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1,956 results for “test data”
SSAM-lite test data
<p>Spatially resolved transcriptomics datasets prepared from different publications to be used as sample data sets for the <a href="https://github.com/HiDiHlabs/ssam-lite">SSAM-lite</a> tool.</p> <p>Each folder contains a dataset including:</p> <ul> <li>one file for mRNA locations, formatted as a comma separated file adhering to the DecodedSpots format defined by the Starfish pipeline (<a href="https://spacetx-starfish.readthedocs.io/en/mcai-api-additions/help_and_reference/spacetx-format/output_formats/DecodedSpots/index.html">https://spacetx-starfish.readthedocs.io/en/mcai-api-additions/help_and_reference/spacetx-format/output_formats/DecodedSpots/index.html</a>). This format is intuitive, with fields for the target mRNA, the x-coordinate and the y-coordinate.</li> <li>a gene signature file, containing expected mRNA expression profiles for cell types, formatted as a comma separated file with rows as cell types, columns as genes, with the matrix populated with numerical or binary values associating mRNA expression to cell types.</li> <li>a csv for a custom color palette for the provided cell types.</li> <li>and a README referencing the original publication the data was retrieved from as well as some dataset specifications.</li> </ul> <p>Datsets specifications:</p> <ul> <li>Codeluppi_osmFISH <ul> <li>method: osmFISH</li> <li>tissue: mouse brain somatosensory cortex</li> <li>mRNA spots: 1802589</li> <li>genes: 33</li> <li>signatures: 31 cell types</li> <li>DOI: 10.1038/s41592-018-0175-z</li> </ul> </li> <li>Tosti_ISS_Pancreas <ul> <li>method: ISS</li> <li>tissue: human pancreas</li> <li>mRNA spots: 461078</li> <li>genes: 138</li> <li>signatures: 16 cell types</li> <li>DOI: <a href="https://doi.org/10.1038/s41592-018-0175-z"> </a>10.1053/j.gastro.2020.11.010</li> </ul> </li> </ul>
Testing the Acoustic Localisation Positioning System-algorithm: Data sets
<p>The data is from 3 separate experimental setups: Tracking a device of constant speed using the Audio1 (single processor) software (B.1); and tracking a faster device using the al-Qt (multi processor) software (B.2) The experiments were also recorded on video. (see Video folder). For the experiments in B.1 a visualisation of the data has been made with the help of a MATLAB script which also included. The dimensions of the room and loudspeaker spacings were identical for both set-ups, namely 3 x 2 meters, with the loudspeakers at the corners of the rectangle. the loudspeakers were situated on the floor, approximately level with the tracked devices.</p> <p>Setup C collects debug log examples of experiments with very short capture cycles with 2 mics and 2 loudspeakers running ALPS al-Qt.</p> <p>The source code for Audio is available from: <a href="https://github.com/spatmus/alps/tree/master/Audio1">https://github.com/spatmus/alps/tree/master/Audio1</a><br> The source code for al-Qt is available from: <a href="https://github.com/spatmus/alps/tree/master/al-Qt">https://github.com/spatmus/alps/tree/master/al-Qt</a><br> A binary of al-Qt for macOS 11, can be found in the assets folder of the release <a href="https://github.com/spatmus/alps/releases">https://github.com/spatmus/alps/releases</a></p>
Test data for double blind submission
<p>Test data for double blind submission</p>
Research data supporting "article test"
<p>Research data supporting "article test"</p>
Data from: Species boundaries in the messy middle – testing the hypothesis of micro-endemism in a recently diverged lineage of coastal fog desert lichen fungi
<p><span><span><span><span><span><span><span><span><span><span><span>Species delimitation among closely related species is challenging because traditional phenotype-based approaches, e.g., morphology, ecological, or chemical characteristics, often produce conflicting results. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, e.g., hybridization/introgression and incomplete lineage sorting, and computational limitations. Here we investigate species <span><span>boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, <i>Niebla </i>Rundel & Bowler in the family Ramalinaceae. The species delimitation models tend to support more specious groupings, but were unable to infer robust, consistent species delimitations. </span></span>The results of our study highlight the problem of delimiting species, particularly in groups such as <i>Niebla</i>, with complex, recent phylogeographic histories.</span></span></span></span></span></span></span></span></span></span></span></p>
Data extraction form - A Systematic Literature Review on Prioritizing Software Test Cases using Markov Chains
<p>A data extraction form was created to gather all relevant data from the identified studies and manage the selection process in this systematic literature review. Some of the main information presented in this form was followed by a protocol, identifier (id) for each returned study, bibliographic reference, and answers to research questions. This catalog helps us in the data extraction and synthesis procedures and may be used by potentially interested, for example, for updating or replication. </p>
Data from: Olfactory testing in Parkinson's disease & REM behavior disorder: a machine learning approach
<p><span><span><span><span><span><span><span><span><span><span><span><b>Objective: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>We sought to identify an abbreviated test of impaired olfaction, amenable for use in busy clinical environments in prodromal (isolated REM sleep Behavior Disorder (iRBD)) and manifest Parkinson's.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>890 PD and 313 control participants in the Discovery cohort study underwent Sniffin' stick odour identification assessment. Random forests were initially trained to distinguish individuals with poor (functional anosmia/hyposmia) and good (normosmia/super-smeller) smell ability using all 16 Sniffin' sticks. Models were retrained using the top 3 sticks ranked by order of predictor importance. One randomly selected 3-stick model was tested in a second independent Parkinson's dataset (n=452) and in two iRBD datasets (Discovery n=241; Marburg n=37) before being compared to previously described abbreviated Sniffin' stick combinations.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>In differentiating poor from good smell ability, the overall area under the curve (AUC) value associated with the top 3 sticks (Anise, Licorice and Banana) was 0.95 in the development dataset (sensitivity:90%, specificity:92%, PPV:92%, NPV:90%). Internal and external validation confirmed AUCs≥0.90. The combination of 3-stick model determined poor smell and an RBD screening questionnaire score of ≥5, separated iRBD from controls with a sensitivity, specificity, PPV and NPV of 65%, 100%, 100% and 30%. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>Our 3-Sniffin'-stick model holds potential utility as a brief screening test in the stratification of individuals with Parkinson's and iRBD according to olfactory dysfunction.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Classification of Evidence: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>This study provides Class III evidence that a 3-Sniffin'-stick model distinguishes individuals with poor and good smell ability and can be used to screen for individuals with iRBD.</span></span></span></span></span></span></span></span></span></span></span></p>
Linkage of hospital records and death certificates by a search engine and machine learning: training and test set data
<p>INTRODUCTION: Vital status is of central importance to hospital clinical research. However, hospital information systems record only in-hospital death information. Recently, the French government released a publicly available dataset containing death-certificate data for over 25 million individuals. The objective of this study was to link French death certificates to the Bordeaux University Hospital records to complete the vital status information.</p> <p>MATERIALS AND METHODS: Our linkage strategy was composed of a search engine to reduce the number of comparisons and machine-learning algorithms. The overall pipeline was evaluated by assembling a file containing 3,565 in-hospital deaths and 15,000 alive persons.</p> <p>RESULTS: The recall and precision of our linkage strategy were 97.5% and 99.97% for the upper threshold and 99.4% and 98.9% for the lower threshold, respectively.</p> <p>CONCLUSION: In this article, we demonstrated the feasibility of accurately linking hospital records with death certificates using a search engine and machine learning.</p>
maxATAC Testing Data
<p>Data for testing maxATAC code.</p>
Data for injection and recovery test performed in the paper "Improved Sensitivity for Space Domain Awareness Observations with the Murchison Widefield Array"
<p>This repo contains the script and the pool of noise images used to perform the injection and recovery test in the paper titled "Improved Sensitivity for Space Domain Awareness Observations with the Murchison Widefield Array"</p>
Experimental data testing CO2 × heatwave effects in Pacific herring offspring including data on vital rates and experimental conditions
<p>Forage fish tend to respond strongly to environmental variability and therefore may be particularly sensitive to marine climate stressors. We used controlled laboratory experiments to assess the vulnerability of Pacific herring (<em>Clupea pallasii</em>) embryos to the combined effects of high <em>p</em>CO<sub>2</sub> and a simulated marine heatwave. The two <em>p</em>CO<sub>2</sub> treatments reflected current conditions (~550 µatm) and a future extreme level (~2,300 µatm). The dynamics of heatwave (i.e., rate of onset: ~0.85°C d-<sup>1</sup>; maximum intensity: +4.4°C) were modeled from the most extreme events detected by a long-term regional temperature dataset. Simultaneous exposure to these potential stressors did not affect embryo survival. However, the heatwave did elicit significant metabolic effects that included higher rates of routine metabolism (Q<sub>10</sub> = 1.15 - 1.72), growth (Q<sub>10</sub> = 1.87), rate of development to hatch (Q<sub>10</sub> = 3.01), and yolk consumption (Q<sub>10</sub> = 3.21) as well as a significant reduction in production efficiency (-10.8%) and a three-fold increase in the rate of developmental anomalies. By contrast, high <em>p</em>CO2 conditions produced comparatively small effects to vital rates, including a significant increase in time to hatch (+0.88 d) and a reduction in routine metabolic rate (-6.3%) under the ambient temperature regime only. We found no evidence that high <em>p</em>CO2 increased routine metabolic rate at either temperature. These results indicate that Pacific herring embryos possess sufficient physiological plasticity to cope with extreme seawater acidification under optimal and heatwave temperature conditions, although lingering metabolic inefficiencies induced by the heatwave may lead to important carry-over effects in later life-stages.</p>
Test data for GUNC+BUSCO filtering workflow
<p>Test data for running GUNC+BUSCO filtering workflow, as described on <a href="https://github.com/trajkovski-lab/Quality-filtering">this GitHub page.</a></p>
Loading tumor test data from eCS (EVONANO)
<p>Loading tumor test data from eCS (EVONANO)</p>
Supplementary material 1 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Gazetteer : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 3 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Supplementary information figure : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 2 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Name and DNA sequences of pairs of primers used for amplification and sequencing of the CYTB gene : Data type: molecular data
Data from: Two dimensions of demographic differentiation of species in a mountain grassland community: an experimental test
1. There is remarkable variation in life histories of coexisting plant species. These 'alternative designs' for the given set of environmental conditions are likely to play a role in species niche differences and thus may underlie species coexistence, although there is no clear demonstration of it. Currently available data on within-community differentiation concern primarily easy and measurable traits that are not fully informative of life history variation. Their relevance for functional differentiation of species and species coexistence is far from clear. 2. Here we examined differentiation of coexisting species in demographic parameters and how it determines species' response to neighbors. We determined these parameters for a set of 21 co-occurring species by fitting a process-based model to a long-term (30 yrs) data series of shoot counts. We examined the functional relevance of these parameters using a field experiment. We further asked with which functional traits they are correlated. 3. Species were differentiated along two largely independent axes: (i) slow vs. fast, separating species according to instantaneous growth rate, competitive response and intraspecific density dependence; and (ii) dispersal vs. local dynamics, which separated species with strong dispersal (by seeds or vegetative) from species that tended to stay in the occupied spot. While the slow-fast axis was associated with commonly used leaf and seed traits, the dispersal axis was best predicted by lateral spreading distance. 4. Each of these two axes predicted different components of species' responses to neighbor competition: the slow-fast axis was a good predictor of the short-term response, whereas dispersal axis was a good predictor of the long-term response. 5. Synthesis. Demographic differentiation of coexisting species resembles to an important degree demographic differentiation known from large-scale comparisons. This differentiation is functionally meaningful also at the fine scale; its role in species' responses to competition implies it is involved in species niche differentiation and coexistence. While seed and leaf traits are important correlates of demographic differentiation, a hitherto underappreciated trait, viz. lateral spreading distance, is an important predictor of the dispersal axis at the fine-scale and should be more widely used.
Data from: Within-trio tests provide little support for post-copulatory selection on MHC haplotypes in a free-living population
<p>Sexual selection has been proposed as a force that could maintain the diversity of major histocompatibility complex (MHC) genes in vertebrates. Potential selective mechanisms can be divided into pre-copulatory and post-copulatory, and in both cases the evidence for occurrence is mixed, especially in natural populations. In this study, we used a large number of parent-offspring trios that were diplotyped for MHC class II genes in a wild population of Soay sheep (<i>Ovis aries</i>) to examine whether there was within-trio post-copulatory selection on MHC genes at both the haplotype and diplotype levels. We found there was transmission ratio distortion of one the eight MHC class II haplotype (E) which was transmitted less than expected by fathers, and transmission ratio distortion of another haplotype (A) which was transmitted more than expected by chance to male offspring. However, in both cases these deviations were not significant after correction for multiple tests. In addition, we did not find any evidence of post-copulatory selection on diplotype level. These results imply given known parents, there is no strong post-copulatory selection on MHC genes in this population.</p>
Hemodynamic data from the Inspired Therapeutics NeoMate Mechanical Circulatory Support System for neonates and infants as tested in static mock circulatory loops, dynamic mock circulatory loops, and acute animal studies
<p>Inspired Therapeutics (Merritt Island, FL) is developing a mechanical circulatory support (MCS) system designed as a single driver with interchangeable, extracorporeal, magnetically levitated pumps. The NeoMate system design features an integrated centrifugal rotary pump, motor, and controller that will be housed in a single compact unit. Conceptually, the primary innovation of this technology will be the combination of disposable, low-cost pumps for use with a single, multi-functional, universal controller to support multiple pediatric cardiopulmonary indications. In response to the paucity of clinically available pediatric devices, Inspired Therapeutics is specifically targeting the underserved neonate and infant heart failure (HF) patient population first. In this article, we present the development of the prototype Inspired Therapeutics NeoMate System for pediatric left ventricular assist device (LVAD) support, and feasibility testing in static mock flow loops (H-Q curves), dynamic mock flow loops (hemodynamics), and in an acute healthy ovine model (hemodynamics and clinical applicability). The resultant hydrodynamic and hemodynamic data demonstrated the ability of this prototype pediatric LVAD and universal controller to function over a range of rotary pump speeds (500-6000 RPM), to provide pump flow rates of up to 2.6 L/min, and to volume unload the left ventricle in acute animals. Key engineering challenges observed and proposed solutions for the next design iteration are also presented.</p>
Test data for BBraun syringe pump - flow rate tests at CMI
<p>Syringe pump BBraun Perfusor Space was tested with two syringes of 50 mL and 10 mL volume. Mass of liquid (water or saline solution) released from the pump is recorded using a reference scale as a function of time with a step of 1s. Flow rate generated by the pump is analysed as a function of time for three values of flow rate set in the pump: 1 mL/h, 10 mL/h and 30 mL/h. </p> <p> </p> <p> </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.