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1,456 results for “parallelism”
Parallel Body Shape Divergence in the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) Along Elevational Gradients of the Western Slopes of the Ecuadorian Andes
<p>TPS files for geometric morphometric analysis of body shape data of Rhoadsia spp. (Teleostei: Characidae) collected in western Ecuador.</p>
Parallel Body Shape Divergence in the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) Along Elevational Gradients of the Western Slopes of the Ecuadorian Andes
<p>Morphological data collected from specimens of Rhoadsia spp. (Teleostei: Characidae) in western Ecuador. Excel file with individual standard length (SL), body depth (BD), size-adjusted fineness ratio (Adj_FR), and size-adjusted canonical variates analysis scores on axes 1 and 2 (Adj_CV1, Adj_CV2).</p>
In-memory integration of existing software components for parallel adaptive unstructured mesh workflows: PHASTA 3D dam break
<p>Input mesh, solution field, configuration files, and job scripts for running the adaptive PHASTA-Chef 3D dam break case.</p> <p>Data stream, POSIX file, and ramdisk results are also included. The python scripts used to generate the bandwidth and open/close time plots are included.</p>
Massively parallel sequencing data of the HIV-1 pol region generated from the plasma of therapy-naïve chronically infected Brazilian blood donors
<p>The submitted massively parallel sequencing (MPS) data were partial data from the pol region of HIV-1 plasma viruses. Samples were obtained from 18 therapy-naive HIV-1 Brazilian blood donors with longstanding infection. Illumina ultra-deep sequencing technology (MiSeq platform) was used to generate the sequences. </p>
Atomistic Fingerprint of Hyaluronan-CD44 Binding: Umbrella Sampling Data, Parallel Mode
<p>Simulation files (Gromacs 4.6.7 format) for the "Free Energy" simulations of parallel mode in Ref. [1]. </p> <p>Files include:</p> <p>-trajectories (.xtc) that are saved every 100ps <br> -initial structures (.gro), <br> -run input files (.tpr)<br> -simulation parameter files (.mdp)<br> -system topology file (.top)<br> -topology files included in the system topology file (.itp)</p> <p>'pullx' ('and pullx2' files, which contain data from the last 80ns) are used to constuct the free energy profile. Command for building the free energy profile is included in 'wham.sh'</p> <p>[1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)</p>
Numerical data set belonging to: 'A Finite Volume Parallel Adaptive Mesh Refinement Method for Solid-Liquid Phase'
<p>This data set corresponds to the paper 'A Finite Volume Parallel Adaptive Mesh Refinement Method for Solid-Liquid Phase Change', submitted to Numerical Heat Transfer, Part A: Applications. The numerical data is included in VTK format (to be read by paraView) for the following cases:</p><p>1) 2D Gallium melting in a rectangular cavity (70x50 elements, 140x100 elements, 280x200 elements, 560x400 elements, 1120x800 elements and adaptive mesh)</p><p>2) 3D Gallium melting in a hexagonal cavity (adaptive mesh)</p><p>3) 2D freeze-plug (both steady-state and melting transient): 110x300 elements, 220x600 elements, 440x1200 elements and adaptive mesh)</p><p>Due to the size of the data-set, the data has been split over 8 tar archives featuring a gzip compression. To unpack the data, run the command: cat paper_<i>amr</i>_<i>data.</i>tar.gz.* | tar xzvf -</p><p> </p>
Dataset: Parallel Empirical Evaluations: Resilience Despite Concurrency
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Dataset for the Paper "Longevity of Artifacts in Leading Parallel and Distributed Systems Conferences: a Review of the State of the Practice in 2023"
<p>Dataset used for the paper "Longevity of Artifacts in Leading Parallel and Distributed Systems Conferences: a Review of the State of the Practice in 2023" submitted at ACM REP'24.</p> <p>The associated analysis scripts are available on Software-Heritage: https://archive.softwareheritage.org/swh:1:dir:3904795a49327b1e9b7ef1a8aff995b1f94ae6fb;origin=https://github.com/GuilloteauQ/artefact-lifetime;visit=swh:1:snp:9adc667f9fefcb6783df076520ef357231030ad4;anchor=swh:1:rev:ad4d19abb5da12fd6df708bc13e444d834c85dfa</p>
Parallel evolution despite low genetic diversity in three-spined sticklebacks
<p>The three-spined stickleback (<em>Gasterosteus aculeatus</em>) is a model organism for studies of parallel evolution in the wild; marine stickleback populations have repeatedly colonized and adapted to different brackish and freshwater habitats. Population genetic studies of European three-spined sticklebacks have usually been conducted only in high-latitude areas. Here, we analysed southern and northern European samples of marine and freshwater three-spined stickleback to test two hypotheses. First, southern European freshwater populations – which currently lack or have limited connection to marine populations – have lost genetic diversity due to population bottlenecks and inbreeding compared to their northern European counterparts. Second, the degree of genetic parallelism in response to freshwater colonisation is higher among northern than southern European populations as the latter have been isolated and likely subjected to strong genetic drift. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss likely happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.</p>
Replication package for article 'Parallel Program Analysis on Path Ranges'
<p>This Replication package contains all the results for the article "Parallel Program Analysis on Path Ranges"</p> <p>Abstract. Symbolic execution is a software verification technique symbolically running programs and thereby checking for bugs. <br> Ranged symbolic execution <br> performs symbolic execution on program parts, so called {\em path ranges}, in parallel.<br> Due to the parallelism, verification is accelerated and hence scales to larger programs.</p> <p>In this paper, we discuss a generalization of ranged symbolic execution to arbitrary program analyses.<br> More specifically, we present a verification approach that splits programs into path ranges and<br> then runs arbitrary analyses on the ranges in parallel. Our approach in particular allows to run {\em different}<br> analyses on different program parts.<br> We have implemented this generalization on top of the tool \textsc{CPAchecker} and evaluated it on programs from the SV-COMP benchmark. Our evaluation shows that verification can benefit from the parallelisation of the verification task,<br> but also needs a form of work stealing (between analysis) as to become efficient.</p>
Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
<p>Photosymbioses between heterotrophic hosts and autotrophic symbionts are evolutionarily prevalent and ecologically significant. However, molecular mechanisms behind such symbioses remain less elucidated, which hinders our understanding of their origin and adaptive evolution. This study compared gene expression patterns in a photosymbiotic bivalve (<em>Fragum sueziense</em>) and a closely related non-symbiotic species (<em>Trigoniocardia granifera</em>) under different light conditions to detect potential molecular pathways involved in mollusk photosymbiosis. We discovered that the presence of algal symbionts greatly impacted host gene expression in symbiont-containing tissues. We found that the host immune functions were suppressed under normal light compared to those in the dark. In addition, we found that cilia in the symbiont-containing tissues play important roles in symbiont regulation or photoreception. Interestingly, many potential photosymbiosis genes could not be annotated or do not exhibit orthologs in <em>T. granifera</em> transcriptomes, indicating unique molecular functions in photosymbiotic bivalves. Overall, we found both novel and known molecular mechanisms involved in animal-algal photosymbiosis within bivalves. Given that many of the molecular pathways are shared among distantly related host lineages, such as mollusks and cnidarians, it indicates that parallel and/or convergent evolution is instrumental in driving host-symbiont adaptations in diverse organisms.</p>
Great Power Dynamics and International Economic Cooperation: Experimental Evidence from Parallel Surveys in China and the United States
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Parallel Recognizer for Regular Texts
<p>parallel recognizer for regular texts</p>
Understanding piRNA-guided Silencing with Massively Parallel Cellular Assays
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Data for: Parallel recolonisations generate distinct genomic sectors in kelp following high magnitude earthquake disturbance
<p>Large-scale disturbance events have the potential to drastically reshape biodiversity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonised by multiple lineages, which can lead to the evolution of distinct spatial 'sectors' of genetic diversity within a species. We test for disturbance-driven sectoring of genetic diversity in intertidal southern bull kelp, <i>Durvillaea antarctica</i> (Chamisso) Hariot following the high-magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping-by-sequencing (GBS) to analyse fine-scale population structure across the uplift zone to assess the fit of alternative recolonisaton models. Our analysis reveals that specimens from the uplift zone carry genomic signatures distinct from populations in other regions, consistent with recolonisation after the 1855 earthquake. Crucially, our analysis identifies two parapatric spatial-genomic sectors of <i>D. antarctica</i> at Turakirae Head, which experienced the most dramatic uplift. We infer that bull kelp in the Wellington region survived moderate uplift and recolonised the devastated Turakirae Head coastline through two parallel, eastward recolonisation events. By identifying multiple parapatric genotypic sectors within a recently recolonised coastal region, the current study confirms that competing lineage expansions can generate striking spatial structuring of genetic diversity, even in highly dispersive taxa.</p>
Dataset of Paper "Optimization and parallelization of the Discrete Ordinate Method for radiation transport simulation in OpenFOAM: Hierarchical combination of shared and distributed memory approaches"
<p>Dataset of Paper "Optimization and parallelization of the Discrete Ordinate Method for radiation transport simulation in OpenFOAM: Hierarchical combination of shared and distributed memory approaches":</p> <ul> <li>Time profiling of the DOM model stages.</li> <li>Speed-up and parallel fraction of the “global results generation” stage in the DOM model.</li> <li>Comparison of computational time between original and modified DOM model stages.</li> <li>Scalability of the peer-to-peer communication (OpenFOAM) and master-slave communication (ANSYS Fluent) architectures.</li> <li>Results of the benchmarking of the model with ANSYS Fluent in three reactors.</li> <li>Mesh of the jerrycan.</li> <li>Mesh of the anular reactor</li> <li>Mesh of the tubular reactor couple to a compound parabolic collector.</li> </ul>
Datasets and scripts from: Sensory-based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space
<p>Parallel evolution, in which independent populations evolve along similar phenotypic trajectories, offers insights into the repeatability of adaptive evolution. Here, we revisit a classic example of parallelism, that of repeated evolution of brighter males in the Trinidadian guppy (<em>Poecilia reticulata</em>). In guppies, colonisation of low predation habitats is associated with emergence of 'more colourful' phenotypes since predator-induced viability selection for crypsis weakens while sexual selection by female preference for conspicuousness remains strong. Our study differs from previous investigations in three respects. First, we adopt a multivariate phenotyping approach to characterise parallelism in multi-trait space. Second, we use ecologically-relevant colour traits defined by the visual systems of the two selective agents (i.e. guppy, predatory cichlid). Third, we estimate population genetic structure to test for adaptive (parallel) evolution against a model of neutral phenotypic divergence. We find strong phenotypic differentiation that is inconsistent with a neutral model but very limited support for the predicted pattern of greater conspicuousness at low predation. Effects of predation regime on each trait were in the expected direction, but weak, largely non-significant, and explained little among-population variation. In multi-trait space, phenotypic trajectories of lineages colonising low from high predation regimes were not parallel. Our results are consistent with reduced predation risk facilitating adaptive differentiation, potentially by female choice, but suggest that this proceeds in independent directions of multi-trait space across lineages. Pool-sequencing data also revealed SNPs showing greater differentiation than expected under neutrality, among which some are found in genes contributing to colour pattern variation, presenting opportunities for future genetic study.</p>
Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
<p>The study "Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution" by Schenk et al. explores the phenotypic and genotypic changes in <em>Escherichia coli </em>after 500 generations of laboratory adaptation to increasing concentrations of an antibiotic (CTX). The source data files and scripts pertaining to the figures in the main manuscript and the extended data are available on the publishers webiste. Here we provide the source data files and scripts pertaining to the supplementary materials, organized according the figures in the supplementary material. Data are provided for Figures S2-S4, S6-S8, and S10-S12.</p>
An automated workflow for parallel processing of large multiview SPIM recordings
<p>Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here, we introduce an automated workflow for processing large multiview, multichannel, multiillumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on <em>snakemake</em> to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it.</p>
Formality annotated Japanese-English parallel data
<p>This is a dataset containing Japanese-English parallel data, annotated according to the formality of the Japanese sentences. The formality classification was automatic and was based on a rule-based formality classifier proposed by Feely et al. 19. The base unannotated parallel corpora that we used can be found at http://www.phontron.com/japanese-translation-data.php, a selection of Japanese-English parallel corpora curated by Graham Neubig.</p>
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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.