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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@home focused its resources on understanding the vulnerabilities in SARS-CoV-2, the virus that causes COVID-19 disease, and working closely with a number of experimental collaborators to accelerate progress toward effective therapies for treating COVID-19 and ending the pandemic. In the process, it created the world's first exascale distributed computing resource, enabling it to generate valuable scientific datasets of unprecedented size. More information about Folding@home's COVID-19 research activities at the Folding@home COVID-19 page. In addition to working directly with experimental collaborators and rapidly sharing new research findings through preprint servers, Folding@home has joined other researchers in committing to rapidly share all COVID-19 research data, and has joined forces with AWS and the Molecular Sciences Software Institute (MolSSI) to share datasets of unprecedented side through the AWS Open Data Registry, indexing these massive datasets via the MolSSI COVID-19 Molecular Structure and Therapeutics Hub. The complete index of all Folding@home datasets can be found here. Th...
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...
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...
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:
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 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 here, and the groups that have contributed data to the current release are listed here. Sign up for the gnomAD...
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 Nanopore RNA-Seq. Transcriptome profiling is done using PCR-cDNA sequencing (PCR-cDNA), amplification-free cDNA sequencing (direct cDNA), direct sequencing of native RNA (direct RNA), 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 samples are sequenced with at least 3 ...
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.
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.
bioinformaticsgenomiclife scienceslong read sequencing
The dataset contains reference samples that will be useful for benchmarking and comparing bioinformatics tools for genome analysis. Currently, there are two samples, which are NA12878 (HG001) and NA24385 (HG002), sequenced on an Oxford Nanopore Technologies (ONT) PromethION using the latest R10.4.1 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 rebasecalling, but also can be used for emerging bioinf...
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.
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.
life sciencesMus musculusneurophysiologyneuroscienceopen source software
Electrophysiological recordings of mouse brain activity acquired using Neuropixels probes and accompanying behavioral data.
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.
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.
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.
bambiologygeneticgenomichealthlife sciencesvcf
This dataset contains alignment files and short nucleotide, copy number, repeat expansion (STR) and structural variant call files from the 1000 Genomes Project Phase 3 dataset (n=3202) using Illumina DRAGEN v3.5.7b and v3.7.6 software. The v3.7.6 dataset also includes results from joint small variant, de novo structural variant, de novo copy number variant and repeat expansion calls on 602 trio families comprised of members from the 1000 Genomes Project Phase 3 dataset, as well as DRAGEN gVCF Genotyper (v3.8.3) analysis on the entire dataset (n=3202). Improvements and new features in the v3.7...
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.
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.
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).
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.
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...
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.
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...
life sciencesMus musculusneurophysiologyneuroscienceopen source software
Behavioral data of mice performing a decision-making task, associated with 2020 publication of the IBL.
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...
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 indextranscriptomics
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 ...
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.
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.
biologycell 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.
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...
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.
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...
bioinformaticsbiologycancergeneticgenomicHomo sapienslife sciencesreference index
Broad maintained human genome reference builds hg19/hg38 and decoy references.
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.
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.
biologycell imagingelectrophysiologyinfrastructurelife sciencesneuroimagingneurophysiologyneuroscience
DANDI is a public archive of neurophysiology datasets, including raw and processed data, and associated software containers. Datasets are shared according to a Creative Commons CC0 or CC-BY licenses. The data archive provides a broad range of cellular neurophysiology data. This includes electrode and optical recordings, and associated imaging data using a set of community standards: NWB:N - NWB:Neurophysiology, BIDS - Brain Imaging Data Structure, and Details →
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...
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.
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 ...
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...
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.
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...
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.
bioinformaticslife sciencesmedicinepharmaceuticalstructural biology
VirtualFlow Versions of Ligand Libraries in Ready-To-Dock Format
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...
agricultureenvironmentalfood securitylife sciencesmachine learning
This dataset contains soil infrared spectral data and paired soil property reference measurements for georeferenced soil samples that were collected through the Africa Soil Information Service (AfSIS) project, which lasted from 2009 through 2018. In this release, we include data collected during Phase I (2009-2013.) Georeferenced samples were collected from 19 countries in Sub-Saharan African using a statistically sound sampling scheme, and their soil properties were analyzed using both conventional soil testing methods and spectral methods (infrared diffuse reflectance spectroscopy). The two ...
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.
biotech blueprintchemistrygeneticgenomiclife sciencesmoleculeparquet
This a parquet representation of The Binding Database's Full BindingDB Database Dump that you can query straight from Athena in under 60 seconds (no Oracle database required). The Binding Database projects aims to make experimental data on the noncovalent association of molecules in solution searchable via the world wide web. The initial focus is on biomolecular systems, but data on host-guest and supramolecular systems are also important and being included over time. It is expected that the enhanced access to data provided by this resource will facilitate drug-discovery, the design of sel...
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...
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...
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.
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/).
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.
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...
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...
genetichealthHomo sapienslife scienceslong read sequencingmappingvariant annotationvcfwhole genome sequencing
Reference data bundle for analyzing HiFi human whole genome sequencing data
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...
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.
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.
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...
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.
geneticgenomiclife 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...
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.
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).
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.
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 general license type:
The PMC Open Access (OA) Subset, which includes all articles in PMC with a machine-readable Creative Commons license
The Author Manuscript Dataset, which includes all articles collected under a funder policy in PMC and made available in machine-readable formats for text mining
These datasets collectively span...
biologycancercomputer visionhealthimage processingimaginglife sciencesmachine learningmagnetic resonance imagingmedical imagingmedicineneurobiologyneuroimagingsegmentation
This dataset contains 8,000+ brain MRIs of 2,000+ patients with brain metastases.
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.
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.
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.
biologyencyclopedicgenomichealthlife 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...
biologyencyclopedicgenomichealthlife 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...
biologyencyclopedicgeneticgenomichealthlife sciencesmedicinesingle-cell transcriptomics
Tabula Sapiens will be a benchmark, first-draft human cell atlas of two million cells from 25 organs of eight normal human subjects. 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. A critical factor in the Tabula projects is our large collaborative network of PI’s with deep expertise at preparation of diverse organs, enabling all organs from a subject to be successfully processed within a single day. Tabula Sapiens leverages our network of human tissue experts and a close collaboration with a Donor Network West, a not-for-profit organ procurement organization. We use their experience to balance and assign cell types from each tissue compartment and optimally mix high-quality plate-seq data and high-volume droplet-based data to provide a broad and deep benchmark atlas. Our goal is to make sequence data rapidly and broadly available to the scientific community as a community resource. Before you use our data, please take note of our Data Release Policy below.Data Release PolicyOur goal is to make sequence data rapidly and broadly available to the scientific community as a community resource. It is our intention to publish the work of this project in a timely fashion, and we welcome collaborative interaction on the project and analyses. However, considerable investment was made in generating these data and we ask that you respect rights of first publication and acknowledgment as outlined in the Toronto agreement. By accessing these data, you agree not to publish any articles containing analyses of genes, cell types or transcriptomic data on a who...
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.
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).
assemblybioinformaticsbiologycontaminationfastageneticgenomehealthlife scienceswhole 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.
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.
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.
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...
biologyimaginglife sciencesneurobiologyneuroimaging
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...
biologylife sciences
PhysioNet offers free web access to large collections of recorded physiologic signals (PhysioBank) and related open-source software (PhysioToolkit).
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.
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.
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.
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.
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.
biotech blueprintchemistrygenomiclife sciencesmoleculeparquet
ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. This representation of ChEMBL is stored in Parquet format and most easily utilized through Amazon Athena. Follow the documentation for install instructions (< 2 minute install). New ChEMBL releases occur sporadically; the most up to date information on ChEMBL releases can be found here.
biotech blueprintchemistrygeneticgenomiclife sciencesparquet
ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported acc...
biotech blueprintchemistrygeneticgenomiclife sciencesmoleculeparquet
This a Parquet representation of the Open Targets Platform's latest export. The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification. The Open Targets Platform (https://www.targetvalidation.org) is a freely available resource for the integration of genetics, genomics, and chemical data to aid systematic drug target identification and prioritisation. This dataset is 'Lakehouse Ready'. Meaning, you can query this data in-place straight out of the Registry of Open Data S3 bucket. Deploy this dataset's corresponding CloudFormation template to create the AWS Glue catalog entries into your account in about 30 seconds. That one step will enable you to write SQL with AWS Athena, build dashboards and charts with Amazon Quick...
bioinformaticsbiologygeneticgenomicHomo sapienslife sciencesparquetpopulation geneticsvcf
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. There were a total of 3202 individuals sequenced as part of Phase 3 of this project. The high coverage samples were processed using the Illumina DRAGEN v3.5.7b pipeline and are available at s3://1000genomes-dragen/. This dataset contains the VCFs transformed to Parquet/ORC in 3 different schemas - partitioned by samples, partitioned by chromosome and a nested data format. These representations ...
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.
bioinformaticsbiologybiotech blueprintgeneticgenomiclife sciencesparquetpopulation geneticsvcfwhole 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 Sign up for the gnomAD mailing list here. This dataset was derived from summary data from gnomAD release 3.1, ava...
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.