This registry exists to help people discover and share datasets that are available via AWS resources. See recent additions and learn more about sharing data on AWS.
See all usage examples for datasets listed in this registry tagged with biology.
You are currently viewing a subset of data tagged with biology.
If you want to add a dataset or example of how to use a dataset to this registry, please follow the instructions on the Registry of Open Data on AWS GitHub repository.
Unless specifically stated in the applicable dataset documentation, datasets available through the Registry of Open Data on AWS are not provided and maintained by AWS. Datasets are provided and maintained by a variety of third parties under a variety of licenses. Please check dataset licenses and related documentation to determine if a dataset may be used for your application.
If you have a project using a listed dataset, please tell us about it. We may work with you to feature your project in a blog post.
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:
bambioinformaticsbiologycramgeneticgenomicgenotypinglife sciencesmachine learningpopulation geneticsshort read sequencingstructural variationtertiary analysisvariant annotationwhole genome sequencing
Overview
This dataset contains alignment files and small variant (includes single nucleotide variants (SNV) and indels), copy number variant (CNV), short tandem repeat (i.e., repeat expansion; STR), structural variant (SV) and other variant call files from the 1000 Genomes Project (1KGP) Phase 3 dataset (3,202 individuals, 602 trios) using Illumina DRAGEN v3.5.7b, v3.7.6, v4.0.3, v4.2.7, and v4.4.7 software. All DRAGEN analyses were performed in the cloud using the Illumina Connected Analytics bioinformatics platform powered by Amazon Web Services (see 'Data solution empowering population genomics' for more infor
...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 ...
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...
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.
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...
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.
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...
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.
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...
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...
acousticsbiodiversitybiologyclimatecoastaldeep learningecosystemsenvironmentalmachine learningmarine mammalsoceansopen source software
This project offers passive acoustic data (sound recordings) from a deep-ocean environment off central California. Recording began in July 2015, has been nearly continuous, and is ongoing. These resources are intended for applications in ocean soundscape research, education, and the arts.
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.
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.
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 ...
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.
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.
bioinformaticsbiologygeneticgenomicinfrastructurelife sciencessingle-cell transcriptomicstranscriptomicswhole genome sequencing
Pre-built refgenie reference genome data assets used for aligning and analyzing DNA sequence data.
biodiversitybiologyecosystemsimage processingmultimediawildlife
The SiPeCaM goal is to create a data source that allows to evaluate changes in the biodiversity state, considering key aspect of how does the ecosystem behaves.
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...
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...
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.
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.
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 ...
agriculturebiodiversitybiologyclimatedigital preservationecosystemsenvironmental
The National Herbarium of New South Wales is one of the most significant scientific, cultural and historical botanical resources in the Southern hemisphere. The 1.43 million preserved plant specimens have been captured as high-resolution images and the biodiversity metadata associated with each of the images captured in digital form. Botanical specimens date from year 1770 to today, and form voucher collections that document the distribution and diversity of the world's flora through time, particularly that of NSW, Austalia and the Pacific.The data is used in biodiversity assessment, syste...
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.
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.
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.
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...
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...
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.
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...
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.
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...
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 ...
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.
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.
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.
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).
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...
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.
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...
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...
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).
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.
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...
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...
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.
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.
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.
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).
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).
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.
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.
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.
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.
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.
biologylife sciences
PhysioNet offers free web access to large collections of recorded physiologic signals (PhysioBank) and related open-source software (PhysioToolkit).
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...
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.
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.
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.
biologychemical biologychemistrymarine mammalsoceans
CTD (Conductivity-Temperature_Depth)-Satellite Relay Data Loggers (CTD-SRDLs) are used to explore how marine animal behaviour relates to their oceanic environment. Loggers developed at the University of St Andrews Sea Mammal Research Unit transmit data in near real-time via the Argo satellite system. Data represented here was collected in the Southern Ocean, from elephant, fur and Weddell Seals. In 2024 data was added from flatback and olive ridley turtles, from a pilot study co-funded by the Royal Australian Navy in collaboration with the Australian Institute of Marine Science and Indigenous ...
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water.There are multiple retrieval algorithms for estimating Chl-a. These data use the Carder method implemented in the SeaDAS processing software l2gen and described in Carder K. L., Chen F. R., Lee Z. P., Hawes S. K. and Cannizzaro J. P. (2003), MODIS Ocean Science Team Algorithm Theoretical Basis Docume...
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the Garver-Siegel-Maritorena (GSM) method implemented in the SeaDAS processing software l2gen and described in “Chapter 11, and references therein, of IOCCG Report 5, 2006, (http://ioccg.org/wp-content/uploads/2015/10/ioc...
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the OC3 method recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen. The OC3 algorithm is described at http://oceancolor.gsfc.nasa.gov/cms/atbd/chlor_a (and links th...
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the OCI method (Hu et al 2012, doi: 10.1029/2011jc007395) recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen. The OCI algorithm is described at https://oceancolor....
biologyoceanssatellite imagery
The NOAA20 satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the Garver-Siegel-Maritorena (GSM) method implemented in the SeaDAS processing software l2gen and described in “Chapter 11, and references therein, of IOCCG Report 5, 2006, (http://ioccg.org/wp-content/uploads/2015/10/ioc...
biologyoceanssatellite imagery
The NOAA20 satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the OC3 method recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen. The OC3 algorithm is described at http://oceancolor.gsfc.nasa.gov/cms/atbd/chlor_a (and links ...
biologyoceanssatellite imagery
The NOAA20 satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the OCI method (Hu et al 2012, doi: 10.1029/2011jc007395) recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen. The OCI algorithm is described at https://oceancolo...
biologyoceanssatellite imagery
The SNPP satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the Garver-Siegel-Maritorena (GSM) method implemented in the SeaDAS processing software l2gen and described in “Chapter 11, and references therein, of IOCCG Report 5, 2006, (http://ioccg.org/wp-content/uploads/2015/10/ioccg...
biologyoceanssatellite imagery
The SNPP satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the OC3 method recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen. The OC3 algorithm is described at http://oceancolor.gsfc.nasa.gov/cms/atbd/chlor_a (and links th...
biologyoceanssatellite imagery
The SNPP satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. There are multiple retrieval algorithms for estimating Chl-a. These data use the OCI method (Hu et al 2012, doi: 10.1029/2011jc007395) recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen. The OCI algorithm is described at https://oceancolor....
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. An empirical relationship is then used to compute an estimate of the relative abundance of three phytoplankton size classes (micro, nano and picoplankton). The methods used to decompose chl_oc3 are described by Brewin et al in two papers in 2010 and 2012. The two methods, denoted Brewin2010at and Br...
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. Modelling is then used to compute an estimate of the Net Primary Productivity (NPP).The model used is based on the standard vertically generalised production model (VGPM). The VGPM is a "chlorophyll-based" model that estimates net primary production from chlorophyll using a temperature-de...
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. Modelling is then used to compute an estimate of the Net Primary Productivity (NPP).The model used is based on the standard vertically generalised production model (VGPM). The VGPM is a "chlorophyll-based" model that estimates net primary production from chlorophyll using a temperature-de...
biologyoceanssatellite imagery
The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. An empirical relationship is then used to compute an estimate of the relative abundance of three phytoplankton size classes (micro, nano and picoplankton). The methods used to decompose chl_oc3 are described by Brewin et al in two papers in 2010 and 2012. The two methods, denoted Brewin2010at and Br...
biologyoceanssatellite imagery
The NOAA20 satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the diffuse attenuation coefficient (Kd) at 490nm wavelength which provides information on how light is attenuated in the water column. It is defined as the scaling length of the exponential decrease of the downwelling irradiance, and has units (m^-1). The VIIRS K490 product estimates Kd at 490nm wavelength, using a semi-empirical model based on the ratio of water leaving radiances at 490nm and 555...
biologyoceanssatellite imagery
The SNPP satellite platform carries a VIIRS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the diffuse attenuation coefficient (Kd) at 490nm wavelength which provides information on how light is attenuated in the water column. It is defined as the scaling length of the exponential decrease of the downwelling irradiance, and has units (m^-1). The VIIRS K490 product estimates Kd at 490nm wavelength, using a semi-empirical model based on the ratio of water leaving radiances at 490nm and 555nm...
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.