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.
13,064
datasets available to search
ShareScore release 0.9.0
Dataset results
13,064 results for “predictions”
Potential Predictability of the Spring Bloom in the Southern Ocean Sea Ice Zone: data and analysis scripts
<p>This repository contains the datasets and notebooks necessary to reproduce the figures in Buchovecky et al. "Potential Predictability of the Spring Bloom in the Southern Ocean Sea Ice Zone". All notebooks, except those deriving quantities from the raw model data, should work "out-of-the-box" after the appropriate local path has been set to the data.</p>
Monthly global grids of lidar-consistent opaque cloud fractions and altitude of attenuation 2008-2034 according to predictions from CESM2 and IPSL-CM6 GCMs
<p>Monthly global grids of opaque cloud fractions and altitude of attenuation 2008-2034 according to predictions from CESM and LMDZ GCMs.</p> <ul> <li>One file describe the CESM2 prediction (cesm.nc); one file describes the IPSL-CM6 predictions (lmdz.nc).</li> <li>Predictions from both models were obtained following the RCP8.5 scenario.</li> <li>The lidar-consistent variables were generated by the COSP lidar simulator (v1.4).</li> </ul> <p>See 10.5194/egusphere-2022-1187 for a description of the dataset and its interpretation</p>
Mean species responses predict effects of environmental change on coexistence
<p>Environmental change research is plagued by the curse of dimensionality: the number of communities at risk and the number of environmental drivers are both large. This raises the pressing question if a general understanding of ecological effects is achievable. These data show that this is indeed possible. It contains code that calculates the feasibility domain size (a proxy for coexistence) for bi- and tritrophic communities challenged by environmental change. Some of this code simply returns the output of a closed-form expressions (i.e. simple equations), while some rely on simulations that require specific packages.</p> <p>The data also contain presence/absence data of macroinvertebrate taxa and water chemistry variables measured across sites (that are either severely or weakly modified by human activity, quantified via land use) at US streams. With these data, we were able to test if sites that share the same community have similar water chemistry, in other words: how tightly is a community linked to a certain water chemistry? This analysis demonstrates how to apply our theory to the analysis of field data, and lends support to effects of land use change on coexistence in natural invertebrate communities.</p>
Data from: Predictive links between petal color and pigment quantities in natural Penstemon hybrids
<p class="MsoNormal">Flowers have evolved remarkable diversity in petal color, in large part due to pollinator-mediated selection. This diversity arises from specialized metabolic pathways that generate conspicuous pigments. Despite the clear link between flower color and floral pigment production, studies determining predictive relationships between pigmentation and petal color are currently lacking. In this study, we analyze a dataset consisting of hundreds of natural <em>Penstemon</em> hybrids that exhibit variation in flower color, including blue, purple, pink, and red. For each individual hybrid, we measured anthocyanin pigment content and petal spectral reflectance. We found that floral pigment quantities are correlated with hue, chroma, and brightness as calculated from petal spectral reflectance data: hue is related to the relative amounts of delphinidin vs. pelargonidin pigmentation, whereas brightness and chroma are correlated with the total anthocyanin pigmentation. We used a partial least squares regression approach to identify predictive relationships between pigment production and petal reflectance. We find that pigment quantity data provide robust predictions of petal reflectance, confirming a pervasive assumption that differences in pigmentation should predictably influence flower color. Moreover, we find that reflectance data enables accurate inferences of pigment quantities, where the full reflectance spectra provide much more accurate inference of pigment quantities than spectral attributes (brightness, chroma, and hue). Our predictive framework provides readily interpretable model coefficients relating spectral attributes of petal reflectance to underlying pigment quantities. These relationships represent key links between genetic changes affecting anthocyanin production and ecological functions of petal coloration.</p>
Seed dispersal syndrome predicts ethanol concentration of fruits in a tropical dry forest
<p><span>Studying fruit traits and their interactions with seed dispersers can improve how we interpret patterns of biodiversity, ecosystem function, and evolution. Mounting evidence suggests that fruit ethanol is common, variable, and may exert selective pressures on seed dispersers. To test this, we comprehensively assess fruit ethanol content in a wild ecosystem and explore sources of variation. We hypothesise that both phylogeny and seed dispersal syndrome explain variation in ethanol levels, and we predict that fruits with mammalian dispersal traits will contain higher levels of ethanol than those with bird dispersal traits. We measured ripe fruit ethanol content in species with mammal- (n = 16), bird- (n = 14), or mixed-dispersal (n = 7) syndromes in a Costa Rican tropical dry forest. Seventy-eight percent of fruit species yielded measurable ethanol concentrations. We detected a phylogenetic signal in maximum ethanol levels (Pagel's λ = 0.82). Controlling for phylogeny, we observed greater ethanol concentrations in mammal-dispersed fruits, indicating that dispersal syndrome helps explain variation in ethanol content and that mammals may be more exposed to ethanol in their diets than birds. Our findings further our understanding of wild fruit ethanol and its potential role as a selective pressure on frugivore sensory systems and metabolism.</span></p>
Analysis Script of Prediction of Self-efficacy in Recognizing Deepfake based on HEXACO Personality Traits
<p><em><strong>Analysis Script (JASP) </strong></em>of Prediction of Self-efficacy in Recognizing Deepfake based on HEXACO Personality Traits </p>
Dataset of historical prediction of ash dispersal of the Sakurajima Taisho eruption
<p>This dataset contains all outputs of the VATDM simulation of the Sakurajima Taisho eruption using the PUFF model with GSM-GPV as the wind fields from July 2018 to December 2022. The details of the simulation process and the model inputs follow Rahadianto et al. (2022). Each file describes the location (latitude and longitude) of the deposit with its depth in cm for each prediction lead time in descending order (24, 18, 12, 6, 0 hours ahead). Only CSV format is available, and each file named based on the date of the simulation, grouped within a yearly folder. Please extract the zip file to access each file.</p>
Virtual Flight Trajectory Prediction and Performance Optimization
<p>Data sets collected from running test flights using Prepar-3D flight simulator; extracted using FS-Flight Control software </p>
Data underlying the article: 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
<p>This repository contains the datasets and results supporting the conclusions of the manuscript "<strong>3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors</strong>". </p> <p>Publicly available data is not included in this repository. The source code to generate the results gathered here can be found on GitHub (https://github.com/CDDLeiden/3ddpd). </p>
CPT-1 pre-computed whole-proteome variant effect predictions and model source code
<p><strong>Cross-protein transfer learning for variant effect prediction</strong></p><p>This repository contains the variant effect predictions of CPT-1 for 18,602 human proteins, initially released with the manuscript "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects". The proteins are split into three files.</p><p><i>CPT1_score_EVE_set.zip</i>: Proteins in the EVE set (<a href="https://www.nature.com/articles/s41586-021-04043-8">Frazer et al., 2021</a>)</p><p><i>CPT1_score_no_EVE_set_1.zip</i> & <i>CPT1_score_no_EVE_set_2.zip</i>: Proteins not in the EVE set. Predictions for these proteins use imputed values for features depending on the EVE MSA.</p><p>The protein names are UniProt gene names.</p><p>We also provide source code to train CPT-1 model and reproduce results in the manuscript :</p><p><i>source_code.zip </i>(corresponds to GitHub repository songlab-cal/CPT version as of Jul 12, 2023)</p><p> </p><p><strong>Citation</strong></p><p>Jagota, M.*, Ye, C.*, Albors, C., Rastogi, R., Koehl, A., Ioannidis, N., and Song, Y.S.†<br>"Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects", bioRxiv (2022)</p><p>*These authors contributed equally to this work.<br>†To whom correspondence should be addressed: <a href="mailto:yss@berkeley.edu">yss@berkeley.edu</a></p><p>DOI: <a href="https://doi.org/10.1101/2022.11.15.516532">https://doi.org/10.1101/2022.11.15.516532</a></p><p> </p>
Poultry Birds Poo Imagery Dataset for Health Status Prediction
<p>Imagery dataset of chicken poo of both healthy and non-healthy collected from poultry farms rearing two species of chickens namely: broilers and layers in Nigeria. The dataset has a total of 14,618 labeled images with 100 × 100 pixels in jpeg format and a label indicating the name of the image from the image number. In the repository, data were uploaded into 2 separate folders; each folder of either healthy or non-healthy contain images taken from different time to the day; morning, afternoon, night and others.</p>
Model output from Snow Ensemble Uncertainty Project (SEUP) as used in Seasonal Snow Predictability Derived from Early-Season Snow in North America
<p>The files provided here are the output from the median peak snow water equivalent (peak_SWE.mat), 1 December snow water equivalent (Dec1_SWE.mat), and 1 January snow water equivalent (Jan1_SWE.mat) model simulations for the Noah-MP run with MERRA-2 forcing, as used in Lundquist et al. (2023) and described in Kim et al. (2021). We also include the model grid's latitude, longitude and elevation data (SEUPlatlon.mat), and example code for plotting the data (Plotmodeldata.m) as in the Lundquist et al. (2023) paper. </p> <p>Kim, R. S., Kumar, S., Vuyovich, C., Houser, P., Lundquist, J., Mudryk, L., et al. (2021). Snow Ensemble Uncertainty Project (SEUP): Quantification of snow water equivalent uncertainty across North America via ensemble land surface modeling. <em>The Cryosphere, 15</em>(2), 771-791.</p> <p>Lundquist, J. D., R. S. Kim, M. Durand, and L. R. Prugh, 2023, Seasonal Peak Snow Predictability Derived from Early-Season Snow in North America, Geophysical Research Letters, (submitted 2023)</p>
Related with: Long-short term memory prediction of user's locomotion in Virtual Reality publication (Dataset)
<p>Dataset: Captured motion data from 44 users.</p> <p>Scenes:</p> <p>SL -> Scene Lab.</p> <p>SR -> Escape Room.</p> <p>MF -> Shooter forest.</p> <p>Since it is recorded inside a game engine and all records take place inside their processing, the timestamp is written down for each register (Time_sice_startup field). Additionally, the anonymized identification of the user is recorded (User field).</p> <p>The dataset includes the following characteristics for Oculus Quest 2 HMD and each controller.</p> <ul> <li> DevicePosition (x, y, z): Position recorded.</li> <li> DeviceRotation (w, x, y, z): Rotation expressed with a quaternion.</li> <li> Forward (x, y, z): The unit vector that points to the specific device in the forward direction used in our new model. It can also be obtained by rotating $(0,0,1)$ with the quaternion.</li> <li> DeviceVelocity (x, y, z): Linear velocity of that device in that frame. It represents the rate of change in position.</li> <li> DeviceAcceleration (x, y, z): Linear acceleration of that device in that frame.</li> <li> DeviceAngularVelocity (x, y, z): The angular velocity vector in that frame of the device is measured in radians per second.</li> <li> DeviceAngularAcceleration (x, y, z): The angular acceleration at that frame. </li> </ul> <p>Also for each goal in the scene:</p> <ul> <li> GoalName (x, y, z): Position of that goal. If the element is static, the same position will always be recorded.</li> <li> GoalName_Quat (w, x, y, z): As in the previously defined fields, a rotation is expressed as a quaternion.</li> <li> GoalName_LocalScale (x, y, z): Scale of that element locally related to its parent in the hierarchy. They have no relatives in their hierarchy, so it is the real scale.</li> </ul>
Multi-Omics Visible Drug Activity Prediction with a Biologically Informed Neural Network Model
<p>Drug discovery is a challenging task, it takes several years for a drug to be introduced on the market, with most of<br> the studied drugs not even passing the first phase. The understanding of the mechanisms influencing response to drugs<br> can reduce failures and accelerate drug development. Virtual drug screening, based on Machine Learning models, is a<br> promising field for the prediction of the outcome of a treatment. However, the complex relationships between the features<br> learned by these models are still poorly understood and not easy to interpret.<br> We have designed a Neural Network model for drug sensitivity prediction that leverages a Visible Neural Network, an<br> easily interpretable model, due to its biologically informed nature. The trained model can be inspected to study which<br> biological processes were fundamental for the prediction and to identify the drug properties that affect sensitivity. It<br> combines multi-omics data from various types of tumor tissues and drug representations based on molecular descriptors.<br> The mechanisms learned from the network can also be exploited to find candidate drugs for synergy to predict the effect<br> of combined therapies. We consider the unbalanced nature of public drug screening datasets and show that our model<br> outperforms state-of-the-art visible machine learning models.</p>
Primary data for: "Remotely sensed localised primary production anomalies predict the burden and community structure of infection in long-term rodent datasets"
<p>Datasets</p>
Supporting Dataset for "Reducing a tropical cyclone weak-intensity bias in a global numerical weather prediction system"
<p>This archive supports the submission of "Reducing a tropical cyclone weak intensity bias in a global numerical weather prediction system" to Monthly Weather Review. It contains model configurations, the software used to create ensemble perturbations, the software used to compute the diagnostics discussed in the text, and the software use to plot figures.</p> <p>After downloading, the contents can be extracted using:</p> <blockquote> <p>tar -xzf idealtc1_archive-1.tgz</p> </blockquote>
Submitted forecasts and analysis code for "Predicting spring phenology in deciduous broadleaf forests: NEON Phenology Forecasting Community Challenge"
<p>Submitted forecasts for the 2021 Ecological Forecasting Initiative NEON Phenology Forecast Challenge and the analysis code for the accompanying manuscript. </p>
In silico subcellular targeting predictions for cytosolic aminoacyl tRNA-synthetases (aaRS) in parasitic plants
<p>Eukaryotic nuclear genomes often encode distinct sets of protein translation machinery for function in the cytosol vs. organelles (mitochondria and plastids). This phenomenon raises questions about why multiple translation systems are maintained even though they are capable of comparable functions, and whether they evolve differently depending on the compartment where they operate. These questions are particularly interesting in land plants because translation machinery, including aminoacyl-tRNA synthetases (aaRS), is often dual-targeted to both the plastids and mitochondria. These two organelles have quite different metabolisms, with much higher rates of translation in plastids to supply the abundant, rapid-turnover proteins required for photosynthesis. Previous studies have indicated that plant organellar aaRS evolve more slowly compared to mitochondrial aaRS in other eukaryotes that lack plastids. Thus, we investigated the evolution of nuclear-encoded organellar and cytosolic translation machinery across a broad sampling of angiosperms, including non-photosynthetic (heterotrophic) plant species with reduced rates of plastid gene expression to test the hypothesis that translational demands associated with photosynthesis constrain the evolution of bacterial-like enzymes involved in organellar tRNA metabolism. Remarkably, heterotrophic plants exhibited wholesale loss of many organelle-targeted aaRS and other enzymes, even though translation still occurs in their mitochondria and plastids. These losses were often accompanied by apparent retargeting of cytosolic enzymes and tRNAs to the organelles, sometimes preserving aaRS-tRNA charging relationships but other times creating surprising mismatches between cytosolic aaRS and mitochondrial tRNA substrates. Our findings indicate that the presence of a photosynthetic plastid drives the retention of specialized systems for organellar tRNA metabolism.</p>
Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15
<p>Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15</p>
Supplementary dataset for "Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking"
<p>The supplementary dataset for the paper "Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking". We include the splits for cora, citeseer, and pubmed, the hard negative samples, and the node2vec embeddings. We also include a jupyter file <em>read_data.ipynb</em> to show how to read the non-txt file.</p> <ul> <li>heart_test_samples.npy, heart_valid_samples.npy: the heard negative samples</li> <li>*-n2v-embedding.pt: node2vec embeddings</li> <li>test_samples_index.pt, valid_samples_index.pt: the node index of the selected samples in ogbl-ppa under HeaRT</li> <li>gnn_feature: the input feature of cora, citeseer, pubmed</li> </ul> <p>More details for our code and how to use the dataset are on the code repository: https://github.com/Juanhui28/HeaRT .</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.