The Cancer Genome Atlas

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TCGA Cancers Selected for Study by National Cancer Institute
  
• Using TCGA Data, Resources, and Materials by National Cancer Institute
  

Publications

• "Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons" by Galen F. Gao, Joel S. Parker, et al.
  
• A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples by Han Chen, Chunyan Li, et al.
  
• An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics by Jianfang Liu, Tara Lichtenberg, et al.
  
• Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer by Katherine A. Hoadley, Christina Yau, et al.
  
• Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas by Yang Liu, Nilay S. Sethi, et al.
  
• Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients by André Kahles, Kjong-Van Lehmann, et al.
  
• Comprehensive Characterization of Cancer Driver Genes and Mutations by Matthew H. Bailey, Collin Tokheim, et al.
  
• Genomic and Functional Approaches to Understanding Cancer Aneuploidy by Alison M. Taylor, Juliann Shih, et al.
  
• Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas by Theo A. Knijnenburg, Linghua Wang, et al.
  
• Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas by Joshua D. Campbell, Christina Yau, et al.
  
• Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types by Zhongqi Ge, Jake S. Leighton, et al.
  
• Machine Learning Detects Pan-Cancer Ras Pathway Activation in The Cancer Genome Atlas by Gregory P. Way, Francisco Sanchez-Vega, et al.
  
• Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation by Tathiane M. Malta, Artem Sokolov, et al.
  
• Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers by Xinxin Peng, Zhongyuan Chen, et al.
  
• Oncogenic Signaling Pathways in The Cancer Genome Atlas by Francisco Sanchez-Vega, Marco Mina, et al.
  
• Pan-Cancer Alterations of the MYC Oncogene and its Proximal Network Across The Cancer Genome Atlas by Franz X. Schaub, Varsha Dhankani, et al.
  
• Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context by Hua-Sheng Chiu, Sonal Somvanshi, et al.
  
• Pathogenic Germline Variants in 10,389 Adult Cancers by Kuan-lin Huang, R. Jay Mashl, et al.
  
• Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines by Kyle Ellrott, Matthew H. Bailey, et al.
  
• Spatial Organization And Molecular Correlation Of Tumor-Infiltrating Lymphocytes Using Deep Learning On Pathology Images by Joel Saltz, Rajarsi Gupta, et al.
  
• The chromatin accessibility landscape of primary human cancers by M. Ryan Corces, Jeffrey M. Granja, et al.
  
• The Immune Landscape of Cancer by Vésteinn Thorsson, David L. Gibbs, et al.
  

Therapeutically Applicable Research to Generate Effective Treatments (TARGET)

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TARGET data matrix by National Cancer Institute
  

Publications

• A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor by Gadd S, Huff V, Walz AL, et al.
  
• Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia by Yang JJ, Cheng C, Devidas M, et al.
  
• Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in osteosarcoma by Nakka M, Allen-Rhoades W, Li Y, et al.
  
• CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AM by Maxson JE, Ries RE, Wang YC, et al.
  
• Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism by Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, et al.
  
• Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways by Chun HJ, Lim EL, Heravi-Moussavi A, et al.
  
• Genomic classification and identification of the cell of origin of pediatric mixed phenotype acute leukemia by Thomas B. Alexander, Zhaohui Gu, Ilaria Iacobucci, et al.
  
• Genomics in childhood acute myeloid leukemia comes of age by Brunner AM, Graubert TA.
  
• Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration by Hye-Jung E. Chun, Pascal D. Johann, Katy Milne et al.
  
• MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia by Lim EL, Trinh DL, Ries RE, et al.
  
• MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours by Perlman EJ, Gadd S, Arold ST, et al.
  
• Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors by Walz AL, Ooms A, Gadd S, et al.
  
• Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations by Eleveld TF, Oldridge DA, Bernard V, Koster J, et al.
  
• Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group by Ooms AH, Gadd S, Gerhard DS, et al.
  
• TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney by Gooskens SL, Gadd S, Guidry Auvil JM, et al.
  
• The genetic landscape of high-risk neuroblastoma by Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, et al.
  
• The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia by Yu Liu, John Easton, Ying Shao, et al.
  
• The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions by Bolouri H, Farrar JE, Triche T Jr, et al.
  

Common Crawl

Tutorials

• Analysing Petabytes of Websites by Mark Litwintschik
  EMR
• Common Crawl Index Athena by Edward Ross
  Athena
• Index to WARC Files and URLs in Columnar Format by Sebastian Nagel
  Athena
• Large-scale graph mining with Spark by Win Suen
  
• Search the Common Crawl Using Lambda Functions by Andres Riancho
  Lambda

Tools & Applications

• CCNet: Extracting high quality monolingual datasets from web crawl data by Facebook AI Research
  
• Dresden Web Table Corpus (DWTC) by Database Systems Group Dresden
  
• Learning word vectors for 157 languages by Facebook AI Research
  

Publications

• Asynchronous pipeline for processing huge corpora on medium to low resource infrastructures by Pedro Javier Ortiz Suárez, Benoît Sagot, Laurent Romary
  
• Building a Web-Scale Dependency-Parsed Corpus from CommonCrawl by Alexander Panchenko, Eugen Ruppert, Stefano Faralli, Simone Paolo Ponzetto, Chris Biemann
  
• C4Corpus: Multilingual Web-Size Corpus with Free License by Ivan Habernal, Omnia Zayed, Iryna Gurevych
  
• CC-News-En: A large English news corpus by Joel Mackenzie, Rodger Benham, Matthias Petri, Johanne R. Trippas, J. Shane Culpepper, Alistair Moffat
  
• CCAligned: A Massive collection of cross-lingual web-document pairs by Ahmed El-Kishky, Vishrav Chaudhary, Francisco Guzmán, Philipp Koehn
  
• Defending against neural fake news by Rowan Zellers, Ari Holtzman, Hannah Rashkin, Yonatan Bisk, Ali Farhadi, Franziska Roesner, et al
  
• Index fun by Philippe Suter
  
• Language models are few-shot learners by Tom B. Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared Kaplan, Prafulla Dhariwal, et al
  
• Large-scale analysis of style injection by relative path overwrite by Sajjad Arshad, Seyed Ali Mirheidari, Tobias Lauinger, Bruno Crispo, Engin Kirda, William Robertson
  
• Mapping languages: The Corpus of Global Language Use by Jonathan Dunn
  
• N-gram counts and language models from the Common Crawl by Christian Buck, Kenneth Heafield, Bas van Ooyen
  
• Of using Common Crawl to play Family Feud by Paul Masurel
  
• On the impact of publicly available news and information transfer to financial markets by Metod Jazbec, Barna Pásztor, Felix Faltings, Nino Antulov-Fantulin, Petter N. Kolm
  
• Using open data to predict market movements by DELL EMC
  
• Web Data Commons - RDFa, microdata, and microformat data sets by Christian Bizer, Robert Meusel, Anna Primpeli
  

Sentinel-2

Tutorials

• Exploring the Chile wildfires with Landsat and Sentinel-2 imagery by Timothy Whitehead
  
• Integrate imagery from the Sentinel-2 archive into your own apps, maps, and analysis with the Sentinel-2 image service by Esri
  
• Learning Custom Scripts to Make Useful and Beautiful Satellite Images by Monja Šebela
  
• Tutorial for using Sentinel-2 data by Antti Lipponen
  
• Using Vector tiles and AWS Lambda, we can build a really simple API to get Landsat and Sentinel images by Remote Pixel
  

Tools & Applications

• EO Browser by Sinergise
  
• EOS Land Viewer by Earth Observing System
  
• FME Landsat-8/Sentinel-2 File Selector by Safe Software
  
• Interactive map with AI detected fields and crops based on Sentinel-2 imagery by OneSoil
  
• Python package for working with Sentinel-2 AWS data by Sinergise
  
• QGIS plugin for Sentinel-2 data by Sinergise
  
• Satellite Search by Remote Pixel by Remote Pixel
  
• Sentinel Hub WMS/WMTS/WCS Service by Sinergise
  
• Sentinel Playground by Sinergise
  
• Sentinel-2 Cloudless Atlas by EOX
  
• Spectator - tracking Sentinel 2, accessing the data and quick preview by Spectator
  
• Sterling Geo Using Sentinel-2 on Amazon Web Services to Create NDVI by Sterling Geo
  
• Use the Sentinel Explorer app to explore, visualize, and analyze the entire Sentinel-2 archive by Esri
  

Publications

• Coral-spawn slicks: Reflectance spectra and detection using optical satellite data by Hiroya Yamano, Asahi Sakuma, Saki Harii
  
• Using Remote Sensing Images and Cloud Services on AWS to Improve Land Use and Cover Monitoring by K. R. Ferreira, et al.
  

Gabriella Miller Kids First Pediatric Research Program (Kids First)

Tools & Applications

• CAVATICA by Seven Bridges Genomics
  
• Kids First DRC Portal by Kids First DRC
  
• Kids First DRC Source Code by Kids First DRC
  
• PedcBioPortal by cBioPortal
  

Publications

• Clinically Relevant and Minimally Invasive Tumor Surveillance of Pediatric Diffuse Midline Gliomas Using Patient-Derived Liquid Biopsy by Eshini Panditharatna, Lindsay B Kilburn, et al.
  
• Decreased ACKR3 (CXCR7) function causes oculomotor synkinesis in mice and humans. by Mary C Whitman, Noriko Miyake, et al.
  
• Deleterious de novo variants of X-linked ZC4H2 in females cause a variable phenotype with neurogenic arthrogryposis multiplex congenita. by Suzanna G M Frints, Friederike Hennig, et al.
  
• Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers. by Fengqi Chang, Fumin Lin, et al.
  
• Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. by Allison H Seiden, Felix Richter, et al.
  
• Genome-Wide Association Study Identifies a Susceptibility Locus for Comitant Esotropia and Suggests a Parent-of-Origin Effect by Sherin Shaaban, Sarah MacKinnon et al.
  
• Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. by Madison R Bishop, Kimberly K Diaz Perez, et al.
  
• Genomic Analyses Implicate Noncoding De Novo Variants in Congenital Heart Disease. by Felix Richter, Sarah U Morton, et al.
  
• Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma. by Laura Egolf, Zalman Vaksman, et al.
  
• Germline microsatellite genotypes differentiate children with medulloblastoma. by Samuel Rivero-Hinojosa, Nicholas Kinney, et al.
  
• MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance by William B Dobyns, Kimberly A Aldinger, et al.
  
• MAGEL2-Related Disorders: A study and case series. by Jameson Patak, James Gilfert, et al.
  
• Phenotype delineation of ZNF462 related syndrome. by Paul Kruszka, Tommy Hu, et al.
  
• The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. by Deanne M Taylor, Bruce J Aronow, et al.
  
• Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21. by Nandita Mukhopadhyay, Madison Bishop, et al.
  

Landsat 8

Tutorials

• A Gentle Introduction to GDAL Part 4: Working with Satellite Data by Planet
  
• Exploring the Chile wildfires with Landsat and Sentinel-2 imagery by Timothy Whitehead
  
• Integrate imagery from the full Landsat archive into your own apps, maps, and analysis with Landsat image services by Esri
  
• Using Cloud-Optimized GeoTIFF by acgeospatial
  
• Using Vector tiles and AWS Lambda, we can build a really simple API to get Landsat and Sentinel images by Remote Pixel
  

Tools & Applications

• Aggi: the fire detecting Twitter bot by Aggi
  
• Apps for exploring and analyzing Landsat imagery on the fly by Esri
  
• COG-Explorer - View Cloud Optimized GeoTIFF images in the browser directly from object storage by EOX
  
• Development Seed Geolambda by Matthew Hanson
  
• Dynamic map tiling with Cloud-Optimized GeoTIFFs by Kyle Barron
  
• EOS Land Viewer by Earth Observing System
  
• FME Landsat-8 on AWS Reader by Safe Software
  
• FME Landsat-8/Sentinel-2 File Selector by Safe Software
  
• landsatlive.live by Development Seed
  
• Sentinel Hub WMS/WMTS/WCS Service for Landsat by Sinergise
  
• Sentinel Playground for Landsat by Sinergise
  
• Spectator - tracking Landsat 8, accessing the data and quick preview by Spectator
  

Publications

• Using Remote Sensing Images and Cloud Services on AWS to Improve Land Use and Cover Monitoring by K. R. Ferreira, et al.
  

Sudachi Language Resources

Tutorials

• analysis-sudachi Tutorial by Works Applications
  
• chiVe Tutorial by Works Applications
  
• Sudachi Tutorial by Works Applications
  
• SudachiPy Tutorial by Works Applications
  

Tools & Applications

• analysis-sudachi: Sudachi pluglin for Elasticsearch by Works Applications
  
• jdartsclone: TRIE Data Structure using Double-Array by Works Applications
  
• Kintoki: Dependency Parser by Works Applications
  
• Sudachi: Japanese Tokenizer for Business by Works Applications
  
• sudachidict_core on pypi.python.org - a Python module to download and install SudachiDict for the python tokenizer by Works Applications
  
• sudachidict_full on pypi.python.org - a Python module to download and install SudachiDict for the python tokenizer by Works Applications
  
• sudachidict_small on pypi.python.org - a Python module to download and install SudachiDict for the python tokenizer by Works Applications
  
• SudachiPy: Python version of Sudachi by Works Applications
  

Publications

• chiVe 2.0: SudachiとNWJCを用いた実用的な日本語単語ベクトルの実現に向けて by 河村宗一郎, 久本空海, 真鍋陽俊, 髙岡一馬, 内田佳孝, 岡照晃, 浅原正幸
  
• chiVe: 製品利用可能な日本語単語ベクトル資源の実現へ向けて ～形態素解析器Sudachiと超大規模ウェブコーパスNWJCによる分散表現の獲得と改良～ by 久本空海, 山村崇, 勝田哲弘, 竹林佑斗, 髙岡一馬, 内田佳孝, 岡照晃, 浅原正幸
  
• Sudachi: a Japanese Tokenizer for Business by Kazuma Takaoka, Sorami Hisamoto, Noriko Kawahara, Miho Sakamoto, Yoshitaka Uchida, Yuji Matsumoto
  
• 形態素解析器『Sudachi』のための大規模辞書開発 by 坂本美保, 川原典子, 久本空海, 髙岡一馬, 内田佳孝
  
• 複数粒度の分割結果に基づく日本語単語分散表現 by 真鍋陽俊, 岡照晃, 海川祥毅, 髙岡一馬, 内田佳孝, 浅原正幸
  
• 詳細化した同義関係をもつ同義語辞書の作成 by 高岡一馬, 岡部裕子, 川原典子, 坂本美保, 内田佳孝
  

Foldingathome COVID-19 Datasets

Tutorials

• Folding@home COVID-19 efforts by Folding@home Consortium
  

Tools & Applications

• SARS-CoV-2 COVID Moonshot absolute free energy calculations by The Voelz lab at Temple University
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) dimer simulations: A 2.9 ms dataset of the SARS-CoV-2 main viral protease (apo, dimer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 2.6 ms equilibrium dataset of the SARS-CoV-2 main viral protease (apo, monomer) by The Chodera lab at MSKCC
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 6.4 ms dataset of the SARS-CoV-2 main viral protease (apo, monomer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp10 dataset: A 6.1 ms dataset of the SARS-CoV-2 nsp10 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp3 macrodomain dataset: An 11 ms dataset of the SARS-CoV-2 nsp3 macrodomain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp3 pl2pro domain dataset: An 731 µs dataset of the SARS-CoV-2 nsp3 pl2pro domain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp7 simulations: A 3.7 ms dataset of the SARS-CoV-2 nsp7 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp8 simulations: A 1.8 ms dataset of the SARS-CoV-2 nsp8 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp9 simulations: A 9 ms dataset of the SARS-CoV-2 nsp9 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 RNA polymerase (nsp12, RdRP) dataset: A 3.4 ms dataset of the SARS-CoV-2 nsp12 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 spike protein dataset: A 1.2 ms dataset of the SARS-CoV-2 spike protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 spike RBD bound to human ACE2 receptor (173.8 us): Wild-type and mutant simulations by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  

Publications

• SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome by Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, View ORCID ProfileRafal P. Wiewiora, Matthew F. D. Hurley, Aoife M Harbison, Carl A Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, Gregory R. Bowman
  

Genome Aggregation Database (gnomAD)

Tools & Applications

• gnomAD quality control GitHub repository by gnomAD Production Team
  
• Hail by Hail Team
  
• Hail on AWS Quick Start by Amazon Web Services and PrivoIT
  
• Hail utilities for gnomAD by gnomAD Production Team
  

Publications

• 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.
  

NEXRAD on AWS

Tutorials

• Mapping Noaa Nexrad Radar Data With CARTO by Stuart Lynn
  
• NEXRAD on EC2 tutorial by openradar
  
• Using Python to Access NCEI Archived NEXRAD Level 2 Data (Jupyter notebook) by Ryan May
  

Tools & Applications

• Into the eye of the storm: NEXRAD Level II open data by Jonni Walker
  
• nexradaws on pypi.python.org - python module to query and download Nexrad data from Amazon S3 by Aaron Anderson
  
• Open NEXRAD Data Access for Level 3 with Lambda@Edge by Zac Flamig
  
• WeatherPipe - Amazon EMR based analysis tool for NEXRAD data stored on Amazon S3 by Stephen Lien Harrell
  

Publications

• Declines in an abundant aquatic insect, the burrowing mayfly, across major North American waterways by Phillip M. Stepanian, Sally A. Entrekin, Charlotte E. Wainwright, Djordje Mirkovic, Jennifer L. Tank, & Jeffrey F. Kelly
  
• Extreme Pyroconvective Updrafts During a Megafire by B. Rodriguez, N. P. Lareau, D. E. Kingsmill, & C. B. Clements
  
• Level 2 Interface Control Document for Message Data Formats: Build 18 by NOAA ROC
  
• Level 2 Interface Control Document for Transfer: Build 18 by NOAA ROC
  
• Level 3 Interface Control Document for Message Data Formats: Build 18 by NOAA ROC
  
• Seasonal abundance and survival of North America’s migratory avifauna determined by weather radar by Adriaan M. Dokter, Andrew Farnsworth, Daniel Fink, Viviana Ruiz-Gutierrez, Wesley M. Hochachka, Frank A. La Sorte, Orin J. Robinson, Kenneth V. Rosenberg & Steve Kelling
  
• Unlocking the Potential of NEXRAD Data through NOAA’s Big Data Partnership by Steve Ansari and Stephen Del Greco
  

Allen Cell Imaging Collections

Tutorials

• Download and train label-free models by Greg Johnson
  
• Integrating single-cell sequencing and nuclear imaging data by Chengxiang Qiu and William Noble
  

Tools & Applications

• AICS Volume Viewer by Dan Toloudis
  
• AICSImageIO by Matthew Bowden, Jackson Brown, Jamie Sherman, Dan Toloudis
  
• Allen Cell Feature Explorer by Allen Institute for Cell Science
  
• Allen Cell Structure Segmenter by Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski
  
• Integrated Mitotic Stem Cell by Allen Institute for Cell Science
  
• Pytorch 3D Integrated Cell by Gregory R. Johnson, Rory M. Donovan-Maiye, Mary M. Maleckar
  
• Visual Guide to Human Cells by Allen Institute for Cell Science
  

Publications

• Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy by Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman & Gregory R. Johnson
  
• Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable? by Matheus P. Viana, Jianxu Chen*, Theo A. Knijnenburg*, Ritvik Vasan*, Calysta Yan*... Allen Institute for Cell Science... Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski
  

CBERS on AWS

Tutorials

• Keeping a SpatioTemporal Asset Catalog (STAC) Up To Date with SNS/SQS by Frederico Liporace
  

Tools & Applications

• aws-sat-api-py by Remote Pixel
  
• CBERS static STAC catalog served by stac-browser by Radiant Earth
  
• CBERS timelapse GIF generator by Frederico Liporace
  
• cbers-tiler by Mapbox
  
• EOS Land Viewer by Earth Observing System
  
• Forest Monitor by Brazil Datacube, INPE
  
• Remote Pixel Viewer by Remote Pixel
  
• rio-tiler by Mapbox
  
• STAC V1.0 search endpoint for archive by AMS Kepler
  

Publications

• Using Remote Sensing Images and Cloud Services on AWS to Improve Land Use and Cover Monitoring by K. R. Ferreira, et al.
  

International Neuroimaging Data-Sharing Initiative (INDI)

Tutorials

• Downloading FCP-INDI Neuroimaging Data from Amazon S3 by INDI
  

Tools & Applications

• Configurable Pipeline for the Analysis of Connectomes (C-PAC) by [INDI C-PAC Team](https://fcp-indi.github.io/)
  

Publications

• Accelerating the Evolution of Nonhuman Primate Neuroimaging by M.P. Milham, C. Petkov
  
• An Open Resource for Non-human Primate Imaging by M.P. Milham, L. Ai, ..., C.E. Schroeder
  
• An open resource for transdiagnostic research in pediatric mental health and learning disorders by L.M. Alexander, J. Escalera, ..., M.P. Milham
  
• Assessment of the impact of shared brain imaging data on the scientific literature by M.P. Milham, R.C. Craddock, ..., A. Klein
  
• Enhancing studies of the connectome in autism using the autism brain imaging data exchange II. by A. Di Martino, D. O'Connor, M.P. Milham
  
• Making data sharing work: The FCP/INDI experience by M. Mennes, B.B. Biswal, F.X. Castellanos, M.P. Milham
  
• The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. by A. Di Martino, C-G Yan, ..., M.P. Milham
  
• The Healthy Brain Network Serial Scanning Initiative: a resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions by D. O'Connor, N.V. Potler, ..., M.P. Milham
  
• The NKI-Rockland sample: a model for accelerating the pace of discovery science in psychiatry by K.B. Nooner, S.J. Colcombe, ..., M.P. Milham
  

Terrain Tiles

Tools & Applications

• EOS Land Viewer by Earth Observing System
  
• Mapzen Terrain Tiles on AWS Reader by Safe Software
  
• On The Go Map by On The Go Map
  
• Open-Source Elevation Service by Racemap
  
• PlanetUtils (GitHub): Scripts and a Docker container to download, merge, and resample terrain tiles by Interline Technologies
  
• PODPAC: Python Library supporting TerrainTiles for analysis by Creare
  
• R package for accessing Terrain Tiles by Jeffrey W. Hollister
  
• Sentinel Hub WMS/WMTS/WCS Service for DEM by Sinergise
  
• Sentinel Playground for DEM by Sinergise
  
• Terradactile: Generate DEM and hillshade Cloud Optimized GeoTIFFs for visualization and download based on terrain tiles by Sparkgeo
  

Publications

• Interactive Visualization of 3D Terrain Data Stored in the Cloud by Gregory Larrick, Yun Tian, Uri Rogers, Halim Acosta, and Fangyang Shen
  

IRS 990 Filings

Tutorials

• Tutorial on using the IRS 990 e-file dataset by 990 Consulting, LLC
  

Tools & Applications

• 990_long by Charity Navigator
  
• aws-irs-990-explorer by Chris Herbert
  
• Grantmakers.io by Chad Kruse
  
• Guide to Open Data for Nonprofit Research by lecy
  
• Non Profit Light by Non Profit Light
  
• Nonprofit Explorer by ProPublica
  
• npo_classifier: Automated coding using machine-learning and remapping the U.S. nonprofit sector by Ji Ma
  
• Open990 by 990 Consulting, LLC
  
• Parse 990 XML using IRSx by Jacob Fenton
  

Multi-Scale Ultra High Resolution (MUR) Sea Surface Temperature (SST)

Tutorials

• Python Jupyter Notebooks by Chelle Gentemann, Rich Signell
  
• Python Reader Software by PO.DAAC
  

Tools & Applications

• HTTPS server by PO.DAAC
  
• OPeNDAP server by Physical Oceanography Distributed Active Archive Center (PO.DAAC)
  
• State of the Ocean (SOTO) server by PO.DAAC
  
• THREDDS server by PO.DAAC
  
• Web discovery service by PO.DAAC
  

Publications

• A multi-scale high-resolution analysis of global sea surface temperature by Chin, Toshio Michael, Jorge Vazquez-Cuervo, and Edward M. Armstrong
  
• GHRSST Data Processing Specification by GHRSST Project
  

NOAA Geostationary Operational Environmental Satellites (GOES) 16 & 17

Tutorials

• Comparison reading GOES-R data from AWS S3 in netCDF versus zarr by Chelle Gentemann
  
• NOAA GOES16 Julia Jupyter Notebook Example by Peter Schmiedeskamp
  
• Visualize GOES-16 in Python using Xarray by Hamed Alemohammad
  

Tools & Applications

• GOES-2-go is a python package for downloading and plotting plotting GOES data. by Brian K. Blaylock
  

Publications

• Billions of Birds Migrate. Where Do They Go? by National Geographic
  
• Comparison of Lightning Forecasts from the High-Resolution Rapid Refresh Model to Geostationary Lightning Mapper Observations by Brian K. Blaylock, and John D. Horel
  
• Embracing the cloud for climate research by North Carolina State University’s North Carolina Institute for Climate Studies
  
• Observations of lightning in relation to transitions in volcanic activity during the 3 June 2018 Fuego Eruption by Christopher J. Schultz, Virginia P. Andrews, Kimberly D. Genareau, and Aaron R. Naeger
  
• Solar irradiance forecasting for the solar powered future by Solcast
  

Cancer Cell Line Encyclopedia (CCLE)

Tools & Applications

• Broad Institute Cancer Cell Line Encyclopedia by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• Genomic Data Commons by National Cancer Institute
  
• ISB CGC BigQuery tables by Institute for Systems Biology
  

Publications

• Next-generation characterization of the Cancer Cell Line Encyclopedia by Ghandi, M., Huang F. et al.
  
• Pharmacogenomic agreement between two cancer cell line data sets by The Cancer Cell Line Encyclopedia Consortium & The Genomics of Drug Sensitivity in Cancer Consortium
  
• The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity by Barretina Caponigro Stransky et al.
  
• The landscape of cancer cell line metabolism by Li, H. et al.
  

NOAA Water-Column Sonar Data Archive

Tutorials

• Frequency Differencing with Raw Data by Carrie Wall
  
• Plotting Raw EK60 Data by Carrie Wall
  
• Reading and Plotting Bottom Data by Carrie Wall
  
• Reading and Plotting Processed CSV Data by Carrie Wall
  

Tools & Applications

• pyEcholab - an open-source, python-based toolkit for reading, processing, plotting, and exporting fisheries acoustic echosounder data by Rick Towler, Chuck Anderson, Veronica Martinez, Pamme Crandell
  
• Water Column Sonar Data Explorer - Map viewer for exploring sonar water column data by NCEI, NOAA
  

Publications

• Building an Accessible Archive for Water Column Sonar Data by Carrie Wall
  
• Increasing the accessibility of acoustic data through global access and imagery by Carrie Wall, Michael Jech, and Susan McLean
  

Sentinel-2 Cloud-Optimized GeoTIFFs

Tutorials

• Create a Dynamic Tiler with TiTiler by Vincent Sarago
  
• Intake-STAC with sat-search by Scott Henderson
  
• STAC, COG, Python and QGIS by Andrew Cutts
  
• Use Sentinel-2 data in the Open Data Cube by Alex Leith
  

Tools & Applications

• rio-tiler-pds by Vincent Sarago, et al.
  
• Sat-search by Matthew Hanson
  
• SpatioTemporal Asset Catalogs by STAC Contriubutors
  

Publications

• STAC and Sentinel-2 COGs (ESIP Summer Meeting 2020) by Matthew Hanson
  

SpaceNet

Tutorials

• Extracting buildings and roads from AWS Open Data using Amazon SageMaker by Yunzhi Shi, Tianyu Zhang, and Xin Chen
  SageMaker
• Getting Started with SpaceNet Data by Adam Van Etten
  

Tools & Applications

• Solaris: an open source Python library for analyzing overhead imagery with machine learning by Nick Weir
  

Publications

• 2nd SpaceNet Competition Winners Code Release by David Lindenbaum
  
• Building Extraction with YOLT2 and SpaceNet Data by Adam Van Etten
  
• Introducing the SpaceNet Road Detection and Routing Challenge and Dataset by David Lindenbaum
  
• Solving SpaceNet Road Detection Challenge With Deep Learning by Jonathan Howe, May Casterline and Abel Brown
  
• SpaceNet: Winning Implementations and New Imagery Release by Todd Stavish
  

eBird Status and Trends Model Results

Tutorials

• eBird Status and Trends FAQ by Cornell Lab of Ornithology
  
• eBird Status and Trends Visualizations by Cornell Lab of Ornithology
  
• ebirdst - Background, Data Access and Data Structure by Tom Auer and Daniel Fink
  
• ebirdst - Generating Seasonal Abundance and Range Maps and Stats by Matt Strimas-Mackey, Tom Auer, and Daniel Fink
  
• ebirdst - Intro Mapping by Tom Auer and Daniel Fink
  
• ebirdst - Non-raster Data by Tom Auer and Daniel Fink
  

Tools & Applications

• ebirdst R Package by Cornell Lab of Ornithology
  

Publications

• Modeling avian full annual cycle distribution and population trends with citizen science data by Fink et al (2019)
  

Clinical Proteomic Tumor Analysis Consortium 2 (CPTAC-2)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer by Hui Zhang, Tao Liu, Zhen Zhang, Samuel H. Payne, Bai Zhang, Jason E. McDermott, Jian-Ying Zhou, Vladislav A. Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A. Gritsenko, Therese R. Clauss, Caitlin Choi, Matthew E. Monroe, Stefani Thomas, Song Nie, Chaochao Wu, Ronald J. Moore, Kun-Hsing Yu, David L. Tabb, David Fenyö, Vineet Bafna, Yue Wang, Henry Rodriguez, Emily S. Boja, Tara Hiltke, Robert C. Rivers, Lori Sokoll, Heng Zhu, Ie-Ming Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, Michael P. Snyder, Douglas A. Levine, Richard D. Smith, Daniel W. Chan, Karin D. Rodland, the CPTAC Investigators
  
• Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities by Suhas Vasaikar, Chen Huang, Xiaojing Wang. Vladislav A. Petyuk, Sara R. Savage, Bo Wen, Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A. Arshad, Marina A. Gritsenko, Lisa J. Zimmerman, Jason E. McDermott, Therese R. Clauss, Ronald J. Moore, Rui Zhao, Matthew E. Monroe, Yi-Ting Wang, Matthew C. Chambers, Robbert J.C. Slebos, Ken S. Lau, Qianxing Mo, Li Ding, Matthew Ellis, Mathangi Thiagarajan, Christopher R. Kinsinger, Henry Rodriguez, Richard D. Smith, Karin D. Rodland, Daniel C. Liebler, Tao Liu, Bing Zhang, Clinical Proteomic Tumor Analysis Consortium
  
• Proteomic analysis of colon and rectal carcinoma using standard and customized databases by Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC
  

Fly Brain Anatomy: FlyLight Gen1 and Split-GAL4 Imagery

Tutorials

• File Operations on AWS S3 by Rob Svirskas
  
• Using Imagery on AWS S3 by Rob Svirskas
  

Tools & Applications

• Color Depth Search Fiji Plugin by Hideo Otsuna
  
• Fly Light Split-GAL4 Driver Collection by Rob Svirskas
  
• FlyLight Project Website by Geoffrey Meissner
  
• NeuronBridge by Jody Clements, Rob Svirskas, Hideo Otsuna, Cristian Goina, Konrad Rokicki
  

Publications

• A GAL4-Driver Line Resource for Drosophila Neurobiology by Jenett, A., Rubin, G. M., Ngo, T., Shepherd, D., Murphy, C., Dionne, H., Pfeiffer, B. D., Cavallaro, A., Hall, D., Jeter, J., Iyer, N., Fetter, D., Hausenfluck, J. H., Peng, H., Trautman, E. T., Svirskas, R. R., Myers, E. W., Iwinski, Z. R., Aso, Y., DePasquale, G. M., Enos, A., Hulamm, P., Lam, S. C. B., Li, H., Laverty, T. R., Long, F., Qu, L., Murphy, S. D., Rokicki, K., Safford, T., Shaw, K., Simpson, J. H., Sowell, A., Tae, S., Yu, Y., & Zugates, C. T.
  
• An unbiased template of the Drosophila brain and ventral nerve cord by Bogovic, J.A., Otsuna, H., Heinrich, L., Ito, M., Jeter, J., Meissner, G., Nern, A., Colonell, J., Malkesman, O., Ito, K., & Saalfeld, S.
  
• Color depth MIP mask search: a new tool to expedite Split-GAL4 creation by Otsuna, H., Ito, M., & Kawase, T.
  
• The neuronal architecture of the mushroom body provides a logic for associative learning by Aso, Y., Hattori, D., Yu, Y., Johnston, R. M., Iyer, N. A., Ngo, T., Dionne, H., Abbott, L., Axel, R., Tanimoto, H., & Rubin, G. M.
  

ICGC on AWS

Tutorials

• AWS Pancancer Workflow Launcher by Solomon Shorser
  

Publications

• Analyses of non-coding somatic drivers in 2,693 cancer whole genomes by Rheinbay et al (2020)
  
• Genomic basis of RNA alterations in cancer by PCAWG Transcriptome Core Group et al. (2020)
  
• Pan-cancer analysis of whole genomes by The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020)
  
• Patterns of somatic structural variation in human cancer genomes by Li et al. (2020)
  
• The evolutionary history of 2,658 cancers by Gerstung et al (2020)
  
• The repertoire of mutational signatures in human cancer by Alexandrov et al (2020)
  

NREL Wind Integration National Dataset

Tutorials

• HSDS Examples by Caleb Phillips, Caroline Draxl, John Readey, Jordan Perr-Sauer, Michael Rossol
  

Tools & Applications

• Wind Prospector by Paul Edwards
  
• Wind Visualization by Jordan Perr-Sauer
  

Publications

• Overview and Meteorological Validation of the Wind Integration National Dataset Toolkit by Caroline Draxl, Bri-Mathias Hodge, Andrew Clifton, Jim McCaa
  
• Power from wind: Open data on AWS by Caleb Phillips, Caroline Draxl, John Readey, Jordan Perr-Sauer
  
• The Wind Integration National Dataset (WIND) Toolkit by Caroline Draxl, Andrew Clifton, Bri-Mathias Hodge, Jim McCaa
  
• Validation of Power Output for the WIND Toolkit by J. King, Andrew Clifton, Bri-Mathias Hodge
  

Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC-3)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics by Clark DJ, Hu Y, Bocik W, Chen L, Schnaubelt M, Roberts R, Shah P, Whiteley G, Zhang H
  
• Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L1, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium
  

Global Database of Events, Language and Tone (GDELT)

Tutorials

• Analysing Brexit Coverage In The Media Over Time by Mark Chopping
  
• Bootstrapping GeoMesa HBase on AWS S3 by Commonwealth Computer Research, Inc.
  
• Creating PySpark DataFrame from CSV in AWS S3 in EMR by Jake Chen
  
• Exploring GDELT with Athena by Julien Simon
  
• Running R on Amazon Athena by Gopal Wunnava
  

Tools & Applications

• Globe Events by thermobook
  

Low Altitude Disaster Imagery (LADI) Dataset

Tutorials

• LADI Tutorials by Andrew Weinert, Jianyu Mao, Kiana Harris, Nae-Rong Chang, Caleb Pennell, Yiming Ren, Ryan Earley, Nadia Dimitrova
  

Tools & Applications

• NIST TRECVID 2020 - Disaster Scene Description and Indexing (DSDI) by TREC Video Retrieval Evaluation (TRECVID)
  
• Remote Sensing for Disaster Response Course by Beaver Works Summer Institute
  

Publications

• Large Scale Organization and Inference of an Imagery Dataset for Public Safety by Jeffrey Liu, David Strohschein, Siddharth Samsi, Andrew Weinert
  
• Train and Deploy an Image Classifier for Disaster Response by Jianyu Mao, Kiana Harris, Nae-Rong Chang, Caleb Pennell, Yiming Ren
  
• Video Testing at the FirstNet Innovation and Test Lab Using a Public Safety Dataset by Chris Budny, Jeffrey Liu, Andrew Weinert
  

NYU Langone & FAIR FastMRI Dataset

Tutorials

• FastMRI Tutorial (Jupyter Notebook) by Tullie Murrell
  
• How to Get Started Working with the FastMRI Dataset (and why you should!) by Kevin Hodges
  

Publications

• Advancing machine learning for MR image reconstruction with an open competition:Overview of the 2019 fastMRI challenge by Knoll et al (2020)
  
• Assessment of the generalization of learned image reconstruction and the potential for transfer learning. by Knoll et al (2019)
  
• Deep Learning Methods for Parallel Magnetic Resonance Image Reconstruction by Knoll et al (2019)
  
• fastMRI:An Open Dataset and Benchmarks for Accelerated MRI by Zbontar et al (2019)
  

Open NeuroData

Tutorials

• Download by Benjamin Falk
  
• Visualization using Neuroglancer by Benjamin Falk
  

Tools & Applications

• CloudVolume by William Silversmith
  
• Igneous by William Silversmith
  
• Neuroglancer by Jeremy Maitin-Shepard
  

Publications

• A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data by J. T. Vogelstein, E. Perlman, B. Falk, A. Baden, W. Gray Roncal, V. Chandrashekhar, F. Collman, S. Seshamani, J. L. Patsolic, K. Lillaney, M. Kazhdan, R. Hider, D. Pryor, J. Matelsky, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. T. Trautman, K. Khairy, E. Bridgeford, D. M. Kleissas, D. J. Tward, A. K. Crow, B. Hsueh, M. A. Wright, M. I. Miller, S. J. Smith, R. J. Vogelstein, K. Deisseroth, and R. Burns
  
• From cosmos to connectomes: The evolution of data-intensive science by R. Burns, J. T. Vogelstein, and A. S. Szalay
  
• The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience by R. Burns, W. G. Roncal, D. Kleissas, K. Lillaney, P. Manavalan, E. Perlman, D. R. Berger, D. D. Bock, K. Chung, L. Grosenick, N. Kasthuri, N. C. Weiler, K. Deisseroth, M. Kazhdan, J. Lichtman, R. C. Reid, S. J. Smith, A. S. Szalay, J. T. Vogelstein, and R. J. Vogelstein.
  
• To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery by J. T. Vogelstein, B. Mensh, M. Häusser, N. Spruston, A. C. Evans, K. Kording, K. Amunts, C. Ebell, J. Muller, M. Telefont, S. Hill, S. P. Koushika, C. Calì, P. A. Valdés-Sosa, P. B. Littlewood, C. Koch, S. Saalfeld, A. Kepecs, H. Peng, Y. O. Halchenko, G. Kiar, M. M. Poo, J. B. Poline, M. P. Milham, A. P. Schaffer, R. Gidron, H. Okano, V. D. Calhoun, M. Chun, D. M. Kleissas, R. J. Vogelstein, E. Perlman, R. Burns, R. Huganir, and M. I. Miller
  

Radiant MLHub

Tutorials

• How to access Radiant MLHub Data by Radiant Earth
  
• Radiant MLHub Tutorials with Jupyter Notebooks by Kevin Booth
  

Tools & Applications

• Challenge on Computer Vision for Crop Detection from Satellite Imagery by Radiant Earth
  

Publications

• A Guide for Collecting and Sharing Ground Reference Data for Machine Learning Applications by Yonah Bromberg Gaber
  
• Creating a Machine Learning Commons for Global Development by Hamed Alemohammad
  
• Geo-Diverse Open Training Data as a Global Public Good by Hamed Alemohammad
  

COVID-19 Data Lake

Tutorials

• A public data lake for analysis of COVID-19 data by AWS Data Lake Team
  GlueAthenaComprehendKendraQuickSight
• Exploring the public AWS COVID-19 data lake by AWS Data Lake Team
  AthenaGlueSageMaker
• 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
  AthenaGlueS3Cloud​Formation

Tools & Applications

• CloudFormation template for Glue Catalog table definitions by AWS Data Lake Team
  
• Explore the COVID-19 data lake public S3 bucket by AWS Data Lake Team
  

CoMMpass from the Multiple Myeloma Research Foundation

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• "Identification of Initiating Trunk Mutations and Distinct Molecular Subtypes: An Interim Analysis of the Mmrf Commpass Study" by Jonathan J Keats, PhD, Gil Speyer, Legendre Christophe, Christofferson Austin, Kristi Stephenson, BS, Ahmet Kurdoglu, Megan Russell, Aldrich Jessica, Cuyugan Lori, Jonathan Adkins, Jackie McDonald, Adrienne Helland, Alex Blanski, Meghan Hodges, Dan Rohrer, Sundar Jagannath, MD, David Siegel, MD PhD, Ravi Vij, MD MBA, Gregory Orloff, MD, Todd Zimmerman, MD, Ruben Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD PhD, Robert M. Rifkin, Norma C Gutierrez, The MMRF CoMMpass Network, Jen Toups, Mary Derome, MS, Winnie Liang, PhD, Seunchan Kim, Daniel Auclair, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John David Carpten, PhD, Sagar Lonial, MD
  
• "Interim Analysis Of The MMRF CoMMpass Trial: a Longitudinal Study In Multiple Myeloma Relating Clinical Outcomes To Genomic and Immunophenotypic Profiles" by Keats JJ, Craig DW, Liang W, Venkata Y, Kurdoglu A, Aldrich J, Auclair D, Allen K, Harrison B, Jewell S, Kidd PG, Correll M, Jagannath S, Siegel DS, Vij R, Orloff G, Zimmerman TM, MMRF CoMMpass Network, Capone W, Carpten J, Lonial S.
  
• "Interim Analysis of the Mmrf Commpass Trial: Identification of Novel Rearrangements Potentially Associated with Disease Initiation and Progression" by Sagar Lonial, MD, Venkata D Yellapantula, Winnie Liang, PhD, Ahmet Kurdoglu, BS, Jessica Aldrich, MSc, Christophe M. Legendre, MD, Kristi Stephenson, Jonathan Adkins, Jackie McDonald, Adrienne Helland, Megan Russell, Austin Christofferson, Lori Cuyugan, Dan Rohrer, Alex Blanski, Meghan Hodges, Mmrf CoMMpass Network, Mary Derome, Daniel Auclair, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, David Craig, PhD, John Carpten, PhD, Jonathan J. Keats, PhD
  
• "Molecular Predictors of Outcome and Drug Response in Multiple Myeloma: An Interim Analysis of the Mmrf CoMMpass Study" by Jonathan J Keats, PhD, Gil Speyer, Austin Christofferson, Christophe Legendre, PhD, Jessica Aldrich, Megan Russell, Lori Cuyugan, Jonathan Adkins, Alex Blanski, Meghan Hodges, Dan Rohrer, Sundar Jagannath, MD, Ravi Vij, MD, Gregory Orloff, MD, Todd Zimmerman, MD, Ruben Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD, Robert M Rifkin, Norma C Gutierrez, MD PhD, Mmrf CoMMpass Network, Jennifer Yesil, MS, Mary Derome, MS, Seungchan Kim, PhD, Winnie Liang, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John David Carpten, PhD, Daniel Auclair, PhD, Sagar Lonial, MD FACP
  

National Renewable Energy Laboratory's (NREL) PV Rooftop Database

Tools & Applications

• NSRDB Viewer by NREL
  

Publications

• Estimating rooftop solar technical potential across the US using a combination of GIS-based methods, lidar data, and statistical modeling by Pieter Gagnon et al 2018 Environ. Res. Lett. 13 024027
  
• Rooftop Solar Photovoltaic Technical Potential in the United States: A Detailed Assessment by Pieter Gagnon, Robert Margolis, Jennifer Melius, Caleb Phillips, and Ryan Elmore
  
• Rooftop Solar Technical Potential for Low-to-Moderate Income Households in the United States by Benjamin Sigrin and Meghan Mooney
  
• Using GIS-based methods and lidar data to estimate rooftop solar technical potential in US cities by Robert Margolis et al 2017 Environ. Res. Lett. 12 074013
  

Ozone Monitoring Instrument (OMI) / Aura NO2 Tropospheric Column Density

Tutorials

• Medium Post: COG Talk — Part 1: What’s new? by Vincent Sarago
  

Tools & Applications

• COG Application Programming Interface (API) by Development Seed
  
• COG metadata example  by Development Seed
  
• COG Viewer by Development Seed
  
• Rasterio (Python Library) for access to geospatial raster data by Mapbox
  

Prefeitura Municipal de São Paulo (PMSP) LiDAR Point Cloud

Tools & Applications

• Entwine by Hobu, Inc.
  
• Fusion by US Department of Agriculture - Forest Service
  
• LAStools by rapidlasso GmbH, GERMANY
  
• PDAL - Point Data Abstraction Library by PDAL Contributors
  

Publications

• Describing the Vertical Structure of Informal Settlements on the Basis of LiDAR Data – A Case Study for Favelas (Slums) in Sao Paulo City by S. C. L. Ribeiro, M. Jarzabek-Rychard, J. P. Cintra, H.-G. Maas
  

Southern California Earthquake Data

Tutorials

• Cactus to Clouds: Processing The SCEDC Open Data Set on AWS by Tim Clements
  
• Getting Started with SCEDC AWS Public Dataset by Ellen Yu
  
• Script to Download Seismic Waveforms from the SCEDC AWS Public Dataset by Aparna Bhaskaran
  
• SeisNoise.jl GPU Computing Tutorial - Another example of accessing data s3://scedc-pds for ambient noise cross-correlation by Tim Clements
  
• Using Lambda to Process Seismograms by Shang-Lin Chen
  

USGS 3DEP LiDAR Point Clouds

Tutorials

• Extracting buildings and roads from AWS Open Data using Amazon SageMaker by Yunzhi Shi, Tianyu Zhang, and Xin Chen
  SageMaker
• Using Lambda Layers with USGS 3DEP LiDAR Point Clouds by Howard Butler
  Lambda
• WebGL Visualization of USGS 3DEP Lidar Point Clouds with Potree and Plasio.js by Connor Manning
  

Tools & Applications

• OpenTopography access to 3DEP lidar point cloud data by OpenTopography
  

Publications

• USGS 3DEP Lidar Point Cloud Now Available as Amazon Public Dataset by Department of the Interior, U.S. Geological Survey
  

1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5

Tutorials

• DRAGEN Quick Start on AWS by AWS Quick Start Team
  

Tools & Applications

• DRAGEN 3.7.5b Release by Illumina Inc.
  
• DRAGEN on BaseSpace Sequence Hub by Illumina Inc.
  

Publications

• precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions (Preprint) by Olson et al (2020)
  

3000 Rice Genomes Project

Tools & Applications

• RiceGalaxy by International Rice Research Institute
  

Publications

• Rice Galaxy: an open resource for plant science by Juanillas V et al (2019)
  
• Structural variants in 3000 rice genomes by Fuentes RR et al (2019)
  
• Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice by Chen J et al (2019)
  

Community Earth System Model Large Ensemble (CESM LENS)

Tutorials

• Analyzing large climate model ensembles in the cloud by Joe Hamman, NCAR
  

Tools & Applications

• Jupyter Notebook and other documentation and tools for CESM LENS on AWS by NCAR Science at Scale team
  
• Rendered (static) version of Jupyter Notebook by Anderson Banihirwe, NCAR
  

Publications

• The Community Earth System Model (CESM) Large Ensemble Project: A Community Resource for Studying Climate Change in the Presence of Internal Climate Variability by Kay et al. (2015), Bull. AMS, 96, 1333-1349
  

DOE's Water Power Technology Office's (WPTO) US Wave dataset

Tools & Applications

• HSDS Examples by Caleb Phillips, Caroline Draxl, John Readey, Jordan Perr-Sauer, Michael Rossol
  

Publications

• Development and validation of a high-resolution regional wave hindcast model for U.S. West Coast wave resource characterization by Wu, Wei-Cheng; Wang, Taiping; Yang, Zhaoqing; Garcia Medina, Gabriel
  
• High-Resolution Regional Wave Hindcast for the U.S. West Coast by Yang, Zhaoqing; Wu, Wei-Cheng; Wang, Taiping; Castrucci, Luca
  
• SWAN Cycle III version 41.31A by The SWAN team
  

Department of Energy's Open Energy Data Initiative (OEDI)

Tools & Applications

• Tracking the Sun Tool by Lawrence Berkeley National Laboratory (LBNL)
  

Publications

• On the Use of Coupled Wind, Wave, and Current Fields in the Simulation of Loads on BottomSupported Offshore Wind Turbines during Hurricanes by E. Kim, L. Manuel, M. Curcic, S. S. Chen, C. Phillips, P. Veers
  
• The Distributed Generation Market Demand Model (dGen):Documentation by B. Sigrin, M. Gleason, R. Preus, I. Baring-Gould, R. Margolis
  
• Tracking the Sun Pricing and Design Trends for Distributed Photovoltaic Systems in the United States: 2019 Edition by G. Barbose, N. Darghouth
  

Encyclopedia of DNA Elements (ENCODE)

Tutorials

• ENCODE CTCF ChIP-seq data correlation across different cell types by Paul Sud
  
• Exploring ENCODE data from EC2 with Jupyter notebook by Keenan Graham
  
• Ingesting ENCODE data into TileDB with S3 backend by Otto Jolanki
  

Publications

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

First Street Foundation (FSF) Flood Risk Summary Statistics

Tools & Applications

• First Street Foundation Flood Lab by First Street Foundation
  

Publications

• Do You Know Your Home’s Flood Risk? by Edward Kearns, Jeremy Porter, Michael Amodeo
  
• Estimating Recent Local Impacts of Sea-Level Rise on Current Real-Estate Losses: A Housing Market Case Study in Miami-Dade, Florida by Steven A. McAlpine, Jeremy R. Porter
  
• Validation of a 30 m resolution flood hazard model of the conterminous United States by Oliver E. J. Wing, Paul D. Bates, Christopher C. Sampson, Andrew M. Smith, Kris A. Johnson, Tyler A. Erickson
  

GEOS-Chem Input Data

Tutorials

• Tutorial on accessing GEOS-Chem data bucket in S3 by Jiawei Zhuang
  

Publications

• Enabling Immediate Access to Earth Science Models through Cloud Computing: Application to the GEOS-Chem Model by Jiawei Zhuang, et al.
  
• Overview of the GEOSChem-on-cloud project by Atmospheric Chemistry Modeling Group, Harvard University
  
• Running GEOS-Chem on Cloud Computing Platforms, presented at the 8th International GEOS-Chem Meeting by Jiawei Zhuang, et al.
  

Genome in a Bottle on AWS

Tools & Applications

• GA4GH Benchmarking Tools by GA4GH Benchmarking Team
  
• The Genome in a Bottle Github Project by Genome In A Bottle Consortium
  

Publications

• Extensive sequencing of seven human genomes to characterize benchmark reference materials by Zook J et al (2016)
  
• High-coverage, long-read sequencing of Han Chinese trio reference samples by Wang Y et al (2019)
  

NIH NCBI Sequence Read Archive (SRA) on AWS

Tutorials

• Access SRA data using Amazon Web Services (AWS) by NCBI SRA
  
• SRA in the Cloud by NCBI SRA
  

Tools & Applications

• SRA Toolkit by NCBI SRA
  

Publications

• The Sequence Read Archive by Leinonen et al (2011)
  

NOAA High-Resolution Rapid Refresh (HRRR) Model

Tutorials

• Conda Enironment Setup Guide by Zach Rieck
  
• What is Zarr? by Taylor Gowan
  
• Zarr File Varable Definitions by Taylor Gowan
  
• Zarr Visualization Example by Taylor Gowan, James Powell, Zach Rieck
  

New York City Taxi and Limousine Commission (TLC) Trip Record Data

Tutorials

• Build a Real-time Stream Processing Pipeline with Apache Flink on AWS by Steffen Hausmann
  
• Deep Dive on Flink & Spark on Amazon EMR by Keith Steward
  
• Exploring data with Python and Amazon S3 Select by Manav Sehgal
  
• Optimizing data for analysis with Amazon Athena and AWS Glue by Manav Sehgal
  

OpenAQ

Tutorials

• Access OpenAQ data via a filterable SNS topic by OpenAQ
  
• Using Athena to access the whole archive by OpenAQ
  

Tools & Applications

• ARISense by Aerodyne Research, Inc.
  
• hackAIR by hackAir
  
• ropenaq R package by Maëlle Salmon
  
• Smokey: Air Quality Bot by Amrit Sharma
  

Publications

• Enabling rapid COVID-19 and air pollution analysis across the globe with OpenAQ and AWS by Christa Hasenkopf
  

OpenStreetMap on AWS

Tutorials

• Develop and Extract Value from Open Data by Daniel Bernao
  
• Querying OpenStreetMap with Amazon Athena by Seth Fitzsimmons
  

Tools & Applications

• OSM+Athena (GitHub) by Development Seed
  
• PlanetUtils (GitHub): Scripts and a Docker container to maintain your own OpenStreetMap planet by Interline Technologies
  

Refgenie reference genome assets

Tutorials

• Basic Refgenie tutorial by Nathan Sheffield
  

Tools & Applications

• Pipeline for ATAC-seq data analysis by Jason Smith and Nathan Sheffield
  
• Pipeline for PRO-seq data analysis by Jason Smith and Nathan Sheffield
  

Publications

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

Sentinel-1

Tools & Applications

• EO Browser by Sinergise
  
• EOS Land Viewer by Earth Observing System
  
• Sentinel Hub WMS/WMTS/WCS Service by Sinergise by Sinergise
  
• Sentinel Playground by Sinergise
  

Sentinel-3

Tutorials

• Accessing Sentinel-3 Data on S3 by MEEO by Meteorological Envionmental Earth Observation
  

Tools & Applications

• Catalogue of data set by Meteorological Envionmental Earth Observation
  
• Sentinel-3 Toolbox by European Space Agency
  

Publications

• Sentinel-3 Document Library by European Space Agency
  

Sentinel-5P Level 2

Tutorials

• Accessing Sentinel-5P Data on S3 by MEEO by Meteorological Envionmental Earth Observation
  

Tools & Applications

• Catalogue of data set by Meteorological Envionmental Earth Observation
  
• The Atmospheric Toolbox by European Space Agency
  

Publications

• Sentinel-5P TROPOMI Document Library by European Space Agency
  

UK Biobank Pan-Ancestry Summary Statistics

Tutorials

• Hail Tutorials by Hail Team
  

Tools & Applications

• Hail by Hail Team
  
• Hail on AWS Quick Start by Amazon Web Services and PrivoIT
  

Publications

• Pan-ancestry genetic analysis of the UK Biobank by Pan UKBB Team
  

Allen Mouse Brain Atlas

Tutorials

• Visualizing Images from the Allen Mouse Brain Atlas by Allen Institute for Brain Science
  

Tools & Applications

• Allen Mouse Brain Atlas by Allen Institute for Brain Science
  

Publications

• Genome-wide atlas of gene expression in the adult mouse brain by Ed Lein, et al.
  

Basic Local Alignment Sequences Tool (BLAST) Databases

Tools & Applications

• 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
  

Beat Acute Myeloid Leukemia (AML) 1.0

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms by Zhang H, Savage S, Schultz AR, Bottomly D, White L, Segerdell E, et al.
  
• Functional Genomic Landscape of Acute Myeloid Leukemia by Jeffrey W. Tyner, Cristina E. Tognon, Dan Bottomly et al.
  

COVID-19 Harmonized Data

Tutorials

• How Talend is joining the fight against COVID-19 by Thomas Bennett
  

Tools & Applications

• Stitch COVID-19 Integration by Jeff Huth
  
• Tap COVID-19 Python by Jeff Huth
  

Clinical Trial Sequencing Project - Diffuse Large B-Cell Lymphoma

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• A multiprotein supercomplex controlling oncogenic signalling in lymphoma by Phelan JD, Young RM, Webster DE, Roulland S, Wright GW, Kasbekar M, Shaffer AL 3rd, Ceribelli M, Wang JQ, Schmitz R, Nakagawa M, Bachy E, Huang DW, Ji Y, Chen L, Yang Y, Zhao H, Yu X, Xu W, Palisoc MM, Valadez RR, Davies-Hill T, Wilson WH, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza LM, Rodriguez FJ, Estephan F, Holdhoff M, Kruhlak MJ, Hewitt SM, Thomas CJ, Pittaluga S, Oellerich T, Staudt LM
  
• Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., Calvin A. Johnson, Ph.D., James D. Phelan, Ph.D., James Q. Wang, Ph.D., Sandrine Roulland, Ph.D., Monica Kasbekar, Ph.D., Ryan M. Young, Ph.D., Arthur L. Shaffer, Ph.D., Daniel J. Hodson, M.D., Ph.D., Wenming Xiao, Ph.D., et al.
  

Deutsche Börse Public Dataset

Tutorials

• 10 visualizations to try in Amazon QuickSight with sample data by AWS Big Data Blog
  
• Stock Price Movement Prediction Using The Deutsche Börse Public Dataset & Machine Learning by Originate
  

Tools & Applications

• Streaming XETRA Data Using Apache Spark by Thermobook
  

Distributed Archives for Neurophysiology Data Integration (DANDI)

Tools & Applications

• DANDI JupyterHub Interface by DANDI Project
  
• DANDI Shell Interface by DANDI Project
  
• DANDI Web Interface by DANDI Project
  

Finnish Meteorological Institute Weather Radar Data

Tutorials

• Handling data with QGIS by Markus Peura
  
• Processing GeoTIFF data with python by Roope Tervo
  
• Processing HDF5 data with python by Roope Tervo
  

Foundation Medicine Adult Cancer Clinical Dataset (FM-AD)

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis by Ryan J. Hartmaier, Lee A. Albacker, Juliann Chmielecki, Mark Bailey, Jie He, Michael E. Goldberg, Shakti Ramkissoon, James Suh, Julia A. Elvin, Samuel Chiacchia, Garrett M. Frampton, Jeffrey S. Ross, Vincent Miller, Philip J. Stephens and Doron Lipson
  
• Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. by Beltran H, Yelensky R, Frampton GM, Park K, Downing SR, MacDonald TY, Jarosz M, Lipson D, Tagawa ST, Nanus DM, Stephens PJ, Mosquera JM, Cronin MT, Rubin MA
  

JMA Himawari-8

Publications

• Himawari-8 Advanced Himawari Imager Data on AWS (pdf file) by NOAA NESDIS
  
• Himawari-8 on AWS (pdf file) by ASDI
  
• Introduction of Himawari-8/9 (pdf file) by JMA
  

Japanese Tokenizer Dictionaries

Tutorials

• Fugashi Word Count Tutorial by Paul O'Leary McCann
  SageMaker

Tools & Applications

• unidic-py by Paul O'Leary McCann
  

Publications

• How to Tokenize Japanese in Python by Paul O'Leary McCann
  

Medical Segmentation Decathlon

Tutorials

• Pytorch-Integrated MSD Data Loader by MONAI Development Team
  

Tools & Applications

• MONAI: Getting Started by MONAI Development Team
  

Publications

• A large annotated medical image dataset for the development and evaluation of segmentation algorithms by Simpson A. L., Antonelli M., Bakas S., Bilello M., Farahana K., van Ginneken B., et al
  

NASA NEX

Tutorials

• Accessing and plotting NASA-NEX data, from GEOSChem-on-cloud tutorial. by Jiawei Zhuang
  

Tools & Applications

• Azavea Climate API by Azavea
  

Publications

• Climate Downscaling Using YNet: a Deep Convolutional Network with Skip Connections and Fusion by Yumin Liu, Auroop Ganguly, and Jennifer Dy
  

NOAA Global Ensemble Forecast System (GEFS) Re-forecast

Tutorials

• Example using GEFS Reforecast Data from AWS by Victor Gensini
  
• Retrospective Dissertation - Part 3: Reforecast Data by Francisco Alvarez
  

Publications

• The GEFS v12 and its reanalyses and reforecasts (Slides) by Tom Hamill
  

NOAA Global Historical Climatology Network Daily (GHCN-D)

Tutorials

• Calculating growing degree days using AWS Registry of Open Data by Karen Hildebrand and Zac Flamig
  
• Explore & Visualize 200+ Years of Global Temperature by Kapil Sreedharan
  
• Visualize over 200 years of global climate data using Amazon Athena and Amazon QuickSight by Conor Delaney
  

NREL National Solar Radiation Database

Tools & Applications

• HSDS Examples by Caleb Phillips, Caroline Draxl, John Readey, Jordan Perr-Sauer, Michael Rossol
  
• NSRDB Viewer by Manajit Sengupta, Yu Xe, Anthony Lopez, Aron Habte, Galen Maclaurin, James Shelby, Paul Edwards
  

Publications

• The National Solar Radiation Data Base (NSRDB) by Manajit Sengupta, Yu Xe, Anthony Lopez, Aron Habte, Galen Maclaurin, James Shelby
  

National Herbarium of NSW

Tutorials

• Accessing the National Herbarium of NSW on AWS by Dr Shelley James
  

Publications

• Atlas of Living Australia by CSIRO
  
• The Australasian Virtual Herbarium by avh@chah.org.au
  

OpenEEW

Tutorials

• Analyzing a magnitude 7.2 earthquake in Mexico using Python by Grillo
  
• Developing a machine learning model for better earthquake detection by Grillo
  

Tools & Applications

• OpenEEW library for Python by Grillo
  

SILO climate data on AWS

Tools & Applications

• Convert NetCDF to ESRI ArcASCII or GeoTIFF by SILO
  
• NetCDF Operators to calculate seasonal means by SILO
  
• Python script to calculate a regional mean by SILO
  

Storm EVent ImageRy (SEVIR)

Tutorials

• Introduction to SEVIR by Mark Veillette
  
• Using Generators for SEVIR data by Mark Veillette
  

Tools & Applications

• sevir -- python utilities for working with SEVIR dataset by Mark Veillette
  

The Human Microbiome Project

Publications

• New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract by Ranjit Kumar, Jayleen Grams, Daniel I. Chu, David K.Crossman, Richard Stahl, Peter Eipers, et al
  
• Strains, functions and dynamics in the expanded Human Microbiome Project by Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, et al.
  
• The Human Microbiome Project by Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight & Jeffrey I. Gordon
  

Variant Effect Predictor (VEP) and the Loss-Of-Function Transcript Effect Estimator (LOFTEE) Plugin

Tools & Applications

• Hail by Neale Lab
  
• Loss-Of-Function Transcript Effect Estimator (LOFTEE) by Konrad Karczewski
  
• Variant Effect Predictor (VEP) by Ensembl
  

Africa Soil Information Service (AfSIS) Soil Chemistry

Tutorials

• AfSIS Soil Chemistry - Usage Tutorial by QED
  

Publications

• Goalkeepers 2018, Soil - The Big Data Beneath Your Feet by QED
  

Amazon Bin Image Dataset

Publications

• Amazon Bin Image Dataset Challenge by silverbottlep
  
• Amazon Inventory Reconciliation using AI by Pablo Rodriguez Bertorello, Sravan Sripada, Nutchapol Dendumrongsup
  

Atmospheric Models from Météo-France

Tools & Applications

• Windguru.cz by Windguru
  
• Windy.com by Windy
  

Broad Genome References

Tutorials

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

Tools & Applications

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

Cancer Genome Characterization Initiatives - Burkitt Lymphoma, HIV+ Cervical Cancer

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma by Grande B. M., Gerhard D. S., Jiang A., Griner N. B., Abramson J. S., Alexander T. B., et al.
  

Copernicus Digital Elevation Model (DEM)

Tools & Applications

• EO Browser by Sinergise
  
• Sentinel Hub WMS/WMTS/WCS Service and Process API by Sinergise
  

ECMWF ERA5 Reanalysis

Tutorials

• Accessing ERA5 Data on S3 Using Boto by Intertrust Technologies Corporation
  
• ERA5 tutorial using the Planet OS API by Intertrust Technologies Corporation
  

Hubble Space Telescope Public Data

Tutorials

• Exploring AWS Lambda with cloud-hosted Hubble public data by Arfon Smith
  

Publications

• Making HST Public Data Available on AWS by Arfon Smith
  

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

Tutorials

• Perform biomedical informatics without a database using MIMIC-III data and Amazon Athena by James Wiggins, Alistair Johnson
  AthenaGlue

Tools & Applications

• MIMIC-code GitHub repository by Alistair Johnson
  

NAIP on AWS

Tools & Applications

• EOS Land Viewer by Earth Observing System
  
• VoyagerSearch showing off Batch + NAIP by Voyager
  

NOAA National Water Model Reanalysis

Tutorials

• Explore the National Water Model Reanalysis in Zarr by Rich Signell
  

Publications

• Simulating storm surge and compound flooding events with a creek-to-ocean model: Importance of baroclinic effects by Fei Ye, et al.
  

NOAA World Ocean Database (WOD)

Publications

• The World Ocean Database Introduction by Tim P. Boyer, Olga K. Baranova, Carla Coleman, Hernan E. Garcia, Alexandra Grodsky, Ricardo A. Locarnini, Alexey V. Mishonov, Christopher R. Paver, James R. Reagan, Dan Seidov, Igor V. Smolyar, Katharine W. Weathers, Melissa M. Zweng
  
• The World Ocean Database User's Manual by Hernan E. Garcia, Tim P. Boyer, Ricardo A. Locarnini, Olga K. Baranova, Melissa M. Zweng
  

National Cancer Institute Center for Cancer Research - Diffuse Large B Cell Lymphoma (DLBCL) Genomics and Expression

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., et al.
  

Open City Model (OCM)

Tutorials

• Running queries on Open City Model using AWS Athena by Allen Gilliland
  
• Using Open City Model with the 3dCityDB by Allen Gilliland
  

Oregon Health & Science University Chronic Neutrophilic Leukemia Dataset

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genomic landscape of neutrophilic leukemias of ambiguous diagnosis by Zhang H, Wilmot B, Bottomly D et al.
  

Pancreatic Cancer Organoid Profiling

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer by Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville TD, et al.
  

RAPID NRT Flood Maps

Publications

• Inundation Extent Mapping by Synthetic Aperture Radar: A Review by Xinyi Shen, Dacheng Wang, Kebiao Mao, Emmanouil Anagnostou, and Yang Hong
  
• Near Real-Time Nonobstructed Flood Inundation Mapping by Synthetic Aperture Radar by Xinyi Shen, Emmanouil N. Anagnostou, George H. Allen, G. Robert Brakenridge, Albert J. Kettner
  

Rapid7 FDNS ANY Dataset

Tutorials

• Creating a Project Sonar FDNS API with AWS by Evan Perotti at SecurityRiskAdvisors
  
• How to Conduct DNS Reconnaissance for $.02 Using Rapid7 Open Data and AWS by Shan Sikdar at Rapid7
  

RarePlanes

Tools & Applications

• RarePlanes Codebase by Thomas Hossler and Jacob Shermeyer
  

Publications

• RarePlanes: Synthetic Data Takes Flight by Jacob Shermeyer, Thomas Hossler, Adam Van Etten, Daniel Hogan, Ryan Lewis, Daeil Kim
  

Sentinel-1 SLC dataset for South and Southeast Asia, Taiwan, Korea and Japan

Tutorials

• Sentinel-1 Opendataset Wiki and Tutorials by Earth Observatory of Singapore
  

Publications

• Rapid flood and damage mapping using synthetic aperture radar in response to Typhoon Hagibis, Japan by Cheryl W. J. Tay, Sang-Ho Yun, Shi Tong Chin, Alok Bhardwaj, Jungkyo Jung & Emma M. Hill
  

Terra Fusion Data Sampler

Tutorials

• Basic Terra fusion product algorithm theoretical basis and data specifications by Zhao, Guangu; Yang, Muqun; Clipp, Landon; Gao, Yizhao; Lee, Joe H.
  

Tools & Applications

• TerraFusion GitHub by University of Illinois
  

UK Met Office Atmospheric Deterministic and Probabilistic Forecasts

Tutorials

• Met Office AWS Earth data - Getting Started by Jacob Tomlinson
  
• Met Office AWS Earth data - Subscribing to data by Jacob Tomlinson
  

1000 Genomes

Publications

• Exploratory data analysis of genomic datasets using ADAM and Mango with Apache Spark on Amazon EMR by Alyssa Marrow
  

AWS iGenomes

Tools & Applications

• nf-core analysis pipelines by Phil Ewels
  

Allen Brain Observatory - Visual Coding AWS Public Data Set

Tutorials

• Use the Allen Brain Observatory – Visual Coding on AWS by Nika Keller, David Feng
  

Answer Reformulation

Publications

• Voice-based Reformulation of Community Answers by Simone Filice, Nachshon Cohen & David Carmel
  

Automatic Speech Recognition (ASR) Error Robustness

Publications

• Using Phoneme Representations to Build Predictive Models Robust to ASR Errors by Anjie Fang, Simone Filice, Nut Limsopatham and Oleg Rokhlenko
  

CMIP6 GCMs downscaled using WRF

Tutorials

• Jupyter Notebook Example by Stefan Rahimi
  

COVID-19 Genome Sequence Dataset

Tools & Applications

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

Cell Painting Image Collection

Publications

• Example submission for the 2018 CytoData Hackathon (in R and Python) by Juan Caicedo, Tim Becker
  

Coupled Model Intercomparison Project 6

Publications

• Special issue | Coupled Model Intercomparison Project Phase 6 (CMIP6) Experimental Design and Organization by V. Eyring
  

CoversBR

Tutorials

• Using the (CoversBR) dataset by Dirceu Silva, Atila Xavier, Edgard Moraes, Marco Grivet and Fernando Perdigão
  

DialoGLUE: A Natural Language Understanding Benchmark for Task-Oriented Dialogue

Publications

• DialoGLUE: A Natural Language Understanding Benchmark for Task-Oriented Dialogue by Shikib Mehri, Mihail Eric, Dilek Hakkani-Tur
  

Enriched Topical-Chat Dataset for Knowledge-Grounded Dialogue Systems

Publications

• Policy-Driven Neural Response Generation for Knowledge-Grounded Dialogue Systems by Behnam Hedayatnia, Karthik Gopalakrishnan, Seokhwan Kim, Yang Liu, Mihail Eric & Dilek Hakkani-Tur
  

Ford Multi-AV Seasonal Dataset

Tutorials

• Ford AV Dataset Tutorial by Ford Motor Company
  

GATK Test Data

Tools & Applications

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

Geosnap Data, Center for Geospatial Sciences

Tools & Applications

• Geosnap User Guide by Eli Knaap
  

Human Cancer Models Initiative (HCMI) Cancer Model Development Center

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Human PanGenomics Project

Publications

• Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes by Shafin et al (2020)
  

IDEAM - Colombian Radar Network

Tutorials

• Guia de como explorar y plotear los archivos de radar utilizando el lenguaje de programación Python by IDEAM
  

LOFAR ELAIS-N1 cycle 2 observations on AWS

Publications

• Calibration of LOFAR ELAIS-N1 data in the Amazon cloud by J. Sabater
  

NOAA Global Forecast System (GFS)

Publications

• GFS Warm Restart Files Additional Information by Fanglin Yang
  

NOAA National Digital Forecast Database (NDFD)

Publications

• NDFD Product Spreadsheet (excel file) by NOAA MDL
  

NOAA Operational Forecast System (OFS)

Tools & Applications

• OFS Data Aggregation and Sub-Setting by NOAA
  

New Jersey Statewide Digital Aerial Imagery Catalog

Tutorials

• Visualize Imagery Changes by stephanie.bosits@tech.nj.gov
  

New Jersey Statewide LiDAR

Tutorials

• 3D Visualization by stephanie.bosits@tech.nj.us
  

Ohio State Cardiac MRI Raw Data (OCMR)

Tutorials

• OCMR Tutorial by Chong Chen
  

Oxford Nanopore Technologies Benchmark Datasets

Tutorials

• ONT Dataset Tutorials by EPI2MELabs
  

QIIME 2 User Tutorial Datasets

Tutorials

• Installing QIIME 2 using Amazon Web Services by The QIIME 2 Development Team
  

SILAM Air Quality

Tutorials

• Simple examples by Roope Tervo
  

Safecast

Tools & Applications

• Safecast Map by Nick Dolezal
  

Tabula Muris

Publications

• Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. by Tabula Muris Consortium (2019)
  

The Multilingual Amazon Reviews Corpus

Publications

• The Multilingual Amazon Reviews Corpus by Phillip Keung, Yichao Lu, György Szarvas, Noah A. Smith
  

Transiting Exoplanet Survey Satellite (TESS)

Publications

• TESS data available on AWS by Arfon Smith
  

U.S. Census ACS PUMS

Tutorials

• Setting up Blazegraph on EC2 by data.world
  

Voices Obscured in Complex Environmental Settings (VOiCES)

Tutorials

• Getting started with VOiCES data by M.A. Barrios
  

Xiph.Org Test Media

Tutorials

• Encoding video with AV1 on EC2 by Thomas Daede
  

Yale-CMU-Berkeley (YCB) Object and Model Set

Publications

• Benchmarking in Manipulation Research: Using the Yale-CMU-Berkeley Object and Model Set by Berk Calli, Aaron Walsman, Arjun Singh, Siddhartha Srinivasa, Pieter Abbeel, Aaron M Dollar
  
• Label Fusion: A Pipeline for Generating Ground Truth Labels for Real RGBD Data of Cluttered Scenes by Pat Marion, Peter R. Florence, Lucas Manuelli, Russ Tedrake
  
• Pre-touch sensing for sequential manipulation by Boling Yang, Patrick Lancaster, Joshua R. Smith
  
• The Closure Signature: A Functional Approach to Model Underactuated Compliant Robotic Hands by Maria Pozzi, Gionata Salvietti, João Bimbo, Monica Malvezzi, Domenico Prattichizzo
  

ZINC Database

Publications

• ZINC Database by John Irwin
  

iHART Whole Genome Sequencing Data Set

Publications

• Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks by Ruzzo et al. (2020)
  

PoroTomo

Tutorials

• PoroTomo DAS Data Processing Tutorial by Nicole Taverna and Ross Ring-Jarvi
  

Publications

• DAS and DTS at Brady Hot Springs: Observations about Coupling and Coupled Interpretations by Douglas E. Miller, Thomas Coleman, Xiangfang Zeng, Jeremy R. Patterson , Elena C. Reinnisch, Michael A. Cardiff, Herbert F. Wang, Dante Fratta, Whitney Trainor-Guitton, Clifford H. Thurber, Michelle ROBERTSON, Kurt FEIGL, and The PoroTomo Team
  
• Ground motion response to an ML 4.3 earthquake using co-located distributed acoustic sensing and seismometer arrays by Herbert F Wang, Xiangfang Zeng, Douglas E Miller, Dante Fratta, Kurt L Feigl, Clifford H Thurber, Robert J Mellors
  

Sophos/ReversingLabs 20 Million malware detection dataset

Tutorials

• SOREL-20M quickstart by Richard Harang
  S3EC2

Tools & Applications

• SOREL-20M dataset interface code by Richard Harang and Ethan M Rudd
  

Publications

• SOREL-20M: A Large Scale Benchmark Dataset for Malicious PE Detection by Richard Harang and Ethan M Rudd
  

Binding DB

Tutorials

• Data Lake as Code Deployment Guide by AWS Biotech Blueprints Team
  AthenaGlueLake Formation

Publications

• Data Lake as Code, Featuring ChEMBL and Open Targets by Paul Underwood
  

Cell Organelle Segmentation in Electron Microscopy (COSEM) on AWS

Publications

• Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. by David P. Hoffman1, Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, H. Amalia Pasolli, Nirmala Iyer, John A. Bogovic, Daniel R. Stabley, Abbas Shirinifard, Song Pang, David Peale, Kathy Schaefer, Wim Pomp, Chi-Lun Chang, Jennifer Lippincott-Schwartz, Tom Kirchhausen1, David J. Solecki, Eric Betzig, Harald F. Hess.
  
• Enhanced FIB-SEM systems for large-volume 3D imaging by C. Shan Xu, Kenneth J. Hayworth, Zhiyuan Lu, Patricia Grob, Ahmed M. Hassan, José G. García-Cerdán, Krishna K. Niyogi, Eva Nogales, Richard J. Weinberg, Harald F. Hess.
  

ChEMBL

Tutorials

• Data Lake as Code Deployment Guide by AWS Biotech Blueprints Team
  AthenaGlueLake Formation

Publications

• Data Lake as Code, Featuring ChEMBL and Open Targets by Paul Underwood
  

Covid Job Impacts - US Hiring Data Since March 1 2020

Tutorials

• Documentation of dataset schemas by Greenwich.HR
  

Tools & Applications

• CovidJobImpats.Greenwich.HR - online visualization of daily hiring data and weekly unemployment data including links to recorded discussions using the data by Greenwich.HR and OneModel Inc.
  

Open Targets

Tutorials

• Data Lake as Code Deployment Guide by AWS Biotech Blueprints Team
  AthenaGlueLake Formation

Publications

• Data Lake as Code, Featuring ChEMBL and Open Targets by Paul Underwood
  

AgricultureVision

Publications

• Agriculture-Vision: A Large Aerial Image Database for Agricultural Pattern Analysis by Mang Tik Chiu, et al.
  

COVID-19 Open Research Dataset (CORD-19)

Tools & Applications

• COVID-19 Open Research Dataset Challenge (CORD-19) by Kaggle
  

Cloud Indexes for Genomic Analyses

Tutorials

• Table of contents for tutorials for constituent tools by Ben Langmead
  

Humor Detection from Product Question Answering Systems

Publications

• Humor Detection in Product Question Answering Systems. by Yftah Ziser, Elad Kravi & David Carmel
  

MODIS MYD13A1, MOD13A1, MYD11A1, MOD11A1, MCD43A4

Tools & Applications

• Astraea Earth OnDemand by Astraea, Inc.
  

Swiss Public Transport Stops

Tools & Applications

• Map Viewer by Swiss Geoportal