Registry of Open Data on AWS

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay by Bray M-A, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancik V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, & Carpenter AE
Cell Painting predicts impact of lung cancer variants by Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, & Singh S
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes by Bray M-A, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, & Carpenter AE
Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects by Singh S, Wu X, Ljosa V, Bray M-A, Piccioni F, Root DE, Doench JG, Boehm JS, & Carpenter AE
Multiplex Cytological Profiling Assay to Measure Diverse Cellular States by Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, and Shamji AF
Systematic morphological profiling of human gene and allele function via Cell Painting by Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, & Carpenter AE
Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling by Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, BodycombeNE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CSK, Duvall JR, Wilson JA, Bittker JA, Dancik V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, & Clemons PA

Genome Aggregation Database (gnomAD)

Tools & Applications

Publications

A genomic mutational constraint map using variation in 76,156 human genomes. Nature 625, 92–100 (2024) by Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., Poterba, T., Wilson, M. W., Tarasova, Y., Phu, W., Yohannes, M. T., Koenig, Z., Farjoun, Y., Banks, E., Donnelly, S., Gabriel, S., Gupta, N., Ferriera, S., Tolonen, C., Novod, S., Bergelson, L., Roazen, D., Ruano-Rubio, V., Covarrubias, M., Llanwarne, C., Petrillo, N., Wade, G., Jeandet, T., Munshi, R., Tibbetts, K., gnomAD Project Consortium, O’Donnell-Luria, A., Solomonson, M., Seed, C., Martin, A. R., Talkowski, M. E., Rehm, H. L., Daly, M. J., Tiao, G., Neale, B. M., MacArthur, D. G. & Karczewski, K. J.
A structural variation reference for medical and population genetics. Nature 581, 444–451 (2020) by Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., Watts, N. A., Solomonson, M., O’Donnell-Luria, A., Baumann, A., Munshi, R., Walker, M., Whelan, C., Huang, Y., Brookings, T., ... Talkowski, M. E.
Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016) by Lek, M., Karczewski, K., Minikel, E. et al.
Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals. Nature Communications 11, 2523 (2020) by Whiffin, N., Karczewski, K. J., Zhang, X., Chothani, S., Smith, M. J., Gareth Evans, D., Roberts, A. M., Quaife, N. M., Schafer, S., Rackham, O., Alföldi, J., O’Donnell-Luria, A. H., Francioli, L. C., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, Cook, S. A., Barton, P. J. R., MacArthur, D. G., & Ware, J. S.
Evaluating potential drug targets through human loss-of-function genetic variation. Nature 581, 459–464 (2020) by Minikel, E. V., Karczewski, K. J., Martin, H. C., Cummings, B. B., Whiffin, N., Rhodes, D., Alföldi, J., Trembath, R. C., van Heel, D. A., Daly, M. J., Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Schreiber, S. L., & MacArthur, D. G.
gnomAD v2.1 by Laurent Francioli, Grace Tiao, Konrad Karczewski, Matthew Solomonson, Nick Watts
gnomAD v3.0 by Laurent Francioli, Daniel MacArthur
Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes. Nature Communications 11, 2539 (2020) by Wang, Q., Pierce-Hoffman, E., Cummings, B. B., Karczewski, K. J., Alföldi, J., Francioli, L. C., Gauthier, L. D., Hill, A. J., O’Donnell-Luria, A. H., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, & MacArthur, D. G.
Technical artifact drives apparent deviation from Hardy-Weinberg equilibrium at CCR5-∆32 and other variants in gnomAD. bioRxiv (p. 784157) by Karczewski, K. J., Gauthier, L. D., Daly, M. J.
The effect of LRRK2 loss-of-function variants in humans. Nature Medicine (2020) by Whiffin, N., Armean, I. M., Kleinman, A., Marshall, J. L., Minikel, E. V., Goodrich, J. K., Quaife, N. M., Cole, J. B., Wang, Q., Karczewski, K. J., Cummings, B. B., Francioli, L., Laricchia, K., Guan, A., Alipanahi, B., Morrison, P., Baptista, M. A. S., Merchant, K. M., Genome Aggregation Database Production Team, ... MacArthur, D. G.
The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020) by Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., Gauthier, L. D., Brand, H., Solomonson, M., Watts, N. A., Rhodes, D., Singer-Berk, M., England, E. M., Seaby, E. G., Kosmicki, J. A., ... MacArthur, D. G.
Transcript expression-aware annotation improves rare variant interpretation. Nature 581, 452–458 (2020) by Cummings, B. B., Karczewski, K. J., Kosmicki, J. A., Seaby, E. G., Watts, N. A., Singer-Berk, M., Mudge, J. M., Karjalainen, J., Kyle Satterstrom, F., O’Donnell-Luria, A., Poterba, T., Seed, C., Solomonson, M., Alföldi, J., The Genome Aggregation Database Production Team, The Genome Aggregation Database Consortium, Daly, M. J., & MacArthur, D. G.

The Singapore Nanopore Expression Data Set

Garvan Institute Long Read Sequencing Benchmark Data

Tutorials

Directly processing on an s3fs mount by Hasindu Gamaarachchi
Fetching subsets with slow5curl and samtools by Bonson Wong

Tools & Applications

buttery-eel: The buttery eel - a slow5 guppy basecaller wrapper by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
Slow5curl: library and tool for accessing remote BLOW5 files. by Wong, B., et al.
Slow5lib: toolkit slow5lib is a software library for reading & writing SLOW5 files. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
Slow5tools: toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.

Publications

Accelerated nanopore basecalling with SLOW5 data format. by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
Fast nanopore sequencing data analysis with SLOW5. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
Flexible and efficient handling of nanopore sequencing signal data with slow5tools. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
Streamlining remote nanopore data access with slow5curl by Wong, B., Ferguson, J.M., Do, J.Y. et al.

PubSeq - Public Sequence Resource

Tutorials

Tools & Applications

Publications

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) by Eichler, N. et al.

Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET)

Tutorials

Finding and Downloading TaRGET II Data files by TaRGET-DCC

Tools & Applications

Visualize TaRGET II data with WashU Epigenome Browser by WashU Epigenome Browser

Publications

Comparison of differential accessibility analysis strategies for ATAC-seq data by Gontarz P, Fu S, Xing X, Liu S, Miao B et.al.
Environmental Determinants of cardiovasular disease: lessons learned from air pollution by Al-Kindi SG, Brook RD, Biswal S, Rajagopalan S.
Epigenetic biomarkers and preterm birth by Park B, Khanam R, Vinayachandran V, et.al.
Metabolic effects of air pollution exposure and reversibility by Rajagopalan S, Park B, Palanivel R, et al.
The NIEHS TaRGET II Consortium and environmental epigenomics by Wang, T., Pehrsson, E., Purushotham, D. et al.
The role of environmental exposures and the epigenome in health and disease. by Perera BPU, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC.

Open Bioinformatics Reference Data for Galaxy

Tutorials

Using Open Bio Ref Data with Galaxy and Bioconductor by Enis Afgan, Alexandru Mahmoud, Nuwan Goonasekera

Tools & Applications

Bioconductor by Bioconductor Project
Galaxy by Galaxy Project

Publications

Accessible, curated metagenomic data through ExperimentHub by Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, and Levi Waldron
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages by Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Wrangling Galaxy's reference data by Daniel Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko

Caenorabditis Diversity Natural Resource

Tutorials

Data Releases - C. briggsae by Erik Andersen
Data Releases - C. elegans by Erik Andersen
Data Releases - C. tropicalis by Erik Andersen
FAQ - AWS API by Erik Andersen

Publications

CaeNDR, the Ceanorhabditis Natural Diversity Resource by Crombie TA, McKeown R, Moya ND, Evans KS, Widmayer SJ, LaGrassa V, et al.

Basic Local Alignment Sequences Tool (BLAST) Databases

Tools & Applications

BLAST on the Cloud with NCBI’s ElasticBLAST by Sixing Huang
BLAST+ Docker by NCBI BLAST

Publications

BLAST+: Architecture and Applications by Christiam Camacho 1 , George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden
Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs by S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman

Encyclopedia of DNA Elements (ENCODE)

Tutorials

Publications

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal by Luo et al 2020

Refgenie reference genome assets

Tutorials

Basic Refgenie tutorial by Nathan Sheffield

Tools & Applications

Publications

Refgenie: a reference genome resource manager by Michał Stolarczyk, Vincent P Reuter, Jason P Smith, Neal E Magee, Nathan C Sheffield

Synthea synthetic patient generator data in OMOP Common Data Model

Tutorials

Create data science environments on AWS for health analysis using OHDSI by James Wiggins
AWS CloudFormationAmazon EC2Amazon RDS
Map clinical notes to the OMOP Common Data Model and healthcare ontologies using Amazon Comprehend Medical by James Wiggins
Amazon ComprehendAWS CloudFormationAmazon EC2Amazon RDS
Predict patient health outcomes using OHDSI and machine learning on AWS by James Wiggins
AWS CloudFormationAmazon EC2Amazon RDS

Tools & Applications

OHDSIonAWS by James Wiggins

Broad Genome References

Tutorials

Using Amazon FSx for Lustre for Genomics Workflows on AWS by W. Lee Pang
AWS BatchAmazon FSx

Tools & Applications

Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang

Publications

Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA by Willey J. C., Morrison T. B., Austermiller B., Crawford E. E., et al (2021)

I-CARE:International Cardiac Arrest REsearch consortium Electroencephalography Database

Tools & Applications

WFDB Software Package by Moody, G., Pollard, T., & Moody, B.

Publications

I-CARE:International Cardiac Arrest REsearch consortium Electroencephalography Database by Amorim E, Zheng WL, Ghassemi MM, Aghaeeaval M, Kandhare P, Karukonda V, et al.
The International Cardiac Arrest Research (I-CARE) Consortium Electroencephalography Database by Amorim E, Zheng WL, Ghassemi MM, Aghaeeaval M, Kandhare P, Karukonda V, et al.

Kraken2 NCBI RefSeq Complete V205 database on AWS

Tutorials

Using an Amazon Machine Image for analysing samples with Kraken2 by Robyn Wright
Amazon EC2

Tools & Applications

Kraken2 by Derrick Wood, Jennifer Lu and Ben Langmead

Publications

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools by Robyn J. Wright, Andre M. Comeau and Morgan G.I. Langille

MIMIC-III (‘Medical Information Mart for Intensive Care’)

Tutorials

Building predictive disease models using Amazon SageMaker with Amazon HealthLake normalized data by Ujjwal Ratan, Nihir Chadderwala, and Parminder Bhatia
AWS GlueAWS HealthLakeAmazon SageMaker
Perform biomedical informatics without a database using MIMIC-III data and Amazon Athena by James Wiggins, Alistair Johnson
Amazon AthenaAWS Glue

Tools & Applications

MIMIC-code GitHub repository by Alistair Johnson

NASA Space Biology Open Science Data Repository (OSDR)

Publications

Advancing the Integration of Biosciences Data Sharing to Further Enable Space Exploration by Ryan T. Scott, Kirill Grigorev, Graham Mackintosh, Samrawit G. Gebre, Christopher E. Mason, Martha E. Del Alto, Sylvain V. Costes
GeneLab: Omics database for spaceflight experiments by Shayoni Ray, Samrawit Gebre, Homer Fogle, Daniel C Berrios, Peter B Tran, Jonathan M Galazka, Sylvain V Costes
NASA GeneLab: interfaces for the exploration of space omics data by Daniel C Berrios, Jonathan Galazka, Kirill Grigorev, Samrawit Gebre, Sylvain V Costes

QIIME 2 Tutorial Data

Tutorials

SPaRCNet data:Seizures, Rhythmic and Periodic Patterns in ICU Electroencephalography

Tools & Applications

IIIC-SPaRCNet Github Repository by Brain Data Science Platform (BDSP)

Publications

Development of Expert-Level Classification of Seizures and Rhythmic and Periodic Patterns During EEG Interpretation by Jing J, Ge W, Hong S, Fernandes MB, Lin Z, Yang C et al., et al.
SPaRCNet data:Seizures, Rhythmic and Periodic Patterns in ICU Electroencephalography by Jing, J., Ge, W., Struck, A. F., Fernandes, M., Hong, S., An, S., et al.

VirtualFlow Ligand Libraries

Tutorials

VirtualFlow tutorial by Christoph Gorgulla

Tools & Applications

VirtualFlow for Virtual Screening (VFVS) Module on GitHub by Christoph Gorgulla

Publications

VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules by Christoph Gorgulla, AkshatKumar Nigam, Matt Koop, Süleyman Selim Çınaroğlu, Christopher Secker, Mohammad Haddadnia, Abhishek Kumar, Yehor Malets, Alexander Hasson, Roni Levin-Konigsberg, Dmitry Radchenko, Aditya Kumar, Minko Gehev, Pierre-Yves Aquilanti, Henry Gabb, Amr Alhossary, Gerhard Wagner, Al, Yurii S. Moroz, Konstantin Fackeldey, Haribabu Arthanari

4D Nucleome (4DN)

Tutorials

Biodiversity Heritage Library Metadata and Page Images

Tools & Applications

BHLIndex by Global Names
BioStor by Roderic Page

Publications

COVID-19 Data Lake

Tutorials

A public data lake for analysis of COVID-19 data by AWS Data Lake Team
AWS GlueAmazon AthenaAmazon ComprehendAmazon KendraAmazon QuickSight
Exploring the public AWS COVID-19 data lake by AWS Data Lake Team
Amazon AthenaAWS GlueAmazon SageMaker
How to use SQL to query data in S3 Bucket with Amazon Athena and AWS SDK for .NET by AWS ProServe US West Applications Team
Amazon AthenaAWS GlueAmazon S3AWS CloudFormation

Tools & Applications

Cloud Indexes for Bowtie, Kraken, HISAT, and Centrifuge

Tutorials

Table of contents for tutorials for constituent tools by Ben Langmead

Publications

Reducing reference bias using multiple population reference genomes by Chen et al (2020)

DNAStack COVID19 SRA Data

Tutorials

Viral lineage assignment by Heather Ward
AWS BatchAmazon EC2Amazon S3

Tools & Applications

Viral AI by DNAstack

Emory Knee Radiograph (MRKR) dataset

Tutorials

Example Notebook by Emory-HITI

Publications

Emory Knee Radiograph Dataset by Brandon Price, Jason Adleberg, Kaesha Thomas, Zach Zaiman, Aawez Mansuri, Beatrice Brown-Mulry, Chima Okecheukwu, Judy Gichoya, Hari Trivedi.

GATK Structural Variation (SV) Data

Tutorials

AWS Setup & Execution by Goldfinch Bio and Loka Inc.

Tools & Applications

Structural Variant Analysis on AWS with Amazon FSx for Lustre by Goldfinch Bio and Loka Inc.

Harvard Electroencephalography Database

Tools & Applications

Harvard-EEG-Database-Tools by Brain Data Science Platform (BDSP)

Publications

Harvard Electroencephalography Database by Zafar, S., Loddenkemper, T., Lee, J. W., Cole, A., Goldenholz, D., Peters, J., et al.

Harvard-Emory ECG Database

Tools & Applications

WFDB Software Package by Moody, G., Pollard, T., & Moody, B.

Publications

Harvard Electroencephalography Database by Moura Junior, V.; Reyna, M.; Hong, S.; Gupta, A.; Ghanta, M.; Sameni, R., et al.

Hecatomb Databases

Tutorials

The Hecatomb Tutorial by Michael Roach

Publications

No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study by Michael Roach,Adrian Cantu,Melissa Krizia Vieri,Matthew Cotten,Paul Kellam,My Phan,Lia van der Hoek,Michel Mandro,Floribert Tepage,Germain Mambandu,Gisele Musinya,Anne Laudisoit,Robert Colebunders,Robert Edwards, John L. Mokili

Indexes for Kaiju

Tutorials

Quickstart Tutorial for downloading the index files and running Kaiju. by Peter Menzel

Publications

Fast and sensitive taxonomic classification for metagenomics with Kaiju by Peter Menzel et al (2016)

Protein Data Bank 3D Structural Biology Data

Publications

Announcing the worldwide Protein Data Bank by Berman, H., Henrick, K. & Nakamura, H.
Protein Data Bank: the single global archive for 3D macromolecular structure data by wwPDB consortium

UniProt

Tutorials

Exploring the UniProt protein knowledgebase with AWS Open Data and Amazon Neptune by Eric Greene, Rafa Xu, Yuan Shi (AWS)
Amazon Neptune
UniProt SPARQL by Swiss-Prot Group at SIB Swiss Institute of Bioinformatics

CMS 2008-2010 Data Entrepreneurs’ Synthetic Public Use File (DE-SynPUF) in OMOP Common Data Model

Tutorials

Create data science environments on AWS for health analysis using OHDSI by James Wiggins
AWS CloudFormationAmazon EC2Amazon RDS
Map clinical notes to the OMOP Common Data Model and healthcare ontologies using Amazon Comprehend Medical by James Wiggins
Amazon ComprehendAWS CloudFormationAmazon EC2Amazon RDS
Predict patient health outcomes using OHDSI and machine learning on AWS by James Wiggins
AWS CloudFormationAmazon EC2Amazon RDS

Tools & Applications

OHDSIonAWS by James Wiggins

COVID-19 Genome Sequence Dataset

Tools & Applications

Download SRA sequence data using Amazon Web Services (AWS) by NCBI SRA

Conformational Space of Short Peptides

Tutorials

Intro to Conformational Space of Short Peptides by Sebastian Bassi and Virginia Gonzalez

GATK Test Data

Tools & Applications

Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang

Global Biodiversity Information Facility (GBIF) Species Occurrences

Tutorials

GBIF and Apache-Spark on AWS tutorial by John Waller
Amazon EMR

Oxford Nanopore Technologies Benchmark Datasets

Tutorials

ONT Dataset Tutorials by EPI2MELabs

Synthea Coherent Data Set

Publications

The “Coherent Data Set”: Combining Patient Data and Imaging in a Comprehensive Synthetic Health Record. by Walonoski J, Hall D, Bates KM, Farris MH, Dagher J, Downs ME, Sivek RT, Wellner B, Gregorowicz A, Hadley M, Campion FX, Levine L, Wacome K, Emmer G, Kemmer A, Malik M, Hughes J, Granger E, Russell S.