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bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The Human Sleep Project (HSP) sleep physiology dataset is a growing collection of clinical polysomnography (PSG) recordings. Beginning with PSG recordings from from ~15K patients evaluated at the Massachusetts General Hospital, the HSP will grow over the coming years to include data from >200K patients, as well as people evaluated outside of the clinical setting. This data is being used to develop CAISR (Complete AI Sleep Report), a collection of deep neural networks, rule-based algorithms, and signal processing approaches designed to provide better-than-human detection of conventional PSG...
cancergenomiclife sciencesSTRIDESwhole genome sequencing
The Cancer Genome Atlas (TCGA), a collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), aims to generate comprehensive, multi-dimensional maps of the key genomic changes in major types and subtypes of cancer. TCGA has analyzed matched tumor and normal tissues from 11,000 patients, allowing for the comprehensive characterization of 33 cancer types and subtypes, including 10 rare cancers. The dataset contains open Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantificati...
alchemical free energy calculationsbiomolecular modelingcoronavirusCOVID-19foldingathomehealthlife sciencesmolecular dynamicsproteinSARS-CoV-2simulationsstructural biology
Folding@home is a massively distributed computing project that uses biomolecular simulations to investigate the molecular origins of disease and accelerate the discovery of new therapies. Run by the Folding@home Consortium, a worldwide network of research laboratories focusing on a variety of different diseases, Folding@home seeks to address problems in human health on a scale that is infeasible by another other means, sharing the results of these large-scale studies with the research community through peer-reviewed publications and publicly shared datasets. During the COVID-19 epidemic, Folding@h...
cancergenomiclife sciencesSTRIDESwhole genome sequencing
Therapeutically Applicable Research to Generate Effective Treatments (TARGET) is the collaborative effort of a large, diverse consortium of extramural and NCI investigators. The goal of the effort is to accelerate molecular discoveries that drive the initiation and progression of hard-to-treat childhood cancers and facilitate rapid translation of those findings into the clinic. TARGET projects provide comprehensive molecular characterization to determine the genetic changes that drive the initiation and progression of childhood cancers.The dataset contains open Clinical Supplement, Biospecimen...
biologycell biologycell imagingHomo sapiensimage processinglife sciencesmachine learningmicroscopy
This bucket contains multiple datasets (as Quilt packages) created by the Allen Institute for Cell Science. The types of data included in this bucket are listed below:
Biohubbioinformaticscell biologylife sciencessingle-cell transcriptomicstranscriptomics
CELLxGENE Discover (cellxgene.cziscience.com) is a free-to-use platform for the exploration, analysis, and retrieval of single-cell data. CELLxGENE Discover hosts the largest aggregation of standardized single-cell data from the major human and mouse tissues, with modalities that include gene expression, chromatin accessibility, DNA methylation, and spatial transcriptomics. This year, CELLxGENE Discover has made available all of its human and mouse RNA single-cell data through Census (https://chanzuckerberg.github.io/cellxgene-census/) – a free-to-use service with an API and data that allows f...
cancergeneticgenomicHomo sapienslife sciencespediatricSTRIDESstructural birth defectwhole genome sequencing
The NIH Common Fund's Gabriella Miller Kids First Pediatric Research Program’s (“Kids First”) vision is to “alleviate suffering from childhood cancer and structural birth defects by fostering collaborative research to uncover the etiology of these diseases and by supporting data sharing within the pediatric research community.” The program continues to generate and share whole genome sequence data from thousands of children affected by these conditions, ranging from rare pediatric cancers, such as osteosarcoma, to more prevalent diagnoses, such as congenital heart defects. In 2018, Kids Fi...
bambioinformaticsbiologycramgeneticgenomicgenotypinglife sciencesmachine learningpopulation geneticsshort read sequencingstructural variationtertiary analysisvariant annotationwhole genome sequencing
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bioinformaticsbiologycancercell biologycell imagingcell paintingchemical biologycomputer visioncsvdeep learningfluorescence imaginggenetichigh-throughput imagingimage processingimage-based profilingimaginglife sciencesmachine learningmedicinemicroscopyorganelle
The Cell Painting Gallery is a collection of image datasets created using the Cell Painting assay. The images of cells are captured by microscopy imaging, and reveal the response of various labeled cell components to whatever treatments are tested, which can include genetic perturbations, chemicals or drugs, or different cell types. The datasets can be used for diverse applications in basic biology and pharmaceutical research, such as identifying disease-associated phenotypes, understanding disease mechanisms, and predicting a drug’s activity, toxicity, or mechanism of action (Chandrasekaran et al 2020). This collection is maintained ...
bambioinformaticsfast5fastafastqgenomiclife scienceslong read sequencingshort read sequencingtranscriptomics
The Singapore Nanopore Expression (SG-NEx) project is an international collaboration to generate reference transcriptomes and a comprehensive benchmark data set for long read RNA-Seq. Transcriptome profiling is done using Nanopore PCR-cDNA sequencing (PCR-cDNA), Nanopore amplification-free cDNA sequencing (direct cDNA), Nanopore direct sequencing of native RNA (direct RNA), PacBio IsoSeq, and short read RNA-Seq. The SG-NEx core data includes 5 of the most commonly used cell lines and it is extended with additional cell lines and samples that cover a broad range of human tissues. All core sampl...
biologycalcium imagingcell imagingelectrophysiologyhdf5life sciencesneuroimagingneurophysiologyneurosciencezarr
DANDI is a public archive of neurophysiology datasets, including raw and processed data, and associated software containers. Datasets are shared according to Creative Commons CC0 or CC-BY licenses. This US BRAIN Initiative supported archive provides a broad range of cellular neurophysiology data including intracellular and extracellular electrophysiology, optophysiology, calcium imaging, fiber photometry, behavioral time-series, and images from immunostaining experiments, from over 20 species.Data is organized using community standards: NWB - Neurodata Without Borders, BIDS - Brain Imaging Data Structure, NGFF - Next Generation File Format for...
bioinformaticsgeneticgenomiclife sciencespopulationpopulation geneticsshort read sequencingwhole genome sequencing
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators that aggregates and harmonizes both exome and genome data from a wide range of large-scale human sequencing projects. The summary data provided here are released for the benefit of the wider scientific community without restriction on use. The v4.1 data set (GRCh38) spans 730,947 exome sequences and 76,215 whole-genome sequences from unrelated individuals, of diverse ancestries, sequenced sequenced as part of various disease-specific and population genetic studies. The gnomAD Principal Investigators and team can be found Details →
biologyfluorescence imagingimage processingimaginglife sciencesmicroscopyneurobiologyneuroimagingneuroscience
This data set, made available by Janelia's FlyLight project, consists of fluorescence images of Drosophila melanogaster driver lines, aligned to standard templates, and stored in formats suitable for rapid searching in the cloud. Additional data will be added as it is published.
cancergeneticgenomicHomo sapienslife sciencesmedical imagingpediatricradiologytranscriptomicswhole genome sequencing
The Real-time Analysis and Discovery in Integrated And Networked Technologies (RADIANT) initiative seeks to develop an extensible, federated framework for rapid exchange of multimodal clinical and research data on behalf of accelerated discovery and patient impact. Coordination and implementation of initial RADIANT deployments will leverage a network of more than 35 partnered health care systems and participating patient families within the Children’s Brain Tumor Network (CBTN) and the Pediatric Neuro-Oncology Consortium (PNOC). This data set is composed of public multi-modal data provisio...
biologyimaginglife sciencesMus musculusneurobiologyneuroimagingneuroscienceniftiRattus norvegicussignal processingvolumetric imaging
ConfUSIus Functional Ultrasound Imaging Dataset Collection is a curated set of public functional ultrasound imaging (fUSI) datasets and derived templates for neuroscience. The collection brings together data from multiple studies and laboratories and makes it available for programmatic access through stable cloud paths and the ConfUSIus Python toolkit. Where possible, datasets are organized or re-exported using fUSI-BIDS/BIDS conventions; original formats, derivatives, provenance, and licenses vary by source dataset.
Homo sapiensimaginglife sciencesmagnetic resonance imagingneuroimagingneuroscience
This bucket contains multiple neuroimaging datasets that are part of the International Neuroimaging Data-Sharing Initiative. Raw human and non-human primate neuroimaging data include 1) Structural MRI; 2) Functional MRI; 3) Diffusion Tensor Imaging; 4) Electroencephalogram (EEG) In addition to the raw data, preprocessed data is also included for some datasets. A complete list of the available datasets can be seen in the documentation lonk provided below.
bioinformaticsbiologydrug discoverygeneticgenomiclife sciencesprotein
The Open Targets Platform is a comprehensive data integration tool that supports systematic identification and prioritisation of potential therapeutic drug targets. By integrating publicly available datasets including data generated by the Open Targets experimental and informatics research programmes, the Platform provides data and services to assist in the task of therapeutic hypothesis building.
bambioinformaticsbiologycancergeneticgenomicHomo sapienslife sciencesshort read sequencingtranscriptomicswhole exome sequencingwhole genome sequencing
This dataset consists of whole genome sequencing (WGS), whole exome sequencing (WES), and RNA sequencing files generated from ~1000 cancer cell lines described in Ghandi et al., 2019.
bioinformaticsbiologyCaenorhabditis elegansDanio rerioDrosophila melanogasterfastagene expressiongeneticgenomegenomicHomo sapienslife sciencesMus musculusproteinRattus norvegicustranscriptomicsvcf
The Alliance of Genome Resources is a consortium that integrates genomic, genetic, and molecular data from leading model organism databases including Drosophila melanogaster, Caenorhabditis elegans, Danio rerio (zebrafish), Mus musculus (mouse), Rattus norvegicus (rat), Saccharomyces cerevisiae (yeast), Xenopus laevis and Xenopus tropicalis (frogs), and human reference data. The Alliance provides comprehensive datasets including gene annotations, disease associations, expression data (bulk and single-cell RNA-Seq), protein and genetic interactions, orthology relationships, variants and alleles...
bioinformaticsgenomiclife scienceslong read sequencing
The dataset contains reference samples that will be useful for benchmarking and comparing bioinformatics tools for genome analysis. Examples include: NA12878 (HG001) and NA24385 (HG002) sequenced on an Oxford Nanopore Technologies (ONT) PromethION using the latest R10.4.1 flowcells; and, UHR RNA (direct-RNA) on an ONT PromethION using the latest RNA004 flowcells. Raw signal data output by the sequencer is provided for these datasets in BLOW5 format, and can be rebasecalled when basecalling software updates bring accuracy and feature improvements over the years. Raw signal data is not only for ...
life sciencesMus musculusneurophysiologyneuroscienceopen source software
Electrophysiological recordings of mouse brain activity acquired during a decision making task.
biologygene expressiongenomegenomicHomo sapienslife sciences
The NHGRI Analysis, Visualization, and Informatics Lab-space (AnVIL) Project (https://anvilproject.org/) is the National Human Genome Research Institute's cloud-based platform for genomic data sharing and analysis. AnVIL hosts widely used human genome reference datasets generated through NHGRI-funded research. AnVIL on Open Data on AWS provides public access to open-access datasets available through AnVIL. The project is a collaborative effort involving NHGRI, the Broad Institute, Johns Hopkins University, the University of California Santa Cruz, Vanderbilt University Medical Center, Brigh...
array tomographybiologyelectron microscopyimage processinglife scienceslight-sheet microscopymagnetic resonance imagingneuroimagingneuroscience
This bucket contains multiple neuroimaging datasets (as Neuroglancer Precomputed Volumes) across multiple modalities and scales, ranging from nanoscale (electron microscopy), to microscale (cleared lightsheet microscopy and array tomography), and mesoscale (structural and functional magnetic resonance imaging). Additionally, many of the datasets include segmentations and meshes.
bambioinformaticsbiologycoronavirusCOVID-19fast5fastafastqgeneticgenomichealthjsonlife scienceslong read sequencingmedicineMERSmetadataopen source softwareRDFSARSSARS-CoV-2SPARQL
COVID-19 PubSeq is a free and open online bioinformatics public sequence resource with on-the-fly analysis of sequenced SARS-CoV-2 samples that allows for a quick turnaround in identification of new virus strains. PubSeq allows anyone to upload sequence material in the form of FASTA or FASTQ files with accompanying metadata through the web interface or REST API.
bioinformaticslife sciencesmetagenomicsopen source softwareproteinprotein folding
The Steinegger Lab Dataset comprises biological databases and resources critical for protein sequence and structure analysis, developed to support ColabFold, MMseqs2, and Foldseek/Foldcomp—three high-performance computational tools widely used in bioinformatics.The MMseqs2 dataset serves as the backbone for our fast structure prediction tool, ColabFold, and includes UniRef30, BFD, and the ColabFold environmental databases. These datasets are specifically designed for the rapid generation of multiple sequence alignments (MSAs), which are essential for high-accuracy structure prediction. Beyond ...
calcium imagingelectron microscopyimaginglife scienceslight-sheet microscopymagnetic resonance imagingneuroimagingneurosciencevolumetric imagingx-rayx-ray microtomographyx-ray tomography
This data ecosystem, Brain Observatory Storage Service & Database (BossDB), contains several neuro-imaging datasets across multiple modalities and scales, ranging from nanoscale (electron microscopy), to microscale (cleared lightsheet microscopy and array tomography), and mesoscale (structural and functional magnetic resonance imaging). Additionally, many of the datasets include dense segmentation and meshes.
biologycell imagingfluorescence imaginghigh-throughput imagingimaginglife sciencesmachine learningmicroscopy
Quantifying cell morphology using images and machine learning models has proven to be a powerful tool to study the response of cells to treatments. However, the models used to quantify cellular morphology are typically trained with a single microscopy imaging type and under controlled experimental conditions. This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels), or because the target experimental conditions are out of distribution. We have created CHAMMI-75, a large-scale dat...
cancergeneticgenomicHomo sapienslife sciencesSTRIDEStranscriptomicswhole genome sequencing
The Cancer Cell Line Encyclopedia (CCLE) project is an effort to conduct a detailed genetic characterization of a large panel of human cancer cell lines. The CCLE provides public access to genomic data, visualization and analysis for over 1100 cancer cell lines. This dataset contains RNA-Seq Aligned Reads, WXS Aligned Reads, and WGS Aligned Reads data.
fastageneticgenomiclife sciencesmetagenomicsSTRIDEStranscriptomicswhole exome sequencingwhole genome sequencing
This repository is a re-analysis of the NCBI Sequence Read Archive (SRA), December 2023 freeze, to make it more accessible. The SRA is an open access database of biological sequences, containing raw data from high-throughput DNA and RNA sequencing platforms. It is the largest database of public DNA sequences worldwide, containing a wealth of genomic diversity across all living organisms. This repository contains Logan, a set of compressed FASTA files for all individual SRA accessions, in the form of unitigs and contigs. Borrowing methods from the realm of genome assembly, unitigs preserve near...
bioinformaticsbiologyepigenomicsgeneticgenomiclife sciences
The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The project has generated high-quality, genome-wide maps of several key histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues. To see what data is available, please check the directory listing: https://roadmapepigenomics.s3.us-west-2.amazonaws.com/index.html.
bioinformaticsbiologyenvironmentalepigenomicsgeneticgenomiclife sciences
The TaRGET (Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription) Program is a research consortium funded by the National Institute of Environmental Health Sciences (NIEHS). The goal of the collaboration is to address the role of environmental exposures in disease pathogenesis as a function of epigenome perturbation, including understanding the environmental control of epigenetic mechanisms and assessing the utility of surrogate tissue analysis in mouse models of disease-relevant environmental exposures.
cancergeneticgenomiclife sciencesvcf
Precision medicine refers to the use of prevention and treatment strategies that are tailored to the unique features of each individual and their disease. In the context of cancer this might involve the identification of specific mutations shown to predict response to a targeted therapy. The biomedical literature describing these associations is large and growing rapidly. Currently these interpretations exist largely in private or encumbered databases resulting in extensive repetition of effort. Realizing precision medicine will require this information to be centralized, debated and interpret...
cancergenomiclife sciencesSTRIDEStranscriptomics
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. CPTAC-2 is the Phase II of the CPTAC Initiative (2011-2016). Datasets contain open RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantification, and miRNA Expression Quantification data.
life sciencesMus musculusneurophysiologyneuroscienceopen source software
Electrophysiological recordings acquired using Neuropixels probes in different mice and labs, targeting the same brain locations (including posterior parietal cortex, hippocampus, and thalamus).
bamcancergeneticgenomiclife sciencesvcf
The International Cancer Genome Consortium (ICGC) coordinates projects with the common aim of accelerating research into the causes and control of cancer. The PanCancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify common patterns of mutation in whole genomes from ICGC. More than 2,400 consistently analyzed genomes corresponding to over 1,100 unique ICGC donors are now freely available on Amazon S3 to credentialed researchers subject to ICGC data sharing policies.
bioinformaticscancergeneticgenomegenomiclife sciencesproteinstructural variationtranscriptomicsvariant annotationvcfwhole exome sequencingwhole genome sequencing
SnpEff is a variant annotation and effect prediction tool that annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes). It supports over 38,000 genomes and provides comprehensive genomic databases for variant annotation. The databases include reference genomes, gene annotations, protein sequences, and regulatory elements from trusted sources like ENSEMBL, RefSeq, and UCSC. SnpSift complements SnpEff by providing tools to annotate genomic variants using databases, filter large genomic datasets, and manipulate annotated variants. Together, these ...
benchmarklife sciencesmachine learningMus musculusneurophysiologyneuroscienceopen source software
BrainWideBench is a large-scale, multi-task benchmark for evaluating neural foundation models, derived from the International Brain Laboratory (IBL) Brainwide Map dataset. It contains preprocessed Neuropixels recordings from 139 mice spanning 276 brain regions during a standardized visual decision-making task. The benchmark is organized around three complementary task suites: behavioral decoding (TS1), neural activity prediction (TS2), and brain region identification (TS3). Data are processed into a standardized format using the torch_brain library and include spike-sorted neural recordings, b...
cancercomputational pathologycomputer visiondeep learninggrand-challenge.orghistopathologylife sciences
"This dataset contains the all data for the CAncer MEtastases in LYmph nOdes challeNge or CAMELYON. CAMELYON was the first challenge using whole-slide images in computational pathology and aimed to help pathologists identify breast cancer metastases in sentinel lymph nodes. Lymph node metastases are extremely important to find, as they indicate that the cancer is no longer localized and systemic treatment might be warranted. Searching for these metastases in H&E-stained tissue is difficult and time-consuming and AI algorithms can play a role in helping make this faster and more accura...
cancergenomiclife sciencesSTRIDEStranscriptomics
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. CPTAC-3 is the Phase III of the CPTAC Initiative. The dataset contains open RNA-Seq Gene Expression Quantification data.
Biohubcell biologycryo electron tomographyelectron tomographylife sciencesmachine learningsegmentationstructural biology
Cryo-electron tomography (cryoET) is a powerful technique for visualizing 3D structures of cellular macromolecules at near atomic resolution in their native environment. Observing the inner workings of cells in context enables better understanding about the function of healthy cells and the changes associated with disease. However, the analysis of cryoET data remains a significant bottleneck, particularly the annotation of macromolecules within a set of tomograms, which often requires a laborious and time-consuming process of manual labelling that can take months to complete. Given the current...
benchmarkBiohubbiologycell biologycell imagingcomputer visionfluorescence imagingimage-based profilinglife sciencesmachine learningmicroscopyzarr
DynaCell is an evaluation framework for dynamic 3D virtual staining of live cells. The dataset pairs label-free transmitted-light volumes (phase reconstructions from brightfield z-stacks) with fluorescence ground truth for four organelles (nucleus, cell membrane, endoplasmic reticulum, mitochondria) across three conditions (uninfected, Zika-infected, Dengue-infected).The v1 release contains images of A549 human lung adenocarcinoma cells acquired on the Mantis correlative label-free and light-sheet fluorescence microscope at Biohub (24 OZX stores, 262 FOVs, ~407 GB), split into train and test s...
Biohubbioinformaticslife sciencesmachine learningmetagenomicsproteinstructural biology
The ESM Atlas is a large-scale public dataset of computational outputs generated by ESMC and ESMFold2, derived from a deduplicated set of over 6.8 billion publicly available protein sequences spanning all domains of life — including viral proteins and previously unannotated sequences representing metagenomic dark matter sampled from a wide range of biomes. The dataset includes two primary components: sparse autoencoder (SAE) features for ~6.8 billion proteins, capturing interpretable biological representations from the ESMC 6B model, and predicted three-dimensional protein structures for ~1.1 ...
life sciencesMus musculusneurophysiologyneuroscienceopen source software
Behavioral data of mice performing a decision-making task, associated with 2020 publication of the IBL.
biologyhealthimage processingimaginglife sciencesmagnetic resonance imagingneurobiologyneuroimaging
This dataset contains deidentified raw k-space data and DICOM image files of over 1,500 knees and 6,970 brains.
biologycomputed tomographyimage processingimaginglife sciencesmagnetic resonance imagingneuroimagingneurosciencevolumetric imagingzarr
This project provides the Open SciVis Datasets in a chunked, highly-compressed, multi-scale format, encodes metadata in JSON according to the OME-Zarr specification, and hosts the datasets on AWS S3 through the AWS Open Data Program, aiming to serve as a web-based resource for the scientific visualization community to enhance reproducibility and facilitate testing and development of OME-Zarr tools.
bioinformaticsbiologygeneticgenomiclife sciencesreference index
This dataset provides genomic reference data and software packages for use with Galaxy and Bioconductor applications. The reference data is available for hundreds of reference genomes and has been formatted for use with a variety of tools. The available configuration files make this data easily incorporable with a local Galaxy server without additional data preparation. Additionally, Bioconductor's AnnotationHub and ExperimentHub data are provided for use via R packag...
bioinformaticselectrophysiologylife sciencesmicroscopyneurophysiologyneuroscience
The SPARC Datasets comprise a collection of scientific data that is focused on bridging the body and the brain. The datasets focus on neural connectivity, organ innervation and detailed anatomical mapping of the peripheral nervous system. SPARC datasets distinguish themselves from other data resources through its multi-modal approach to scientific data and integrates molecular, imaging, timeseries and other datatypes associated with the interaction between the peripheral nervous system and organs. SPARC data provides a unique integrated effort to develop next generation mapping of anatomical ...
bamCOVID-19geneticgenomiclife sciencesMERSSARSSARS-CoV-2virus
Serratus is a collaborative open science project for ultra-rapid discovery of known and unknown coronaviruses in response to the COVID-19 pandemic through re-analysis of publicly available genomic data. Our resulting vertebrate viral alignment data is explorable via the Serratus Explorer and directly accessible on Amazon S3.
agriculturefood securitygeneticgenomiclife sciences
The 3000 Rice Genome Project is an international effort to sequence the genomes of 3,024 rice varieties from 89 countries.
biologycell biologycomputer visionelectron microscopyimaginglife sciencesmicroscopysegmentation
The Automated Segmentation of intracellular substructures in Electron Microscopy (ASEM) project provides deep learning models trained to segment structures in 3D images of cells acquired by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Each model is trained to detect a single type of structure (mitochondria, endoplasmic reticulum, golgi apparatus, nuclear pores, clathrin-coated pits) in cells prepared via chemically-fixation (CF) or high-pressure freezing and freeze substitution (HPFS). You can use our open source pipeline to load a model and predict a class of sub-cellular structur...
bambioinformaticsbiologyCaenorhabditis elegansfastqgatk-svgenetic mapsgenomegenome wide association studygenomiclife sciencesshort read sequencingvariant annotationvcf
The Caenorhabditis Natural Diversity Resource (CaeNDR) is a data repository and analysis hub of wild strains of selfing Caenhorabditis species C. elegans, C. briggsae, and C. tropicalis from around the world to facilitate discovery of genetic variation across all three species through genome-wide association mappings to correlate genotype with phenotype and identify genetic variation underlying quantitative traits.
cancergeneticgenomiclife sciencesSTRIDESwhole genome sequencing
The Relating Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile study is the Multiple Myeloma Research Foundation (MMRF)’s landmark personalized medicine initiative. CoMMpass is a longitudinal observation study of around 1000 newly diagnosed myeloma patients receiving various standard approved treatments. The MMRF’s vision is to track the treatment and results for each CoMMpass patient so that someday the information can be used to guide decisions for newly diagnosed patients. CoMMpass checked on patients every 6 months for 8 years, collecting tissue samples, gene...
deep learninglife sciencesmachine learningneuroimagingneuroscience
The EEG-DaSh (EEG Data Sharing) data archive is a large-scale data-sharing resource for magnetoencephalography and electroencephalography (MEEG) data hosted at the Swartz Center for Computational Neuroscience (SCCN), UC San Diego. It provides curated, BIDS-formatted datasets for neuroscience research, machine learning, and deep learning applications. The archive spans three S3 buckets: (1) the EEGDash bucket for data served through the EEGDash platform, (2) the NEMAR archive containing datasets contributed through the NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) platform, which...
autism spectrum disorderlife sciencesMus musculusneurophysiologyneuroscienceopen source software
Electrophysiological recordings of mouse brain activity acquired during a decision making task in multiple autism mice models.
cancerclassificationcomputational pathologycomputer visiondeep learningdigital pathologygrand-challenge.orghistopathologyimaginglife sciencesmachine learningmedical image computingmedical imaging
This dataset contains the training data for the Machine learning for Optimal detection of iNflammatory cells in the KidnEY or MONKEY challenge. The MONKEY challenge focuses on the automated detection and classification of inflammatory cells, specifically monocytes and lymphocytes, in kidney transplant biopsies using Periodic acid-Schiff (PAS) stained whole-slide images (WSI). It contains 80 WSI, collected from 4 different pathology institutes, with annotated regions of interest. For each WSI up to 3 different PAS scans and one IHC slide scan are available. This dataset and challenge support th...
brain imagesbrain modelshdf5life sciencesmachine learningneuroimagingneuroscience
This extensible dataset, MOSAIC, aggregates individual functional magnetic resonance imaging (fMRI) datasets by leveraging a shared preprocessing pipeline and stimulus curation procedure. This dataset aggregation procedure achieves the scale necessary for neural network training and the diversity needed for generalizable results.
bamcramfastqgeneticgenomiclife sciencesSTRIDEStranscriptomicswhole exome sequencingwhole genome sequencing
The Sequence Read Archive (SRA), produced by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) at the National Institutes of Health (NIH), stores raw DNA sequencing data and alignment information from high-throughput sequencing platforms. The SRA provides open access to these biological sequence data to support the research community's efforts to enhance reproducibility and make new discoveries by comparing data sets. Buckets in this registry contain public SRA data in the original (user submitted) format from select high value and newly-rel...
amino acidarchivesbioinformaticsbiomolecular modelingcell biologychemical biologyCOVID-19electron microscopyelectron tomographyenzymelife sciencesmoleculenuclear magnetic resonancepharmaceuticalproteinprotein templateSARS-CoV-2structural biologyx-ray crystallography
The "Protein Data Bank (PDB) archive" was established in 1971 as the first open-access digital data archive in biology. It is a collection of three-dimensional (3D) atomic-level structures of biological macromolecules (i.e., proteins, DNA, and RNA) and their complexes with one another and various small-molecule ligands (e.g., US FDA approved drugs, enzyme co-factors). For each PDB entry (unique identifier: 1abc or PDB_0000001abc) multiple data files contain information about the 3D atomic coordinates, sequences of biological macromolecules, information about any small molecules/ligan...
biologyimaginglife sciencesneurobiologyneuroimagingneuroscience
The Human Connectome Project (HCP Young Adult, HCP-YA) is mapping the healthy human connectome by collecting and freely distributing neuroimaging and behavioral data on 1,200 normal young adults, aged 22-35.
cancerlife sciencesmagnetic resonance imagingmedical imagingmedicineradiologysegmentation
This dataset provides 973 prostate MRI exams performed between January 2016 and March 2019 for patients who underwent MRI/ultrasound fusion biopsy within one year at UCSF.
analysis ready databrain imagesbrain modelsimaginginfrastructurejsonlife sciencesmachine learningmetadatamicroscopyneuroimagingneuroscienceniftizarr
The BRAIN Initiative Connectivity Across Scales (CONNECTS) program is working to create detailed maps of brain wiring across different species and scales, using advanced imaging technologies. APEX supports this effort by serving as a central hub that brings together and coordinates data and tools from research focused on brain connectivity in humans and animals. Together, these efforts aim to improve our understanding of how the brain is structured and functions.
assemblybacteriabioinformaticsgenomiclife sciencesmetagenomicsopen source softwareproteinvirus
Lineage datasets for use with BUSCO software package. Each dataset contains HMM profiles for clade specific, universal, single-copy marker genes. Datasets are available across archaea, bacteria, eukaryota and virus domains. The repository also includes necessary data files for phylogenetic placement of an input assembly.
bioinformaticsbiologygeneticgenomichealthlife sciencesproteinreference indexSTRIDEStranscriptomics
A centralized repository of pre-formatted BLAST databases created by the National Center for Biotechnology Information (NCBI).
bioinformaticsbiologygeneticgenomiclife sciences
The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE investigators employ a variety of assays and methods to identify functional elements. The discovery and annotation of gene elements is accomplished primarily by sequencing a ...
bioinformaticsbiologyepigenomicsgeneticgenomiclife sciences
The Human Pangenome Reference Consortium (HPRC) Release 2 represents a landmark achievement in genomics, providing high-quality phased genome assemblies from over 200 individuals with comprehensive functional genomics data. The HPRC Epigenome Browser provides researchers a way to explore all epigenomics data generated by release 2. The HPRC Epigenome Browser (HPRCEB) is a modern, interactive web portal that democratizes access to HPRC Release 2 epigenomics data through an intuitive interface supporting genome selection, data visualization, and bulk download capabilities. The portal integrates ...
bioinformaticselectrophysiologylife sciencesmedicineneuroscience
Epilepsy.Science comprise a set of datasets focused on Epilepsy Research that span both Clinical Data and Pre-clinical data. Datasets are contributed by the Epilepsy Research community and published using a standardized structure and metadata. Clinical datasets include de-identified subject information, EEG, and clinical imaging.
geneticgenomiclife sciencesreference indexvcf
Several reference genomes to enable translation of whole human genome sequencing to clinical practice. On 11/12/2020 these data were updated to reflect the most up to date GIAB release.
biologycancerclassificationcomputational pathologydicomgrand-challenge.orghealthHomo sapiensimaginglife sciencesmachine learningmedical image computingmedical imagingmedicinemicroscopysegmentation
A public-access archive of skin lesion images, supporting teaching, research, and the development and evaluation of diagnostic algorithms.
cancergenomiclife sciencesSTRIDESwhole genome sequencing
The Molecular Profiling to Predict Response to Treatment (MP2PRT) program is part of the NCI's Cancer Moonshot Initiative. The aim of this program is the retrospective characterization and analysis of biospecimens collected from completed NCI-sponsored trials of the National Clinical Trials Network and the NCI Community Oncology Research Program. This study, titled "Identification of Genetic Changes Associated with Relapse and/or Adaptive Resistance in Patients Registered as Favorable Histology Wilms Tumor on AREN03B2", performs genomic characterization (WGS 30X, Total RNAseq, mi...
biologyfluorescence imagingimage processingimaginglife sciencesmicroscopyneurobiologyneuroimagingneuroscience
This data set, made available by Janelia's MouseLight project, consists of images and neuron annotations of the Mus musculus brain, stored in formats suitable for viewing and annotation using the HortaCloud cloud-based annotation system.
Biohubbiologycell biologycell imagingcomputer visionfluorescence imagingimaginglife sciencesmachine learningmicroscopy
The OpenCell project is a proteome-scale effort to measure the localization and interactions of human proteins using high-throughput genome engineering to endogenously tag thousands of proteins in the human proteome. This dataset consists of the raw confocal fluorescence microscopy images for all tagged cell lines in the OpenCell library.These images can be interpreted both individually, to determine the localization of particular proteins of interest, and in aggregate, by training machine learning models to classify or quantify subcellular localization patterns.
life sciencesmsaopen source softwareopenfoldproteinprotein foldingprotein template
This dataset contains MSAs and predicted structures used to train OpenFold3 preview, an open-source, all-atom ligand, RNA and protein structure prediction software. This includes -
alphafoldlife sciencesmsaopen source softwareopenfoldproteinprotein foldingprotein template
Multiple sequence alignments (MSAs) for 140,000 unique Protein Data Bank (PDB) chains and 16,000,000 UniClust30 clusters. Template hits are also provided for the PDB chains and 270,000 UniClust30 clusters chosen for maximal diversity and MSA depth. MSAs were generated with HHBlits (-n3) and JackHMMER against MGnify, BFD, UniRef90, and UniClust30 while templates were identified from PDB70 with HHSearch, all according to procedures outlined in the supplement to the AlphaFold 2 Nature paper, Jumper et al. 2021. We expect the database to be broadly useful to structural biologists training or valid...
computer visionhealthlife sciencesmachine learningrobotics
A comprehensive multimodal dataset capturing real-world caregiving routines from 21 occupational therapists performing 15 daily caregiving tasks. The dataset includes synchronized RGB-D video, tactile sensing, eye-gaze tracking, pose annotations, and action labels across 315 sessions totaling 19.8 hours of expert demonstrations. Data modalities include anonymized RGB images, depth maps, 44-sensor tactile readings, 2D/3D pose tracking, temporal action annotations, and first/third-person videos, enabling research in robot learning from demonstration, multimodal perception, and safe human-robot i...
bioinformaticsbiologygeneticgenomicinfrastructurelife sciencessingle-cell transcriptomicstranscriptomicswhole genome sequencing
Pre-built refgenie reference genome data assets used for aligning and analyzing DNA sequence data.
bioinformaticshealthlife sciencesnatural language processingus
The Synthea generated data is provided here as a 1,000 person (1k), 100,000 person (100k), and 2,800,000 persom (2.8m) data sets in the OMOP Common Data Model format. SyntheaTM is a synthetic patient generator that models the medical history of synthetic patients. Our mission is to output high-quality synthetic, realistic but not real, patient data and associated health records covering every aspect of healthcare. The resulting data is free from cost, privacy, and security restrictions. It can be used without restriction for a variety of secondary uses in academia, research, industry, and gov...
bioinformaticsbiologygeneticgenomiclife sciences
The IGVF (Impact of Genomic Variation on Function) Consortium aims to understand how genomic variation affects genome function,
which in turn impacts phenotype. The NHGRI is funding this collaborative program that brings together teams of investigators who
will use state-of-the-art experimental and computational approaches to model, predict, characterize and map genome function, how
genome function shapes phenotype, and how these processes are affected by genomic variation. These joint efforts will produce a
catalog of the impact of genomic variants on genome function and phenotypes.
The Da...
geneticgenome wide association studygenomiclife sciencespopulation genetics
Linkage disequilibrium (LD) matrices of UK Biobank participants of a British ancestry, based on imputed genotypes.
geneticgenome wide association studygenomiclife sciencespopulation genetics
A multi-ancestry analysis of 7,221 phenotypes using a generalized mixed model association testing framework, spanning 16,119 genome-wide association studies. We provide standard meta-analysis across all populations and with a leave-one-population-out approach for each trait. The data are provided in tsv format (per phenotype) and Hail MatrixTable (all phenotypes and variants). Metadata is provided in phenotype and variant manifests.
bioinformaticscsvepigenomicsgenomicHomo sapienslife sciencesMus musculuszarr
The WashU Repeat Browser dataset provides processed genomic and epigenomic profiles for studying repetitive elements in human (hg38) and mouse (mm10). It contains 8,774 indexed entries spanning CAGE, epigenomic, conservation, transcription-factor and repeat-overlap resources in CSV, BigWig and Zarr formats. The data support genome-wide, repeat-family and consensus-level analysis in Repeat Browser and standard bioinformatics tools.
fastqgeneticgenomiclife scienceswhole genome sequencing
The 1000 Genomes Project is an international collaboration which has established the most detailed catalogue of human genetic variation, including SNPs, structural variants, and their haplotype context. The final phase of the project sequenced more than 2500 individuals from 26 different populations around the world and produced an integrated set of phased haplotypes with more than 80 million variants for these individuals.
bioinformaticsbiologygeneticgenomicimaginglife sciences
The goal of the National Institutes of Health (NIH) Common Fund’s 4D Nucleome (4DN) program is to study the three-dimensional organization of the nucleus in space and time (the 4th dimension). The nucleus of a cell contains DNA, the genetic “blueprint” that encodes all of the genes a living organism uses to produce proteins needed to carry out life-sustaining cellular functions. Understanding the conformation of the nuclear DNA and how it is maintained or changes in response to environmental and cellular cues over time will provide insights into basic biology as well as aspects of human health...
healthlife sciencesmachine learningmolecular dynamicspharmaceuticalproteinsimulations
The rapid advancement of computing technologies, particularly artificial intelligence (AI), has revolutionized various domains, including drug discovery. Curated datasets are crucial for developing reliable, generalizable, and accurate models for practical applications. Generating experimental data on a large scale is an expensive and arduous process. In domains such as medical diagnostics where real-life data is hard to obtain, synthetic data has been shown to be extremely valuable. We, teams from IIIT Hyderabad, Intel, AWS, and Insilico Medicine, have performed physics-based calculations (mo...
brain imagescomputer visionelectrophysiologylife sciencesmachine learningmagnetic resonance imagingnatural language processingneuroimagingneuroscience
The Active Visual Semantics (AVS) Dataset is a multimodal neuroimaging dataset combining magnetoencephalography (MEG), eye-tracking, and structural MRI, recorded from 5 participants (sub-01-sub-05) as they actively explored 4,080 natural scenes (subsampled from the Natural Scenes Dataset, NSD) across 10 recording sessions each, yielding more than 200,000 fixation epochs in total. Unlike neuroimaging datasets that rely on passive viewing with enforced central fixation, AVS captures brain activity during active, self-directed scene exploration, including natural saccades and fixations. A semanti...
bioinformaticslife sciencesmedicinepharmaceuticalstructural biology
AdaptiveFlow Versions of Ligand Libraries in Ready-To-Dock Format
biologycancercomputer visiongene expressiongeneticglioblastomaHomo sapiensimage processingimaginglife sciencesmachine learningneurobiology
This dataset consists of images of glioblastoma human brain tumor tissue sections that have been probed for expression of particular genes believed to play a role in development of the cancer. Each tissue section is adjacent to another section that was stained with a reagent useful for identifying histological features of the tumor. Each of these types of images has been completely annotated for tumor features by a machine learning process trained by expert medical doctors.
biologygene expressiongeneticimage processingimaginglife sciencesMus musculusneurobiologytranscriptomics
The Allen Mouse Brain Atlas is a genome-scale collection of cellular resolution gene expression profiles using in situ hybridization (ISH). Highly methodical data production methods and comprehensive anatomical coverage via dense, uniformly spaced sampling facilitate data consistency and comparability across >20,000 genes. The use of an inbred mouse strain with minimal animal-to-animal variance allows one to treat the brain essentially as a complex but highly reproducible three-dimensional tissue array. The entire Allen Mouse Brain Atlas dataset and associated tools are available through an...
cancergeneticgenomicHomo sapienslife sciencesSTRIDES
Beat AML 1.0 is a collaborative research program involving 11 academic medical centers who worked collectively to better understand drugs and drug combinations that should be prioritized for further development within clinical and/or molecular subsets of acute myeloid leukemia (AML) patients. Beat AML 1.0 provides the largest-to-date dataset on primary acute myeloid leukemia samples offering genomic, clinical, and drug response.This dataset contains open Clinical Supplement and RNA-Seq Gene Expression Quantification data.This dataset also contains controlled Whole Exome Sequencing (WXS) and R...
calcium imagingimaginglife sciencesMus musculusneurosciencevideo
The BraiDyn-BC (Brain Dynamics underlying emergence of Behavioral Change) Database offers an extensive, multimodal dataset that links wide-field calcium imaging of the mouse neocortex to comprehensive behavioral measurements during a behavioral task. As one of the contents in this database, we newly provide a dataset that includes 15 sessions spanning two weeks of motor skill learning, in which 25 mice were trained to pull a lever to obtain water rewards. Simultaneous high-speed videography captures body, facial, and eye movements, and environmental parameters are monitored. The dataset also ...
cancercomputational pathologycomputer visiondeep learninghistopathologylife sciences
This page describes the COBRA (Classification Of Basal cell carcinoma, Risky skin cancers and Abnormalities) skin pathology dataset, which comprises over 7000 histopathology whole-slide-images related to the diagnosis of basal cell carcinoma skin cancer, the most commonly diagnosed cancer. The dataset includes biopsies and excisions and is divided into four groups. The first group contains about 2,500 BCC biopsies with subtype labels, while the second group includes 2,500 non-BCC biopsies with different types of skin dysplasia. The third group has 1,000 labelled risky cancer biopsies, includin...
coronavirusCOVID-19life sciences
A harmonized collection of the core data pertaining to COVID-19 reported cases by geography, in a format prepared for analysis
cell biologycomputer visionelectron microscopyimaginglife sciencesorganelle
High resolution images of subcellular structures.
agriculturecomputer visionIMUlidarlife scienceslocalizationmappingrobotics
CitrusFarm is a multimodal agricultural robotics dataset that provides both multispectral images and navigational sensor data for localization, mapping and crop monitoring tasks.
cancergenomiclife sciencesSTRIDEStranscriptomicswhole genome sequencing
The goal of the project is to identify recurrent genetic alterations (mutations, deletions, amplifications, rearrangements) and/or gene expression signatures. National Cancer Institute (NCI) utilized whole genome sequencing and/or whole exome sequencing in conjunction with transcriptome sequencing. The samples were processed and submitted for genomic characterization using pipelines and procedures established within The Cancer Genome Analysis (TCGA) project.
bioinformaticslife sciencesmachine learningproteinstructural biology
DPEB is a multimodal database of human protein embeddings integrating four biologically complementary representations—AlphaFold2, BioEmbeddings, ESM-2, and ProtVec—designed for enhanced protein-protein interaction prediction and functional classification.
cancerepigenomicsgenomiclife sciencesSTRIDEStranscriptomicswhole exome sequencingwhole genome sequencing
The Exceptional Responders Initiative is a pilot study to investigate the underlying molecular factors driving exceptional treatment responses of cancer patients to drug therapies. Study researchers will examine molecular profiles of tumors from patients either enrolled in a clinical trial for an investigational drug(s) and who achieved an exceptional response relative to other trial participants, or who achieved an exceptional response to a non-investigational chemotherapy. An exceptional response is defined as achievement of either a complete response or a partial response for at least 6 mon...
cancergenomiclife sciences
The Foundation Medicine Adult Cancer Clinical Dataset (FM-AD) is a study conducted by Foundation Medicine Inc (FMI). Genomic profiling data for approximately 18,000 adult patients with a diverse array of cancers was generated using FoundationeOne, FMI's commercially available, comprehensive genomic profiling assay. This dataset contains open Clinical and Biospecimen data.
genomegenotypinggolden retriever lifetime studylife sciencesmorris animal foundation
Morris Animal Foundation’s Golden Retriever Lifetime Study is a longitudinal, prospective study following 3044 golden retrievers. The Study’s purpose is to identify the nutritional, environmental, lifestyle and genetic risk factors for cancer and other diseases. The Golden Oldie’s study enrolled an additional cohort of golden retrievers that had reached the age of 12 years or older and had not yet been diagnosed with a malignant cancer. This population can be used as a control group for conditions with high mortality in younger age. This dataset contains the data for ~1.1 million genetic marke...
agriculturecarbonclimateenvironmentalfood securityjsonlife sciencesparquetsustainability
National and global weighted averages of the environmental impacts of agricultural and food production, aggregated from the farm-level cycles published on the HESTIA platform.Each release is a self-contained snapshot in JSON-LD: validated aggregated impact assessments with the cycles they describe, those cycles' sites, and every glossary term and bibliographic source any of them reference, so a release resolves without leaving the bucket. Alongside it sits a flat Parquet mirror of the mid-point and end-point indicators, for querying without parsing JSON-LD, and an index mapping product to ...
biologycell biologycell imaginggene expressiongenomegenomicHomo sapienslife sciencesMus musculussingle-cell transcriptomicstranscriptomics
The Human Cell Atlas (HCA) is a collaborative community of international scientists. Our mission is to create comprehensive reference maps of all the cells in the human body as a basis for both understanding human health and diagnosing, monitoring, and treating disease. The HCA registry has more than one thousand member scientists from hundreds of institutions around the world. The project is steered and governed by an Organizing Committee, co-chaired by Aviv Regev and Sarah Teichmann.
biologygene expressionHomo sapienslife sciencesMus musculusneurobiologynon-human primatesingle-cell transcriptomics
Human and Mammalian Brain Atlas (HMBA) is a major atlas of the BRAIN Initiative Cell Atlas Network (BICAN) that proposes to establish a comprehensive, highly granular cell atlas in complete adult human, macaque, and marmoset brains that links brain structure, function and cellular architecture. Release artifacts have been made available in this OpenData bucket to enable utilization along with their paper publications by the neuroscience community.
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The International Cardiac Arrest REsearch consortium (I-CARE) Database includes baseline clinical information and continuous electroencephalography (EEG) recordings from 1,020 comatose patients with a diagnosis of cardiac arrest who were admitted to an intensive care unit from seven academic hospitals in the U.S. and Europe. Patients were monitored with 18 bipolar EEG channels over hours to days for the diagnosis of seizures and for neurological prognostication. Long-term neurological function was determined using the Cerebral Performance Category scale.
biodiversityBiohubbioinformaticsbiologybiomolecular modelingbrain imagescell biologycell imagingimaginglife sciencesmachine learningmicroscopymodelproteinzarr
This dataset contains a diverse range of imaging biological data and models. The data is sourced and curated by a team of experts at Biohub and is made available as part of these datasets only when it is not publicly accessible or requires transformations to support model training.
benchmarkbioinformaticslife sciencesmetagenomicsmicrobiome
Database for use with Kraken2 (taxonomic annotation of metagenomic sequencing reads) including all NCBI RefSeq genomes available in release V205
bioinformaticshealthlife sciencesnatural language processingus
MIMIC-III (‘Medical Information Mart for Intensive Care’) is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. Data includes vital signs, medications, laboratory measurements, observations and notes charted by care providers, fluid balance, procedure codes, diagnostic codes, imaging reports, hospital length of stay, survival data, and more. The database supports applications including academic and industrial research, quality improvement initiatives, and higher education coursework. The MIMIC-I...
computed tomographyhealthimaginglife sciencesmagnetic resonance imagingmedicineniftisegmentation
With recent advances in machine learning, semantic segmentation algorithms are becoming increasingly general purpose and translatable to unseen tasks. Many key algorithmic advances in the field of medical imaging are commonly validated on a small number of tasks, limiting our understanding of the generalisability of the proposed contributions. A model which works out-of-the-box on many tasks, in the spirit of AutoML, would have a tremendous impact on healthcare. The field of medical imaging is also missing a fully open source and comprehensive benchmark for general purpose algorithmic validati...
bioinformaticsbiologyGeneLabgenomicimaginglife sciencesspace biology
NASA’s Space Biology Open Science Data Repository (OSDR) introduces a one-stop site where users can explore and contribute a variety of NASA open science biological data. This site consolidates data from the Ames Life Sciences Data Archive (ALSDA) and GeneLab and includes information about the broader NASA Open Science and Open Data initiatives, all at one centralized location. Our mission is to maximize the utilization of the valuable biological research resources and enable new discoveries.
OSDR introduces access to data generated from spaceflight and space relevant experiments that explore ...
cancerdigital pathologyfluorescence imagingimage processingimaginglife sciencesmachine learningmedical imagingmicroscopyradiology
Imaging Data Commons (IDC) is a repository within the Cancer Research Data Commons (CRDC) that manages imaging data and enables its integration with the other components of CRDC. IDC hosts a growing number of imaging collections that are contributed by either funded US National Cancer Institute (NCI) data collection activities, or by the individual researchers.Image data hosted by IDC is stored in DICOM format.
bambenchmarkbioinformaticsepigenomicsgenomiclife scienceslong read sequencing
ONT Methylation Benchmarking Datasets are generated to benchmark existing methylation-calling tools on the Oxford Nanopore sequencing platform using their recent R10.4.1 flowcell chemistry. It spans a diverse range of species, including bacteria (E. coli, H. pylori J99, H. pylori 26695, A. variabilis, T. denticola), plants (Rice, Arabidopsis), and mammals (mouse, human).In addition, the dataset includes EMSeq data for E. coli, plant, and mouse samples, which can serve as ground truth for methylation studies. It also provides unmethylated whole-genome amplified (WGA) DNA for H. pylori 26695 and...
bioinformaticsbiologygenomiclife sciences
The Open Human Genome Library (OpenHGL) is a collection of high-quality de novo human assemblies that are publicly available in genomic databases (e.g. NCBI and CNCB) or from individual research papers. It provides consistent naming and uniform formats across datasets, supporting efficient subsequence retrieval and approximate string search.
benchmarkcomputational pathologycomputer visiondeep learningdigital pathologyhistopathologyimaginglife sciencesmachine learningmedical imagingnatural language processing
This dataset contains the data for the Pathologist Reasoning-Guided Report Generation challenge (REG2026), a computational pathology benchmark for pathology report generation from hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) with paired Chain-of-Thought (CoT) data. Participants are tasked with generating pathology reports based on WSIs, and their models are evaluated not only on report generation but also on the reasoning process underlying report generation. WSIs have been preprocessed to anonymize patient information and retain only 20x magnification images. The dataset ...
bioinformaticsbiologydeep learninglife sciencesmachine learningprotein
ProteinGym is a benchmark suite for assessing the performance of protein fitness prediction and design models. It comprises a large curated collection of 200+ high-throughput experimental assays (~3M mutated sequences), as well as clinical annotations from experts about the pathogenicity of mutants in over 3k human genes.
bioinformaticsbiologyecosystemsenvironmentalgeneticgenomichealthlife sciencesmetagenomicsmicrobiome
QIIME 2 (pronounced “chime two”) is a microbiome multi-omics bioinformatics and data science platform that is trusted, free, open source, extensible, and community developed and supported.
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The IIIC dataset includes 50,697 labeled EEG samples from 2,711 patients' and 6,095 EEGs that were annotated by physician experts from 18 institutions. These samples were used to train SPaRCNet (Seizures, Periodic and Rhythmic Continuum patterns Deep Neural Network), a computer program that classifies IIIC events with an accuracy matching clinical experts.
computed tomographycomputer visioncoronavirusCOVID-19grand-challenge.orgimaginglife sciencesSARS-CoV-2
The STOIC project collected Computed Tomography (CT) images of 10,735 individuals suspected of being infected with SARS-COV-2 during the first wave of the pandemic in France, from March to April 2020. For each patient in the training set, the dataset contains binary labels for COVID-19 presence, based on RT-PCR test results, and COVID-19 severity, defined as intubation or death within one month from the acquisition of the CT scan. This S3 bucket contains the training sample of the STOIC dataset as used in the STOIC2021 challenge on grand-challenge.org.
bioinformaticscancergenomiclife sciencesspatial omics
Sid was diagnosed with osteosarcoma in November 2022 and after running out of standard of care treatment options he began: maximum diagnostics, created new treatments, started doing treatments in parallel, and scaling this for others. This dataset includes the clinical and molecular data generated by and for Sid throughout this journey: longitudinal single cell and bulk RNA and DNA sequencing, spatial transcriptomics, residual disease testing (MRD), flow cytometry, imaging, and clinical lab results. This data is being freely shared with the community to advance cancer research.
bioinformaticslife sciencesmetagenomicsmicrobiome
SoilMicrobeDB is a Kraken2 genome database with extensive representation of high-quality genomes of soil organisms, including uncultured and fungal species.
bioinformaticsbiomolecular modelinglife sciencesmetagenomicsmsaproteinprotein foldingstructural biology
A collection of prebuilt protein sequence databases for multiple sequence alignment (MSA) search. MSAs are the main input of protein structure prediction and are also used to study conservation, coevolution and protein function. The nine databases, in the native formats of MMseqs2 and HH-suite, derive from UniProt UniRef100 (release 2026_01), the reduced BFD, MGnify (release 2024_04), EnVhogDB and the Logan protein catalogue from the NCBI Sequence Read Archive. The sequences of UniRef100, MGnify and the reduced BFD were re-clustered, EnVhogDB was re-clustered at its upstream standard level, an...
amino acidfastafastqgeneticgenomiclife sciencesmetagenomicsmicrobiome
The NIH-funded Human Microbiome Project (HMP) is a collaborative effort of over 300 scientists from more than 80 organizations to comprehensively characterize the microbial communities inhabiting the human body and elucidate their role in human health and disease. To accomplish this task, microbial community samples were isolated from a cohort of 300 healthy adult human subjects at 18 specific sites within five regions of the body (oral cavity, airways, urogenital track, skin, and gut). Targeted sequencing of the 16S bacterial marker gene and/or whole metagenome shotgun sequencing was performe...
bioinformaticsbiologyepigenomicsgene expressiongenomicgenotypingHomo sapiensimaginglife sciencesmedicineneurobiologyneuroscienceproteinRNA-seqtranscriptomicswhole genome sequencing
The Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP) are ongoing longitudinal clinical-pathologic cohort studies of aging and Alzheimer's disease. Participants enroll without known dementia, undergo annual clinical and cognitive evaluations, and agree to organ donation at death. The ROSMAP study provides genomic, transcriptomic, epigenomic, proteomic, metabolomic, imaging, and related metadata generated from these cohorts to support research into cognitive decline, neuropathology, brain aging, and the molecular mechanisms of Alzheimer's disease.
biodiversityBiohubbiologybiomolecular modelingcell biologyhdf5life sciencesmachine learningmodelproteintranscriptomics
This dataset contains a transcriptomics biological data and models. The models embed transcriptomic data and facilitate transcriptomic analysis. The data is sourced and curated by a team of experts at Biohub and is made available as part of these datasets only when it is not publicly accessible or requires transformations to support model training.
cancercomputed tomographylife sciencesmedical imagingmedicineradiology
This dataset provides a set of 831 3D Multiphase CT exams of renal masses, registered across phases with annotations identifying the masses
genome wide association studygenomiclife scienceslofteevep
VEP determines the effect of genetic variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. The European Bioinformatics Institute produces the VEP tool/db and releases updates every 1 - 6 months. The latest release contains 267 genomes from 232 species containing 5567663 protein coding genes. This dataset hosts the last 5 releases for human, rat, and zebrafish. Also, it hosts the required reference files for the Loss-Of-Function Transcript Effect Estimator (LOFTEE) plugin as it is commonly used with VEP.
benchmarkbioinformaticslife sciencesmetagenomicsmicrobiome
Database for use with run_dbcan (CAZyme and CGC annotation), including CAZyme, Transporter, Transcription factor, Signaling Transduction Protein, Sulfatase, Peptidase, and Polysaccharide utilization Loci.
electrophysiologyHomo sapienslife sciencesMus musculusneurobiologysignal processing
This is a large-scale survey that describes the physiology (strength, kinetics, and short term plasticity) of thousands of synapses from patch clamp experiments in mouse visual cortex and human middle temporal gyrus.
electrophysiologylife sciencesMus musculusneurobiologysignal processing
Extracellular electrophysiology data is growing at a remarkable pace. This data, collected neuropixels probes by the Allen Institute and the International Brain Lab can be used to benchmark throughput rates and storage ratios of various data compression algorithms.
electrophysiologylife sciencesMus musculusneurobiologysignal processing
Evaluation of spike sorting methods is a challenging task, as it requires both ground-truth data and a variety of sorting algorithms to compare against. This dataset contains a set of hybrid data specifically designed for benchmarking spike sorting methods.
electrophysiologyimage processingimaginglife sciencesMus musculusneurobiologyneuroimagingsignal processing
The Allen Institute for Neural Dynamics (AIND) is committed to FAIR, Open, and Reproducible science. We therefore share all of the raw and derived data we collect publicly with rich metadata, including preliminary data collected during methods development, as near to the time of collection as possible.
connectomicselectron microscopyimaginglife sciencesneuroscience
organized and data files for plotting figures in the manuscript of VISp intratelencephalic (IT) neuron connectivity using MICrONS EM dataset
biologylife sciencesmarine mammalsoceans
Since 2007, the Integrated Marine Observing System’s Animal Tracking Facility (formerly known as the Australian Animal Tracking And Monitoring System (AATAMS)) has established a permanent array of acoustic receivers around Australia to detect the movements of tagged marine animals in coastal waters. Simultaneously, the Animal Tracking Facility developed a centralised national database (https://animaltracking.aodn.org.au/) to encourage collaborative research across the Australian research community and provide unprecedented opportunities to monitor broad-scale animal movements. The resulting da...
agriculturecomputer visiondeep learningfood securitygeospatialimage processingimaginglabeledlife sciencesmachine learningsustainability
Artemis and Image Safari are complementary large-scale agricultural imaging datasets containing approximately 7.5 million field images (7,469,218) from smallholder and phenotyping farming systems across 18 crop species in 11 countries spanning sub-Saharan Africa, Latin America, and the United States. Artemis (1,387,663 images) pairs imagery with linked agronomic, genotypic, and environmental metadata across four crops and four countries. Image Safari (6,081,555 images) captures diversity across 18 crops and nine countries. A subset of 40,558 images includes organ-level annotations (10,887 Arte...
biodiversitybioinformaticslife sciences
The Biodiversity Heritage Library (BHL) is the world’s largest open access digital library for biodiversity literature and archives. BHL operates as a worldwide consortium of natural history, botanical, research, and national libraries working together to digitize the natural history literature held in their collections and make it freely available for open access.
fluorescence imagingGeneLabgeneticgenetic mapslife sciencesmicroscopyNASA SMD AI
Fluorescence microscopy images of individual nuclei from mouse fibroblast cells, irradiated with Fe particles or X-rays with fluorescent foci indicating 53BP1 positivity, a marker of DNA damage. These are maximum intensity projections of 9-layer microscopy Z-stacks.
gene expressionGeneLabgeneticgenetic mapslife sciencesNASA SMD AIspace biology
RNA sequencing data from spaceflown and control mouse liver samples, sourced from NASA GeneLab and augmented with generative adversarial network.
brain modelscomputer visiondeep learninglife sciencesmachine learningneuroimagingneuroscience
Brain Encoding Response Generator (BERG) is a resource consisting of multiple pre-trained encoding models of the brain and an accompanying Python package to generate accurate in silico neural responses to arbitrary stimuli with just a few lines of code.
brain imagesimaginglife sciencesmicroscopyneurobiologyneuroimagingneuroscienceniftinon-human primate
Brain/MINDS Marmoset Connectivity Resource (BMCR) is a resource that provides access to anterograde and retrograde neuronal tracer data, made available by Brain/MINDS project. It is currently restricted to injections into the prefrontal cortex of a marmoset brain but is planned to include injections into entire cortical areas and representative subcortical brain regions.
biologydigital preservationHomo sapiensimage processingimaginglife scienceslight-sheet microscopymagnetic resonance imagingmedical imagingmicroscopyMus musculusneurobiologyneuroimagingneuroscienceRattus norvegicusvolumetric imagingzarr
BrainGlobe provides an archive and standardised interface to anatomical atlases from multiple species. This dataset includes these atlases, and other data (e.g. sample neuroanatomy data) to allow the greatest use of the atlases.
gene expressiongenotypinglife sciencestranscriptomics
This ambitious project seeks to characterize the genetic and epigenetic regulation of multiple facets of transcription in distinct brain regions across the human lifespan in samples of major neuropsychiatric disorders and controls. Initially focused on schizophrenia and mood disorders, the goal of this consortium is to elucidate the underlying molecular mechanisms of genetic associations with the goal of identifying novel therapeutic targets. The consortium currently consists of seven pharmaceutical companies and a not-for-profit medical research institution working as a precompetitive team to...
bioinformaticsbiologycancergeneticgenomicHomo sapienslife sciencesreference index
Broad maintained human genome reference builds hg19/hg38 and decoy references.
amazon.sciencebioinformaticsbiologycoronavirusCOVID-19healthlife sciencesmedicineMERSSARS
A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19. Globally, there are several efforts underway to gather this data, and we are working with partners to make this crucial data freely available and keep it up-to-date. Hosted on the AWS cloud, we have seeded our curated data lake with COVID-19 case tracking data from Johns Hopkins and The New York Times, hospital bed availability from Definitive Healthcare, and over 45,000 research articles about COVID-19 and rela...
cancergenomiclife sciencesSTRIDEStranscriptomics
The Cancer Genome Characterization Initiatives (CGCI) program supports cutting-edge genomics research of adult and pediatric cancers. CGCI investigators develop and apply advanced sequencing methods that examine genomes, exomes, and transcriptomes within various types of tumors. The program includes Burkitt Lymphoma Genome Sequencing Project (BLGSP) project and HIV+ Tumor Molecular Characterization Project - Cervical Cancer (HTMCP-CC) project. The dataset contains open Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantificati...
biologycell imagingcell paintingfluorescence imaginghigh-throughput imagingimaginglife sciencesmicroscopy
The Cell Painting Image Collection is a collection of freely downloadable microscopy image sets. Cell Painting is an unbiased high throughput imaging assay used to analyze perturbations in cell models. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth" (expected results). Researchers are encouraged to use these image sets as reference points when developing, testing, and publishing new image analysis algorithms for the life sciences. We hope that the this data set will lead to a better understanding of w...
bioinformaticsbiologygenomiclife sciencesmappingmedicinereference indexwhole genome sequencing
Genomic tools use reference databases as indexes to operate quickly and efficiently, analogous to how web search engines use indexes for fast querying. Here, we aggregate genomic, pan-genomic and metagenomic indexes for analysis of sequencing data.
life sciencesmachine learningstructural biology
The “Cryo-EM SPA Workflow Records” contains all outputs of all processing steps involved in cryogenic electron microscopy (cryo-EM) single particle analysis (SPA), including both intermediate and final output data. The primary focus will be on data generated by RELION and CryoSPARC, two widely used software packages for :Cryo-EM SPA. These records will be archived systematically. To ensure the data remains reproducible while minimizing storage demands, large-sized files that can be regenerated will be excluded prior to registration. The aim is to retain only the essential metadata, processing ...
bambioinformaticscoronavirusCOVID-19fastafastqgeneticgenomicglobalhealthlife scienceslong read sequencingSARS-CoV-2vcfviruswhole genome sequencing
The Sequence Read Archive (SRA) is the primary archive of high-throughput sequencing data, hosted by the National Institutes of Health (NIH). The SRA represents the largest publicly available repository of SARS-CoV-2 sequencing data. This dataset was created by DNAstack using SARS-CoV-2 sequencing data sourced from the SRA. Where possible, raw sequence data were processed by DNAstack through a unified bioinformatics pipeline to produce genome assemblies and variant calls. The use of a standardized workflow to produce this harmonized dataset allows public data generated using different methodol...
brain imagesbrain modelselectron microscopyelectrophysiologyimaginglife sciencesMus musculusneurobiologyneuroimagingneurophysiologyneurosciencesimulation neurosciencesingle neuron models
The Dendritic Consortium provides a multimodal dataset integrating calcium and voltage imaging, electrophysiology, electron microscopy, proteomics, and computational models of Baz1a pyramidal neurons in the mouse primary visual cortex (V1).
bioinformaticsbiologybrain imagescell imagingcomputer visionfluorescence imaginghigh-throughput imagingimage processingimagingion channelslife sciencesmachine learningmicroscopymorphological reconstructionsMus musculusneurobiologyneuroimagingneuroscienceproteinsegmentationzarr
This dataset was generated using E11.bio's PRISM technology (Protein Reconstruction and Identification through Multiplexing), a platform that combines viral barcoding, expansion microscopy, and iterative immunolabeling for large-scale neuronal reconstruction.Neurons in the mouse hippocampal CA3 were transduced with a library of adeno-associated viruses (AAVs) encoding diverse “protein bits”—small epitope tags that act as combinatorial barcodes. Tissue was then processed with an expansion microscopy protocol, physically enlarging the sample ~5× to achieve an effective voxel size of ~35 × 3...
activity detectionactivity recognitionanalyticsbioinformaticsbrain imagesbrain modelscloud computingcomputer visiondeep learningelectrophysiologyGPSh5hdf5Homo sapiensjsonlife scienceslocalizationmachine learningmagnetic resonance imagingMus musculusneurobiologyneuroimagingneurophysiologyneurosciencenon-human primatesignal processingspeech processingzarr
This is data from, Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER), It contains time series behavioral and neuroscience data from animal and deidentified human subjects across multiple modalities.
biasbiologycancerhealthimaginglife sciencesmammographyx-ray
EMBED is a racially diverse mammography dataset containing 3.4M screening and diagnostic images from 110,000 patients collected from 2013-2020, with an equal representation of black and white women. The dataset is comprised of 2D, synthetic 2D (C-view), and 3D (digital breast tomosynthesis, i.e. DBT) images. It contains 60,000 annotated lesions linked to structured imaging descriptors and ground truth pathologic outcomes grouped into six severity classes. This release represents 20% of the total 2D and C-view dataset and is available for research use. DBT, US, and MRI exams will be added at a ...
bioinformaticsbiologycomputer visioncsvhealthimaginglabeledlife sciencesmachine learningmedical image computingmedical imagingradiologyx-ray
The Emory Knee Radiograph (MRKR) dataset is a large, demographically diverse collection of 503,261 knee radiographs from 83,011 patients, 40% of which are African American. This dataset provides imaging data in DICOM format along with detailed clinical information, including patient- reported pain scores, diagnostic codes, and procedural codes, which are not commonly available in similar datasets. The MRKR dataset also features imaging metadata such as image laterality, view type, and presence of hardware, enhancing its value for research and model development. MRKR addresses significant gaps ...
life sciencesmachine learningproteinprotein template
FLAb is the largest publicly available therapeutic antibody dataset designed to train and benchmark protein AI models. It provides open-access, high-quality developability data on diverse therapeutic properties, including expression, thermostability, immunogenicity, aggregation, polyreactivity, binding affinity, and pharmacokinetics.
bioinformaticsbiologycromwellgatk-svgeneticgenomiclife sciencesstructural variation
This dataset holds the data needed to run a structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data in AWS.
cancergenomiclife sciencesSTRIDESwhole genome sequencing
Biopsies of castration resistant prostate cancer metastases were subjected to whole genome sequencing (WGS), along with RNA-sequencing (RNA-Seq). The overarching goal of the study is to illuminate molecular mechanisms of acquired resistance to therapeutic agents, and particularly androgen signaling inhibitors, in the treatment of metastatic castration resistant prostate cancer (mCRPC). This study is made available on AWS via the NIH STRIDES Initiative.
geneticgenomiclife sciencesvariant annotationwhole exome sequencingwhole genome sequencing
Genoxus Annotation is a harmonized and curated collection of human genetic variant databases designed to support accurate and salable variant annotation. Variant annotation following genetic testing such as whole genome sequencing (WGS) or whole exome sequencing (WES) is a critical step in identifying and interpreting disease-associated genetic factors. As sequencing technologies continue to generate large volumes of genomic data, robust and well-structured annotation resources are essential for translating raw variant calls into clinically meaningful insights. Genoxus Annotation v1.0 integrat...
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The Harvard EEG Database will encompass data gathered from four hospitals affiliated with Harvard University:Massachusetts General Hospital (MGH), Brigham and Women's Hospital (BWH), Beth Israel Deaconess Medical Center (BIDMC), and Boston Children's Hospital (BCH).
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
The Harvard-Emory ECG database (HEEDB) is a large collection of 12-lead electrocardiography (ECG) recordings, prepared through a collaboration between Harvard University and Emory University investigators.
bioinformaticsgeneticgenomiclife sciencesmetagenomicsviruswhole genome sequencing
Preprocessed databases for use with the Hecatomb pipeline for viral and phage sequence annotation.
bioinformaticsbiologygenomiclife sciencesmetagenomicsmicrobiomereference indexwhole genome sequencing
This dataset comprises pre-built indexes for the bioinformatics software Kaiju, which is used for taxonomic classification of metagenomic sequencing data. Various indexes for different source reference databases are available.
cancerepigenomicsgenomiclife sciencesSTRIDESwhole exome sequencingwhole genome sequencing
We performed whole genome sequencing and whole exome sequencing of 31 lung adenocarcinoma (LUAD) samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. The EAGLE study is made available on AWS via the NIH STRIDES Initiative (https://aws.amazon.com/blogs/publicsector/aws-and-national-institutes-of-health-collaborate-to-accelerate-discoveries-with-strides-initiative/).
image processingimaginglife sciencesmicroscopyMus musculusneurobiologyneuroimagingneuroscience
This dataset contains high-resolution ExA-SPIM (Expansion-Assisted Selective Plane Illumination Microscopy) light-sheet imaging data of interhemispheric cortical connectivity in the mouse brain. Whole-brain volumes are acquired at near-isotropic sub-micron resolution following tissue expansion and clearing, enabling visualization and reconstruction of individual callosal projection neurons and their axonal arbors spanning both hemispheres. Data is stored in OME-Zarr format for efficient cloud-based access and multiscale visualization.
brain imagescomputer visiondeep learningimaginglife sciencesmachine learningmagnetic resonance imagingneuroimagingneurosciencenifti
LAION-fMRI is one of the largest and most comprehensive high-resolution imaging datasets of brain responses to visually-presented photographs which we built to uncover how the human brain sees and understands the world. Five participants viewed over 25,000 unique natural images in 165 hours across 165 sessions, capturing hundreds of thousands of brain responses every second with an ultra-high-field 7-Tesla MRI scanner. This extraordinary scale means results can be replicated across individuals and generalized across a very broad range of visual experiences, overcoming critical barriers that pr...
cancercomputational pathologycomputer visiondeep learninggrand-challenge.orghistopathologylife sciences
"This dataset contains the all data for the LEarning biOchemical Prostate cAncer Recurrence from histopathology sliDes challenge or LEOPARD.Prostate cancer, impacting 1.4 million men annually, is a prevalent malignancy (H. Sung et al., 2021). A substantial number of these individuals undergo prostatectomy as the primary curative treatment. The efficacy of this surgery is assessed, in part, by monitoring the concentration of prostate-specific antigen (PSA) in the bloodstream. While the role of PSA in prostate cancer screening is debatable (W. F. Clark et al., 2018; E. A. M. Heijnsdijk et al., 2018), it serves as a valuable biomarker for postprostatectomy follow-up in patients. Following successful surgery, PSA concentration is typically undetectable (<0.1 ng/mL) within 4-6 weeks (S. S. Goonewardene et al., 2014). However, approximately 30% of patie...
life sciencesmachine learningmagnetic resonance imagingmedical imaging
The MAPSMR dataset is a multi-organ, post-surgical MRI benchmark dataset focused on organ absence and altered anatomy after common abdominal and pelvic surgeries. The dataset includes cases such as cholecystectomy, prostatectomy, nephrectomy, colectomy, hepatectomy, and related procedures, with annotations identifying surgically absent organs and post-treatment anatomical changes.
3d-meshcardiovasculardicomhealthlife sciencesmagnetic resonance imagingmedical imagingmedicineneuroimagingradiologyroboticssegmentationsimulationsstrokestrokex-ray
As part of the ARPA-H AIR program, we are collecting prospective and retrospective Computed Tomography Angiography (CTA), Magnetic Resonance Angiography (MRA), and video fluoroscopy recordings. In total, we will collect 2,500 CTA/MRA and 1,500 video fluoroscopy recordings. The 1,500 video fluoroscopy recordings will be paired with the corresponding CTA/MRA data. We will also upload annotations for 150 of the recordings and images and 100 anatomic segmentations. These data will be collected in a multi-institutional effort under the ARPA-H AIR program. The immediate goal of the program is to dev...
csvlife sciencesSTRIDEStxtxml
PubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal article at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). The PubMed Central (PMC) Article Datasets include full-text articles archived in PMC and made available under license terms that allow for text mining and other types of secondary analysis and reuse. The articles are organized on AWS based on PMCID and version number:
The PMC Open Access (OA) Subset, which includes all articles in PMC that are available for reuse based on terms specified by the publisher. The majority of avai...
cancergenomiclife sciences
The study describes integrative analysis of genetic lesions in 574 diffuse large B cell lymphomas (DLBCL) involving exome and transcriptome sequencing, array-based DNA copy number analysis and targeted amplicon resequencing. The dataset contains open RNA-Seq Gene Expression Quantification data.
chemistrydrug discoverylife sciencesmachine learningmoleculeparquetpharmaceutical
122,454,458 PubChem compounds with RDKit physicochemical descriptors, ADMET/toxicity predictions from NovoMCP's own models (most trained on the public Therapeutics Data Commons ADMET benchmark; a few base heads on other public toxicology data such as Tox21), a machine-learned logP, and PAINS structural-alert flags. One row per PubChem CID, stored as Apache Parquet (Snappy) for direct in-place querying (Athena, DuckDB, PyArrow, pandas). An analysis-ready cheminformatics substrate for drug discovery: virtual screening, drug-likeness (QED) filtering, similarity search, chemical-space explorat...
geneticgenomiclife sciencessqlitetertiary analysisvariant annotation
OpenCRAVAT is a module variant annotation tool developed by KarchinLab at Johns Hopkins. This dataset is a mirror of the OpenCRAVAT store available at https://store.opencravat.org. You can configure OpenCRAVAT to use this mirror by editing the "cravat-system.yml" file. The path to this file is in the first output line of the command "oc config system". In that file, change the value of "store_url" to "https://opencravat-store-aws.s3.amazonaws.com".
cancergenomiclife sciences
The OHSU-CNL study offers the whole exome and RNA-sequencing on a cohort of 100 cases with rare hematologic malignancies such as Chronic neutrophilic leukemia (CNL), atypical chronic myeloid leukemia (aCML), and unclassified myelodysplastic syndrome/myeloproliferative neoplasms (MDS/MPN-U). This dataset contains open RNA-Seq Gene Expression Quantification data.
cancergeneticgenomiclife sciencesSTRIDEStranscriptomicswhole genome sequencing
This study generated a collection of patient-derived pancreatic normal and cancer organoids and it was sequenced using Whole Genome Sequencing (WGS), Whole Exome Sequencing (WXS) and RNA-Seq as well as matched tumor and normal tissue if available. The study provides a valuable resource for pancreatic cancer researchers. The dataset contains open RNA-Seq Gene Expression Quantification data and controlled WGS/WXS/RNA-Seq Aligned Reads, WXS Annotated Somatic Mutation, WXS Raw Somatic Mutation, and RNA-Seq Splice Junction Quantification.
coronavirusCOVID-19information retrievallife sciencesnatural language processingtext analysis
The REaltime DAta Synthesis and Analysis (REDASA) COVID-19 snapshot contains the output of the curation protocol produced by our curator community. A detailed description can be found in our paper. The first S3 bucket listed in Resources contains a large collection of medical documents in text format extracted from the CORD-19 dataset, plus other sources deemed relevant by the REDASA consortium. The second S3 bucket contains a series of documents surfaced by Amazon Kendra that were considered relevant for each medical question asked. The final S3 bucket contains the GroundTruth annotations cr...
bioinformaticsgenomiclife sciencestranscriptomics
The fragSTRUC project devises a software to extract RNA secondary structure information from Illumina datasets, based on divalent ions in standard RNA-seq library preparation fragmenting sequences at non-base-paired regions of RNA.
bioinformaticslife sciencesmetagenomicsmicrobiomereference index
krepp is an alignment-free method for estimating distances and phylogenetic placement of individual reads to many thousands of reference genomes in a scalable manner using k-mers. This dataset includes k-mer-based indexes consisting of ultra-large reference genome sets that can be efficiently analyzed using krepp.
genetichealthHomo sapienslife scienceslong read sequencingmappingvariant annotationvcfwhole genome sequencing
Reference data bundle for analyzing HiFi human whole genome sequencing data
bambioinformaticsbiologygeneticgenomicimaginglife scienceswhole genome sequencing
The Somatic Mosaicism across Human Tissues (SMaHT) project is an NIH Common Fund consortium (2023-) aimed to comprehensively characterize somatic variation ("mosaicism") in normal human tissues. While most genetic studies have relied on blood-derived DNA, SMaHT captures the full spectrum of DNA variation across cell types, tissues, and organs from phenotypically normal individuals to better understand the role of somatic mosaicism in human development, aging, and disease progression.Researchers in the consortium develop and apply experimental and computational methods, paired with th...
biodiversitybiologyecosystemsgeospatiallandlife sciencesnatural resourcesurvey
Archival soundscapes recorded in the rainforest landscapes of Central Africa, with a focus on the vocalizations of African forest elephants (Loxodonta cyclotis).
cancercomputational pathologycomputer visiondeep learninggrand-challenge.orghistopathologylife sciences
"This dataset contains the training data for the Tumor InfiltratinG lymphocytes in breast cancER or TIGER challenge. TIGER is the first challenge on fully automated assessment of tumor-infiltrating lymphocytes (TILs) in breast cancer histopathology slides. TILs are proving to be an important biomarker in cancer patients as they can play a part in killing tumor cells, particularly in some types of breast cancer. Identifying and measuring TILs can help to better target treatments, particularly immunotherapy, and may result in lower levels of other more aggressive treatments, including chemo...
Biohubbiologyencyclopedicgeneticgenomichealthlife sciencesmedicinesingle-cell transcriptomics
Tabula Sapiens is a benchmark, first-draft human cell atlas of over 1.1M cells from 28 organs of 24 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects, and allows detailed analysis and comparison of cell types that are shared between tissues. Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments. We...
bioinformaticsbiologygene expressiongenomicgenotypingHomo sapienslife sciencesmedicineneurobiologyneuroscienceRNA-seqsingle-cell transcriptomicstranscriptomics
The Mount Sinai PsychAD Study provides population-scale single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex of 1,494 postmortem brain donors. The study encompasses more than 6.3 million nuclei from individuals with neurodegenerative diseases, serious mental illnesses, and neurotypical controls. Represented conditions include Alzheimer's disease, Parkinson's disease, schizophrenia, bipolar disorder, diffuse Lewy body dementia, vascular dementia, and additional neurological and psychiatric disorders. The study also includes genotype, clinical, neuropathological, an...
bioinformaticsbiologychemistryenzymegraphlife sciencesmoleculeproteinRDFSPARQL
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium and host institutions EMBL-EBI, SIB Swiss Institute of Bioinformatics and PIR are committed to the long-term preservation of the UniProt databases.
bioinformaticsbiologydemographicsepigenomicsethnicitygene expressiongenomicgenotypingHomo sapienslife sciencesmedicineneurobiologyneuroscienceproteinRNA-seqsingle-cell transcriptomicstranscriptomicswhole genome sequencing
The Accelerating Medicines Partnership Alzheimer's Disease (AMP-AD) Diverse Cohorts Study is a cross-consortium project generating harmonized datasets from diverse human cohorts. It provides post-mortem multi-omic data from more than 850 individuals representing the spectrum of Alzheimer's disease phenotypes, with substantial representation of Black or African American and Hispanic or Latino individuals. Data were generated by research teams at Rush University, Emory University, Mayo Clinic, Columbia University, and the Icahn School of Medicine at Mount Sinai.
bamcramfastqgeneticgenomiclife sciencestranscriptomicswhole exome sequencingwhole genome sequencing
Aging is a major risk factor for neurodegenerative diseases, yet underlying epigenetic mechanisms remain unclear. Here, we generated a comprehensive single-nucleus cell atlas of brain aging across multiple brain regions, comprising 132,551 single-cell methylomes and 72,666 joint chromatin conformation-methylome nuclei. Integration with companion transcriptomic and chromatin accessibility data yielded a cross-modality taxonomy of 36 major cell types.
electrophysiologyimage processingimaginglife sciencesMus musculusneurobiologyneuroimagingsignal processing
The Allen Brain Observatory – Visual Coding is a large-scale, standardized survey of physiological activity across the mouse visual cortex, hippocampus, and thalamus. It includes datasets collected with both two-photon imaging and Neuropixels probes, two complementary techniques for measuring the activity of neurons in vivo. The two-photon imaging dataset features visually evoked calcium responses from GCaMP6-expressing neurons in a range of cortical layers, visual areas, and Cre lines. The Neuropixels dataset features spiking activity from distributed cortical and subcortical brain regions, c...
cancercomputational pathologycomputer visiondeep learningdigital pathologygrand-challenge.orghistopathologylife sciencesmachine learningmedical image computingmedical imaging
This dataset contains the training data for the CHIMERA - Combining HIstology, Medical imaging (radiology) and molEcular data for medical pRognosis and diAgnosis challenge. The CHIMERA Challenge aims to advance precision medicine in cancer care by addressing the critical need for multimodal data integration. Despite significant progress in AI, integrating transcriptomics, pathology, and radiology across clinical departments remains a complex challenge. Clinicians are faced with large, heterogeneous datasets that are difficult to analyze effectively. AI has the potential to unify multimodal dat...
amazon.sciencebioinformaticshealthlife sciencesnatural language processingus
DE-SynPUF is provided here as a 1,000 person (1k), 100,000 person (100k), and 2,300,000 persom (2.3m) data sets in the OMOP Common Data Model format. The DE-SynPUF was created with the goal of providing a realistic set of claims data in the public domain while providing the very highest degree of protection to the Medicare beneficiaries’ protected health information. The purposes of the DE-SynPUF are to:
bambioinformaticsbiologycoronavirusCOVID-19cramfastqgeneticgenomichealthlife sciencesMERSSARSSTRIDEStranscriptomicsviruswhole genome sequencing
This repository within the ACTIV TRACE initiative houses a comprehensive collection of datasets related to SARS-CoV-2. The processing of SARS-CoV-2 Sequence Read Archive (SRA) files has been optimized to identify genetic variations in viral samples. This information is then presented in the Variant Call Format (VCF). Each VCF file corresponds to the SRA parent-run's accession ID. Additionally, the data is available in the parquet format, making it easier to search and filter using the Amazon Athena Service. The SARS-CoV-2 Variant Calling Pipeline is designed to handle new data every six ho...
coronavirusCOVID-19life sciencesMERSSARS
Full-text and metadata dataset of COVID-19 and coronavirus-related research articles optimized for machine readability.
amino acidbioinformaticsbiomolecular modelinglife sciencesmolecular dynamicsproteinstructural biology
Co-managed by Toyoko and the Structural Biology Group at the Universidad Nacional de Quilmes, this dataset allows us to explore the conformational space of all possible peptides using the 20 common amino acids. It consists of a collection of exhaustive molecular dynamics simulations of tripeptides and pentapeptides.
biodiversitybioinformaticsconservationearth observationlife sciences
The Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure funded by the world's governments providing global data that document the occurrence of species. GBIF currently integrates datasets documenting over 1.6 billion species occurrences, growing daily. The GBIF occurrence dataset combines data from a wide array of sources including specimen-related data from natural history museums, observations from citizen science networks and environment recording schemes. While these data are constantly changing at GBIF.org, periodic snapshots are taken a...
cancergenomiclife sciencesSTRIDESwhole genome sequencing
The Human Cancer Models Initiative (HCMI) is an international consortium that is generating novel, next-generation, tumor-derived culture models annotated with genomic and clinical data. HCMI-developed models and related data are available as a community resource. The NCI is contributing to the initiative by supporting four Cancer Model Development Centers (CMDCs). CMDCs are tasked with producing next-generation cancer models from clinical samples. The cancer models include tumor types that are rare, originate from patients from underrepresented populations, lack precision therapy, or lack ca...
cramfast5fastqgeneticgenomiclife sciences
This dataset includes sequencing data, assemblies, and analyses for the offspring of ten parent-offspring trios.
life sciencesmagnetic resonance imagingneuroimagingneurosciencepediatric
Infant 3T/7T MRI precision imaging data, including raw BIDS, preprocessed Infant fMRIPrep derivatives, and XCP-D derivatives (N=6 highly sampled infant participants)
geneticgenome wide association studylife sciences
At the Knowledge Portal Network, we aggregate and analyze genetic association results for a wide range of diseases and traits. For any given disease, a large number of individual genetic association datasets may have been generated. To make these results more interpretable, we meta-analyze all datasets for each phenotype, using a method that we term "bottom-line integrative analysis". Here we provide the bottom-line summary statistic files for public download.
bambenchmarkbioinformaticscancerfastqlife scienceslong read sequencingshort read sequencingsingle-cell transcriptomicsvcf
LongBench is a comprehensive benchmark dataset of the latest long-read transcriptomics technologies from Oxford Nanopore (ON) and Pacific Biosciences, alongside a comparison with next-generation sequencing from Illumina. We generated bulk and single-cell libraries from lung cancer cell lines which include different cancer subtypes to capture real biological variation. To further compare and assess sequencing platform performance, Sequins and SIRVs (Set 4) synthetic spike-ins have been included.
geneticlife sciencesRNA-seqtranscriptomics
The NIH Sequence Read Archive (SRA), hosted by the [National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) stores sequencing data and alignment information from high-throughput next-generation sequencing platforms. SRA has conducted gene expression analysis of publicly released human and mouse RNA-Seq experiments to process raw RNA-seq reads into concise formats that summarize the expression results. The un-normalized feature counts for each SRA record are available in tab-delimited (*.tsv) format. The tsv files include two columns, the gene id and count...
biologycancercomputer visionhealthimage processingimaginglife sciencesmachine learningmagnetic resonance imagingmedical imagingmedicineneurobiologyneuroimagingsegmentation
This dataset contains 8,000+ brain MRIs of 2,000+ patients with brain metastases.
biodiversitybiologyclimatedigital preservationenvironmentalimage processingimaginglife sciences
Our collection encompasses approximately one million vascular plant specimens from the Mediterranean and Middle East biodiversity hotspot, representing flora from Israel, Jordan, Hermon, Sinai, Egypt, the Caucasus, Arabia, North Africa, and throughout the Mediterranean basin. This scientifically significant repository includes published voucher specimens, original specimens used for "Flora Palaestina" illustrations, and critical references for the Israeli gene bank collections. The ongoing digitization process captures high-resolution images of each specimen while systematically inco...
biodiversityclimatecoastalconservationecosystemsenvironmentalgeospatiallife sciencesoceanswater
This dataset provides access to species distribution models (SDMs) for marine species, initially developed as part of the MPA Europe project (https://mpaeurope.eu/). SDMs are statistical models used to predict the potential geographic distribution of a species based on the relationship between observed species occurrence records and environmental predictors. The models were built using marine occurrence data from the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF), together with environmental data from Bio-ORACLE v3.0 (Assis et al. 2024, DOI...
biodiversitybioinformaticsbiologyconservationgeneticgenomiclife sciencesmetagenomics
Minderoo Foundation OceanOmics aims to establish environmental DNA (eDNA) as a tool to measure, understand, and protect oceans. OceanOmics mainly generates two types of data: eDNA sequencing data (metabarcoding, metagenomics), and genome assembly data (marine vertebrates).
Homo sapiensimage processingimaginglife sciencesmagnetic resonance imagingsignal processing
OCMR is an open-access repository that provides multi-coil k-space data for cardiac cine. The fully sampled MRI datasets are intended for quantitative comparison and evaluation of image reconstruction methods. The free-breathing, prospectively undersampled datasets are intended to evaluate their performance and generalizability qualitatively.
biologyimaginglife sciencesneurobiologyneuroimagingneuroscience
OpenNeuro is a database of openly-available brain imaging data. The data are shared according to a Creative Commons CC0 license, providing a broad range of brain imaging data to researchers and citizen scientists alike. The database primarily focuses on functional magnetic resonance imaging (fMRI) data, but also includes other imaging modalities including structural and diffusion MRI, electroencephalography (EEG), and magnetoencephalograpy (MEG). OpenfMRI is a project of the Center for Reproducible Neuroscience at Stanford University. Development of the OpenNeuro resource has been funded by th...
biodiversitybiologycoastalconservationdeep learningecosystemsenvironmentalgeospatiallabeledlife sciencesmachine learningmappingoceansopen source softwaresignal processing
Live-streamed and archived audio data (~2018-present) from underwater microphones (hydrophones) containing marine biological signals as well as ambient ocean noise. Hydrophone placement and passive acoustic monitoring effort prioritizes detection of orca sounds (calls, clicks, whistles) and potentially harmful noise. Geographic focus is on the US/Canada critical habitat of Southern Resident killer whales (northern CA to central BC) with initial focus on inland waters of WA. In addition to the raw lossy or lossless compressed data, we provide a growing archive of annotated bioacoustic bouts.
bioinformaticsbiologyfast5fastqgenomicHomo sapienslife scienceswhole genome sequencing
The ont-open-data registry provides reference sequencing data from Oxford Nanopore Technologies to support, 1) Exploration of the characteristics of nanopore sequence data. 2) Assessment and reproduction of performance benchmarks 3) Development of tools and methods. The data deposited showcases DNA sequences from a representative subset of sequencing chemistries. The datasets correspond to publicly-available reference samples (e.g. Genome In A Bottle reference cell lines). Raw data are provided with metadata and scripts to describe sample and data provenance.
computed tomographycomputer visioncsvlabeledlife sciencesmachine learningmedical image computingmedical imagingradiologyx-ray tomography
Blunt force abdominal trauma is among the most common types of traumatic injury, with the most frequent cause being motor vehicle accidents. Abdominal trauma may result in damage and internal bleeding of the internal organs, including the liver, spleen, kidneys, and bowel. Detection and classification of injuries are key to effective treatment and favorable outcomes. A large proportion of patients with abdominal trauma require urgent surgery. Abdominal trauma often cannot be diagnosed clinically by physical exam, patient symptoms, or laboratory tests. Prompt diagnosis of abdominal trauma using...
computed tomographycomputer visioncsvlabeledlife sciencesmachine learningmedical image computingmedical imagingradiologyx-ray tomography
Blunt force abdominal trauma is among the most common types of traumatic injury, with the most frequent cause being motor vehicle accidents. Abdominal trauma may result in damage and internal bleeding of the internal organs, including the liver, spleen, kidneys, and bowel. Detection and classification of injuries are key to effective treatment and favorable outcomes. A large proportion of patients with abdominal trauma require urgent surgery. Abdominal trauma often cannot be diagnosed clinically by physical exam, patient symptoms, or laboratory tests. Prompt diagnosis of abdominal trauma using...
computed tomographycomputer visioncsvlabeledlife sciencesmachine learningmedical image computingmedical imagingradiologyx-ray tomography
Over 1.5 million spine fractures occur annually in the United States alone resulting in over 17,730 spinal cord injuries annually. The most common site of spine fracture is the cervical spine. There has been a rise in the incidence of spinal fractures in the elderly and in this population, fractures can be more difficult to detect on imaging due to degenerative disease and osteoporosis. Imaging diagnosis of adult spine fractures is now almost exclusively performed with computed tomography (CT). Quickly detecting and determining the location of any vertebral fractures is essential to prevent ne...
computer visioncsvlabeledlife sciencesmachine learningmedical image computingmedical imagingradiology
The Radiological Society of North America Intracranial Aneurysm Detection (RSNA-ICA) dataset is a collection of over 4,000 CT brain scans annotated by a cohort of over 40 volunteer radiologists from RSNA and the American Society of Neuroradiology to show the presence and location of intracranial aneurysms. It also includes a set of about 200 imaging studies that are annotated with AI-generated segmentations highlighting abnormalities. The imaging data was provided by 18 institutions. Initially compiled in 2025 for the RSNA Intracranial Aneurysm Detection AI Challenge hosted on Kaggle competiti...
computed tomographycomputer visioncsvlabeledlife sciencesmachine learningmedical image computingmedical imagingradiologyx-ray tomography
RSNA assembled this dataset in 2019 for the RSNA Intracranial Hemorrhage Detection AI Challenge (https://www.kaggle.com/c/rsna-intracranial-hemorrhage-detection/). De-identified head CT studies were provided by four research institutions. A group of over 60 volunteer expert radiologists recruited by RSNA and the American Society of Neuroradiology labeled over 25,000 exams for the presence and subtype classification of acute intracranial hemorrhage.
computer visioncsvlabeledlife sciencesmachine learningmedical image computingmedical imagingradiology
The Radiological Society of North America Lumbar Spine Degenerative Classification dataset (RSNA-LSDD) is a collection of over 2,600 magnetic resonance imaging (MR) scans of the lumbar spine annotated by a cohort of about 60 volunteer radiologists recruited by the RSNA, the American Society for Spine Radiology and the American Society of Neuroradiology to identify the location and severity of five degenerative conditions across the five intervertebral disc levels (L1/L2, L2/L3, L3/L4, L4/L5, and L5/S1). The imaging data, comprising over 8,500 image series (Sagittal “T2”, Axial T2 and Sagittal ...
computed tomographycomputer visioncsvlabeledlife sciencesmachine learningmedical image computingmedical imagingradiologyx-ray tomography
RSNA assembled this dataset in 2020 for the RSNA STR Pulmonary Embolism Detection AI Challenge (https://www.kaggle.com/c/rsna-str-pulmonary-embolism-detection/). With more than 12,000 CT pulmonary angiography (CTPA) studies contributed by five international research centers, it is the largest publicly available annotated PE dataset. RSNA collaborated with the Society of Thoracic Radiology to recruit more than 80 expert thoracic radiologists who labeled the dataset with detailed clinical annotations.
biologycell biologycell imagingepigenomicsgene expressionhistopathologyHomo sapiensimaginglife sciencesmedicinemicroscopyneurobiologyneurosciencesingle-cell transcriptomicstranscriptomics
The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) consortium strives to gain a deep molecular and cellular understanding of the early pathogenesis of Alzheimer's disease and is funded by the National Institutes on Aging (NIA U19AG060909). The SEA-AD datasets available here comprise single cell profiling (transcriptomics and epigenomics) and quantitative neuropathology. To explore gene expression and chromatin accessibility information, the single-cell profiling data includes: snRNAseq and snATAC-seq data from the SEA-AD donor cohort (aged brains which span the spectrum of Alzhe...
bioinformaticsbiologycell biologyepigenomicsgene expressiongenomicgenotypingHomo sapienslife sciencesmedicineneurobiologyneurosciencesingle-cell transcriptomicstranscriptomics
The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) study provides transcriptomic and chromatin accessibility data from single nuclei isolated from postmortem brain tissue from individuals spanning the Alzheimer's disease spectrum. The study supports investigation of cellular and molecular changes associated with Alzheimer's disease progression and includes data generated as part of the broader SEA-AD effort to characterize brain cell types, disease-associated cellular states, and related neuropathology.
life sciencesproteinsingle-cell transcriptomics
Comprehensive, large-scale single-cell profiling of healthy human blood at different ages is one of the critical pending tasks required to establish a framework for systematic understanding of human aging. Here, using single-cell RNA/TCR/BCR-seq with protein feature barcoding (20 antibodies), we profiled 317 samples from 166 healthy individuals aged 25 to 85 years old drawn over 3-year period. Dataset spanning ~2 million cells describes 50 subpopulations of blood immune cells, with 14 subpopulations changing with age, including a novel NKG2C+ CD8 Tcm population that decreases with age. We desc...
bioinformaticscsvdicomgenomichealthimaginglife sciencesmedicine
This is a synthetic data set that includes FHIR resources, DICOM images, genomic data, physiological data (i.e., ECGs), and simple clinical notes. FHIR links all the data types together.
Biohubbiologyencyclopedicgenomichealthlife sciencesmedicine
Tabula Muris is a compendium of single cell transcriptomic data from the model organism Mus musculus comprising more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations, and allow for direct and controlled comparison of gene expression in cell types shared between tissues, such as T-lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3’-end counting, enabled the s...
Biohubbiologyencyclopedicgenomichealthlife sciencesmedicinesingle-cell transcriptomics
Tabula Muris Senis is a comprehensive compendium of single cell transcriptomic data from the model organism Mus musculus comprising more than 500,000 cells from 18 organs and tissues across the mouse lifespan. We discovered cell-specific changes occurring across multiple cell types and organs, as well as age related changes in the cellular composition of different organs. Using single-cell transcriptomic data we were able to assess cell type specific manifestations of different hallmarks of aging, such as senescence, changes in the activity of metabolic pathways, depletion of stem-cell populat...
bioinformaticsbiologyepigenomicsgene expressionHomo sapienslife sciencesmedicineneurobiologyneuroscienceRNA-seqsingle-cell transcriptomicstranscriptomics
The MIT ROSMAP Single-Nucleus Multiomics Study provides single-nucleus transcriptomic and chromatin accessibility data generated from postmortem brain tissue from participants in the Religious Orders Study and Rush Memory and Aging Project (ROSMAP). The study includes single-nucleus RNA sequencing, single-nucleus ATAC sequencing, and paired multiome data from 427 prefrontal cortex samples, as well as single-nucleus RNA sequencing data from multiple brain regions. These data support investigation of cell-type-specific molecular changes, cellular vulnerability, cognitive resilience, and Alzheime...
bioinformaticsbiologygeneticgenomiclife sciences
The UCSC Genome Browser is an online graphical viewer for genomes, a genome browser, hosted by the University of California, Santa Cruz (UCSC). The interactive website offers access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. This dataset is a copy of the MySQL tables in MyISAM binary and tab-sep format and all binary files in custom formats, sometimes referred as 'gbdb'-files. Data from the UCSC Genome Browser is free and open for use by anyone. However, every genome...
brain imagescancerlife sciencesmagnetic resonance imagingmedical imagingmedicineneuroimagingradiology
This BIDS-formatted dataset provides multimodal brain MRI data from 150 patients with primary central nervous system lymphoma (PCNSL), including T1-weighted, contrast-enhanced T1-weighted, FLAIR, and ADC sequences. The dataset includes expert-annotated lesion segmentations with radiomic features, along with anonymized clinical data including demographics, diagnosis history, and medications.
genome wide association studylife sciencespopulation genetics
The UKB-PPP is a collaboration between the UK Biobank (UKB) and thirteen biopharmaceutical companies characterising the plasma proteomic profiles of 54,219 UKB participants. As part of a collaborative analysis across the thirteen UKB-PPP partners, we conducted comprehensive protein quantitative trait loci (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 85% are newly discovered, in addition to ancestry-specific pQTL mapping in non-Europeans. We identify independent secondary associations in 87% of cis and 30% of trans loci, expanding the catalogue ...
biologyhealthlife sciencesmedicinesignal processing
VitalDB, a high-fidelity multi-parameter vital signs database in surgical patients.
biologychemical biologylife sciencesmolecular dockingpharmaceuticalprotein
3D models for molecular docking screens.
autism spectrum disorderbamgeneticgenomiclife sciencesvcfwhole genome sequencing
iHART is the Hartwell Foundation’s Autism Research and Technology Initiative. This release contains whole genome data from over 1000 families with 2 or more children with autism, of which biomaterials were provided by the Autism Genetic Resource Exchange (AGRE).
bioinformaticsbiologycancercsvgene expressiongeneticgenomicHomo sapienslife sciencesMus musculusneurosciencetranscriptomics
recount3 is an online resource consisting of RNA-seq gene, exon, and exon-exon junction counts as well as coverage bigWig files for 8,679 and 10,088 different studies for human and mouse respectively. It is the third generation of the ReCount project and part of recount.bio. recount2 is also included for historical purposes. The pipeline used to generate the data in recount3 (but not recount2) is available here.
healthlife sciencesmedicine
In collaboration with the IEEE Conference on Biomedical and Health Informatics (BHI) 2018 and the IEEE Conference on Body Sensor Networks (BSN), we are hosting a challenge to explore real clinical questions in critically ill patients using the MIMIC-III database. Participants in the challenge will be invited to present at the BHI & BSN Annual Conference in Las Vegas, USA (4-7 March 2018): https://bhi-bsn.embs.org/2018/
healthlife sciencesmedicine
We introduce here the Research CardioVascular SIMulator (RCVSIM) software in order to complement research with the experimental data sets provided by PhysioBank. The human cardiovascular model upon which RCVSIM is based includes three major components. The first component is a lumped parameter model of the pulsatile heart and circulation. The second component is a short-term regulatory system model which includes an arterial baroreflex system, a cardiopulmonary baroreflex system, and a direct neural coupling mechanism between respiration and heart rate.
healthlife sciencesmedicine
The pattern electroretinogram (PERG) is a valuable tool in ophthalmic electrophysiology, offering a non-invasive and objective method to evaluate central retinal function. By measuring electrical activity in the macula and retinal ganglion cells, PERG provides essential quantitative insights, especially when distinguishing between macular and optic nerve diseases remains challenging. This dataset comprises 1354 transient PERG responses from 304 subjects in 336 records, representing a comprehensive collection of ocular electrophysiological data. The evaluations took place at the Institute of Ap...
healthlife sciencesmedicine
We introduce a cost-effective public health analysis solution for low- and middle-income countries—the Multi-Modal Satellite Imagery Dataset in Colombia. By leveraging high-quality, spatiotemporally aligned satellite images and corresponding metadata, the dataset integrates economic, demographic, meteorological, and epidemiological data. Employing a single forwards and a forward-backward technique ensures clear satellite images with minimal cloud cover for every epi-week, significantly enhancing overall data quality. The extraction process utilizes the satellite extractor package powered by th...
healthlife sciencesmedicine
In this project, we collected in-bed posture pressure data from multiple adult participants using two different types of pressure sensing mats. To the best of our knowledge, our dataset, PmatData is the first publicly-available dataset of pressure sensor data which includes various sleeping postures. PmatData contains pressure data from two separate experiments.
healthlife sciencesmedicine
Preliminary datasets containing skin conductance recordings where experiments involve artificial stimuli are available online. However, recordings of a longer duration acquired during real-world cognitive stressors are lacking significantly. This dataset seeks to bridge the gap between a body of knowledge concerning the human stress response primarily built up on laboratory acquired data, and how people’s skin conductance fluctuates in reality when they undergo a stressful exam experience. The data contains electrodermal activity, heart rate, blood volume pulse, skin surface temperature, inter...
healthlife sciencesmedicine
This newly inaugurated research database for 12-lead electrocardiogram (ECG) signals was created under the auspices of Chapman University, Shaoxing People’s Hospital (Shaoxing Hospital Zhejiang University School of Medicine), and Ningbo First Hospital. It aims to enable the scientific community in conducting new studies on arrhythmia and other cardiovascular conditions. Certain types of arrhythmias, such as atrial fibrillation, have a pronounced negative impact on public health, quality of life, and medical expenditures. As a non-invasive test, ECG is a major and vital diagnostic tool for dete...
healthlife sciencesmedicine
Gait and posture analysis while using assisting robotic devices is of utmost importance to attain effective assistance. This work provides a multi-camera, multimodal, and detailed dataset for vision-based applications using a wheeled robotic walker equipped with a pair of affordable cameras. Depth data was acquired at 30 fps from a total of 14 healthy participants walking at 3 different gait speeds, across 3 different walking scenarios/paths at 3 different locations. Simultaneously, accurate skeleton joint data was recorded using an inertial-based commercial motion capture system that provides...
healthlife sciencesmedicine
Gait is a fundamental motor function, and its analysis is essential for understanding locomotor control, rehabilitation, and the early detection of neurological and musculoskeletal disorders. While many datasets capture either biomechanical or neural aspects of gait, publicly available multimodal datasets that integrate brain, muscle, kinematic, and ground reaction force recordings remain scarce. This limitation restricts advances in modeling neuromechanical interactions and the development of machine learning approaches for gait classification and rehabilitation technologies. To address this ...
healthlife sciencesmedicine
Detecting the presence of chaos in a dynamical system is an important problem that is solved by measuring the largest Lyapunov exponent. Lyapunov exponents quantify the exponential divergence of initially close state-space trajectories and estimate the amount of chaos in a system.
healthlife sciencesmedicine
The 2017 PhysioNet/CinC Challenge aims to encourage the development of algorithms to classify, from a single short ECG lead recording (between 30 s and 60 s in length), whether the recording shows normal sinus rhythm, atrial fibrillation (AF), an alternative rhythm, or is too noisy to be classified.
healthlife sciencesmedicine
This database of two-channel ECG recordings has been created for use in the Computers in Cardiology Challenge 2004, an open competition with the goal of developing automated methods for predicting spontaneous termination of atrial fibrillation (AF).
healthlife sciencesmedicine
AFVP generates a synthesized beat-to-beat interval sequence of ventricular excitations with a realistic structure observed during AF.
healthlife sciencesmedicine
The files available here are not part of the AHA Database. The 0001.* and 0201.* files have been derived from a sample given to us in 1980 by the creators of the AHA Database. The original recording had been a candidate for inclusion in the database and was digitized and annotated using the same methods used for the AHA Database records. After the annotation process was complete, the recording was excluded from the AHA Database since it was found to contain ectopy of a higher grade than the class for which it had been chosen as a candidate.
healthlife sciencesmedicine
The files in this set can be used for testing a variety of devices that monitor the electrocardiogram. The recordings include both synthetic and real waveforms.
healthlife sciencesmedicine
The research material included in the Abdominal and Direct Fetal Electrocardiogram Database contains multichannel fetal electrocardiogram (FECG) recordings obtained from 5 different women in labor, between 38 and 41 weeks of gestation. The recordings were acquired in the Department of Obstetrics at the Medical University of Silesia, by means of the KOMPOREL system for acquisition and analysis of fetal electrocardiogram (ITAM Institute, Zabrze, Poland). Each recording comprises four differential signals acquired from maternal abdomen and the reference direct fetal electrocardiogram registered f...
healthlife sciencesmedicine
The analysis and identification of abnormal ventricular potentials (AVPs) in intracardiac electrograms (EGMs) are paramount in radiofrequency catheter ablation (RFCA) of post-ischemic ventricular tachycardia (VT). The ARGO dataset represents the first open-access dataset of post-ischemic VT EGMs featuring invasive and noninvasive electrophysiological recordings, as well as electroanatomical (EA) map data, including data annotation by three expert electrophysiologists and their final consensus. The dataset includes unipolar and bipolar EGMs, 12-lead surface ECGs, and EA maps, for a total of 196...
healthlife sciencesmedicine
Hilbert Transform based Sleep Apnea Detection using a Single Lead Electrocardiogram.
healthlife sciencesmedicine
The data consist of 70 records, divided into a learning set of 35 records (a01 through a20, b01 through b05, and c01 through c10), and a test set of 35 records (x01 through x35), all of which may be downloaded from this page. Recordings vary in length from slightly less than 7 hours to nearly 10 hours each. Each recording includes a continuous digitized ECG signal, a set of apnea annotations (derived by human experts on the basis of simultaneously recorded respiration and related signals), and a set of machine-generated QRS annotations (in which all beats regardless of type have been labeled n...
healthlife sciencesmedicine
This data set consists of over 240 two-minute EEG recordings obtained from 20 volunteers. Resting-state and auditory stimuli experiments are included in the data. The goal is to develop an EEG-based Biometric system. The data includes resting-state EEG signals in both cases: eyes open and eyes closed. The auditory stimuli part consists of six experiments; Three with in-ear auditory stimuli and another three with bone-conducting auditory stimuli. The three stimuli for each case are a native song, a non-native song, and neutral music.
biodiversitybiologyconservationgeneticgenomiclife sciencestranscriptomicswildlife
Australasian Genomes is the genomic data repository for the Threatened Species Initiative (TSI) and the ARC Centre for Innovations in Peptide and Protein Science (CIPPS). This repository contains reference genomes, transcriptomes, resequenced genomes and reduced representation sequencing data from Australasian species. Australasian Genomes is managed by the Australasian Wildlife Genomics Group (AWGG) at the University of Sydney on behalf of our collaborators within TSI and CIPPS.
healthlife sciencesmedicine
Pacing artifacts in electrocardiogram (ECG) signals can interfere with accurate waveform analysis, making their detection and removal essential for reliable interpretation. We present an algorithm and provide MATLAB code to detect and remove pacing artifacts from raw digital 12-lead ECG recordings. The algorithm was developed using the Chronic Renal Insufficiency Cohort (CRIC) data, which includes 493 paced ECGs, and validated on an external dataset (273 paced ECGs). A graphical user interface (GUI) was designed to allow user-friendly quality control of automated algorithm performance. Users c...
healthlife sciencesmedicine
Autonomic function regulating blood pressure and cardiac rhythm progressively declines with increasing age. Impaired cardiovascular control promotes a variety of age-related conditions such as dementia, or Alzheimer’s disease. This study aims to provide a database of high-resolution biological signals to describe the effect of healthy aging on cardiovascular regulation. Electrocardiogram and continuous non-invasive blood pressure signals were recorded simultaneously at rest in 1,121 healthy volunteers.
healthlife sciencesmedicine
This database includes long-term ECG recordings from 15 subjects (11 men, aged 22 to 71, and 4 women, aged 54 to 63) with severe congestive heart failure (NYHA class 3–4). This group of subjects was part of a larger study group receiving conventional medical therapy prior to receiving the oral inotropic agent, milrinone.
healthlife sciencesmedicine
This study aimed to determine the feasibility and effectiveness of wearable devices in detecting early physiological changes prior to the development of prediabetes [1-3]. The study generated digital biomarkers for remote, mHealth-based prediabetes and hyperglycemia risk to classify which individuals should undergo further clinical testing. The primary inclusion criteria were subjects aged 35-65 years, inclusive, including only post-menopausal females, with a point of care A1C measurement between 5.2-6.4%, inclusive. Blood was collected during the study for measurement of glucose, hemoglobin A...
life sciencesmagnetic resonance imagingneuroimagingneuroscienceniftipediatricsegmentation
Manually curated and reviewed infant brain segmentations and accompanying T1w and T2w images for a range of 1-9 month old participants from the Baby Connectome Project (BCP)
bioinformaticschemistrylife sciencesmolecular dockingmoleculeproteinstructural biology
BioLiP is a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions. The structure data are collected primarily from the Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. BioLiP aims to construct the most comprehensive and accurate database for serving the needs of ligand-protein docking, virtual ligand screening and protein function annotation.
healthlife sciencesmedicine
This database contains continuous blood pressure recordings for 9 Dahl SS rats and 6 Dahl SS.13BN rats, under high and low salt conditions.
healthlife sciencesmedicine
The increased likelihood of falls as a consequence of aging or disease is generally associated with rising levels of body sway during stance. The use of virtual reality (VR) for studying the role in vision in regulating body sway is well established, however the extent to which music incorporated into a virtual environment can influence sway is not understood. This dataset was collected as part of a study to explore the hypothesis that music manipulated to match VR motion provided by an Oculus Rift head mounted display can lead to increased levels of body sway. Twenty-eight subjects stood for ...
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
This collection unifies multiple brain datasets spanning critical care, sleep medicine, cardiopulmonary health, infectious diseases, and other aspects of clinical neuroscience. It includes a variety of types of clinical neuroscience data including electroencephalography (EEG) and polysomnography (PSG) recordings, and supporting data to enable research in diverse areas of clinical neuroscience such as epilepsy, delirium, coma, and sleep medicine. All data is de-identified and includes code to reproduce results in accompanying research publications. The data is available for non-commercial resea...
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
This collection unifies multiple brain datasets spanning critical care, sleep medicine, cardiopulmonary health, infectious diseases, and other aspects of clinical neuroscience. It includes large-scale electroencephalography (EEG) and polysomnography (PSG) recordings, brain imaging data (MRI, CT, PET), and supporting data to enable research in diverse areas of clinical neuroscience such as epilepsy, delirium, coma, sleep depth, sleep-related breathing disorders, meditation, subarachnoid hemorrhage, cardiac arrest, neuroinfectious diseases, and audiology. All data is de-identified and includes a...
bioinformaticsdeep learninglife sciencesmachine learningmedicineneurophysiologyneuroscience
This collection unifies multiple brain datasets spanning critical care, sleep medicine, cardiopulmonary health, infectious diseases, and other aspects of clinical neuroscience. It includes large-scale electroencephalography (EEG) and polysomnography (PSG) recordings, brain imaging data (MRI, CT, PET), and electronic health records (EHR) data supporting research in areas such as epilepsy, delirium, coma, sleep depth, sleep-related breathing disorders, burst suppression, meditation, subarachnoid hemorrhage, cardiac arrest, and neuroinfectious diseases. All data is de-identified and includes algo...
healthlife sciencesmedicine
BHX is a public available dataset with bounding box annotations for 5 types of acute hemorrhage as an extension of the qure.ai CQ500 dataset. This dataset intends to provide data resources to help advance hemorrhage detection towards machine learning localization tasks. Key Points: BHX contains up to 39,668 bounding boxes in 23,409 images annotated for hemorrhage, out of a total of ~170k images from qure.ai CQ500 dataset. The dataset was built through an efficient method to obtain automatic annotated images (thin slices) from sparse initial labeling (thick slices). We hope this dataset can con...
healthlife sciencesmedicine
BUT QDB is a database created by the cardiology team at the Department of Biomedical Engineering, Brno University of Technology, for the purpose of evaluating ECG quality. The data comprises 18 long-term recordings of single-lead ECGs and associated 3-axis accelerometer data, collected from 15 subjects (9 female, 6 male) aged between 21 to 83 years. Recordings were carried out between August 2018 and October 2019 while the subjects were undertaking ordinary everyday activities ("free-living conditions"). Data was collected using a mobile ECG and accelerometer (Bittium Faros 180) with...
healthlife sciencesmedicine
Brno University of Technology ECG Signal Database with Annotations of P Wave (BUT PDB) is an ECG signal database with marked peaks of P waves created by the cardiology team at the Department of Biomedical Engineering, Brno University of Technology. The database consists of 50 2-minute 2-lead ECG signal records with various types of pathology. The ECGs were selected from three existing databases of ECG signal - the MIT-BIH Arrhythmia Database, the MIT-BIH Supraventricular Arrhythmia Database, and the Long Term AF Database. The P waves positions were manually annotated by two ECG experts in all ...
healthlife sciencesmedicine
Brno University of Technology Smartphone PPG Database (BUT PPG) is a database created by the cardiology team at the Department of Biomedical Engineering, Brno University of Technology, for the purpose of evaluating PPG quality and estimation of heart rate (HR). The data comprises 3,888 10-second recordings of PPGs and associated ECG signals used for determination of reference HR. All of the signals contain QRS complex positions, most signals contain moreover accelerometric data (ACC), and single-value annotations of blood pressure, blood oxygen saturation and glycaemia. The data were collected...
healthlife sciencesmedicine
We present a novel dataset of 12-lead electrocardiogram (ECG) recordings developed to support the study and classification of Brugada syndrome, a rare but potentially fatal cardiac arrhythmia. The data were collected retrospectively from patients evaluated at the Cardiology Department of the Hospital Universitario Central de Asturias (HUCA) and reviewed by clinical experts. Diagnostic labels were assigned according to internationally accepted criteria. The dataset comprises 363 subjects in total, including 76 patients diagnosed with Brugada syndrome and 287 healthy control subjects. Each recor...
healthlife sciencesmedicine
The CAP Sleep Database is a collection of 108 polysomnographic recordings registered at the Sleep Disorders Center of the Ospedale Maggiore of Parma, Italy. The waveforms (contained in the .edf files of the database) include at least 3 EEG channels (F3 or F4, C3 or C4 and O1 or O2, referred to A1 or A2), EOG (2 channels), EMG of the submentalis muscle, bilateral anterior tibial EMG, respiration signals (airflow, abdominal and thoracic effort and SaO2) and EKG. Additional traces include EEG bipolar traces, according to the 10-20 international system (Fp1-F3, F3-C3, C3-P3, P3-O1 and/or Fp2-F4, F...
healthlife sciencesmedicine
The Cardiac Arrhythmia Suppression Trial (CAST) was a landmark NHLBI-sponsored study designed to test the hypothesis that the suppression of asymptomatic or mildly symptomatic ventricular premature complexes (PVCs) in survivors of myocardial infarction (MI) would decrease the number of deaths from ventricular arrhythmias and improve survival. Enrollment required an acute MI within the preceding 2 years and 6 or more PVCs per hour during a pre-treatment (qualifying) long-term ECG (Holter) recording. Those subjects enrolled within 90 days of the index MI were required to have left ventricular ej...
healthlife sciencesmedicine
We present CGMacros, a dataset containing multimodal information from two continuous glucose monitors (CGM), food macronutrients, food photographs, and physical activity, in addition to anonymized participant demographics, anthropometric measurements and health parameters from blood analyses and gut microbiome profiles. CGMacros contains data from 45 study participants (15 healthy adults, 16 with pre-diabetes, and 14 with Type 2 diabetes) who consumed meals with varying and known macronutrient compositions in a free-living setting for ten consecutive days. To our knowledge, this is the first d...
healthlife sciencesmedicine
The CHARIS database contains multi-channel recordings of ECG, arterial blood pressure (ABP), and intracranial pressure (ICP) of patients diagnosed with traumatic brain injury (TBI). The data is contributed by members of the CHARIS project which aims to systematize the analysis of relevant physiological signals, and create data-driven algorithms to search for potential predictors of acute clinical events for patients with acute brain injury.
healthlife sciencesmedicine
This database, collected at the Children’s Hospital Boston, consists of EEG recordings from pediatric subjects with intractable seizures. Subjects were monitored for up to several days following withdrawal of anti-seizure medication in order to characterize their seizures and assess their candidacy for surgical intervention. The recordings are grouped into 23 cases and were collected from 22 subjects (5 males, ages 3–22; and 17 females, ages 1.5–19).
bioinformaticsbiologycoronavirusCOVID-19life sciencesmolecular dockingpharmaceutical
Aggregating critical information to accelerate drug discovery for the molecular modeling and simulation community. A community-driven data repository and curation service for molecular structures, models, therapeutics, and simulations related to computational research related to therapeutic opportunities for COVID-19 (caused by the SARS-CoV-2 coronavirus).
healthlife sciencesmedicine
A pressure and flow dataset for CPAP (continuous positive airway pressure) breathing obtained from 30 subjects for model-based identification of patient-specific lung mechanics using a specially designed sensor system comprising an array of differential pressure sensors (Sensirion AG SDP816-125PA) and gauge pressure sensors (NXP MPVZ4006GW7U). Relevant medical information was collected using a questionnaire, including: sex; age; weight; height; smoking history; and history of asthma. Subjects were tasked with breathing at five different rates (including passive) from very slow to very fast bre...
healthlife sciencesmedicine
This database, from the Czech Technical University (CTU) in Prague and the University Hospital in Brno (UHB), contains 552 cardiotocography (CTG) recordings, which were carefully selected from 9164 recordings collected between 2010 and 2012 at UHB.
healthlife sciencesmedicine
This database includes 35 eight-minute ECG recordings of human subjects who experienced episodes of sustained ventricular tachycardia, ventricular flutter, and ventricular fibrillation.
healthlife sciencesmedicine
The Concept Unique Identifier (CUI)-less database contains a corpus of "CUI-less" concepts taken from the SemEval2015 Task 14 that have been assigned CUIs. The annotation process allows assignment of CUIS from any Unified Medical Language System (UMLS) semantic group and compositional normalization using more than one CUI per disease entity. Concepts are mapped to SNOMED CT as represented in the September 2016 version found in Unified Medical Language System (UMLS) 2016AB.
healthlife sciencesmedicine
CVSim is a lumped-parameter model of the human cardiovascular system that has been developed and used for research and for teaching quantitative physiology courses at MIT and Harvard Medical School since 1984. The versions presented here have a graphical user interface implemented in Java, with computational components in C.
healthlife sciencesmedicine
The present database is an ensemble of cardiorespiratory measurements acquired during 18 cycloergometer maximal graded exercise tests performed in the "Adaptation, Climat Tropical, Exercice et Santé" (ACTES) laboratory of the French West Indies University. Data correspond to heart R-wave to R-wave intervals, Oxygen consumption, and mechanical power output on a beat-to-beat basis recorded all along the graded exercise test sessions. Participants are 18 teenagers athletes (15.2±2 years) from the Regional Physical and Sports Education Centre (CREPS) of French West Indies (Guadeloupe, Fr...
bioinformaticsgenomiclife sciencesspatial omicsspatial transcriptomics
Cross-Platform Repository for High-resolution Spatial Transcriptomics Datasets.
healthlife sciencesmedicine
Acute Brain injury (ABI) is a devastating event requiring intensive acute treatment and post-injury rehabilitation, both delivered for indeterminate periods of time. For severe ABIs, acute treatment is aimed at stabilizing the patient to prevent secondary brain injury from ischemia and swelling. This requires a balance between adequate levels of cerebral blood flow and safely low intracranial pressure (ICP) - a task normally done by autoregulatory (AR) processes of the brain. In the absence of normal AR, hemodynamic stability is difficult to maintain because there are no reliable predictors to...
healthlife sciencesmedicine
This observational study evaluated the effects of type 2 diabetes on cerebral vasoregulation and functional outcomes, measured by blood flow responses to hypocapnia and hypercapnia, Valsalva maneuver, head-up tilt, and sit-to-stand test. This dataset contains 37 diabetic participants and 49 controls (aged 55 to 75 years) with continuous measurements of cerebral blood flow using transcranial Doppler and MRI, heart rate, blood pressure, and respiratory parameters, balance, walking, laboratory and retinopathy measures.
healthlife sciencesmedicine
This database contains multimodal data from a large study investigating the effects of ischemic stroke on cerebral vasoregulation. The cross sectional study compared 60 subjects who suffered strokes, to 60 control subjects, collecting the following data for each patient across multiple days: transcranial doppler of cerebral arteries, 24-h blood pressure numerics, high resolution waveforms (ECG, blood pressure, CO2 and respiration) during various movement tasks, 24-h ECG, EMG, and accelerometer recordings, and gait pressure recordings during a walking test.
healthlife sciencesmedicine
This dataset was collected as part of a prospective observational study to evaluate the effects of type 2 diabetes mellitus (DM) on cerebral vasoregulation, perfusion and functional outcomes, measured by blood flow responses to hypocapnia and hypercapnia, Valsalva maneuver, head-up tilt, and sit-to-stand test. The dataset comprises of observations from 69 diabetic and control participants (aged 55 to 75 years) with continuous measurements of cerebral blood flow using transcranial Doppler and MRI (magnetic resonance imaging), heart rate, blood pressure, and respiratory parameters, balance, walk...
healthlife sciencesmedicine
ECG effects of ranolazine, verapamil, lopinavir+ritonavir, chloroquine, dofetilide, diltiazem, and dofetilide+diltiazem in a small sample size clinical study. The ECGCIPA database contains multi-channel ECG recordings of 60 subjects participating in the CiPA ECG validation study.
healthlife sciencesmedicine
The 2016 PhysioNet/CinC Challenge aims to encourage the development of algorithms to classify heart sound recordings collected from a variety of clinical or nonclinical (such as in-home visits) environments. The aim is to identify, from a single short recording (10-60s) from a single precordial location, whether the subject of the recording should be referred on for an expert diagnosis.
life sciencesmachine learningmedical imagingmedicine
Generic Clinical Ultrasound Data from Random Subjects acquired for Clinical Reasons, to be used for Developing Artificial Intelligence Applications. This dataset is complete with 2000 studies from 2000 subjects (one third each from abdominal, cardiac, and OB/GYN cases)
healthlife sciencesmedicine
The CogWear database consists of two datasets: pilot and survey gamification experiment. The pilot dataset includes physiological signals from 11 volunteers captured by three wearable devices (Empatica E4 watch, Samsung Galaxy Watch4 and Muse S EEG headband) during cognitively demanding task (Stroop test) and baseline condition (no engagement in any activity). The pilot dataset was collected to evaluate the experimental setup and the signal captured by the wearables. In particular, can we detect when people perform a cognitively demanding task using data from consumer-grade smartwatches. The s...
biologybrain imagesDrosophila melanogasterelectrophysiologyfluorescence imagingHomo sapiensimaginglife sciencesmagnetic resonance imagingneuroimagingneurophysiologyneurosciencesimulation neuroscience
CRCNS.org is a repository of high quality neuroscience datasets which are expected to be useful for testing computational models of the brain and new analysis methods. The data include physiological recordings from sensory and memory systems, as well as eye movement and other behavioral data. The repository and sharing of the data sets was initially funded by the NSF CRCNS (Collaborative Research in Computational Neuroscience) program.
healthlife sciencesmedicine
This database contains the combined measurement of ECG, breathing and seismocardiogram from 20 healthy volunteers. The purpose of the database was twofold: To check if slight errors in the detection of the RR time series when measuring it using two different leads are influenced by breathing. To compare the RR time series obtained from the ECG and its surrogate measure obtained from the seismocardiogram or SCG (and to optimize beat detectors for SCG).
healthlife sciencesmedicine
This database includes beat annotation files for 29 long-term ECG recordings of subjects aged 34 to 79, with congestive heart failure (NYHA classes I, II, and III).
brain imagescomputer visionlife sciencesmicroscopyneurobiologysegmentation
We introduce DHARANI, the first online platform with three-dimensional (3D) histological reconstructions of the developing human brain from 14 to 24 gestational weeks (GW) across the five fetal brains. DHARANI features 5132 Nissl, hematoxylin and eosin stained, 20 µm coronal and sagittal sections, postmortem MRI, and a neuroanatomical atlas with 466 annotated sections covering ∼500 brain structures. It is accessible online at https://brainportal.humanbrain.in/publicview/index.html. The 3D reconstruction enables a volumetric view of the fetal brain, allowing visualization in all three planes ak...
healthlife sciencesmedicine
Analysis of biomedical time series plays a key role in clinical management and basic investigation. However, most conventional monitors streaming data in real-time show only the most recent values, not referenced to past dynamics. The proposed visualization method (termed “data chromatix”) was developed to address this challenge by bringing memory of the system’s past behavior into the current display window. The function DataChromatix.m (version 1.0) assigns a color to each data point of a time series. The color is determined by the values of a normalized histogram (estimated probability dens...
healthlife sciencesmedicine
Obstructive sleep apnea (intermittent cessation of breathing) is a common problem with major health implications, ranging from excessive daytime drowsiness to serious cardiac arrhythmias. Obstructive sleep apnea is associated with increased risks of high blood pressure, myocardial infarction, and stroke, and with increased mortality rates. Standard methods for detecting and quantifying sleep apnea are based on respiration monitoring, which often disturbs or interferes with sleep and is generally expensive. A number of studies during the past 15 years have hinted at the possibility of detecting...
healthlife sciencesmedicine
The ninth annual PhysioNet/Computers in Cardiology Challenge aims to improve understanding of methods for identification and analysis of T-wave alternans in the ECG.
healthlife sciencesmedicine
The method of detrended fluctuation analysis has proven useful in revealing the extent of long-range correlations in time series.
healthlife sciencesmedicine
We present a Python-based utility for real-time ingestion of digital physiological signals and study enrollment metadata into an Oracle database. The application combines filesystem event monitoring, a GUI data entry form, and thin-mode Oracle connectivity to ensure timely and accurate data capture at the point of file creation. The system is designed for research assistants to enter metadata for digital signal recordings (e.g., ECG, PCG, and other physiological datasets), with automated database field assignments (e.g., study_date, study_id) and compliance with pre-defined enumerations and co...
healthlife sciencesmedicine
For the fourth annual PhysioNet/Computers in Cardiology Challenge, we propose a provocative question of considerable clinical interest: Is it possible to tell the difference between transient ST changes in the ECG that are due to myocardial ischemia, and those that are not?
healthlife sciencesmedicine
This project contains Matlab functions for visualizing the behavior of complex systems by means of the dynamical density delay mapping ("D3-Map") technique . This simple-to-implement visualization method provides an animated representation of a system's dynamics.
healthlife sciencesmedicine
The ECGRDVQ database contains multi-channel ECG recordings of 22 healthy subjects partaking in a randomized, double‐blind, 5‐period crossover clinical trial aimed at comparing the effects of four known QT prolonging drugs versus placebo on electrophysiological and other clinical parameters.
healthlife sciencesmedicine
The database contains a set of 2 second fragments of ECG signals with rhythm disturbances, which are grouped into separate classes according to the degree of threat to the patient's life. It is intended for practical use to develop and test the efficiency of algorithms for detecting dangerous arrhythmias for continuous monitoring systems. The “MIT-BIH Malignant Ventricular Ectopy Database” (MVED) was selected as the primary source of ECG records. This database contains heart rhythm disturbances necessary for research and is widely used for testing and comparative analysis of various algori...
healthlife sciencesmedicine
ECGwaveGen generates a synthesized ECG signal with user-settable heart rate, signal duration, sampling frequency, QRS amplitude and duration, and T-wave amplitude; it uses QRSpulse to create premature beats followed by compensatory pauses.
healthlife sciencesmedicine
The ECG-Derived Respiration (EDR) technique is an approach to obtain a respiration signal from an ECG.. It is based on the observation that the positions of ECG electrodes on the chest surface move relative to the heart, and transthoracic impedance varies, as the lungs fill and empty. Thus the lead axes vary at different points in the respiratory cycle, and any sufficiently precise measurement of the mean cardiac electrical axis shows variations that are correlated with respiration. This method is particularly effective if two or more ECG signals are available, but a single lead is sufficient....
healthlife sciencesmedicine
The database contains 310 ECG recordings, obtained from 90 persons. Each recording contains: ECG lead I, recorded for 20 seconds, digitized at 500 Hz with 12-bit resolution over a nominal ±10 mV range; 10 annotated beats (unaudited R- and T-wave peaks annotations from an automated detector); information (in the .hea file for the record) containing age, gender and recording date.
healthlife sciencesmedicine
This toolbox is a collection of Matlab tools that Mariano Llamedo Soria used, adapted or developed during his PhD and post-doc work with the Besicos group at University of Zaragoza, Spain and at the National Technological University of Buenos Aires, Argentina.
healthlife sciencesmedicine
ecgpuwave analyses an ECG signal from the specified record, detecting the QRS complexes and locating the beginning, peak, and end of the P, QRS, and ST-T waveforms. The output of ecgpuwave is written as a standard WFDB-format annotation file associated with the specified annotator.
healthlife sciencesmedicine
ECGSYN generates a synthesized ECG signal with user-settable mean heart rate, number of beats, sampling frequency, waveform morphology (P, Q, R, S, and T timing, amplitude,and duration), standard deviation of the RR interval, and LF/HF ratio (a measure of the relative contributions of the low and high frequency components of the RR time series to total heart rate variability).
healthlife sciencesmedicine
The database contains EEG recordings of subjects before and during the performance of mental arithmetic tasks.
healthlife sciencesmedicine
The EEG Motor Movement/Imagery Dataset provides 64-channel electroencephalography recordings collected with the BCI2000 system during real and imagined motor tasks. Participants completed 14 experimental runs, including two one-minute baseline recordings with eyes open and eyes closed, followed by three repetitions of four two-minute task conditions. These conditions involved either executing or imagining unilateral fist movements in response to left/right visual targets, or executing or imagining bilateral fist or foot movements in response to top/bottom visual targets. EEG signals were recor...
healthlife sciencesmedicine
This project contains EEG data from 11 healthy participants upon rapid presentation of images through the Rapid Serial Visual Presentation (RSVP) protocol at speeds of 5, 6, and 10 Hz.
cancerlife sciencesmedical imagingniftiradiologysegmentation
Open, multi-center dataset of 1,597 whole-/total-body FDG-PET/CT studies with 130 CT-derived, expert-verified anatomical segmentations per scan (~250 GB). Provided as anonymized NIfTI (PET, CT, labels) with spreadsheet metadata. Designed for segmentation benchmarking, multi-organ analysis, radiomics, and PET/CT AI research.
healthlife sciencesmedicine
The electro-phono-cardiogram (EPHNOGRAM) project focused on the development of low-cost and low-power devices for recording simultaneous electrocardiogram (ECG) and phonocardiogram (ECG) data, with auxiliary channels for capturing environmental audio noise, which could be used for PCG quality enhancement through signal processing. The current database, recorded by version 2.1 of the developed hardware, has been acquired from 24 healthy adults aged between 23 and 29 (average: 25.4 ± 1.9 years) in 30min stress-test sessions during resting, walking, running and biking conditions, using indoor fit...
healthlife sciencesmedicine
This dataset — created and contributed by Luca Citi, Riccardo Poli, and Caterina Cinel — was generated as part of a study aimed at identifying the factors limiting the performance of brain-computer interfaces (BCIs) based on event-related potentials (ERPs), in order to improve the transfer rate and the usability of these interfaces. In this study, each participant was asked to spell a total of 20 characters using a traditional matrix speller (shown at left). Each record in the dataset contains the signals, triggers and annotations corresponding to a single run, i.e. the spelling of a single ch...
healthlife sciencesmedicine
The EVAL_ST tool is an open source tool to evaluate and compare performance and robustness of ST episode detection algorithms. The tool supports all standard and other relevant performance measures, aggregate gross and average statistics, and bootstrap statistical procedure to predict real-world clinical performance. The tool (written in C) is compilable an a wide variety of platforms and contains an additional graphic user interface module (LessTif/Motif environment) for use on the LINUX/UNIX operating systems.
healthlife sciencesmedicine
Sepsis is a life-threatening condition that occurs when the body's response to infection causes tissue damage, organ failure, or death (Singer et al., 2016). In the U.S., nearly 1.7 million people develop sepsis and 270,000 people die from sepsis each year; over one third of people who die in U.S. hospitals have sepsis (CDC). Internationally, an estimated 30 million people develop sepsis and 6 million people die from sepsis each year; an estimated 4.2 million newborns and children are affected (WHO). Sepsis costs U.S. hospitals more than any other health condition at $24 billion (13% of U....
healthlife sciencesmedicine
Sleep deprivation (SD) is associated with decreased cognitive performance, but the underlying mechanisms are poorly understood. To assess the impact of SD on cerebral hemodynamics in the frontal lobe, functional near-infrared spectroscopy (fNIRS) measurements were carried out on young subjects. Ten young healthy adults (males, age of 27.6±3.7 years, one left-handed participant) were recruited for this study conducted in 2018 at University of Oklahoma, Translational Geroscience Laboratory. The examination protocol began with assessment of cognitive performance with the aid of Cambridge Neuropsy...
healthlife sciencesmedicine
The recordings of this database are of rest tremor velocity in the index finger of 16 subjects with Parkinson's disease (PD) who receive chronic high frequency electrical deep brain stimulation (DBS).
healthlife sciencesmedicine
This project contains electrocardiogram, skin conductance and respiration as raw data (unfiltered, unprocessed) recorded from consented, spider-fearful individuals using the wearable BITalino biosignal measurement device (PLUX – Wireless Biosignals S.A., Lisbon, Portugal) with the sampling rate set to 100 Hz per channel having 10-bit resolution. All subjects were introduced to the exposure procedure and rationale that is mainly based on the principles of the one-session exposure treatment. The main focus of this study was to investigate if the use of an HRV biofeedback intervention could be a ...
healthlife sciencesmedicine
The aim of Challenge 2007 is to establish how well one can characterize the location and extent of moderate to large, relatively compact infarcts using electrocardiographic evidence (supplemented by a model of the torso geometry and conductivity), in comparison with a "gold standard" expert analysis of gadolinium-enhanced MRI data.
healthlife sciencesmedicine
Surgical training and patient safety depend on objective and accurate performance evaluation. Robot-assisted surgery (RAS) is newer and its training less well defined, but resources are not easily accessed to support data collection from participants with various RAS skill levels. This work describes and makes available for public use electroencephalogram (EEG) and eye-gaze data collected from 25 participants performing RAS simulator tasks with varying levels of RAS experience.Twenty-seven tasks from six modules of the da Vinci®;Skills Simulator ™, which are standard elements of most RAS surgi...
healthlife sciencesmedicine
The database contains acceleration signals from accelerometers attached directly on the epicardium in canines and porcines during various interventions that altered cardiac function and myocardial motion. The tri-axial accelerometer was attached in the anterior, apical region of the left ventricle (LV). The database contains a total of 289 recordings from 19 canines and 27 porcines with an average duration of 15 seconds, ranging from 5 to 30 seconds. Acceleration data was recorded simultaneously with ECG and LV pressure (LVP).
healthlife sciencesmedicine
Using only a heart rate time series, it is possible to measure a number of features that reflect the level of physical activity. Here we provide software for deriving an "activity index" based on measurements of mean heart rate, total power of the instantaneous heart rate time series over a given interval, and stationarity.
healthlife sciencesmedicine
The European ST-T Database is intended to be used for evaluation of algorithms for analysis of ST and T-wave changes. This database consists of 90 annotated excerpts of ambulatory ECG recordings from 79 subjects. The subjects were 70 men aged 30 to 84, and 8 women aged 55 to 71.
healthlife sciencesmedicine
The Evoked Auditory Responses in Hearing Impaired database contains evoked Auditory Brainstem Response (ABR) and Otoacoustic Emission (OAE) recordings in eight hearing impaired listeners, in response to tone-burst stimuli across a wide range of levels.
healthlife sciencesmedicine
This database, created and contributed by Michael J. Epstein and Ikaro Silva, was generated as part of a study examining evoked potentials and loudness growth. The database consists of two sets of physiological signals: auditory brainstem response (ABR) and otoacoustic emissions (OAE) and two sets of psychoacoustical estimates of loudness as a function of peak sound pressure level (peSPL).
healthlife sciencesmedicine
An electromyogram (EMG) is a common clinical test used to assess function of muscles and the nerves that control them. EMG studies are used to help in the diagnosis and management of disorders such as the muscular dystrophies and neuropathies. Nerve conduction studies that measure how well and how fast the nerves conduct impulses are often performed in conjunction with EMG studies. Examples of EMG studies (courtesy of Seward Rutkove, MD, Department of Neurology, Beth Israel Deaconess Medical Center/Harvard Medical School) are given here.
healthlife sciencesmedicine
This dataset contains collected eye tracking data from medical practitioners and students with different expertise levels to understand their electrocardiogram interpretation behavior. These medical practitioners encounter electrocardiograms during their daily medical practice. The end goal of the collection of this dataset was to use it for analysis to uncover insights about key best practices as well as pitfall in the ECG interpretation process. The data consists of quantitative eye tracking measurements for different eye gaze features for 63 participants. These participants belong to six ex...
healthlife sciencesmedicine
The FECGSYN toolbox is a reference open-source platform for NI-FECG research, product of a collaboration between the Department of Engineering Science, University of Oxford (DES-OX), the Institute of Biomedical Engineering, TU Dresden (IBMT-TUD) and the Biomedical Engineering Faculty at the Technion Israel Institute of Technology (BME-IIT).
healthlife sciencesmedicine
To evaluate the benefit of implementing standardized deployment and acquisition practices in the measurement of elevated body temperature (EBT) with infrared thermographs (IRTs), we conducted a clinical study with more than one thousand subjects. Subject oral temperatures were measured and facial thermal images captured with two evaluated IRTs. Based on the thermal images, temperatures from different locations on the face were extracted based on developed method and are listed in six CSV file as the open database. All data in these files has been de-identified. Based on these data, we publishe...
healthlife sciencesmedicine
Twenty young (21 - 34 years old) and twenty elderly (68 - 85 years old) rigorously-screened healthy subjects underwent 120 minutes of continuous supine resting while continuous electrocardiographic (ECG), and respiration signals were collected; in half of each group, the recordings also include an uncalibrated continuous non-invasive blood pressure signal. Each subgroup of subjects includes equal numbers of men and women.
healthlife sciencesmedicine
The FECGSYNDB is a large database of simulated adult and non-invasive fetal ECG (NI-FECG) signals, which provides a robust resource that enables reproducible research in the field. The data is generated using the FECGSYN simulator (visit website).
healthlife sciencesmedicine
The project collects a series of 26 fetal phonocardiographic (PCG) signals from different pregnant women during the last months of their singleton physiological pregnancies (gestational week between 31 and 40).
bioinformaticsbiologycancergeneticgenomiclife sciences
The GATK test data resource bundle is a collection of files for resequencing human genomic data with the Broad Institute's Genome Analysis Toolkit (GATK).
healthlife sciencesmedicine
This dataset is an extension of the Gesture Recognition and Biometrics Electromyogram (GRABMyo) dataset, a comprehensive collection of surface electromyography (sEMG) signals from the forearm and wrist while performing static gestures, designed for hand gesture recognition (HGR) and biometric authentication research. The study extends the dataset in two key aspects: 1) by adding wrist-only recordings from 20 newly recruited healthy adults, and 2) by including a dynamic trial at the end of each session. The extension study follows the protocol established in the original study to ensure methodo...
assemblybioinformaticsbiologycontaminationfastageneticgenomehealthlife sciencesSTRIDESwhole genome sequencing
Sequence database used by FCS-GX (Foreign Contamination Screen - Genome Cross-species aligner) to detect contamination from foreign organisms in genome sequences.
healthlife sciencesmedicine
The data contained here are from 50 healthy children ranging in age from 40 months to 163 months. Each data file is named with a subject identifier (1-50) and the subject's age (e.g., the file name 2-45.txt indicates that subject #2 is 45 months old). Each data file contains two columns of data in text format. The first column is the time (in seconds), and the second column is the stride interval (in seconds) or the gait cycle duration, the time from heel strike to heel strike of the same foot.
healthlife sciencesmedicine
Walking stride interval time series included are from 15 subjects: 5 healthy young adults (23 - 29 years old), 5 healthy old adults (71 - 77 years old), and 5 older adults (60 - 77 years old) with Parkinson's disease. The file name indicates old (o), young (y) or Parkinson's disease (pd). For the old and young subjects, the age (in years) is also included in the filename.
healthlife sciencesmedicine
Neuro-degenerative disease often affects gait and mobility. To understand better the pathophysiology of these diseases and to improve our ability to measure responses to therapeutic interventions, it may be helpful to quantify gait dynamics accurately. The records in this database are from patients with Parkinson's disease (n = 15), Huntington's disease (n = 20), or amyotrophic lateral sclerosis (n = 13). Records from 16 healthy control subjects are also included here.
healthlife sciencesmedicine
This database contains measures of gait from 93 patients with idiopathic PD (mean age: 66.3 years; 63% men), and 73 healthy controls (mean age: 66.3 years; 55% men). The database includes the vertical ground reaction force records of subjects as they walked at their usual, self-selected pace for approximately 2 minutes on level ground.
healthlife sciencesmedicine
The method of generalized multiscale entropy (GMSE) analysis is useful for investigating complexity in physiologic signals and other series that have correlations at multiple (time) scales. It represents a generalization of the original method of multiscale entropy analysis.
biodiversitybioinformaticsbiologyconservationgeneticgenomiclife sciences
The Genome Ark hosts genomic information for the Vertebrate Genomes Project (VGP) and other related projects. The VGP is an international collaboration that aims to generate complete and near error-free reference genomes for all extant vertebrate species. These genomes will be used to address fundamental questions in biology and disease, to identify species most genetically at risk for extinction, and to preserve genetic information of life.
healthlife sciencesmedicine
We present the Gesture Recognition and Biometrics ElectroMyogram (GRABMyo) dataset, an open-access dataset of electromyogram (EMG) recordings collected from the wrist and forearm muscles while performing hand gestures. Data were collected from 43 healthy participants (age range: 24-35 years) on three different days while performing 16 hand and finger gestures in identical experimental sessions on each day. The GRABMyo dataset can be used for research on: 1) EMG-based biometrics for personal identification and verification, and 2) EMG-based gesture recognition for neurorehabilitation and home a...
healthlife sciencesmedicine
In finding an optimal stimulus waveform for inducing switches in neuronal states, analytical techniques from optimal control theory are often found to be difficult to use or extremely time intensive. Here, we present the code for a gradient-based algorithm approach that has been used to find energetically optimal stimulus waveforms to trigger an action potential in the Hodgkin-Huxley model as well as initiating and repressing repetitive firing in the FitzHugh-Nagumo models. These two models serve just as examples and the code can be easily adapted to any other system.
biologyconservationecosystemsenvironmentallabeledlife sciencesobject detection
For this project, The Water Institute (the Institute) and subcontractor Colibri Ecological Consulting, LLC (Colibri) utilized established methods and protocols capable of assessing changes of colonial waterbird populations and their important habitats within individual states and the broader northern Gulf of Mexico region. Data collection activities included: Aerial Photographic Nest Surveys: Implementation of fixed-wing aircraft surveys intended to assess waterbird colonies and document associated nesting within select portions of the northern Gulf of Mexico. Additional detail is provide...
biologybreast cancercancercomputational pathologyhistopathologylife sciences
This is a retrospective dataset of 1523 H&E-stained whole slide images (WSI) of lymph nodes from breast cancer patients. The cohort consisted of 177 patients (122 LN-positive - metastasis was reported in at least 1 LN - and 55 LN-negative patients) with invasive breast carcinoma treated between 1984 and 2002 at Guy’s Hospital London, UK. Slides were scanned and digitised at 40x magnification (0.23 µm/pixel), NanoZoomer H.T2.0 2.0-HT (Hamamatsu Photonics UK, Ltd, Welwyn Garden City, UK). WSIs are in .ndpi format.
healthlife sciencesmedicine
A collection of 151 whole-night polysomnographic (PSG) sleep recordings (85 Male, 66 Female, mean Age of 53.9 ± 15.4) collected during 2018 at the Haaglanden Medisch Centrum (HMC, The Netherlands) sleep center. Patient recordings were randomly selected and include a heterogeneous population which was referred for PSG examination on the context of different sleep disorders. The dataset contains electroencephalographic (EEG), electrooculographic (EOG), chin electromyographic (EMG), and electrocardiographic (ECG) activity, as well as event annotations corresponding to scoring of sleep patterns (h...
healthlife sciencesmedicine
Congenital heart diseases affect about 1% of newborns, representing an important morbidity and mortality factor for several severe conditions, including advanced heart failure [1]. In a 2019 survey, it was estimated that congenital heart diseases affect over 500,000 children in East Africa [2], and about 8 in every 1000 live births [3]. Acquired heart diseases include rheumatic fever and the Kawasaki disease, the former being a serious public health problem in developing regions, e.g., rural Brazil [4]. Several regions of developing countries have difficulties in diagnosing and treating both c...
healthlife sciencesmedicine
Heart rate time series for 5 different groups of healthy subjects performing meditation techniques.
healthlife sciencesmedicine
The "HeartCycle" dataset offers a comprehensive collection of synchronized impedance cardiography (ICG) and echocardiography (ECHO) signals, supplemented with finger photoplethysmography (PPG), heart sounds, and electrocardiography (ECG) data from 17 healthy volunteers. Collected during the HeartCycle project (FP7-216695), this dataset aims to address biases in the ICG waveform, particularly the ABEXYOZ complex, where the B and X points do not precisely align with the aortic valve opening and closing notches. The biases in B and X point detection are critical for hemodynamic predicti...
healthlife sciencesmedicine
Glaucomatous optic neuropathy (GON) is a leading cause of irreversible blindness worldwide, affecting an estimated 64.3 million people globally with projections reaching 111.8 million by 2040. Approximately 50% of cases remain undiagnosed until advanced stages when vision loss becomes noticeable. Traditional diagnosis requires comprehensive ophthalmic examinations by specialists, creating accessibility barriers in many regions. The Hillel Yaffe Glaucoma Dataset (HYGD) addresses a critical limitation in existing GON datasets: the lack of gold-standard annotations. Unlike most publicly available...
healthlife sciencesmedicine
The HBEDB contains force platform recordings from subjects undergoing stabilography tests. The subjects performed standing tasks under four different conditions: with their eyes opened or closed, while standing on a rigid or unstable surface. Each condition was tested three times, with the order of the conditions being randomized among subjects. A total of 1930 trials performed by 163 different subjects are given in this database.
healthlife sciencesmedicine
This database consists of 122 16-electrode EHG recordings performed on 45 pregnant women. The recordings were performed between 2008 and 2010 in Iceland.
healthlife sciencesmedicine
This is a dataset of continuous raw electrocardiogram (ECG) signals containing 11 thousand patients and 2 billion labelled beats. The signals were recorded with a 16-bit resolution at 250Hz with a fixed chest mounted single lead probe for up to 2 weeks. The average age of the patient is 62.2±17.4 years. 20 technologists annotated each beat's type (Normal, Premature Atrial Contraction, Premature Ventricular contraction) and rhythm (Normal Sinusal Rhythm, Atrial Fibrillation, Atrial Flutter).
biodiversityBiohubbioinformaticsbiologybiomolecular modelingbrain imagescell biologycell imagingimaginglife sciencesmachine learningmicroscopymodelproteinzarr
This dataset contains a diverse range of imaging biological data and models. The data is sourced and curated by a team of experts at Biohub and is made available as part of these datasets only when it is not publicly accessible or requires transformations to support model training.
healthlife sciencesmedicine
The aim of the PhysioNet/Computing in Cardiology Challenge 2011 is to develop an efficient algorithm able to run in near real-time within a mobile phone, that can provide useful feedback to a layperson in the process of acquiring a diagnostically useful ECG recording.
healthlife sciencesmedicine
We conducted a field study at a K-12 private school in the suburbs of Melbourne, Australia. The datasets contained two elements: (1) In-Gauge dataset: we conducted a 5-month longitudinal field study using two outdoor weather stations, as well as indoor weather stations in 17 classrooms and temperature sensors on the vents of occupant-controlled room air-conditioners; these were collated into individual datasets for each classroom at a 5-minute logging frequency, including additional data on occupant presence. (2) En-Gage dataset: we tracked 23 students and 6 teachers in a 4-week cross-sectiona...
bioinformaticscoronavirusCOVID-19healthlife sciencesmedicineSARS
This dataset is a collection of anonymized thoracic radiographs (X-Rays) and computed tomography (CT) scans of patients with suspected COVID-19. Images are acommpanied by a positive or negative diagnosis for SARS-CoV2 infection via RT-PCR. These images were provided by Hospital das Clínicas da Universidade de São Paulo, Hospital Sirio-Libanes, and by Laboratory Fleury.
healthlife sciencesmedicine
The Indian Institute of Science Fetal Heart Sound Database (IIScFHSDB) has 60 fetal phonocardiography (fPCG) recordings obtained from expecting mothers of age 18-27 years of age with gestation weeks 30-40. The recordings are made at St. John’s Hospital, Bangalore with an electronic stethoscope. The data is collected from the antenatal and labor wards by placing the electronic stethoscope on the lower abdomen of the subject. The fPCG recordings are obtained from 60 subjects with the gain of 500X and the average duration of the recordings is 8 minutes with a sampling frequency of 2 kHz.
healthlife sciencesmedicine
The surface electrohysterogram (EHG) has emerged as a promising diagnostic tool for non-invasive automated preterm birth prediction. The existing automated preterm birth prediction methods rely on the use of uterine EHG records coming from spontaneous preterm and term deliveries, and are indifferent to term induced and cesarean deliveries. In order to enhance current publicly available pool of term EHG records, we developed a new EHG dataset containing 126 30-minute EHG records, recorded either early (23rd week), or later during pregnancy (31st week), of those pregnancies that were expected to...
healthlife sciencesmedicine
This ECG dataset was acquired in different magnetic resonance imaging (MRI) scanners to study the magnetohydrodynamic (MHD) effect. The MHD effect, which is caused an interaction of the MRI’s strong static magnetic field and the patient’s blood flow, superimposes the ECG signal during MRI exams. As a consequence, a detailed morphological analysis of the ECG (e.g. of the P wave, ST segment or the T wave) is prevented. The MHD effect might be a useful signal for extracting further physiological information, e.g. about blood flow or stroke volume. The 12-lead and 3-lead ECG signals were acquired ...
healthlife sciencesmedicine
IBS is a novel method for comparing time series based on linguistic analysis of "word" frequency and rank order statistics. It has been applied successfully in a variety of applications, including analysis of interbeat (RR) intervals, classification of the SARS coronavirus, and study of literary works of disputed authorship.
healthlife sciencesmedicine
Laparoscopic surgery represents a significant advancement in healthcare, aiming to enhance patient outcomes. However, evaluating performance in laparoscopic surgery tasks can be challenging due to subjective assessments. To address this, this study provides a comprehensive description and public access to electroencephalogram (EEG) and eye-gaze data collected from 25 participants with varying levels of robotic surgery experience. The participants performed Fundamentals of Laparoscopic Surgery (FLS) tasks using a trainer box (Pyxus®), focusing on three standard FLS elements. The dataset, named ...
healthlife sciencesmedicine
This database consists of endocardial recordings from the right atria of 8 patients in atrial fibrillation or flutter. A decapolar catheter with 2-5-2mm spacing (7mm spacing between bipoles) was placed in four separate regions of the heart. In each region, the 5 bipolar signals were recorded along with 3 surface ECG leads.
healthlife sciencesmedicine
In its June 2008 issue, the editors of Chaos announced a new feature, "Controversial Topics in Nonlinear Dynamics". The first controversial topic to be aired is "Is the Normal Heart Rate Chaotic?". Since major impediments to achieving consensus on the statistical properties of biologic time series have included the lack of open access time series, PhysioNet has provided a set of 15 heart beat (RR-interval) time series in health and disease (congestive heart failure and atrial fibrillation). Each time series is about 24 hours long (roughly 100,000 intervals), and is provided...
healthlife sciencesmedicine
The field of human action recognition has made great strides in recent years, much helped by the availability of a wide variety of datasets that use Kinect to record human movement. Conversely, progress towards using Kinect in clinical practice has been hampered by the lack of appropriate data. In particular, datasets that contain clinically significant movements and appropriate metadata. This paper proposes a dataset to address this issue, namely KINECAL. It contains the recordings of 90 individuals carrying out 11 movements, commonly used in the clinical assessment of balance. The dataset co...
healthlife sciencesmedicine
The Kiel Cardio Database, which includes magnetocardiography (MCG) measurements of seven healthy male volunteers, is presented in this publication. QuSpin QZFM Gen 1 sensors were used in a magnetically shielded chamber at the University of Kiel. Each subject underwent 25 one-minute measurements, resulting in magnetic field recordings at 200 different positions for each subject. The dataset is intended to facilitate MCG research by making this expensive method accessible to researchers without the necessary equipment. Future versions of the database will expand its utility for cardiac research ...
healthlife sciencesmedicine
The database contains raw accelerometry data collected during outdoor walking, stair climbing, and driving for 32 healthy adults. Accelerometry data were collected simultaneously at four body locations: left wrist, left hip, left ankle, and right ankle, at a sampling frequency of 100 Hz. The 3-axial ActiGraph GT3X+ devices were used to collect the data. The data include labels of activity type performed (walking, descending stairs, ascending stairs, driving, clapping) for each time point of data collection. Basic demographic information of participants is also provided. All data are anonymized...
healthlife sciencesmedicine
Interpretation of Electrocardiograms (ECG) is increasingly complemented by algorithms. These algorithms are based on large datasets. This ECG database consists of children and adults with congenital heart defects (CHD) including many arrhythmia annotations. This dataset, notable for its manual annotations and inclusion of intracardiac electrograms alongside traditional 12-lead ECGs, offers 1075.85 minutes of recordings (in total 113924 annotated beats) that capture various cardiac rhythms and arrhythmias such as supraventricular tachycardia and ventricular tachycardia. The data were meticulous...
healthlife sciencesmedicine
Lobachevsky University Electrocardiography Database (LUDB) is an ECG signal database with marked boundaries and peaks of P, T waves and QRS complexes. The database consists of 200 10-second 12-lead ECG signal records representing different morphologies of the ECG signal. The ECGs were collected from healthy volunteers and patients of the Nizhny Novgorod City Hospital No 5 in 2017–2018. The patients had various cardiovascular diseases while some of them had pacemakers. The boundaries of P, T waves and QRS complexes were manually annotated by cardiologists for all 200 records. Also, each record ...
healthlife sciencesmedicine
The identification of the exact positions of the first and second heart sounds within a phonocardiogram (PCG), or heart sound segmentation, is an essential step in the automatic analysis of heart sound recordings, allowing for the classification of pathological events. While threshold-based segmentation methods have shown modest success, probabilistic models, such as hidden Markov models, have recently been shown to surpass the capabilities of previous methods. Segmentation performance is further improved when apriori information about the expected duration of the states is incorporated into t...
healthlife sciencesmedicine
This database includes 84 long-term ECG recordings of subjects with paroxysmal or sustained atrial fibrillation (AF). Each record contains two simultaneously recorded ECG signals digitized at 128 Hz with 12-bit resolution over a 20 mV range; record durations vary but are typically 24 to 25 hours.
healthlife sciencesmedicine
The LTMM database contains 3-day 3D accelerometer recordings of 71 elder community residents, used to study gait, stability, and fall risk.
healthlife sciencesmedicine
Stride interval fluctuations were studied in ten young, healthy men. Participants had no history of any neuromuscular, respiratory or cardiovascular disorders, and were taking no medications. Mean age was 21.7 years (range: 18-29 years). Height was 1.77 ± 0.08 meters (mean ± S.D.) and weight was 71.8 ± 10.7 kg. All subjects provided informed written consent. Subjects walked continuously on level ground around an obstacle free, long (either 225 or 400 meters), approximately oval path and the stride interval was measured using ultra-thin, force sensitive switches taped inside one shoe.
healthlife sciencesmedicine
This dataset includes longitudinal data from 59 mice assigned to four drug treatment groups (lemborexant 10 mg/kg, lemborexant 30 mg/kg, zolpidem 30 mg/kg, and vehicle), assessed at five timepoints: baseline (pre-treatment), maximal deficit (post-stroke 48 hours), and weeks 2, 4, and 8 post-treatment. Designed to evaluate drug efficacy over time, the dataset captures functional or physiological changes across stroke acute and recovery phases via the behavioral test of cylinder rearing. The shared data specifically comprises 295 video recordings (.mp4) of these sessions, paired with correspondi...
healthlife sciencesmedicine
Released by the Information Technologies Institute (CERTH-ITI) and powered by MAMEM HORIZON 2020, the MSSVEP database contains EEG recordings of 11 subjects under the stimulation of flickering lights, used to study the steady state visually evoked potentials. The data is divided into three sets in which the experimental procedures and capturing devices differ.
healthlife sciencesmedicine
The Massachusetts General Hospital/Marquette Foundation (MGH/MF) Waveform Database is a comprehensive collection of electronic recordings of hemodynamic and electrocardiographic waveforms of stable and unstable patients in critical care units, operating rooms, and cardiac catheterization laboratories. It is the result of a collaboration between physicians, biomedical engineers and nurses at the Massachusetts General Hospital. The database consists of recordings from 250 patients and represents a broad spectrum of physiologic and pathophysiologic states. Individual recordings vary in length fro...
healthlife sciencesmedicine
This dataset comprises head motion observations collected as part of an experiment in which a group of people were asked to stand still for 6 minutes, with the first 3 minutes in silence, followed by 3 minutes with music. Head motion was captured in units of mm at 100Hz using a Qualisys infra-red optical system. The experiment was carried out at the University of Oslo on March 8th 2012 from a total of 113 participants. Code to read and process these files is available. The paper corresponding to the work is Jensenius et al., "The Musical Influence on People's Micromotion when Standing...
healthlife sciencesmedicine
This project contains head movement data recorded from groups of participants asked to stand as still as possible and presented with a series of auditory stimuli. Data was collected in units of mm with a Qualisys motion capture system at 100Hz. Data was collected at the University of Oslo on March 12th 2015 from a total of 108 participants. Code to read and process these files has been made publicly available.
healthlife sciencesmedicine
The Medical Information Mart for Intensive Care (MIMIC)-IV database is comprised of deidentified electronic health records for patients admitted to the Beth Israel Deaconess Medical Center. Access to MIMIC-IV is limited to credentialed users. Here, we have provided an openly-available demo of MIMIC-IV containing a subset of 100 patients. The dataset includes similar content to MIMIC-IV, but excludes free-text clinical notes. The demo may be useful for running workshops and for assessing whether the MIMIC-IV is appropriate for a study before making an access r...
healthlife sciencesmedicine
Interoperability of healthcare data has become increasingly important given the increase in deployment of data driven algorithms in clinical settings. The Fast Healthcare Interoperability Resources (FHIR) standard has emerged as a promising mechanism to share healthcare data across vendors in real-time and batch settings. Real-world datasets available in FHIR would accelerate research and development of data-driven algorithms. Existing datasets in FHIR are primarily synthetic, and cover a limited number of resources. To address this gap, we have reformatted the Medical Information Mart for Int...
healthlife sciencesmedicine
This dataset is an automated ETL conversion of the MIMIC-IV Clinical Database Demo into the Medical Event Data Standard (MEDS). MEDS is a data schema for storing streams of medical events such as those sourced from Electronic Health Records or claims records. MEDS is intentionally a minimal standard, designed for maximum interoperability across datasets, existing tools, and model architectures. By providing a simple standardization layer between datasets and model-specific code, MEDS is intended to help make machine learning research for EHR data more reproducible, robust, computationally perf...
healthlife sciencesmedicine
The MIMIC-IV-ECG module contains approximately 800,000 diagnostic electrocardiograms across nearly 160,000 unique patients. These diagnostic ECGs use 12 leads and are 10 seconds in length. They are sampled at 500 Hz. This subset contains all of the ECGs for patients who appear in the MIMIC-IV Clinical Database. When a cardiologist report is available for a given ECG, we provide the needed information to link the waveform to the report. The patients in MIMIC-IV-ECG have been matched against the MIMIC-IV Clinical Database, making it possible to link to information across the MIMIC-IV modules.
healthlife sciencesmedicine
The MIT-BIH Arrhythmia Database contains 48 approximately half-hour, two-channel ambulatory electrocardiogram (ECG) recordings from 47 subjects. The recordings were collected at Boston's Beth Israel Hospital between 1975 and 1979 and include both randomly selected excerpts and recordings selected to represent less common, clinically significant arrhythmias. Signals were digitized at 360 samples per second per channel with 11-bit resolution over a 10 mV range. Each recording includes expert-reviewed reference annotations, comprising approximately 110,000 beat annotations across the database...
healthlife sciencesmedicine
This database provides manually reviewed P-wave annotations for twelve ECG recordings from the MIT-BIH Arrhythmia Database [1]. The recordings were selected to support evaluation of P-wave detection across a range of rhythms, including pathological conditions that can make detection difficult. One expert annotated the recordings, a second expert reviewed the annotations, and ambiguous segments were discussed jointly. The annotations are supplied in standard WFDB format alongside the corresponding ECG signals and header files. They support the development and evaluation of automated P-wave dete...
healthlife sciencesmedicine
This database includes 25 long-term ECG recordings of human subjects with atrial fibrillation (mostly paroxysmal).
healthlife sciencesmedicine
This database contains 168 short ECG recordings (20.48 seconds each) selected to pose a variety of challenges for ECG compressors, in particular for lossy compression methods.
healthlife sciencesmedicine
The MIT-BIH Long-Term ECG Database is a collection of 7 long-duration electrocardiogram (ECG) recordings (14 to 22 hours each), with manually reviewed beat annotations. The database was primarily developed to support research in the field of cardiac arrhythmia detection and analysis, and is a collaborative effort between the Massachusetts Institute of Technology (MIT) and the Beth Israel Hospital (BIH).
healthlife sciencesmedicine
This database includes 22 half-hour ECG recordings of subjects who experienced episodes of sustained ventricular tachycardia, ventricular flutter, and ventricular fibrillation.
healthlife sciencesmedicine
This database includes 18 long-term ECG recordings of subjects referred to the Arrhythmia Laboratory at Boston's Beth Israel Hospital (now the Beth Israel Deaconess Medical Center). Subjects included in this database were found to have had no significant arrhythmias; they include 5 men, aged 26 to 45, and 13 women, aged 20 to 50.
healthlife sciencesmedicine
The MIT-BIH Polysomnographic Database is a collection of recordings of multiple physiologic signals during sleep. Subjects were monitored in Boston's Beth Israel Hospital Sleep Laboratory for evaluation of chronic obstructive sleep apnea syndrome, and to test the effects of constant positive airway pressure (CPAP), a standard therapeutic intervention that usually prevents or substantially reduces airway obstruction in these subjects.
healthlife sciencesmedicine
This database includes 28 ECG recordings of varying lengths, most of which were recorded during exercise stress tests and which exhibit transient ST depression. The last five records (323 through 327) are excerpts of long-term ECG recordings and exhibit ST elevation.
healthlife sciencesmedicine
This database includes 78 half-hour ECG recordings chosen to supplement the examples of supraventricular arrhythmias in the MIT-BIH Arrhythmia Database.
healthlife sciencesmedicine
The MUSIC (MUerte Subita en Insuficiencia Cardiaca) study is a prospective, multicentre, longitudinal study designed to assess risk predictors of cardiac mortality and sudden cardiac death (SCD) in ambulatory patients with chronic heart failure (CHF). The study population consisted of 992 patients with CHF consecutively enrolled from the specialized HF clinics of eight University Spanish Hospitals between April 2003 and December 2004, and followed up for a median of 44 months (until November 2008). All patients had a 3-lead resting electrocardiogram (ECG), a 24 h, 2-(4%) or 3-lead (96%) Holter...
analysis ready databiodiversitybioinformaticsbiologyfastagenomegenomicgraphinformation retrievallife sciencesmedicinemetagenomicsmicrobiometranscriptomicswhole exome sequencingwhole genome sequencing
The MetaGraph Sequence Indexes dataset comprises full-text searchable index files for raw sequencing data hosted in major public repositories. These include the European Nucleotide Archive (ENA) managed by the European Bioinformatics Institute (EMBL-EBI), the Sequence Read Archive (SRA) maintained by the National Center for Biotechnology Information (NCBI), and the DNA Data Bank of Japan (DDBJ) Sequence Read Archive (DRA).All index files can be used with the MetaGraph framework for sequence search. Indexes can be jointly used for aggregated search in the cloud or can be individually downloaded...
bioinformaticsbiologygenomiclife sciencesmetagenomicsmicrobiome
Metagenomic indexes for use with the Slacken taxonomic classification tool
benchmarkBiohubbiologybiomolecular modelingcell biologylife sciencesmachine learningmodel
This dataset includes data and models relevant to benchmarking multimodal biological models. The data has been sourced and curated by a team of experts at Biohub and is provided as part of these datasets only when it is not publicly available or requires transformation to support effective model benchmarking.
healthlife sciencesmedicine
Short duration ECG signals are recorded from a healthy 25-year-old male performing different physical activities to study the effect of motion artifacts on ECG signals and their sparsity.
healthlife sciencesmedicine
This data collection, contributed to PhysioBank by Kevin Sweeney and colleagues at the National University of Ireland in Maynooth, contains examples of functional near-infrared spectroscopy (fNIRS) and electroencephalogram (EEG) recordings that have been created for evaluating artifact removal methods.
healthlife sciencesmedicine
This project contains acceleration (in units of g) and heart rate (bpm, measured from photoplethysmography) recorded from the Apple Watch, as well as labeled sleep scored from gold-standard polysomnography. Data were collected at the University of Michigan from June 2017 to March 2019, and there are 31 subjects in total. Code to read and process these files is available on GitHub. The paper corresponding to the work is Walch et al., "Sleep stage prediction with raw acceleration and photoplethysmography heart rate data derived from a consumer wearable device", SLEEP (2019).
healthlife sciencesmedicine
Multilevel Monitoring of Activity and Sleep in Healthy people (MMASH) dataset provides 24 hours of continuous beat-to-beat heart data, triaxial accelerometer data, sleep quality, physical activity and psychological characteristics (i.e., anxiety status, stress events and emotions) for 22 healthy participants. Moreover, saliva bio-markers (i.e.cortisol and melatonin) and activity log were also provided in this dataset. The MMASH dataset will enable researchers to test the correlations between physical activity, sleep quality, and psychological characteristics.
healthlife sciencesmedicine
The method of multiscale entropy (MSE) analysis is useful for investigating complexity in physiologic signals and other series that have correlations at multiple (time) scales.
healthlife sciencesmedicine
Multiscale multifractal analysis (MMA) (Gierałtowski et al., 2012) is a time series analysis method, designed to describe scaling properties of fluctuations within the signal analyzed. The main result of this procedure is the so called Hurst surface h(q,s) , which is a dependence of the local Hurst exponent h (fluctuation scaling exponent) on the multifractal parameter q (Kantelhardt et al., 2002) and the scale of observation s (data window width).
healthlife sciencesmedicine
Poincaré delay maps are widely used in the analysis of cardiac interbeat interval (RR) dynamics. To facilitate visualization of the structure of these complex time series, we introduced a methodology called multiscale Poincaré (MSP) plots.
healthlife sciencesmedicine
This database provides a collection of myocardial perfusion scintigraphy images in DICOM format with all metadata and segmentations (masks) in NIfTI format. The images were obtained from patients undergoing scintigraphy examinations to investigate cardiac conditions such as ischemia and myocardial infarction. The dataset encompasses a diversity of clinical cases, including various perfusion patterns and underlying cardiac conditions. All images have been properly anonymized, and the age range of the patients is from 20 to 90 years. This database represents a valuable source of information for ...
healthlife sciencesmedicine
The development of algorithms for the extraction of the foetal ECG (fECG) from non-invasive recordings is hampered by the lack of publicly-available reference datasets, which could be used to benchmark different algorithms while providing a ground truth on the foetal heart activity when an invasive scalp lead is unavailable. By enriching the electrophysiological recordings with simultaneous multimodal signals, these datasets could also help the investigation of the foetal cardiac physiology, providing ground truth for the analysis in early pregnancy, when the fECG is not directly accessible. T...
geneticgenomiclife scienceswhole genome sequencing
This dataset includes the sequencing and assembly of a reference standard human genome (GM12878) using the MinION nanopore sequencing instrument with the R9.4 1D chemistry.
computer visionimage processingimaginglife sciencesmachine learningmagnetic resonance imagingneuroimagingneurosciencenifti
Here, we collected and pre-processed a massive, high-quality 7T fMRI dataset that can be used to advance our understanding of how the brain works. A unique feature of this dataset is the massive amount of data available per individual subject. The data were acquired using ultra-high-field fMRI (7T, whole-brain, 1.8-mm resolution, 1.6-s TR). We measured fMRI responses while each of 8 participants viewed 9,000–10,000 distinct, color natural scenes (22,500–30,000 trials) in 30–40 weekly scan sessions over the course of a year. Additional measures were collected including resting-state data, retin...
healthlife sciencesmedicine
This database contains postural sway measurements for 15 healthy young (mean age 23, standard deviation 2), and 12 healthy elderly (mean age 73, standard deviation 3) volunteers. Each subject's postural sway was recorded during a test of 10 minutes for the young subjects, or 5 minutes for the elderly subjects, in all cases with a 2-minute seated break midway through the test. Each test was divided into 30-second trials, and each file of the database contains data for one of these 30-second trials.
healthlife sciencesmedicine
Fetal cardiac arrhythmias are defined as any irregular fetal cardiac rhythm or regular rhythm at a rate outside the reference range of 100 to 200 beat per minute (bpm). Arrhythmias are discovered in about 1% of fetuses with about 10% of these being considered potential sources of morbidity. Although most fetal arrhythmias are benign, some can cause fetal hydrops and lead to fetal death. This means that up to 1 fetus in 100 need their arrhythmias to be closely monitored and if indicated treated in-utero using antiarrhythmic therapy. The Non-Invasive Fetal ECG Arrhythmia Database (NIFEA DB) prov...
healthlife sciencesmedicine
This database contains a series of 55 multichannel abdominal non-invasive fetal electrocardiogram (FECG) recordings, taken from a single subject between 21 to 40 weeks of pregnancy. The records have variable durations, and were taken weekly (two or more records were acquired during some weeks). These records may be very useful for testing signal separation algorithms.
healthlife sciencesmedicine
The aim of this year's PhysioNet/Computing in Cardiology Challenge is to encourage development of accurate algorithms for locating QRS complexes and estimating the QT interval in noninvasive FECG signals.
healthlife sciencesmedicine
This database includes beat annotation files for 54 long-term ECG recordings of subjects in normal sinus rhythm (30 men, aged 28.5 to 76, and 24 women, aged 58 to 73). The original ECG recordings (not available) were digitized at 128 samples per second, and the beat annotations were obtained by automated analysis with manual review and correction.
healthlife sciencesmedicine
The Norwegian Endurance Athlete ECG Database contains 12-lead ECG recordings from 28 elite athletes from various sports in Norway. All recordings are 10 seconds resting ECGs recorded with a General Electric (GE) MAC VUE 360 electrocardiograph. All ECGs are interpreted with both the GE Marquette SL12 algorithm (version 23 (v243)) and one cardiologist with training in interpretation of athlete's ECG. The data was collected at the University of Oslo in February and March 2020.
healthlife sciencesmedicine
This project is developing a set of recordings of fetal scalp electrograms and uterine muscular activity, with beat-by-beat annotations of the fetal ECG, to support studies of fetal heart rate variability.
healthlife sciencesmedicine
We provide an open access dataset of High densitY Surface Electromyogram (HD-sEMG) Recordings (named "Hyser"). We acquired data from 20 subjects with each subject participating in our experiment twice on separate days following the same experiment paradigm. Our Hyser dataset contains five sub-datasets: (1) pattern recognition (PR) dataset acquired during 34 hand gestures, (2) maximal voluntary muscle contraction (MVC) dataset while subjects contracted each individual finger, (3) one-degree of freedom (DoF) dataset acquired during force-varying contraction of each individual finger, (...
biodiversityfastqgeneticgenomelife sciencesmuseumwildlife
DNA sequence data of UCE loci collected from the world's bird species (n=10,560).
archiveslife sciencespharmaceuticaltext analysistxt
The OIDA Data on AWS contain the metadata, documents, and extracted text for all of the documents in the UCSF-JHU Opioid Industry Documents Archive, a growing corpus of internal corporate records and other documents arising from the opioid industry.
healthlife sciencesmedicine
Parkinson’s disease (PD) is the second-most common neurodegenerative disorder, while incidence and worldwide burden are further increasing. In the era of digital health transformation, smart devices and mobile sensors, including smartphones and smartwatches, can provide an affordable source to capture and analyse digital objective biomarkers. These can aid in early diagnosis and studying phenotypical characteristics. The Parkinson’s Disease Smartwatch (PADS) dataset comprises clinical assessments of a broad spectrum of PD patients, other similar movement disorders and healthy controls. The ass...
healthlife sciencesmedicine
This database of two-channel ECG recordings has been created for use in the Computers in Cardiology Challenge 2001, an open competition with the goal of developing automated methods for predicting paroxysmal atrial fibrillation (PAF). See the challenge announcement for information about the competition, and see Predicting Onset of Atrial Fibrillation for a brief overview of the clinical problem, its significance, and suggestions for further reading on the subject.
healthlife sciencesmedicine
This dataset, named PolySomnoGraphic Inter-scorer Performance Assessment (PSG-IPA) database, comprises 20 polysomnography (PSG) recordings and related multi-expert scoring annotations. It was utilized in a study to evaluate inter-scorer variability, specifically assessing reliability and scoring times associated with various PSG review tasks. The study also aimed to compare the impact of computer-assisted (semi-automatic) scoring versus unassisted visual analysis on these factors. The dataset includes recordings of common raw PSG signal activity, such as electroencephalography (EEG), electrooc...
healthlife sciencesmedicine
Physikalisch-Technische Bundesanstalt (PTB), the National Metrology Institute of Germany, has provided this compilation of digitized ECGs for research, algorithmic benchmarking or teaching purposes to the users of PhysioNet. The ECGs were collected from healthy volunteers and patients with different heart diseases by Professor Michael Oeff, M.D.
healthlife sciencesmedicine
The PTB-XL+ dataset is a comprehensive feature dataset that supplements the PTB-XL ECG dataset. It includes ECG features extracted via two commercial and one open-source algorithm in a harmonized format as well as median beats or, where applicable, fiducial points extracted by the respective algorithms. In addition, it provides automatic diagnosis statements from one commercial ECG analysis algorithm at different processing levels that are ready to be used for training and evaluation of machine learning models.
healthlife sciencesmedicine
Electrocardiography (ECG) is a key diagnostic tool to assess the cardiac condition of a patient. Automatic ECG interpretation algorithms as diagnosis support systems promise large reliefs for the medical personnel - only on the basis of the number of ECGs that are routinely taken. However, the development of such algorithms requires large training datasets and clear benchmark procedures. In our opinion, both aspects are not covered satisfactorily by existing freely accessible ECG datasets. The PTB-XL ECG dataset is a large dataset of 21799 clinical 12-lead ECGs from 18869 patients of 10 second...
healthlife sciencesmedicine
Atrial fibrillation (AF) is the most frequent arrhythmia, but paroxysmal atrial fibrillation (PAF) often remains unrecognized. Early detection of PAF is of great value for AF surgery options, drug intervention and diagnosis and treatment of various clinical complications. Although accurate detection of paroxysmal AF is very important, there is currently no algorithm that can efficiently measure the onset and end of AF episode in dynamic or wearable ECGs. Previous AF detection algorithms usually focus on the classification of AF rhythm instead of locating the onsets and ends of AF episodes. Thu...
healthlife sciencesmedicine
Multiple Sclerosis (MS) is an inflammatory autoimmune disease of the central nervous system, causing increased vulnerability to infections and disability among young adults. Ever since the coronavirus disease 2019 (COVID-19) outbreak, caused by severe acute respiratory syndrome coronavirus 2 infections, there have been concerns among people with MS (PwMS) about the potential interactions between various disease-modifying therapies and COVID-19. The COVID-19 in MS Global Data Sharing Initiative (GDSI) was initiated in 2020 to address these concerns. This paper focuses on the anonymisation and o...
healthlife sciencesmedicine
This database contains one hour oxygen saturation measurements of 36 patients, used for the analysis of oxygen saturation variability.
healthlife sciencesmedicine
A better understanding of the permittivity of skeletal muscle is essential for the development of new diagnostic tools and approaches for neuromuscular evaluation. However, there remain important knowledge gaps in our understanding of this property in healthy and diseased skeletal muscle, which hinder its translation into clinical application. The aim of this project is to provide a platform for the researchers to contribute and share the dissemination of this property in healthy and diseased muscle. Ultimately, the normative data reported will offer the scientific community the opportunity to...
healthlife sciencesmedicine
The PhysioNet Cardiovascular Signal Toolbox is an open-source modular program for calculating heart rate variability (HRV) implemented in Matlab with evidence-based algorithms and output formats. The Toolbox is compatible with 64-bit MATLAB on GNU/Linux, Mac OS X, and MS-Windows.
healthlife sciencesmedicine
To develop robust algorithms for automated diagnosis of medical conditions such as cardiac arrhythmias, researchers require large collections of data with human expert annotations. Currently, there is a lack of accessible, open-source platforms for human experts to collaboratively develop these annotated datasets through a web interface. In this work, we developed a flexible, generalizable, web-based framework to enable multiple users to create and share annotations on multi-channel physiological waveforms. The software is simple to install and offers a range of features, including: user manag...
healthlife sciencesmedicine
The PhysioZoo database contains electrocardiographic recordings (ECG) taken from multiple types of mammals (dogs, rabbits, mice). Each record is provided in 3 different formats: MATLAB (.mat), simple text (.txt), PhysioNet (.hea,.dat,.qrs). For each record the following data is available: the raw ECG signal, reference (human corrected) R-peak annotations and the signal quality annotations. All of the files formats are compatible with the PhysioZoo open source software available at physiozoo.com. When the recordings were taken, all the mammals were conscious, and no drugs were administered prio...
healthlife sciencesmedicine
A collection of physiological signals in ten healthy subjects in response to a slow tilt, a fast tilt, and a standing-up maneuver.
biologylife sciences
PhysioNet offers free web access to large collections of recorded physiologic signals (PhysioBank) and related open-source software (PhysioToolkit).
healthlife sciencesmedicine
This database contains “post-ictal heart rate oscillations in a heterogeneous group of patients with partial epilepsy.
healthlife sciencesmedicine
The focus of the PhysioNet/CinC Challenge 2012 is to develop methods for patient-specific prediction of in-hospital mortality. Participants will use information collected during the first two days of an ICU stay to predict which patients survive their hospitalizations, and which patients do not.
healthlife sciencesmedicine
Following the success of the first Computers in Cardiology Challenge, we are pleased to offer a new challenge from PhysioNet and Computers in Cardiology 2001. The challenge is to develop a fully automated method to predict the onset of paroxysmal atrial fibrillation/flutter (PAF), based on the ECG prior to the event. The goal of the contest is to stimulate effort and advance the state of the art in this clinically significant problem, and to foster both friendly competition and wide-ranging collaborations.
healthlife sciencesmedicine
A respiratory pressure, flow, and dynamic circumference (chest and abdominal) dataset was collected from 30 healthy adults at the University of Canterbury under Human Research Ethics Committee (HREC) ethics. Pressure and flow data was collected using a bi-directional Venturi, with data combined in post-collection processing. Dynamic circumferences were measured using inelastic band tape measures attached to rotary encoders capturing expansion and contraction. Data was collected at zero end-expiratory pressure (ZEEP) and with continuous positive airway pressure (CPAP) ventilation, at positive e...
healthlife sciencesmedicine
Puka calculates descriptive statistics such as heart rate variability (HRV), peak-valley respiratory sinus arrhythmia (RSA), and respiratory variables from EKG and strain gauge respiration data.
healthlife sciencesmedicine
We provide an open access, high resolution and time synchronised dataset from multiple sensors worn at different body locations including Photoplethysmogram (PPG), Inertial, Pressure and ECG. The recordings are from 22 healthy subjects performing 3 physical activities. This dataset contains 66 waveform records from multi-site and multi-wavelength PPGs, sensors’ attachment pressures, sensors’ temperatures, inertial data from accelerometer and gyroscope, along with annotated ECG data for a total of 19 channels. Additionally, systolic and diastolic blood pressures, as well as blood oxygenation sa...
healthlife sciencesmedicine
We introduce Q-Pain, a dataset for assessing bias in medical QA in the context of pain management. We developed 55 medical question-answer pairs across five different types of pain management: each question includes a detailed patient-specific medical scenario ("vignette") designed to enable the substitution of multiple different racial and gender "profiles" and to evaluate whether bias is present when answering whether or not to prescribe medication. Along with the dataset, we propose a new framework, including a sample experimental design, to measure the potential bias pr...
healthlife sciencesmedicine
Over 100 fifteen-minute two-lead ECG recordings (many excerpted from other databases), with onset, peak, and end markers for P, QRS, T, and (where present) U waves of from 30 to 50 selected beats in each recording.
healthlife sciencesmedicine
The seventh annual PhysioNet/Computers in Cardiology Challenge addresses a question of high clinical interest: Can the QT interval be measured by fully automated methods with an accuracy acceptable for clinical evaluations?
healthlife sciencesmedicine
Quantitative estimation of dehydration (total body water loss) using bioimpedance measurements, temperature measurements, salivary samples, and sweat samples.
healthlife sciencesmedicine
Many of the existing ECG toolboxes focus on the derivation of heart rate variability features from RR-intervals. By doing so, they assume correct detection of the QRS-complexes. However, it is highly likely that not all detections are correct. Therefore, it is recommended to visualize the actual R-peak positions in the ECG signal and allow manual adaptations. As a solution, we present R-DECO, an easy-to-use graphical user interface for the detection and correction of R-peaks. Within R-DECO, the R-peaks are detected by an adaptation of the Pan-Tompkins algorithm. Instead of using all the pre-pr...
healthlife sciencesmedicine
Heart rate variability (HRV) is mainly controlled by the autonomic nervous system (ANS) interacting with receptors on the sinoatrial node (SAN). HRV is influenced by many several factors such as chemical, hormonal and neural modulations, circadian changes, exercise, emotions, posture, and preload. The heart rate adaptation to changing factors is carried out by the activity of a variety of regulatory subsystems and results in a complex linear and non-linear time behaviour, which changes with age, gender and pathological conditions. Many studies explore an age range of 1-99 years. This study foc...
breast cancercancercomputer visioncsvlabeledlife sciencesmachine learningmammographymedical image computingmedical imagingradiology
According to the WHO, breast cancer is the most commonly occurring cancer worldwide. In 2020 alone, there were 2.3 million new breast cancer diagnoses and 685,000 deaths. Yet breast cancer mortality in high-income countries has dropped by 40% since the 1980s when health authorities implemented regular mammography screening in age groups considered at risk. Early detection and treatment are critical to reducing cancer fatalities, and your machine learning skills could help streamline the process radiologists use to evaluate screening mammograms. Currently, early detection of breast cancer requi...
healthlife sciencesmedicine
The Radiology Report Generation Models Evaluation Dataset For Chest X-rays (RadEvalX) is publicly available and developed similarly to the ReXVal dataset. Just like ReXVal, RadEvalX focuses on radiologist evaluations of errors found in automatically generated radiology reports. The dataset includes annotations from two board-certified radiologists, who identified clinically significant and clinically insignificant errors across eight different categories of errors. Compared to the ground-truth reports from the IU-Xray dataset, the evaluations were done on candidate radiology reports. For every...
healthlife sciencesmedicine
A major issue with many signal processing and machine learning algorithms is the lack of optimisation methods for determining the numerous hyper-parameters associated with the model as well as the knowledge of which hyper-parameters are relevant. These parameters are usually tunned by trial and error (manual search) or by grid search. In 2012 Bergstra et al. showed empirically that random search was performing similar or better than grid search while reducing the computational cost substantially.
healthlife sciencesmedicine
The recordings in this collection were originally selected for inclusion in the MIT-BIH Normal Sinus Rhythm Database, but were excluded after study revealed low-grade arrhythmias.
healthlife sciencesmedicine
This dataset contains airway gauge pressure, inspiratory differential pressure, and pulse oximetry waveforms collected from 20 healthy adult participants (10 females, 10 males) during simulated obstructive sleep apnoea (OSA) trials. Recordings include photoplethysmography (PPG) signals from a custom neck-worn reflectance oximeter, which records both arterial and venous blood waveforms from the carotid artery and internal jugular vein, respectively. Each subject completed a a series of 8 × 60-second breathing trials with varying positive airway pressures (0, 4, and 8 cmH₂O) set with a continuou...
healthlife sciencesmedicine
A study was conducted to collect respiratory pressure and flow data for model-based assessment, alongside electrical impedance tomography (EIT) aeration, electrocardiogram (ECG), and heart-rate belt (HRB) data. A 20 subjects set was selected with no known significant respiratory abnormalities, under University of Canterbury Human Research Ethics Committee (HREC) consent (HREC 2023/30/LR-PS). Subject demographic data was collected using a combination of measurements and a self-reported questionnaire. Subject demographic information to ascertain: sex; height; weight; age; any history of asthma, ...
healthlife sciencesmedicine
A trial was conducted to collect gauge pressure and flow from a venturi-based flow-meter, dynamic abdominal and thoracic circumference from rotary-encoder based tape measures, and aeration data from electrical impedance tomography (EIT). Data was collected from 80 adults, breathing with continuous positive airway pressure (CPAP) ventilation, under ethical consent from the University of Canterbury Human Research Ethics Committee (HREC 2023/04/LR-PS). In each subject’s recording the positive end expiratory pressure (PEEP) was increased from 4 to 12 cmH2O in 0.5 cmH2O increments, with data record...
healthlife sciencesmedicine
Functional metrics of autonomic control of heart rate, including baroreflex sensitivity, have been shown to be strongly associated with cardiovascular risk. A decrease in baroreflex sensitivity with aging is hypothesized to represent a contributing causal factor in the etiology of primary hypertension. To assess baroreflex function in human subjects, two complementary methods to simulate the response in heart rate elicited by the Valsalva maneuver were developed and applied to data obtained from a cohort of healthy normal volunteers.
healthlife sciencesmedicine
Saitama Heart Database Atrial Fibrillation (SHDB-AF) is a novel open-sourced Holter ECG database from Japan, containing data from 122 unique subjects with paroxysmal atrial fibrillation. Among the 128 recordings, 98 contain raw ECG data with rhythm annotations at the beat level, manually performed by a cardiology fellow. The remaining recordings consist only of ECG traces without annotations. The dataset was collected as part of a study evaluating the generalization performance of a deep learning atrial fibrillation event detection model across different distribution shifts.
healthlife sciencesmedicine
This dataset was collected as part of a study that aimed to determine the effects of intranasal insulin (INI) on cognition and motor performance in PD. The study was a proof of concept, randomized, double-blinded, placebo-controlled trial evaluating the effects of 40 international units (IU) of insulin or saline once daily for four weeks on cognitive and functional performance. Of 16 subjects enrolled, eight in the INI group and six in the placebo group completed verbal fluency (FAS), Unified Parkinson Disease Scale (UPDRS), and modified Hoehn and Yahr scale (HY, PD severity) at baseline and p...
healthlife sciencesmedicine
Sample Entropy is a useful tool for investigating the dynamics of heart rate and other time series. Sample Entropy is the negative natural logarithm of an estimate of the conditional probability that subseries (epochs) of length m that match pointwise within a tolerance r also match at the next point.
healthlife sciencesmedicine
These magnetic resonance angiography (MRA) images show coronal slices acquired from consecutive anteroposterior positions within the torso. The study was performed on a 1.5T General Electric (GE) Signa imaging system with gadolinium-contrast-enhancement for visualization of the cardiopulmonary vasculature. The pulse sequence used was a 3D time-of-flight fast spoiled gradient recalled acquisition in steady state (FSPGR, TR=6.3, TE=1.4, NEX=1, FOV = 40cm, slice thickness = 1.2mm).
healthlife sciencesmedicine
This is a multivariate data set recorded from a patient in the sleep laboratory of the Beth Israel Hospital (now the Beth Israel Deaconess Medical Center) in Boston, Massachusetts. This data set was extracted from record slp60 of the MIT-BIH Polysomnographic Database, and it was submitted to the Santa Fe Time Series Competition in 1991 by our group. The data are presented in text form and have been split into two sequential parts. Each line contains simultaneous samples of three parameters; the interval between samples in successive lines is 0.5 seconds. The first column is the heart rate, the...
healthlife sciencesmedicine
Existing datasets containing physiological data are mostly acquired at rest or in controlled scenarios. As a result, algorithms developed using such data may not perform as well as with biosignals acquired in dynamic and uncontrolled environments. ScientiSST MOVE is a multimodal dataset recording natural everyday activities, including lifting a chair, greeting, gesticulating, walking and running. Data was collected using three wearable devices, namely: a chestband, an armband, and the Empatica E4 wristband. This setup enabled recording of multi-channel Electrodermal Activity (EDA), Photoplethy...
healthlife sciencesmedicine
The SensSmartTech database comprises cardiovascular signals synchronously recorded by electrocardiograph (ECG), phonocardiograph (PCG), photoplethysmograph (PPG) and accelerometer (ACC) at heart rates at rest and after activity (HRs). It is composed of 338 30-s recordings taken from 32 healthy volunteers. Recordings contain information from 10 channels: 4 ECG (limb, V3 and V4 leads), 1 PCG (measured at heart apex), 4 PPG (measured at carotid and brachial arteries at two light wavelengths each) and 1 ACC (measured between V3 and V4 ECG electrodes), along with the recording time of each signal. ...
healthlife sciencesmedicine
The Shiraz University (SU) fetal heart sounds database (SUFHSDB) contains fetal and maternal phonocardiogram (PCG) recordings from 109 pregnant women in single and twin pregnancies. The recordings were made at Hafez Hospital of Shiraz University of Medical Sciences, Shiraz, Iran, from mothers aged from 16 to 47 years with a digital stethoscope placed on the lower maternal abdomen. In total, 99 subjects had one signal recorded, three subjects had two and seven cases of twins were recorded individually, resulting in 119 recordings. The average duration of each record is about 90 seconds. The sam...
healthlife sciencesmedicine
The database consists of EEG recordings of 14 patients acquired at the Unit of Neurology and Neurophysiology of the University of Siena. Subjects include 9 males (ages 25-71) and 5 females (ages 20-58). Subjects were monitored with a Video-EEG with a sampling rate of 512 Hz, with electrodes arranged on the basis of the international 10-20 System. Most of the recordings also contain 1 or 2 EKG signals. The diagnosis of epilepsy and the classification of seizures according to the criteria of the International League Against Epilepsy were performed by an expert clinician after a careful review of...
healthlife sciencesmedicine
This data set is a series of synthetic fetal phonocardiographic signals (PCGs) relative to different fetal states and recording conditions.
healthlife sciencesmedicine
This open database contains physiological measurements from 13 adult and healthy subjects during a standardized experimental setup. The physiology was examined with five different devices (NeXus-10 MKII, eMotion Faros 360°, SOMNOtouch NIBP, Hexoskin Hx1, Polar RS800 Multi), which, in contrast to other studies, were recorded simultaneously. The experiment included a five minute baseline measurement, five minute walking on the treadmill, a five minute cognitive audio test, and a five minute uphill walking on the treadmill. Measurements included electrocardiography (ECG), photoplethysmography, ac...
healthlife sciencesmedicine
The database contains 32 records of non-contact sleep monitoring by a bioradar. The records are accompanied by results of sleep scoring, based on polysomnography according to the rules of the American Academy of Sleep Medicine.
healthlife sciencesmedicine
The Sleep Heart Health Study (SHHS) is a prospective cohort study designed to investigate the relationship between sleep disordered breathing and cardiovascular disease.
healthlife sciencesmedicine
The sleep-edf database contains whole-night PolySomnoGraphic sleep recordings, containing EEG, EOG, chin EMG, and event markers.
healthlife sciencesmedicine
The sleep-edf database contains 197 whole-night PolySomnoGraphic sleep recordings, containing EEG, EOG, chin EMG, and event markers. Some records also contain respiration and body temperature. Corresponding hypnograms (sleep patterns) were manually scored by well-trained technicians according to the Rechtschaffen and Kales manual, and are also available.
healthlife sciencesmedicine
Software for calculating multifractal partitions and moments of a time series.
healthlife sciencesmedicine
Heart rate fragmentation (HRF) is a new method for assessing neuroautonomic integrity based on the analysis of short-term (high-frequency [HF]) heart rate dynamics. The code (in AWK) provided here is for the computation of three different metrics, PIP, PNNLS, and PNNSS introduced in 2017 by Costa and colleagues. The motivation for developing HRF was the recognition that changes in heart rate (HR) above the respiratory frequency not only inflate the value of traditional heart rate variability (HRV) metrics, such as rMSSD and HF power, but are a dynamical marker of cardioautonomic dysfunction. I...
healthlife sciencesmedicine
This database contains 135 pairs of RR interval time series, recorded by implanted cardioverter defibrillators (Medtronic Jewel PlusTM ICD 7218) in 78 subjects. Each series contains between 986 and 1022 RR intervals. One series of each pair includes a spontaneous episode of ventricular tachycardia (VT) or ventricular fibrillation (VF), and the other is a sample of the intrinsic (usually sinus) rhythm.
healthlife sciencesmedicine
The SGAMP database contains single-unit neuronal recordings of North Atlantic squid (Loligo pealei) giant axons in response to stimulus currents. The membrane potential and stimulus current are given for a total of 170 trials across 8 different axons.
healthlife sciencesmedicine
This database consists of 75 annotated recordings extracted from 32 Holter records. Each record is 30 minutes long and contains 12 standard leads, each sampled at 257 Hz, with gains varying from 250 to 1100 analog-to-digital converter units per millivolt.
healthlife sciencesmedicine
This database contains 25 full overnight polysomnograms with simultaneous three-channel Holter ECG, from adult subjects with suspected sleep-disordered breathing. A revised version of this database was posted on 1 September 2011.
healthlife sciencesmedicine
This database, contributed to PhysioNet by its creator, Jennifer Healey, contains a collection of multiparameter recordings from healthy volunteers, taken while they were driving on a prescribed route including city streets and highways in and around Boston, Massachusetts. The objective of the study for which these data were collected was to investigate the feasibility of automated recognition of stress on the basis of the recorded signals, which include ECG, EMG (right trapezius), GSR (galvanic skin resistance) measured on the hand and foot, and respiration.
healthlife sciencesmedicine
PhysioNet has inaugurated a Sudden Cardiac Death Database to support research and to stimulate progress in this important area of electrophysiology. We initiate this database with 23 complete Holter recordings (originally collected by Scott Greenwald while he was at MIT), from which half-hour excerpts have been available to researchers since 1989 as the MIT-BIH Malignant Ventricular Arrhythmia Database. The database currently includes 18 patients with underlying sinus rhythm (4 with intermittent pacing), 1 who was continuously paced, and 4 with atrial fibrillation. All patients had a sustained...
healthlife sciencesmedicine
The present dataset is composed of long-lasting (around 5 minutes) surface electromyographic (sEMG) signals recorded from 2011 and 2018 during ground walking of 31 young (20 years < age < 30 years) able-bodied subjects in the Movement Analysis Lab, Università Politecnica delle Marche, Ancona, Italy. Underweight, overweight, and obese people (body mass index, BMI < 18.5 Kg/m2 and BMI > 25 Kg/m2) and subjects affected by any pathological condition, joint pain, or undergone orthopedic surgery are not included in the present dataset. sEMG signals are acquired from the following ten dif...
healthlife sciencesmedicine
The data in this collection include: (1) 6 surrogate stationary signals with different correlations; (2) 7 surrogate correlated signals with linear, sinusoidal and power-law trends; and (3) 15 surrogate correlated signals with different types of nonstationarities. Each data file contains one column of data in ASCII format.
healthlife sciencesmedicine
This database has been assembled for the PhysioNet/Computers in Cardiology Challenge 2008. It contains 100 multichannel ECG records sampled at 500 Hz with 16 bit resolution over a ± 32 mV range. The subjects include patients with myocardial infarctions, transient ischemia, ventricular tachyarrhythmias, and other risk factors for sudden cardiac death, as well as healthy controls and synthetic cases with calibrated amounts of T-wave alternans.
healthlife sciencesmedicine
This is the keystroke dataset for the study titled 'High-accuracy detection of early Parkinson's Disease using multiple characteristics of finger movement while typing'. This research report is currently under review for publication by PLOS ONE. The dataset contains keystroke logs collected from over 200 subjects, with and without Parkinson's Disease (PD), as they typed normally on their own computer (without any supervision) over a period of weeks or months (having initially installed a custom keystroke recording app, Tappy). This dataset has been collected and analyzed in ord...
healthlife sciencesmedicine
The Term-Preterm ElectroHysteroGram DataSet with Tocogram (TPEHGT DS) contains 26 four-signal 30-min uterine EHG records, i.e., three EHG signals accompanied by a simultaneously recorded external tocogram measuring mechanical uterine activity (TOCO signal) of pregnant women, and another five 30-min uterine records (EHG signals and TOCO signal) of non-pregnant women.
healthlife sciencesmedicine
The Electrohysterogram records (uterine EMG records) included in the Term-Preterm ElectroHysteroGram DataBase (TPEHG DB) were obtained from 1997 to 2005 at the University Medical Centre Ljubljana, Department of Obstetrics and Gynecology. The records were obtained during regular check-ups either around the 22nd week of gestation or around the 32nd week of gestation.
healthlife sciencesmedicine
A total number of 5272 heart sound recordings were collected from the main four auscultation locations of 1568 subjects, aged between 0 and 21 years (mean ± STD = 6.1 ± 4.3 years), with a duration between 4.8 to 80.4 seconds (mean ± STD = 22.9 ± 7.4 s), totaling more than 33.5 hours of recording. Each cardiac murmur in the dataset has been annotated in detail by a human annotator, in terms of timing, shape, pitch, grading, quality and location. Moreover, segmentation annotations regarding the location of fundamental heart sounds (S1 and S2) in the recordings have been obtained using a semi-sup...
healthlife sciencesmedicine
Our popular series of challenges presented in cooperation with Computers in Cardiology continues this year in a new mode. Participants are invited to choose one of the five previous challenges as a topic for a follow-up study: Detecting sleep apnea from the ECG Predicting paroxysmal atrial fibrillation RR interval time series modeling Distinguishing ischemic from non-ischemic ST changes Spontaneous termination of atrial fibrillation The problems posed by these challenges have continued to interest many researchers long after the final deadlines have passed. We encourage you to read the papers ...
geneticgenomiclife sciences
The Genome Institute at Washington University has developed a high-throughput, fault-tolerant analysis information management system called the Genome Modeling System (GMS), capable of executing complex, interdependent, and automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. GMS includes a full system image with software and services, expandable from one workstation to a large compute cluster.
bioinformaticsbiologyepigenomicsgene expressiongenomicHomo sapienslife sciencesmedicineneurobiologyneuroscienceRNA-seqsingle-cell transcriptomicstranscriptomics
The Seattle Alzheimer's Disease Brain Cell Atlas Integrative Analysis Center (SEA-AD IAC) reprocesses datasets from SEA-AD and other large-scale Alzheimer's disease and related dementia studies to support harmonized cross-study analyses. The study provides uniformly processed single-cell genomics and multiomic data, harmonized metadata, and representations of disease pathology mapped to highly annotated BRAIN Initiative Cell Atlas Network (BICAN) and SEA-AD cell classifications. These resources support investigation of cell-type-specific molecular changes across Alzheimer's disease...
cancerlife sciencesmagnetic resonance imagingmedical imagingmedicineradiology
The University of California San Francisco Brain Metastases Stereotactic Radiosurgery (UCSF-BMSR) dataset is a public, clinical, multimodal brain MRI dataset consisting of 560 brain MRIs from 412 patients with expert annotations of 5136 brain metastases. Data consists of registered and skull stripped T1 post-contrast, T1 pre-contrast, FLAIR and subtraction (T1 pre-contrast - T1 post-contrast) images and voxelwise segmentations of enhancing brain metastases in NifTI format.
bioinformaticsbiologygenomicgenotypingHomo sapienslife sciencesmedicineneurobiologyneurosciencewhole genome sequencing
The Whole Genome Sequence Harmonization Study provides uniformly processed whole-genome sequencing data generated from the three primary AMP-AD cohort studies: the Religious Orders Study and Memory and Aging Project (ROSMAP), the Mount Sinai Brain Bank (MSBB), and the Mayo RNAseq Study. The project harmonizes whole-genome sequence data across these cohorts to support cross-study analyses of genomic variation associated with aging, Alzheimer's disease, and related dementias.
healthlife sciencesmedicine
This is a repository of MATLAB functions that can estimate transfer entropy (information flow) from one time series to another using a non-parametric partitioning algorithm.
healthlife sciencesmedicine
Sharing patient data such as clinical notes among clinicians and researchers is fundamental to advancements in clinical practice and biomedical research. Prior to distribution, it is often necessary and legally mandated to remove identifiers such as names, contact details, identification numbers, and dates to safeguard patient privacy. This process is known as deidentification. Here we provide a neural network model for the removal of patient identifiers from clinical text based upon Bidirectional Encoder Representations from Transformers (BERT) and two variations of BERT, namely Robustly Opti...
healthlife sciencesmedicine
The present database is an ensemble of the cardiorespiratory measurements acquired during 992 treadmill maximal graded exercise tests (GET) performed in the Exercise Physiology and Human Performance Lab of the University of Malaga. Heart rate, oxygen consumption, carbon dioxide generation, and pulmonary ventilation are measured on a breath-to-breath basis along with the treadmill speed during maximal effort tests. Participants are amateur and professional athletes are of ages ranging from 10 to 63 years old. The age, height, and weight of the participants are provided, as well as the temperatu...
healthlife sciencesmedicine
The authors used this dataset to evaluate the responsiveness of the cardiorespiratory-cerebrovascular networks by capturing linear and nonlinear interdependencies to postural changes. Ten young healthy adults participated in our study between December 2009 and February 2010 at Semmelweis University, Faculty of Medicine. Non-invasive measurements of arterial blood pressure (ABP), cardiac cycle duration (derived from ABP signals), breath-to-breath interval (capnography), cerebral blood flow velocity (BFV, recorded by transcranial Doppler sonography), and cerebral hemodynamics (hemoglobin signals...
biologychemical biologylife sciencespharmaceutical
Collection of 7 billion small molecules in SMILES notation with 28 billion fingerprints, including MACCS, ECFP4, FCFP4, and PubChem, with pre-constructed USearch indexes over them.
healthlife sciencesmedicine
The UniCA ElectroTastegram Database (PROP) contains 39 differential biopotential measurements recorded from the tongues of as many healthy voluntary human subjects (16 males, 23 females, equally divided into the three PROP taster status classes), during a stimulation with 30uL, 3.2 mmol/L solution of 6-n-propylthiouracil (PROP).
agriculturebiodiversitybioinformaticsbiologyfood securitygeneticgenomiclife scienceswhole genome sequencing
This dataset captures Sunflower's genetic diversity originating from thousands of wild, cultivated, and landrace sunflower individuals distributed across North America.The data consists of raw sequences and associated botanical metadata, aligned sequences (to three different reference genomes), and sets of SNPs computed across several cohorts.
healthlife sciencesmedicine
This database includes 208 voice samples, from 150 pathological, and 58 healthy voices.
healthlife sciencesmedicine
The data set contains 40 pulse signal recordings obtained from 15 healthy volunteers (12 men and 3 women between 23 and 35 years). For each subject, there is a simultaneous face video recording, and a finger pulse recording reference system, in a sitting position.
healthlife sciencesmedicine
This database is from a cohort study of pregnant women up to 20 weeks of pregnancy and followed until delivery. Measurement of maternal visceral adipose tissue (VAT) was performed during routine obstetric ultrasound. At this time, the biometric evaluation was also performed, and information obtained from prenatal care. Gestational outcomes, including gestational diabetes mellitus (GDM), were obtained through evaluating the patients' medical records at the hospitals where they took place. The data was collected as part of a study that sought to evaluate if maternal VAT could predict GDM at ...
healthlife sciencesmedicine
Vital File Web Viewer is an open-source, browser-based tool for visualizing high-resolution vital signs data stored in the .vital format, commonly used during surgery or intensive care monitoring. The viewer enables seamless access to time-series waveform data across operating systems without requiring installation or server-side processing. This tool facilitates rapid data exploration and quality assessment in clinical research environments, particularly when centralized software infrastructure is unavailable.
healthlife sciencesmedicine
Intraoperative cardiac arrhythmias present distinct characteristics and clinical challenges compared to non-surgical environments, yet publicly available electrocardiogram (ECG) databases have primarily focused on ambulatory and intensive care environments. To address this gap, we present the VitalDB Arrhythmia Database, a comprehensive collection of annotated intraoperative ECG recordings specifically designed for developing and validating arrhythmia detection algorithms in the surgical context. The database comprises 734,528 seconds of continuous ECG data from 482 surgical patients, with ove...
healthlife sciencesmedicine
The wfdb-swig package provides interfaces between the WFDB library and software written in a variety of other languages, so that such software can have access to the full range of capabilities supported by current and future versions of the WFDB library. The package provides interfaces for software written using Perl, Python, C# (and other .NET languages), and Java. The wfdb-swig package can be readily extended for use with other target languages supported by SWIG, such as PHP, Ruby, TCL, and several versions of Lisp.
healthlife sciencesmedicine
The WFDB SWIG Toolbox for MATLAB is a collection of applications for reading, writing, manipulating, and plotting PhysioBank data, implemented as functions in MATLAB.
healthlife sciencesmedicine
Effective processing and analysis of physiological data requires specialized software. We have developed a large collection of such software over the past thirty years, and much of it is contained within the WFDB (Waveform Database) Software Package. The WFDB Software Package comprises over 70 applications for signal processing and automated analysis. A comprehensive collection of documentation, including tutorials and reference manuals, is also included in the package. The package is written in highly portable C and can be used on all popular platforms, including GNU/Linux, MacOS, MS-Windows,...
healthlife sciencesmedicine
Physiological waveforms - such as electrocardiograms (ECG), electroencephalograms (EEG), electromyograms (EMG) - are generated during the course of routine care. These signals contain information that can be used to understand underlying conditions of health. Effective processing and analysis of physiological data requires specialized software. The WaveForm DataBase (WFDB) Toolbox for MATLAB and Octave is a collection of over 30 functions and utilities that integrate PhysioNet's open-source applications and databases with the high-precision numerical computational and graphics environment ...
healthlife sciencesmedicine
Physiological waveforms - such as electrocardiograms (ECG), electroencephalograms (EEG), electromyograms (EMG) - are generated during the course of routine care. These signals contain information that can be used to understand underlying conditions of health. Effective processing and analysis of physiological data requires specialized software. The waveform-database (WFDB) package for Python is a library of tools for reading, writing, and processing physiological signals and annotations, written in the Python programming language. Core components of the Python package are loosely based on the ...
healthlife sciencesmedicine
This original dataset contains physiological signals collected during structured acute stress induction and aerobic and anaerobic exercise sessions using a wearable device. Blood volume pulse, motion-based activity, skin temperature, and electrodermal activity were recorded with the Empatica E4, a research-grade wearable. The stress induction protocol involved math and emotional tasks designed to provoke stress responses, interleaved with rest periods. Self-reported stress levels were also recorded during this procedure. For the exercise sessions, distinct routines on a stationary bike were cr...
healthlife sciencesmedicine
This data collection contains a single-lead electrocardiogram and triaxial acceleration signals of 80 elderly frailty patients, who entered a cardiac rehabilitation program after open-heart surgery. The signals were collected using a chest-based heart rate monitor worn by the patients performing a series of exercise tests for health status assessment. The tests include veloergometry, 6-minute walk test, stair climbing test, timed up and go test, and gait analysis on a treadmill. The signals are supplemented with the demographic and clinical characteristics of the patients including the Edmonto...
healthlife sciencesmedicine
A collection of wide-field calcium imaging (WFCI) sleep and wake recordings collected from twelve transgenic mice expressing GCaMP6f in excitatory neurons. Each mouse underwent a three-hour undisturbed WFCI recording session where wake, REM (rapid eye movement) sleep and NREM (non-REM) sleep was recorded. Each WFCI recording is manually scored by sleep scoring experts in 10-second epochs as wake, NREM or REM by use of adjunct EEG/EMG. The dataset contains annotated WFCI recordings, brain mask and the Paxinos atlas used for defining the brain regions. The dataset was collected as part of a stud...
healthlife sciencesmedicine
The electrocardiogram (ECG) is a non-invasive representation of the electrical activity of the heart. Although the twelve-lead ECG is the standard diagnostic screening system for many cardiological issues, the limited accessibility of twelve-lead ECG devices provides a rationale for smaller, lower-cost, and easier to use devices. While single-lead ECGs are limiting [1], reduced-lead ECG systems hold promise, with evidence that subsets of the standard twelve leads can capture useful information [2], [3], [4] and even be comparable to twelve-lead ECGs in some limited contexts. In 2017 we challen...
healthlife sciencesmedicine
The Wilson Central Terminal ECG Database (WCTECGdb) contains the Wilson Central Terminal (WCT), the voltage of right arm (RA), left arm (LA) and left leg (LL), six unipolar chest leads associated with three limb leads and six precordial leads. With our ECG device, the potentials of RA, LA, LL and six true unipolar leads are measured using the right leg as the reference point. Having this configuration, we have been able to overcome the difficulty of recording the WCT in a clinical setting. Our data confirmed once again that the WCT does not have a small value, and could be as high as 241% of l...
healthlife sciencesmedicine
This database contains wrist PPGs recorded during walking, running and bike riding. Simultaneous motion estimates are collected using both accelerometers and gyroscopes to give multiple options for the removal of motion interference from the PPG traces. A reference chest ECG is included to allow a gold-standard comparison of heart rate during exercise.
healthlife sciencesmedicine
The goal of the challenge is use information from the available signals to correctly classify target arousal regions.
healthlife sciencesmedicine
Brain–computer interfaces (BCIs) have wide-ranging applications as solutions for replacing or substituting neural output that has been lost because of severe neuromuscular injury or disease, such as individuals with late-stage amyotrophic lateral sclerosis (ALS). The P300-based BCI is one of the most commonly researched BCI for communication. This BCI dataset is curated from data originally generated from previous visual P300-based BCI speller studies, which include single- and multi-session experiments under a wide range of conditions. The BCI data are provided in an enriched and standardised...
healthlife sciencesmedicine
edf-anonymize reads an EDF or EDF+ file (input), writing an anonymized copy of it as output.
biodiversitybioinformaticsconservationearth observationlife sciences
iNaturalist is a community science effort in which participants share observations of living organisms that they encounter and document with photographic evidence, location, and date. The community works together reviewing these images to identify these observations to species. This collection represents the licensed images accompanying iNaturalist observations.
healthlife sciencesmedicine
The neuroQWERTY MIT-CSXPD database contains keystroke logs collected from 85 subjects with and without parkinsons disease (PD). This dataset has been collected and analyzed in order to indicate that the routine interaction with computer keyboards can be used to detect motor signs in the early stages of PD.
healthlife sciencesmedicine
The pNNx software package expands the analysis capabilities of the widely used pNN50 measure, providing researchers with the flexibility to test various thresholds for optimal discrimination of HRV in populations of interest.
healthlife sciencesmedicine
plt is a non-interactive plotting utility originally written for Unix by Paul Albrecht. plt can produce publication-quality 2D plots in PostScript from easily-produced text or binary data files, and can also create screen plots under the X Window System.
genetic mapslife sciencespopulation geneticsrecombination mapssimulations
Contains all resources (genome specifications, recombination maps, etc.) required for species specific simulation with the stdpopsim package. These resources are originally from a variety of other consortium and published work but are consolidated here for ease of access and use. If you are interested in adding a new species to the stdpopsim resource please raise an issue on the stdpopsim GitHub page to have the necessary files added here.
healthlife sciencesmedicine
Our team previously introduced an innovative concept for an "invisible" Electrocardiography (ECG) system, incorporating electrodes and sensors into a toilet seat design to enable signal acquisition from the thighs. Building upon that work, we now present a novel dataset featuring real-world, single-lead ECG signals captured at the thighs, offering a valuable resource for advancing research on thigh-based ECG for cardiovascular disease assessment. To our knowledge, this is the first dataset of its kind. The tOLIet dataset comprises 149 ECG recordings collected from 86 individuals (50 ...
bioinformaticsgenomegenomicHomo sapienslife sciencesMus musculusnon-human primateopen source softwareRattus norvegicusvariant annotation
GenomeKit is Deep Genomics’ Python library for fast and easy access to genomic resources such as sequence, data tracks, and annotations. The goal is to let machine learning researchers build data sets easily, and to be creative about how those data sets are designed. Out of the box, GenomeKit provides access to pre-built optimized genomic data files that are required for its operation.
life sciencesneuroimagingtransportationworkload analysis
Commercial pilot simulation data during safety-of-flight scenarios.
bioinformaticsgenomicgenotypingHomo sapienslife scienceslong read sequencingwhole genome sequencing
The Platinum Pedigree Consortium (PCC) is a collaborative project to create a comprehensive reference for human genetic variation using a four-generation, 28-member family (CEPH-1463). We employed five different short and long-read sequencing technologies to generate phased assemblies and characterize both inherited and de novo variation, including at some of the most difficult to genotype genomic regions such as tandem repeats, centromeres, and the Y chromosome. This extensive "truth set" is publicly available and can be used to test and benchmark new algorithms and technologies to ...
bioinformaticsgenomiclife sciencesmetagenomicsmsaRNA-seqstructural biology
The elDORS (elevated Database Of RNA Sequences) database provides a massive-scale, updated repository of RNA sequence data curated from diverse genomic, non-coding RNA, and metagenomic sources. Following a rigorous hierarchical redundancy removal workflow, the dataset features two distinct tiers: the baseline elDORS_raw database (elDORS_raw_v1) containing ~1.91 billion sequences, and a clustered and optimized elDORS version (elDORS_v1) containing ~1.32 billion sequences (clustered at 80% sequence identity and 80% overlap, keeping sequences between 10 and 4096 nucleotides). To bypass seve...
fast5fastqgeneticgenomiclife scienceswhole genome sequencing
The 1KG-ONT-VIENNA panel comprises medium coverage ONT sequencing data for 1.019 samples from the 1000 Genomes Project collection, structural variants, and their haplotype context.
agricultureamazon.sciencebiologyCaenorhabditis elegansDanio reriogeneticgenomicHomo sapienslife sciencesMus musculusRattus norvegicusreference index
Common reference genomes hosted on AWS S3. Can be used when aligning and analysing raw DNA sequencing data.
assemblybacteriabioinformaticsfastagenomiclife sciencesmicrobial genomicsshort read sequencingwhole genome sequencing
All bacterial isolate whole-genome sequencing data from INSDC, uniformly assembled, quality-controlled, annotated, and searchable.
deep learninglife sciencesmolecular dockingopen source softwareprotein folding
This is the data used to train the Boltz-1 model. It contains the following datasets:
amazon.sciencebioinformaticsfastqgeneticgenomiclife scienceslong read sequencingshort read sequencingwhole exome sequencingwhole genome sequencing
To facilitate benchmarking and development, the Google Brain group has sequenced 9 human samples covering the Genome in a Bottle truth sets on different sequencing instruments, sequencing modalities (Illumina short read and Pacific BioSciences long read), sample preparation protocols, and for whole genome and whole exome capture. The original source of these data are gs://google-brain-genomics-public.
archiveschemistryfossil fuelhealthlife sciencesmedicinepharmaceuticaltext analysistxt
The IDL Data on AWS contain the metadata, documents, and extracted text for all of the documents in the UCSF Industry Documents Library, a growing corpus of internal corporate records and other documents arising from the tobacco, opioids, chemical, drug, food, fossil fuel industries.
biodiversitycoastalconservationecosystemsenvironmentalgeospatiallife sciencesoceanswater
The Ocean Biodiversity Information System (OBIS) was founded in 2000 under the Census of Marine Life. It is now a programme component of the International Oceanographic Data and Information Exchange (IODE) programme of the Intergovernmental Oceanographic Commission (IOC) of UNESCO. OBIS aims to be the most comprehensive data and information gateway on the diversity, distribution and abundance of marine life to support its Member States in achieving a healthy and resilient ocean ecosystem. The OBIS network consists of over 30 regional and thematic nodes, and provides access to more than 5,000 d...
brain imagesbrain modelselectrophysiologyion channelslife sciencesmicrocircuit modeling and simulationmorphological reconstructionsMus musculusneurosciencesimulation neurosciencesingle neuron models
The Blue Brain Open Data represents an extensive neuroscience dataset encompassing a diverse range of data types, including experimental, model, and simulation data, along with images and videos depicting reconstructed neurons and brain regions.
SocialGene RefSeq Databases
amino acidbioinformaticschemical biologygenomicgraphlife sciencesmetagenomicsmicrobiomepharmaceuticalprotein
Precomputed SocialGene Neo4j graph databases of various sizes built from RefSeq genomes and MIBiG BGCs.
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