Figure 2 from: Owen D, Groom Q, Hardisty A, Leegwater T, Livermore L, van Walsum M, Wijkamp N, Spasić I (2020) Towards a scientific workflow featuring Natural Language Processing for the digitisation of natural history collections. Research Ideas and Outcomes 6: e58030. https://doi.org/10.3897/rio.6.e58030
Figure 2 A possible semi-automatic digitisation workflow to extract data from the labels of collection specimens.
PHASTA incompressible test case for 48 processes
<p>Input files and execution instructions for a PHASTA incompressible 'crossflow' flow case using 48 processes. The expected results are listed in the included README.md.</p>
Supporting model data for paper: Measuring the impact of a new snow model using surface energy budget process relationships
<p>Supporting model data for paper: Measuring the impact of a new snow model using surface energy budget process relationships which has been submitted to the Journal of Advances in Modelling Earth Systems: https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020MS002144</p> <p>The experiment id h3hh corresponds to simulations with the ECMWF IFS with a single layer snow model. h3eg corresponds to the experimental 5-layer snow model.</p> <p>The timeseries are made by concatenating hourly data from day2 of forecasts initialised at 00UTC each day between Dec 1st 2013 and 1 June 2014.</p>
Environmental filtering and spatial processes shape the beta diversity of liana communities in a valley savanna in Southwest China
<p><b><span>Questions:</span></b> Lianas contribute substantially to diversity and function of ecosystems. What is the relative importance of environmental filtering and spatial processes on structuring liana beta diversity at taxonomic, functional and phylogenetic levels? Is there any synergy between these drivers (environmental factors and spatial distance) on shaping three dimensions of beta diversity in a savanna liana community?</p> <p><b><span>Location:</span></b> A dry-hot valley savanna in Yunnan Province, southwest China.</p> <p><b><span>Methods: </span></b>We established 30 20×20 m plots in the savanna to collect data on the distribution of 22 liana species, 19 functional traits, and plot-level soil nutrients, elevation, and slope. The relative contributions of these environmental factors and spatial distance to liana taxonomic, functional and phylogenetic dissimilarity were analyzed using multiple regression on distance matrices. We also tested which environmental factors influence the beta diversity of liana community using permutational multivariate analysis of variance.</p> <p><b><span>Results: </span></b>Both environmental and spatial distances were significantly correlated with taxonomic, functional and phylogenetic dissimilarity. Spatial distance explained more variation in taxonomic beta diversity than environmental factors. But for both nearest neighbor functional and phylogenetic distance <i><span>D</span></i><i><sub><span><span>nn</span></span></sub></i><sub><span>'</span></sub>, environment explained a relatively higher variation than space did. Moreover, the proportion explained by environmental variables was ranked in decreasing order as follows: functional <i><span>D</span></i><i><sub><span><span>nn</span></span></sub></i><sub><span>'</span></sub>, phylogenetic <i><span>D</span></i><i><sub><span><span>nn</span></span></sub></i><sub><span>'</span></sub>, and taxonomic beta diversity. We found soil pH had the highest contribution to taxonomic and functional beta diversity, while soil total nitrogen contributed most to phylogenetic beta diversity.</p> <p><b><span>Conclusions: </span></b>This study revealed that liana taxonomic, functional and phylogenetic beta diversity in the study hot-dry savanna ecosystem are affected and maintained by both environmental filtering and spatial processes. Moreover, the functional and phylogenetic diversities were more strongly subject to environmental filtering. Our study provides the information on mechanisms underlying liana diversity maintenance in savanna, which are necessary to inform conservation management in this vulnerable ecosystem. </p>
Assessment of companies' safety processes maturity in requirements engineering with Uni-REPM SCS
<p>Video presentation of the paper "<em>Assessment of companies’ safety processes maturity in requirements engineering with Uni-REPM SCS</em>" to appear at<strong> the Industry Track </strong>of CBSOFT 2020.</p> <p><strong>Abstract.</strong> Safety is an important quality attribute in the development of safety-critical systems (SCS). This attribute can be achieved by improving safety processes maturity to reduce accidents and safety incidents. In this work, we present a safety module called Uni-REPM SCS for the Uni-REPM maturity model. We describe the methodology used to develop the module, how we built and validated it and further research and possibilities of collaboration.</p>
Toward a Metamodel Quality Evaluation Framework: Requirements, Model, Measures, and Process
<p>The quality of metamodel considerably affects the models and transformations that conform to it. Despite that, there is still little discussion about a comprehensive form to evaluate the quality of metamodels and its consequences in model-driven development processes. This paper proposes a metamodel quality evaluation framework called MQuaRE (Metamodel Quality Requirements and Evaluation). MQuaRE comprises metamodel quality requirements and measures, a quality model, and an evaluation process, with the evident influence of international standards for software product quality, such as ISO/IEC 25000 series. We present a simple use case of MQuaRE describing how requirements, measures, and the quality model should be used during the evaluation process of a metamodel for software patterns. Among other benefits, MQuaRE can help determine final metamodel quality, decide on the acceptance of a metamodel, and also assess the positive and negative aspects of a metamodel, contributing to its quality evolution.</p>
Processed multibeam bathymetry data collected around the Ria de Aveiro, Portugal, onboard the NEREIDE research vessel.
<p>A Kongsberg EM 2040 C multibeam echo sounder transducer installed on the scientific vessel NEREIDE, was used to collect multibeam bathymetry data during graduation activities and equipment testing. This particular dataset was collected around the Ria de Aveiro, Portugal during March, 2020.</p> <p>The range of opening angles of the EM 2040 C multibeam varies between 60 and 65 degrees. The positioning system used was supported by the Real Time Kinematic (RTK) technique with the transmission of differential data in Ultra High Frequency (UHF) mode.</p> <p>The data is calibrated and corrected for the surface sound velocity. The processing of hydrographic data was performed using specific algorithms for hydrography - Combined Uncertainty and Bathymetric Estimator (CUBE). In its processing, data was referenced to the hydrographic Zero of Portugal and projected in the WGS84-UTM29N coordinate system.</p>
The spatial landscape of lung pathology during COVID-19 progression - processed IMC data
<p>Recent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19). However thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking. We use high parameter imaging mass cytometry9 targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of human acute lung injury including SARS-CoV-2. This spatially resolved, single-cell data unravels the disordered structure of the infected and injured lung alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyper-inflammatory cell state associated with lung damage. By leveraging the temporal range of COVID-19 severe fatal disease in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19, and lung pathology in general.</p>
Code and processed data accompanying "Widespread haploid-biased gene expression enables sperm-level natural selection"
<p>Code and processed data required to reproduce the analysis in "Widespread haploid-biased gene expression enables sperm-level natural selection".</p>
Towards a Process for Migrating Legacy Systems into Microservice Architectural Style
<p>Microservice architectural style is a paradigm to develop systems as a suite of small and autonomous services, communicating thought a light weight protocol. Currently, one of the most common ways of adopting microservice architectures is by the modernization of legacy monolith systems. The migration of a legacy system into a microservice architecture is not a trivial task. In addition, there is a lack of recommendation or guidelines on how to perform such process. In view of this, this paper presents a preliminary process for conducting the migration of legacy systems into microservice architectures. This process was defined by analyzing and discussing pieces of work on the topic. As result, we propose a process composed of eight steps, grouped in four phases, which we describe together with their common input and output.</p>
ClairCity Process Diagram
<p>The ClairCity Process of citizen-inclusive policy making</p>
Dataset accompanying article: On Linear and Circular Approach to GPS Data Processing: Analyses of the Horizontal Positioning Deviations Based on the Adriatic Region IGS Observables
<p>The dataset accompanies journal article: On Linear and Circular Approach to GPS Data Processing: Analyses of the Horizontal Positioning Deviations Based on the Adriatic Region IGS Observables published on 21 January 2021 in Data. </p> <p>SINEX, RINEX, position solution files, logs used for positional accuracy and deviation distribution of IGS observables and additional figures with results are included. Dataset covers period from 10th to 20th of March 2017. </p> <p>IGS SINEX combined weekly station position/velocity solutions were retrieved from the online archives of the Crustal Dynamics Data Information System (CDDIS), NASA Goddard Space Flight Center, Greenbelt, MD, USA, available at: ftp://cddis.nasa.gov/gnss/products/. Please note that from from October 31, 2020 anonymous ftp service has been discontinued. Access with examples is available via HTTPS or ftp-ssl from <a href="https://cddis.nasa.gov/Data_and_Derived_Products/CDDIS_Archive_Access.html">CDDIS Archive</a></p> <p>RINEX observation and navigation files were retrieved from IGS repository available at: ftp://igs.ign.fr/pub/igs/data/</p> <p>Position solution files were determined with <a href="https://github.com/tomojitakasu/RTKLIB_bin/">RTKLIB</a>: An Open Source Program Package for GNSS Positioning, version 2.4.3 b33 available</p> <p>Please cite respective sources accordingly.</p> <p> </p>
Data from: Beyond a single patch: local and regional processes explain diversity patterns in a seagrass epifaunal metacommunity
<p>Ecological communities are jointly structured by dispersal, density-independent responses to environmental conditions and density-dependent biotic interactions. Metacommunity ecology provides a framework for understanding how these processes combine to determine community seagrass meadows along the British Columbia coast, we tested the hypothesis that eelgrass (<i>Zostera marina</i> L.) epifaunal invertebrate assemblages are influenced by local environmental conditions, but that high dispersal rates at larger spatial scales dampen effects of environmental differences. We used hierarchical joint species distribution modelling to understand the contribution of environmental conditions, spatial distance between meadows, and species co-occurrences to epifaunal invertebrate abundance and distribution across the region. We found that patterns of taxonomic compositional similarity among meadows were inconsistent with dispersal limitation, and meadows in the same region were often no more similar to each other than meadows over 1000 km away. Abiotic environmental conditions (temperature, dissolved oxygen) explained a small fraction of variation in taxonomic abundances patterns across the region. We found novel co-occurrence patterns among taxa that could not be explained by shared responses to environmental gradients, suggesting the possibility that interspecific interactions influence seagrass invertebrate abundance and distribution. Our results suggest that biodiversity and ecosystem functions provided by seagrass meadows reflect ecological processes occurring both within meadows and across seascapes, and that management of eelgrass habitat for biodiversity may be most effective when both local and regional processes are considered.</p>
Visualization of the process of lightning initiation in a thundercloud via coalescence of multiple simultaneously developing bipolar streamer/leader systems
<p>This movie visualizes the evolution of 3D streamer / hot-channel systems at 6 km altitude in a uniform upward directed electric field, the magnitude of which is equal to 65 kV/m. Positive and negative streamer channels are shown in green and gray, respectively. Red channels indicate hot leader sections with conductivity exceeding 1 S/m. All three axes are labeled in meters.</p>
Drought risk of global terrestrial gross primary productivity in recent 40 years detected by a remote sensing-driven process model
<p class="Abstract"><span>Gross primary productivity (GPP) is the largest flux in the global terrestrial carbon cycle and affected by multiple factors. In recent decades, drought has significantly impacted global terrestrial GPP and been projected to occur with increasing frequency and intensity. However, the drought risk of global terrestrial GPP has not been well investigated. In this study, global terrestrial GPP over the period from 1981 to 2016 was simulated with the process-based Boreal Ecosystem Productivity Simulator (BEPS) model. Then, the drought risk of terrestrial GPP was quantified as the product of frequency of drought and reduction of GPP caused by drought, which were determined using the standardized precipitation evapotranspiration index (SPEI). During the study period, the drought risk of terrestrial GPP exhibited detectable spatial heterogeneity, high in southeastern United States, most of South America, southern Europe, central and eastern Africa, eastern and southeastern Asia, and eastern Australia. In these regions, the maximum reduction of GPP might be above 30% in drought years relative to that in normal years. The drought risk of GPP was low at high latitudes of the Northern Hemisphere, in which terrestrial GPP increased slightly in drought years. The spatial pattern of the drought risk of GPP simulated by the BEPS model was close to that of FLUXCOM GPP, which was scaled from tower observations with a machine learning algorithm forced by remote sensing and meteorological data. This study advances our understanding on the impact of drought on terrestrial GPP over the globe.</span></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.