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9,113 results for “Sampling”
Cray-HPC Data Sample
<p>Sample of console and job logs of Cray system shared in the SC 18 <a href="https://dl.acm.org/doi/abs/10.5555/3291656.3291668">paper</a> (Doomsday: Predicting Which Node Will Fail When on Supercomputers). </p> <p>If you use this data, please cite the following paper that first released the logs:</p> <pre>@inproceedings{DBLP:conf/sc/DasMHRB18, author = {Anwesha Das and Frank Mueller and Paul Hargrove and Eric Roman and Scott B. Baden}, title = {Doomsday: predicting which node will fail when on supercomputers}, booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis, {SC} 2018, Dallas, TX, USA, November 11-16}, pages = {9:1--9:14}, publisher = {{IEEE} / {ACM}}, year = {2018} } </pre>
HIGH-REDSHIFT NARROW LINE SEYFERT 1 GALAXIES: A CANDIDATE SAMPLE
<p>The study of Narrow line Seyfert 1 galaxies (NLS1s) is now mostly limited to low redshift (z < 0.8). This is because their definition requires the presence of the Hβ emission line, which is red-shifted out of the spectral coverage of major ground-based spectroscopic surveys at z > 0.8. We studied the correlation between the properties of Hβ and Mg II lines of a large sample of SDSS DR14 quasars to find high-z NLS1 candidates. Based on the strong correlation of FWHM(MgII)=(0.880±0.005)×FWHM(Hβ)+(0.438±0.018), we present a sample of high-z NLS1 candidates having FWHM of Mg II < 2000 km s−1. The high-z sample contains 2684 NLS1s with redshift z = 0.8 − 2.5 with a median logarithmic bolometric luminosity of 46.16 ± 0.42 erg s−1, logarithmic black hole mass of 8.01 ± 0.35M⊙, and logarithmic Eddington ratio of 0.02 ± 0.27. The fraction of radio-detected high-z NLS1s is similar to that of the low-z NLS1s and SDSS DR14 quasars at a similar redshift range and their radio luminosity is found to be strongly correlated with their black hole mass.</p> <p>This page contains the catalog of high-z NLS1 candidates. </p>
Sample dataset from RNA-Seq analysis of Ostreococcus tauri
<p>Sample dataset from:</p> <p>Lelandais et al. "<em>Ostreococcus tauri</em> is a new model green alga for studying iron metabolism in eukaryotic phytoplankton", <em>BMC Genomics</em> (2016).<br> DOI <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2666-6">10.1186/s12864-016-2666-6</a></p>
Predatory arthropod community composition in apple orchards: Orchard management, landscape structure and sampling method
<p>Studies on predatory arthropods in agricultural areas seldom include Diptera other than hover flies, partly because common sampling methods are less effective for capturing species that easily fly off when disturbed. To study the effect from this bias when describing the predator community, we compared traditional beat sampling of branches and suction sampling for describing the community of predatory arthropods in Swedish apple orchards, both organic orchards and orchards using integrated pest management. Our results indicate that the proportion of both predatory dipterans and parasitic hymenopterans increase dramatically when using suction sampling (Diptera: 32% vs 20%, Hymenoptera: 25% vs 7%). In fact, predatory dipterans were the most abundant predatory group when using suction sampling, in contrast to beat sampling where spiders were the most abundant group. One group of predatory flies that was particularly rich in both species and individuals in the surveyed apple orchards was dance flies in the family Hybotidae. Even though the bias of sampling method was evident, it was encouraging that the method choice did not affect the conclusions concerning management on predatory arthropod communities. With both methods, dipteran and coleopteran predators were more abundant in organic apple orchards whereas opilionids were more abundant in orchards managed according to integrated pest management. The inclusion of landscape variables further indicated effects of landscape diversity and of deciduous forest cover, but the response varied in sign between predatory groups. Whereas both Coleoptera and Heteroptera were more abundant in orchards surrounded by more complex landscapes (high landscape diversity and/or high deciduous forest cover), spiders, opilionids and dipterans were rather less abundant in these orchards. To conclude, our study points to the potential importance of predatory dipterans in apple orchards, and we highly recommend future studies of arthropod predators in apple and other crops to actively include predatory Diptera.</p>
Bioinformatic pipeline from: Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River
<p>Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcode assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcode assays and a customized bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e)DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned in comparison to four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcode assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcode assays than with morphological sampling and identifications, especially with the combined assays. At the population-level, metabarcode analyses targeting the invasive round goby <i>Neogobius melanostomus</i> and the silver carp <i>Hypophthalmichthys molitrix</i> identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcode assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.</p>
Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions
<p><span><span><span><span><span><span><span><span><span><span><span>Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (<b>new definition</b>), as the sister group of scorpions. Panscorpiones (<b>new name</b>) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.</span></span></span></span></span></span></span></span></span></span></span></p>
Supporting publication for 'Prevalence sample-based guidance for reporting 2020 data'
<p>These two Excel documents help in mapping terms from the matrix catalogue ZOO_CAT_MATRIX used in the aggregated prevalence data model to FoodEx2 codes and offer examples on how prevalence data can be reported using SSD2.</p>
The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases
There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 38,711 fossil occurrences, we show that the spatial extent of the 'global' terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic, and that this spatial variation explains around 75% of the variation in known fossil species counts. Controlling for this bias, we find that regional-scale terrestrial tetrapod diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. The Cretaceous/Paleogene mass extinction, 66 million years ago, fundamentally disrupted terrestrial ecosystems, catalysing an abrupt increase in its aftermath. Nevertheless, this was followed by general stasis and recent diversity levels do not exceed those of the Paleogene. These findings parallel those recovered in analyses of local community-level richness, suggesting that tetrapod beta diversity has also not shown a general increase through time. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases over the last 100 million years.
Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of substitution among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Weekly travel times by direction and sample count for each link in Development of AIS Model of Texas Gulf Intracoastal Waterway Travel Times
<p>Excel spreadsheet containing all of the travel times and sample counts for each link (by direction).</p>
Data from: Overcoming the challenge of small effective sample sizes in home-range estimation
Technological advances have steadily increased the detail of animal tracking datasets, yet fundamental data limitations exist for many species that cause substantial biases in home‐range estimation. Specifically, the effective sample size of a range estimate is proportional to the number of observed range crossings, not the number of sampled locations. Currently, the most accurate home‐range estimators condition on an autocorrelation model, for which the standard estimation frame‐works are based on likelihood functions, even though these methods are known to underestimate variance—and therefore ranging area—when effective sample sizes are small. Residual maximum likelihood (REML) is a widely used method for reducing bias in maximum‐likelihood (ML) variance estimation at small sample sizes. Unfortunately, we find that REML is too unstable for practical application to continuous‐time movement models. When the effective sample size N is decreased to N ≤ urn:x-wiley:2041210X:media:mee313270:mee313270-math-0001(10), which is common in tracking applications, REML undergoes a sudden divergence in variance estimation. To avoid this issue, while retaining REML's first‐order bias correction, we derive a family of estimators that leverage REML to make a perturbative correction to ML. We also derive AIC values for REML and our estimators, including cases where model structures differ, which is not generally understood to be possible. Using both simulated data and GPS data from lowland tapir (Tapirus terrestris), we show how our perturbative estimators are more accurate than traditional ML and REML methods. Specifically, when urn:x-wiley:2041210X:media:mee313270:mee313270-math-0002(5) home‐range crossings are observed, REML is unreliable by orders of magnitude, ML home ranges are ~30% underestimated, and our perturbative estimators yield home ranges that are only ~10% underestimated. A parametric bootstrap can then reduce the ML and perturbative home‐range underestimation to ~10% and ~3%, respectively. Home‐range estimation is one of the primary reasons for collecting animal tracking data, and small effective sample sizes are a more common problem than is currently realized. The methods introduced here allow for more accurate movement‐model and home‐range estimation at small effective sample sizes, and thus fill an important role for animal movement analysis. Given REML's widespread use, our methods may also be useful in other contexts where effective sample sizes are small.
Data from: Population genomics and demographic sampling of the ant-plant Vachellia drepanolobium and its symbiotic ants from sites across its range in East Africa.
The association between the African ant plant, Vachellia drepanolobium, and the ants that inhabit it has provided insight into the boundaries between mutualism and parasitism, the response of symbioses to environmental perturbations, and the ecology of species coexistence. We use a landscape genomics approach at sites sampled throughout the range of this system in Kenya to investigate the demographics and genetic structure of the different partners in the association. We find that different species of ant associates of V. drepanolobium show striking differences in their spatial distribution throughout Kenya, and these differences are only partly correlated with abiotic factors. A comparison of the population structure of the host plant and its three obligately arboreal ant symbionts, Crematogaster mimosae, Crematogaster nigriceps, and Tetraponera penzigi, shows that the ants exhibit somewhat similar patterns of structure throughout each of their respective ranges, but that this does not correlate in any clear way with the respective genetic structure of the populations of their host plants. A lack of evidence for local coadaptation in this system suggests that all partners have evolved to cope with a wide variety of biotic and abiotic conditions.
Data from: Landscape genetic inferences vary with sampling scenario for a pond breeding amphibian
A critical decision in landscape genetic studies is whether to use individuals or populations as the sampling unit. This decision affects the time and cost of sampling and may affect ecological inference. We analyzed 334 Columbia spotted frogs at 8 microsatellite loci across 40 sites in northern Idaho to determine how inferences from landscape genetic analyses would vary with sampling design. At all sites, we compared a proportion available sampling scheme (PASS), in which all samples were used, to resampled datasets of 2-11 individuals. Additionally, we compared a population sampling scheme (PSS) to an individual sampling scheme (ISS) at 18 sites with sufficient sample size. We applied an information theoretic approach with both restricted maximum likelihood and maximum likelihood estimation to evaluate competing landscape resistance hypotheses. We found that PSS supported a low-density forest model (0.87) and ISS supported this model as well as additional models when testing hypotheses of landcover types that create the greatest resistance to gene flow for Columbia spotted frogs. Increased sampling density and study extent, seen by comparing PSS to PASS, showed a change in model support from a model of only low-density forest to a model of only high-density forest. As number of individuals increased, model support converged at 7 individuals for ISS to PSS. ISS may be useful to increase study extent and sampling density, but may lack power to provide strong support for the correct model with microsatellite datasets. Our results highlight the importance of additional research on sampling design effects on landscape genetics inference.
Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events
• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. • We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. • We identified twenty-six ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. • Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macro-evolutionary implications compared to autopolyploidy.
Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions
<p>Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (TACT: Taxonomic Addition for Complete Trees) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling.</p>
Data from: Sampling effects drive the species-area relationship in lake zooplankton
<p><b>The Island Species-Area relationship (ISAR) describes how the numbers of species increases with increasing size of an island (or island-like habitat, such as lakes), and is one of the oldest laws in ecology. Despite its conceptual importance, there remains a great deal of ambiguity regarding the ISAR and its underlying processes. We compiled data from sampled zooplankton assemblages from several hundred lakes in North America and Europe to examine the influence of the three main hypothesized mechanisms leading to ISARs - passive sampling, disproportionate effects, and habitat heterogeneity. We compiled data on lake zooplankton assemblages that reported sample-level and lake level species richness estimates, as well as relative abundance data. In both North American and European lakes, we found a consistent and strong increase in total species richness with increasing lake area. However, when we compared the number of species standardized by number of individuals, there was no relationship between lake area and sample-level species richness or an estimate of species relative abundances, calculated as the Probability of Interspecific Encounter (PIE; a measure of evenness). This was true even when multiple samples were taken across lakes and combined, reducing the likelihood that habitat heterogeneity was driving the results. Overall, our results suggest that the ISAR of zooplankton in these lakes was most likely determined by sampling effects rather than disproportionate effects or habitat heterogeneity leading to more species in larger lakes. Understanding the mechanisms driving ISAR results such as ours can also help us develop predictions for biodiversity change when the area of these habitats changes. </b></p>
Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.
Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses.
Data from: Genetic sampling for estimating density of common species
Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single-session NGS sampling of hares. We compared spatial capture–recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost-effective sampling protocols.
Hearth Soil Sample, 150,000-40,000 BCE
Upper Mousterian (ca. 150,000-40,000 BCE) Flint, bone, and soil Europe; France; St. Leon 5.5 x 3 in. MH 2016.16.664 View this object on the Database: http://museums.fivecolleges.edu/detail.php?museum=all&t=objects&type=all&f=&s=mh+2016+16+664&record=0 Photographs and photogrammetry by Laura Shea (Digital Collections Coordinator and Museum Photographer), Mount Holyoke College Art Museum; Copyright info: Contact the Mount Holyoke College Art Museum South Hadley, Massachusetts, USA 01075 413-538-2245 http://www.mtholyoke.edu/artmuseum/ The Mount Holyoke College Art Museum is dedicated to teaching and learning; therefore, we value your feedback and welcome any scholarly observations. Please feel free to contact us if you would like to learn more about the objects you see here or to request 3D models of other objects in our collections. Description: Specimen of hearth site - to show how the material lies when dug. Contains tools and/or flakes, ash, charcoal, bone - from Saint Leon dig in France. Source: Objaverse 1.0 / Sketchfab
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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.