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.
  

Foldingathome COVID-19 Datasets

Tutorials

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

Tools & Applications

• SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2 (953.7 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• 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 (with glycosylation) (1.8 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD (without glycosylation) (1.9 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• 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
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97 (623.7 us) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S309 (1.1 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337A mutation bound to monoclonal antibody S309 (907.0 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309 (923.2 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  

Publications

• Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity by Emma C. Thomson, Laura E, Rosen, James G. Shepherd, et al.
  
• SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape by Tyler N. Starr, Nadine Czudnochowski, Zhuoming Liu, et al.
  
• 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
  

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

• Detecting deforestation in the using unsupervised K-means clustering on Sentinel-2 satellite imagery and SageMaker Studio Lab (SMSL) by Parth Patel
  SageMaker Studio Lab
• Exploring the Chile wildfires with Landsat and Sentinel-2 imagery by Timothy Whitehead
  
• Getting Started With Geospatial Data Analysis by Sam Palani
  SageMaker Studio Lab
• How to Work with Landsat and Sentinel-2 on AWS with Python by Martin D. Maas
  
• 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
  
• Vegetation Analysis Pre/Post Lava Fire Using SentinelHub and Sentinel-2 Imagery on AWS by Mike Jeffe
  SageMaker Studio Lab

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
  
• 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.
  

Sudachi Language Resources

Tutorials

• analysis-sudachi Tutorial by Works Applications
  
• chiTra 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
  
• chiTra: SudachiPy for hugging face Transformers 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
  

USGS Landsat

Tutorials

• A Gentle Introduction to GDAL Part 4: Working with Satellite Data by Planet
  
• Cloud Segmentation in Landsat-8 Images by Ingrid Grenet
  
• Creating a STAC of Landsat data by PySTAC Contributors
  
• Exploring the Chile wildfires with Landsat and Sentinel-2 imagery by Timothy Whitehead
  
• How to Work with Landsat and Sentinel-2 on AWS with Python by Martin D. Maas
  
• Integrate imagery from the full Landsat archive into your own apps, maps, and analysis with Landsat image services by Esri
  
• Landsat Cloud Direct Access Requester Pays Tutorial by USGS
  
• Landsat Data is Moving to the Cloud by USGS
  
• Landsat in the Cloud – Supporting Current Workflows by USGS
  
• Using Cloud-Optimized GeoTIFF by acgeospatial
  

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
  
• EO Browser by Sinergise
  
• 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
  
• 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.
  

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.
  

NASA Prediction of Worldwide Energy Resources (POWER)

Tutorials

• About the Prediction Of Worldwide Energy Resources (POWER) Project ArcGIS StoryMap. by The POWER Project
  
• Accessing and Subsetting POWER data, from AWS S3 using Python. by The POWER Project
  

Tools & Applications

• NASA POWER NetCDF Data Download by The POWER Project
  
• POWER Application Programming Interface (API) by The POWER Project
  
• POWER Data Access Viewer (DAV) by The POWER Project
  

Publications

• A solar azimuth formula that renders circumstantial treatment unnecessary without compromising mathematical rigor: Mathematical setup, application and extension of a formula based on the subsolar point and atan2 function by Zhang, T., P. W. Stackhouse, B. Macpherson, and J. C. Mikovitz
  
• Application of a global-to-beam irradiance model to the NASA GEWEX SRB dataset: An extension of the NASA Surface meteorology and Solar Energy datasets by Zhang, T., P. W. Stackhouse, W. S. Chandler, and D. J. Westberg
  
• Application of Satellite Sensor Data and Models for Energy Management by Zell, E., J. Engel-Cox, R. Eckman, and P. Stackhouse
  
• Association between solar insolation and a history of suicide attempts in bipolar I disorder by Bauer M, et al., Stackhouse PW Jr., et al.
  
• CEOS contributions to informing energy management and policy decision making using space-based Earth observations by Eckman, R. S., and P. W. Stackhouse
  
• Enhancing Climate Resilience at NASA Centers: A Collaboration between Science and Stewardship by Rosenzweig, C., and Coauthors
  
• Evaluation of NASA satellite- and assimilation model-derived long-term daily temperature data over the continental US by White, J. W., G. Hoogenboom, P. W. Stackhouse, and J. M. Hoell
  
• Evaluation of Satellite-Based, Modeled-Derived Daily Solar Radiation Data for the Continental United States by White, J. W., G. Hoogenboom, P. W. Wilkens, P. W. Stackhouse, and J. M. Hoel
  
• Global Surface Solar Energy Anomalies Including El Nino and La Nina Years. by C. H., and Coauthors
  
• Modeling the potential for thermal concentrating solar power technologies by Zhang, Y., S. J. Smith, G. P. Kyle, and P. W. Stackhouse
  
• NASA Climatological Data for Renewable Energy Assessment by Chandler, W. S., C. H. Whitlock, and P. W. Stackhouse
  
• The Contribution of Solar Brightening to the US Maize Yield Trend by Tollenaar, T., J. Fridgen, P. Tyagi, P. W. Stackhouse Jr., and S. Kumudini
  
• Variations in seasonal solar insolation are associated with a history of suicide attempts in bipolar I disorder by Bauer, M., and Coauthors
  

NOAA Geostationary Operational Environmental Satellites (GOES) 16 & 17

Tutorials

• Comparison reading GOES-R data from AWS S3 in netCDF versus zarr by Chelle Gentemann
  
• Forecasting Hurricane Tracks with TensorFlow and data from AWS S3 by Kyle Archie
  
• NOAA GOES16 Julia Jupyter Notebook Example by Peter Schmiedeskamp
  CloudFormationEC2SageMaker
• Processing GOES-16 data with Dask & AWS Fargate by Zac Flamig
  CloudFormationFargateSageMaker
• 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

• Beginner’s Guide to GOES-R Series Data by Danielle Losos
  
• 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
  
• GOES Quick Guides (Spanish) by Anthony Segura García
  
• Imaging Considerations From a Geostationary Orbit Using the Short Wavelength Side of the Mid-Infrared Water Vapor Absorption Band by N.B. Miller, M.M. Gunshor, A.J. Merrelli, T.S. L'Ecuyer, T.J. Schmit, J.J. Gerth, N.J. Gordillo
  
• 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
  
• SunCast: Solar Irradiance Nowcasting from Geosynchronous Satellite Data by Dhileeban Kumaresan, Richard Wang, Ernesto Martinez, Richard Cziva, Alberto Todeschini, Colorado J Reed, Hossein Vahabi
  
• The Use of Composite GOES-R Satellite Imagery to Evaluate a TC Intensity and Vortex Structure Forecast by an FV3GFS-Based Hurricane Forecast Model by Shaowu Bao, Zhan Zhang, Evan Kalina, and Bin Liu
  

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

• Get NEXRAD data from AWS, get severe reports from SPC archive, and plot a loop of them by Russ Schumacher
  
• Mapping Noaa Nexrad Radar Data With CARTO by Stuart Lynn
  
• NEXRAD on EC2 tutorial by openradar
  EC2
• 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
  

Terrain Tiles

Tutorials

• Using GDAL to Produce a Geotiff for an Area by Chris Henrick
  

Tools & Applications

• Customizable Terrain Tiles by Clockwork Micro
  
• 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
  
• ShadeMap: Simulate sun shadows for any time and place on Earth by Ted Piotrowski
  
• 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
  
• Landscape transformations produce favorable roosting conditions for turkey vultures and black vultures by Jacob E. Hill, Kenneth F. Kellner, Bryan M. Kluever, Michael L. Avery, John S. Humphrey, Eric A. Tillman, Travis L. DeVault & Jerrold L. Belant
  

Sentinel-2 Cloud-Optimized GeoTIFFs

Tutorials

• Create a Dynamic Tiler with TiTiler by Vincent Sarago
  
• How to process Sentinel-2 data in a serverless Lambda on AWS? by Alvaro Huarte
  LambdaSNS
• How to Work with Landsat and Sentinel-2 on AWS with Python by Martin D. Maas
  
• Intake-STAC with sat-search by Scott Henderson
  
• STAC, COG, Python and QGIS by Andrew Cutts
  
• Transforming Geospatial Data to Cloud-Native Frameworks with Element 84 on AWS by Matt Hanson, Imtranur Rahman, Mary-Elizabeth Morin, and Ariel Walcutt
  EKSSageMakerS3
• Use Sentinel-2 data in the Open Data Cube by Alex Leith
  

Tools & Applications

• Fire detection Twitter bot using satellite imagery by Firewatch
  
• rio-tiler-pds by Vincent Sarago, et al.
  
• Sat-search by Matthew Hanson
  
• SITS - Satellite Image Time Series Analysis for Earth Observation Data Cubes by e-Sensing
  
• SpatioTemporal Asset Catalogs by STAC Contriubutors
  

Publications

• OpenSentinelMap: A Large-Scale Land Use Dataset using OpenStreetMap and Sentinel-2 Imagery by Noah Johnson, Wayne Treible, Daniel Crispell
  
• STAC and Sentinel-2 COGs (ESIP Summer Meeting 2020) by Matthew Hanson
  

Digital Earth Africa Landsat Collection 2 Level 2

Tutorials

• Digital Earth Africa Training by Digital Earth Africa Contributors
  

Tools & Applications

• Digital Earth Africa Explorer (LS5 Surface Reflectance) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (LS5 Surface Temperature) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (LS7 Surface Reflectance) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (LS7 Surface Temperature) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (LS8 Surface Reflectance) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (LS8 Surface Temperature) by Digital Earth Africa Contributors
  
• Digital Earth Africa Geoportal by ESRI
  
• Digital Earth Africa Map by Digital Earth Africa Contributors
  
• Digital Earth Africa Notebook Repo by Digital Earth Africa Contributors
  
• Digital Earth Africa Sandbox by Digital Earth Africa Contributors
  
• Digital Earth Africa web services by Digital Earth Africa Contributors
  

Publications

• Introduction to DE Africa by Dr Fang Yuan
  

Fly Brain Anatomy: FlyLight Gen1 and Split-GAL4 Imagery

Tutorials

• File Operations on AWS S3 by Rob Svirskas
  
• Scaling Neuroscience Research on AWS by Konrad Rokicki
  LambdaAppSyncDynamoDBStep Functions
• Tutorial for neuronbridger (R API) by Alexander Bates
  
• 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 Arnim Jenett, Gerald M Rubin, Teri-TB Ngo, David Shepherd, Christine Murphy, Heather Dionne, Barret D Pfeiffer, Amanda Cavallaro, Donald Hall, Jennifer Jeter, Nirmala Iyer, Dona Fetter, Joanna H Hausenfluck, Hanchuan Peng, Eric T Trautman, Robert R Svirskas, Eugene W Myers, Zbigniew R Iwinski, Yoshinori Aso, Gina M DePasquale, Adrianne Enos, Phuson Hulamm, Shing Chun Benny Lam, Hsing-Hsi Li, Todd R Laverty, Fuhui Long, Lei Qu, Sean D Murphy, Konrad Rokicki, Todd Safford, Kshiti Shaw, Julie H Simpson, Allison Sowell, Susana Tae, Yang Yu, Christopher T Zugates
  
• An image resource of subdivided Drosophila GAL4-driver expression patterns for neuron-level searches by Geoffrey W Meissner, Zachary Dorman, Aljoscha Nern, Kaitlyn Forster, Theresa Gibney, Jennifer Jeter, Lauren Johnson, Yisheng He, Kelley Lee, Brian Melton, Brianna Yarbrough, Jody Clements, Cristian Goina, Hideo Otsuna, Konrad Rokicki, Robert R Svirskas, Yoshinori Aso, Gwyneth M Card, Barry J Dickson, Erica Ehrhardt, Jens Goldammer, Masayoshi Ito, Wyatt Korff, Ryo Minegishi, Shigehiro Namiki, Gerald M Rubin, Gabriella Sterne, Tanya Wolff, Oz Malkesman, FlyLight Project Team
  
• An unbiased template of the Drosophila brain and ventral nerve cord by John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
  
• Color depth MIP mask search: a new tool to expedite Split-GAL4 creation by Hideo Otsuna, Masayoshi Ito, Takashi Kawase
  
• The neuronal architecture of the mushroom body provides a logic for associative learning by Yoshinori Aso, Daisuke Hattori, Yang Yu, Rebecca M Johnston, Nirmala A Iyer, Teri-TB Ngo, Heather Dionne, LF Abbott, Richard Axel, Hiromu Tanimoto, Gerald M Rubin
  

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

• Accelerating Ukraine Intelligence Analysis with Computer Vision on Synthetic Aperture Radar Imagery by Ritwik Gupta, Colorado Reed, Anja Rohrbach, and Trevor Darrell
  
• Creating Training Datasets for the SpaceNet Road Detection and Routing Challenge by Adam Van Etten and Jake Shermeyer
  
• Deploying the SpaceNet 6 Baseline on AWS by Adam Van Etten and Nick Weir
  
• FCAU-Net for the Semantic Segmentation of Fine-Resolution Remotely Sensed Images by Xuerui Niu, Qiaolin Zeng, Xiaobo Luo and Liangfu Chen
  
• Introducing the SpaceNet Off-Nadir Imagery Dataset by David Lindenbaum
  
• Introducing the SpaceNet Road Detection and Routing Challenge and Dataset by David Lindenbaum
  
• SpaceNet 5 Dataset Release by Adam Van Etten and Ryan Lewis
  
• SpaceNet 6: Dataset Release by Jake Shermeyer
  
• SpaceNet: Winning Implementations and New Imagery Release by Todd Stavish
  
• The SpaceNet 7 Multi-Temporal Urban Development Challenge: Dataset Release by Adam Van Etten
  

Cell Painting Gallery

Tutorials

• Cell Painting wiki by Multiple
  
• Center for Open Bioimage Analysis (COBA) YouTube Channel - video tutorials of CellProfiler and other softwares by Multiple
  
• Image-based Profiling Handbook - for processing image-based profiling datasets using CellProfiler and pycytominer by Multiple
  
• Scientific Community Image Forum - for software-oriented aspects of scientific imaging including analysis, processing, and acquisition by Multiple
  

Tools & Applications

• Deep Profiler - Morphological profiling using deep learning by Multiple
  
• Distributed CellProfiler - Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure by Multiple
  
• Image-based Profiling Recipe by Multiple
  
• Pycytominer - Data processing functions for profiling perturbations by Multiple
  

Publications

• 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
  

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
  

Digital Earth Africa GeoMAD

Tutorials

• Digital Earth Africa Training by Digital Earth Africa Contributors
  

Tools & Applications

• Digital Earth Africa Explorer (Landsat 5 and 7 GeoMAD) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (Landsat 8 GeoMAD) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (Sentinel-2 Annual GeoMAD) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (Sentinel-2 Semi-Annual GeoMAD) by Digital Earth Africa Contributors
  
• Digital Earth Africa Geoportal by Digital Earth Africa Contributors
  
• Digital Earth Africa Map by Digital Earth Africa Contributors
  
• Digital Earth Africa Notebook Repo by Digital Earth Africa Contributors
  
• Digital Earth Africa Sandbox by Digital Earth Africa Contributors
  
• Digital Earth Africa web services by Digital Earth Africa Contributors
  

Publications

• Introduction to DE Africa by Dr Fang Yuan
  

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
  

NOAA Operational Forecast System (OFS)

Tools & Applications

• OFS Data Aggregation and Sub-Setting by NOAA
  

Publications

• Chesapeake Bay OFS Flyer by NOAA
  
• Chesapeake Bay OFS: Model Development and Skill Assessment by NOAA
  
• Delaware Bay and River OFS Flyer by NOAA
  
• Skill Assessment of the Delaware River and Bay OFS (DBOFS) by NOAA
  
• Tampa Bay OFS Flyer by NOAA
  
• Tampa Bay OFS: Model Development and Skill Assessment by NOAA
  
• Technical Implementation Notice for Chesapeake Bay OFS by NOAA
  
• Technical Implementation Notice for Delaware River and Bay OFS by NOAA
  
• Technical Implementation Notice for Tampa Bay OFS by NOAA
  
• Three-Dimensional Hydrodynamic Model Developments for a Delaware River and Bay Nowcast/Forecast System by NOAA
  

Digital Earth Africa Sentinel-2 Level-2A

Tutorials

• Digital Earth Africa Training by Digital Earth Africa Contributors
  
• Downloading and streaming data using STAC metadata by Digital Earth Africa Contributors
  
• Use Sentinel-2 data in the Open Data Cube by Alex Leith
  

Tools & Applications

• Digital Earth Africa Explorer by Digital Earth Africa Contributors
  
• Digital Earth Africa Geoportal by Digital Earth Africa Contributors
  
• Digital Earth Africa Map by Digital Earth Africa Contributors
  
• Digital Earth Africa Notebook Repo by Digital Earth Africa Contributors
  
• Digital Earth Africa Sandbox by Digital Earth Africa Contributors
  
• Digital Earth Africa web services by Digital Earth Africa Contributors
  

Publications

• Introduction to DE Africa by Dr Fang Yuan
  

Digital Earth Africa Water Observations from Space

Tutorials

• Digital Earth Africa Training by Digital Earth Africa Contributors
  

Tools & Applications

• Digital Earth Africa Explorer (Water Observations from Space All-Time Summary) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (Water Observations from Space Annual Summary) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (Water Observations from Space) by Digital Earth Africa Contributors
  
• Digital Earth Africa Geoportal by Digital Earth Africa Contributors
  
• Digital Earth Africa Map by Digital Earth Africa Contributors
  
• Digital Earth Africa Notebook Repo by Digital Earth Africa Contributors
  
• Digital Earth Africa Sandbox by Digital Earth Africa Contributors
  
• Digital Earth Africa web services by Digital Earth Africa Contributors
  

Publications

• Introduction to DE Africa by Dr Fang Yuan
  

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
  
• Improving our knowledge about the oceans by providing cloud-based access to large datasets by Chelle Gentemann
  

RADARSAT-1

Tutorials

• PCI Geomatics Webinar | Cloud enabling earth observation archives by CATALYST
  

Tools & Applications

• Catalyst Professional by CATALYST
  
• ENVI SARscape by L3Harris Geospatial
  
• EODMS RAPI Client Python Script by Earth Observation Data Management System - Natural Resources Canada
  
• Gamma by Gamme Remote Sensing
  
• GDAL by GDAL
  
• MapReady by NASA
  
• OpenEV by Frank Warmerdam
  
• QGIS by German QGIS user group
  
• RADARSTAC by Sparkgeo Consulting Inc.
  

CBERS on AWS

Tutorials

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

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
  
• rio-tiler by Mapbox
  

Publications

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

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

Tools & Applications

• NSRDB Viewer by National Renewable Energy Laboratory (NREL)
  
• Tracking the Sun Tool by Lawrence Berkeley National Laboratory (LBNL)
  

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
  
• 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
  
• 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
  
• 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
  
• 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
  

Digital Earth Africa ALOS PALSAR, ALOS-2 PALSAR-2 and JERS-1

Tutorials

• Digital Earth Africa Training by Digital Earth Africa Contributors
  

Tools & Applications

• Digital Earth Africa Explorer (ALOS PALSAR and ALOS-2 PALSAR-2) by Digital Earth Africa Contributors
  
• Digital Earth Africa Explorer (JERS) by Digital Earth Africa Contributors
  
• Digital Earth Africa Geoportal by Digital Earth Africa Contributors
  
• Digital Earth Africa Map by Digital Earth Africa Contributors
  
• Digital Earth Africa Notebook Repo by Digital Earth Africa Contributors
  
• Digital Earth Africa Sandbox by Digital Earth Africa Contributors
  
• Digital Earth Africa web services by Digital Earth Africa Contributors
  

Publications

• Introduction to DE Africa by Dr Fang Yuan
  

Digital Earth Africa Sentinel-1 Radiometrically Terrain Corrected

Tutorials

• Digital Earth Africa Training by Digital Earth Africa Contributors
  

Tools & Applications

• Digital Earth Africa Explorer by Digital Earth Africa Contributors
  
• Digital Earth Africa Geoportal by Digital Earth Africa Contributors
  
• Digital Earth Africa Map by Digital Earth Africa Contributors
  
• Digital Earth Africa Notebook Repo by Digital Earth Africa Contributors
  
• Digital Earth Africa Sandbox by Digital Earth Africa Contributors
  
• Digital Earth Africa web services by Digital Earth Africa Contributors
  

Publications

• An Operational Analysis Ready Radar Backscatter Dataset for the African Continent by Fang Yuan, Marko Repse, Alex Leith, Ake Rosenqvist, Grega Milcinski, Negin F. Moghaddam, Tishampati Dhar, Chad Burton, Lisa Hall, Cedric Jorand and Adam Lewis
  
• Introduction to DE Africa by Dr Fang Yuan
  

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
  

PubSeq - Public Sequence Resource

Tutorials

• PubSeq Documentation by PubSeq development team
  
• PubSeq FAQ by PubSeq development team
  
• Query metadata by PubSeq development team
  
• REST API by PubSeq development team
  
• Submitting a sequence by PubSeq development team
  

Tools & Applications

• Source code for (meta)data uploader by PubSeq development team
  
• Source code for CWL workflows by PubSeq development team
  
• Source code for website by PubSeq development team
  

Publications

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

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.
  

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
  
• Development and validation of a regional-scale high-resolution unstructured model for wave energy resource characterization along the US East Coast by Allahdadi, M.N., Gunawan, J. Lai, R. He, V.S. Neary
  
• High-resolution hindcasts for U.S. wave energy resource characterization by Yang, Z. and V.S. Neary
  
• High-Resolution Regional Wave Hindcast for the U.S. West Coast by Yang, Zhaoqing; Wu, Wei-Cheng; Wang, Taiping; Castrucci, Luca
  
• Nearshore wave energy resource characterization along the East Coast of the United States by Ahn, S. V.S. Neary, Allahdadi, N. and R. He
  
• Predicting ocean waves along the US East Coast during energetic winter storms: sensitivity to whitecapping parameterizations by Allahdadi, M.N., He, R., and Neary, V.S
  
• SWAN Cycle III version 41.31A by The SWAN team
  

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
  

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

• A Twenty-Year Analysis of Winds in California for Offshore Wind Energy Production Using WRF v4.1.2 by Alex Rybchuk, Mike Optis, Julie K. Lundquist, Michael Rossol, Walt Musial
  
• 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
  

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.
  

World Bank - Light Every Night

Tutorials

• Open Nighttime Lights by Daynan Crull, Trevor Monroe
  

Tools & Applications

• High Resolution Electricity Access Indicators (HREA) - Settlement-level measures of electricity access, reliability, and usage. by Brian Min, Zachary O'Keeffe
  
• Twenty Years of India Lights by Kwawu Mensan Gaba, Brian Min, Anand Thakker, Christopher Elvidge
  

Publications

• Detection of Rural Electrification in Africa using DMSP-OLS Night Lights Imagery. International Journal of Remote Sensing by Brian Min, Kwawu Mensan Gaba, Ousmane Fall Sarr, Alassane Agalassou.
  
• Mainstreaming Disruptive Technologies in Energy. World Bank Report. 2019 by Kwawu Mensan Gaba, Brian Min, Olaf Veerman, Kimberly Baugh
  
• Mapping city lights with nighttime data from the DMSP Operational Linescan System. Photogrammetric Engineering and Remote Sensing, 63(6)727-734. by Elvidge, C.D., Baugh, K.E., Kihn, E.A., Kroehl, H.W. and Davis, E.R.
  
• Nighttime lights compositing using the VIIRS day-night band - Preliminary results. Proceedings of the Asia-Pacific Advanced Network 35 (2013)70-86. by Kimberly Baugh, Feng-Chi Hsu, Christopher D. Elvidge, and Mikhail Zhizhin.
  
• Power and the Vote - Elections and Electricity in the Developing World. Cambridge. 2015. by Brian Min
  

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
  

Coupled Model Intercomparison Project 6

Tutorials

• Analyze terabyte-scale geospatial datasets with Dask and Jupyter on AWS by Ethan Fahy and Zac Flamig
  EC2EKSS3CloudFormation
• Comparing CMIP6 Zarr vs NetCDF Holdings by Aparna Radhakrishnan
  S3
• Finding CMIP6 data using intake-esm and plotting time series for points by Zac Flamig
  CloudFormationSageMaker
• Getting Started with CMIP6 Data by Aparna Radhakrishnan
  
• Processing CMIP6 data in Zarr format with Dask & AWS Fargate by Zac Flamig
  CloudFormationFargateSageMaker

Publications

• CMIP6 Data Informational Session Video Recording by ASDI
  
• Special issue | Coupled Model Intercomparison Project Phase 6 (CMIP6) Experimental Design and Organization by V. Eyring
  

Earth Observation Data Cubes for Brazil

Tutorials

• Tile Map Service to view Image Collections from Brazil Data Cube Catalog by Brazil Data Cube
  
• Using Python to Access Image Collections Data (Jupyter notebook) by Brazil Data Cube
  

Tools & Applications

• cube-builder-aws - Application to generate data cubes on AWS environment. by Brazil Data Cube
  
• rstac - R library to query and download Image Collections from Brazil Data Cube Catalog on Amazon S3 by Brazil Data Cube
  

Publications

• Building Earth Observation Data Cubes on AWS by Ferreira, K R; Queiroz, G R; Marujo, R F B; Costa, R W. 
  
• Earth Observation Data Cubes for Brazil: Requirements, Methodology and Products. by K. R. Ferreira, et al.
  
• Using Remote Sensing Images and Cloud Services on AWS to Improve Land Use and Cover Monitoring by K. R. Ferreira, et al.
  

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)
  

NOAA Joint Polar Satellite System (JPSS)

Tutorials

• JPSS Satellites (COMET) by UCAR
  
• JPSS Short Course from the 2018 Annual Meeting of American Meteorological Society by Colorado State University
  
• JPSS Training Resources by NOAA
  
• VIIRS Active Fire Quick Guide by NOAA
  
• VIIRS Products (NASA SPoRT) by NASA
  

Tools & Applications

• JPSS Proving Ground by NOAA
  

Publications

• JPSS Science Seminar Annual Digest 2020 by NOAA
  

OpenAQ

Tutorials

• Access OpenAQ data via a filterable SNS topic by OpenAQ
  SNS
• Analyze Global Air Pollution Using Apache Spark & BigQuery by Kapil Sreedharan
  
• Build your own Air Quality Monitor with OpenAQ and EMR on EKS by Damon Cortesi
  EMREKS
• Using Athena to access the whole archive by OpenAQ
  AthenaGlue

Tools & Applications

• ARISense by Aerodyne Research, Inc.
  
• hackAIR by hackAir
  
• OpenAQ Aggregator by Kapil Sreedharan
  
• 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
  

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
  
• Radiant MLHub Dataset Registry 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
  

Scottish Public Sector LiDAR Dataset

Tutorials

• LiDAR Tutorial using QGIS by Michal Michalski
  
• LiDAR Tutorial using R by Michal Michalski
  

Tools & Applications

• Scottish Remote Sensing Portal by Scottish Government and Joint Nature Conservation Committee (JNCC)
  

Publications

• Large area archaeological survey in the age of big data and machine learning by Dave Cowley, George Geddes, Łukasz Banaszek, Kirsty Millican and Iris Kramer
  
• Making LiGHT Work of Large Area Survey? Developing Approaches to Rapid Archaeological Mapping and the Creation of Systematic National-scaled Heritage Data by Dave Cowley, Łukasz Banaszek, George Geddes, Angela Gannon, Mike Middleton and Kirsty Millican
  
• New light on medieval settlement in lowland Scotland by Dave Cowley and Piers Dixon
  
• Towards National Archaeological Mapping. Assessing Source Data and Methodology - A Case Study from Scotland by Łukasz Banaszek, Dave Cowley and Mike Middleton
  

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

• Equator - View, Process, and Download USGS 3DEP LiDAR data in-browser by Equator Studios
  
• Facebook Line of Sight Check by Facebook
  
• 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 and 3.7

Tutorials

• DRAGEN Quick Start on AWS by AWS Quick Start Team
  

Tools & Applications

• DRAGEN 3.7 User Guide by Illumina Inc.
  
• DRAGEN 3.7.5b Release by Illumina Inc.
  
• DRAGEN on BaseSpace Sequence Hub by Illumina Inc.
  

Publications

• DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes by Illumina Inc. (2021)
  
• precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions (Preprint) by Olson et al (2020)
  

BossDB Open Neuroimagery Datasets

Tutorials

• Data access and download by Jordan Matelsky
  

Tools & Applications

• bossDB by bossDB Team
  
• CloudVolume by Seung Lab
  

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
  
• intern: Integrated Toolkit for Extensible and Reproducible Neuroscience by Jordan K Matelsky, Luis Rodriguez, Daniel Xenes, Timothy Gion, Robert Hider Jr., Brock Wester, William Gray-Roncal
  
• The Block Object Storage Service (bossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery by Robert Hider Jr., Dean M. Kleissas, Derek Pryor, Timothy Gion, Luis Rodriguez, Jordan Matelsky, William Gray-Roncal, Brock Wester
  

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
  

GeoNet Aotearoa New Zealand Data

Tutorials

• Aotearoa/New Zealand GeoNet Coastal Tsunami Gauge Digital Waveform Dataset by GNS Science - Te Pū Ao
  
• Available GeoNet GNSS event high rate data by GNS Science - Te Pū Ao
  
• GeoNet continuous GNSS network RAW files by GNS Science - Te Pū Ao
  
• GeoNet continuous GNSS network RINEX by GNS Science - Te Pū Ao
  

Publications

• The development and evolution of the GeoNet and PositioNZ GNSS continuously operating network in New Zealand by P. Gentle; K. Gledhill; G. Blick
  
• Tsunami Forecasting and Monitoring in New Zealand by W. Power; N. Gale
  

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)
  

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
  
• Build and run streaming applications with Apache Flink and Amazon Kinesis Data Analytics for Java Applications 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
  
• Machine learning on distributed Dask using Amazon SageMaker and AWS Fargate by Ram Vittal
  
• Optimizing data for analysis with Amazon Athena and AWS Glue by Manav Sehgal
  

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
  

Pacific Ocean Sound Recordings

Tutorials

• Tutorials on machine learning and signal processing methods for anthropogenic and cetacean study using the pacific-sound archives by MBARI
  

Publications

• Animal-borne metrics enable acoustic detection of blue whale migration by Oestreich et al. (2020)
  
• Humpback whale song occurrence reflects ecosystem variability in feeding and migratory habitat of the northeast Pacific by Ryan et al. (2019)
  
• New Passive Acoustic Monitoring in Monterey Bay National Marine Sanctuary by Ryan et al. (2016)
  
• Reduction of Low-Frequency Vessel Noise in Monterey Bay National Marine Sanctuary During the COVID-19 Pandemic by Ryan et al. (2021)
  
• Seal bomb noise as a potential threat to Monterey Bay harbor porpoise by Simonis et al. (2020)
  

PoroTomo

Tutorials

• PoroTomo DAS Data Processing Tutorial for hdf5 Files by Nicole Taverna and Michael Rossol
  
• PoroTomo DAS Data Processing Tutorial for hdf5 Files via HSDS and h5pyd by Michael Rossol and Nicole Taverna
  
• PoroTomo DAS Data Processing Tutorial for SEG-Y Files 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
  
• PoroTomo Final Technical Report: Poroelastic Tomography by Adjoint Inverse Modeling of Data from Seismology, Geodesy, and Hydrology by Kurt L. Feigl, Lesley M. Parker, and the PoroTomo Team
  

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
  

Publications

• Southern California Earthquake Data Now Available in the AWS Cloud by Ellen Yu; Aparna Bhaskaran; Shang‐Lin Chen; Zachary E. Ross; Egill Hauksson; Robert W. Clayton
  

3000 Rice Genomes Project

Tools & Applications

• RiceGalaxy by International Rice Research Institute
  

Publications

• Identification and Allele Combination Analysis of Rice Grain Shape-Related Genes by Genome-Wide Association Study by Meng B et al (2022)
  
• 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)
  

CAM6 Data Assimilation Research Testbed (DART) Reanalysis: Cloud-Optimized Dataset

Tutorials

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

Tools & Applications

• Intake-ESM Catalog by Brian Bonnlander, NCAR
  
• Jupyter Notebook and other documentation and tools for DART Reanalysis on AWS by NCAR Science at Scale team
  
• Rendered (static) version of Jupyter Notebook by Brian Bonnlander, NCAR
  

Publications

• A new CAM6 + DART reanalysis with surface forcing from CAM6 to other CESM models by Raeder, K., Hoar, T.J., El Gharamti, M. et al (2021)
  

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
  

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
  
• Urban Climate Explorer by Zhonghua Zheng
  

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
  

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
  
• Intro to Amazon EMR Studio by Damon Cortesi
  EMR
• Processing ERA5 data in NetCDF Format by Zac Flamig
  
• Processing ERA5 data in Zarr Format by Zac Flamig
  

ESA WorldCover

Tutorials

• Global Fire Spread Prediction System by SatelliteVu
  

Tools & Applications

• TerraScope Viewer by TerraScope
  
• WorldCover Viewer by ESA/Vito
  

Publications

• Release of the 10 m WorldCover map by Ruben Van De Kerchove
  
• Remote Sensing Mapping of Build-Up Land with Noisy Label via Fault-Tolerant Learning by Gang Xu, Yongjun Fang, Min Deng, Geng Sun and Jie Chen.
  

First Street Foundation (FSF) Flood Risk Summary Statistics

Tools & Applications

• First Street Foundation Flood Lab by First Street Foundation
  

Publications

• Communicating a national flood risk assessment using AWS by Ed Kearns, Mike Amodeo
  
• 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
  

Global Seasonal Sentinel-1 Interferometric Coherence and Backscatter Data Set

Tutorials

• Jupyter Notebook to access and visualize global mosaics of the global data set by Josef Kellndorfer
  
• Jupyter Notebook to access and visualize sub regions of the global data set by Josef Kellndorfer
  

Publications

• Generating Global Temporal Coherence Maps from one year of Sentinel-1 C-band data, ESA Fringe 2021 Poster (Youtube) by Oliver Cartus, Josef Kellndorfer, Shadi Oveisgharan, Batu Osmanoglu, Paul Rosen, Urs Wegmüller
  
• Global seasonal Sentinel-1 interferometric coherence and backscatter data set by Josef Kellndorfer, Oliver Cartus, Marco Lavalle, Christophe Magnard, Pietro Milillo, Shadi Oveisgharan, Batu Osmanoglu, Paul A. Rosen, Urs Wegmüller
  
• Webinar: The new era of SAR Time Series Analysis and Visualization: Cloud meets Big SAR Data. IEEE GRSS Bay Area Chapter (Dec. 3rd 2021) by Josef Kellndorfer
  

NIH NCBI Sequence Read Archive (SRA) on AWS

Tutorials

• Access SRA data using Amazon Web Services (AWS) by NCBI SRA
  
• Get started with the SRA and Amazon Athena 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 National Water Model CONUS Retrospective Dataset

Tutorials

• Explore Repository of Tutorials on National Water Model V2.1 Retrospective Dataset in Zarr by James McCreight
  
• Explore the National Water Model V2.0 Retrospective in Zarr by Rich Signell
  
• Explore the National Water Model V2.1 Retrospective Dataset in Zarr by James McCreight, Ishita Srivastava, Rich Signell
  

Publications

• On Strictly Enforced Mass Conservation Constraints for Modeling the Rainfall-Runoff Process by Jonathan M. Frame, Frederik Kratzert, Hoshin V. Gupta, Paul Ullrich and Grey S. Nearing
  
• Simulating storm surge and compound flooding events with a creek-to-ocean model: Importance of baroclinic effects by Fei Ye, et al.
  

NOAA Rapid Refresh Forecast System (RRFS) Ensemble [Prototype]

Publications

• A Limited Area Modeling Capability for the Finite-Volume Cubed-Sphere (FV3) Dynamical Core and Comparison With a Global Two-Way Nest by Black, T. L., J. A. Abeles, B. T. Blake, D. Jovic, E. Rogers, X. Zhang, E. A. Aligo, L. C. Dawson, Y. Lin, E. Strobach, P. C. Shafran, and J. R. Carley
  
• Community modeling framework underpinning the RRFS - The UFS Short Range Weather Application by UFS community
  
• Details for the configuration used during the 2021 Hazardous Weather Testbed Spring Forecast Experiment may be found in Table 11 of the Program Overview and Operations Plan by NOAA
  
• Prototype UFS-Based Rapid Refresh Forecast System (RRFS) on the Cloud by Holt, C., D. Abdi, J. A. Abeles, J. R. Carley, C. W. Harrop, R. Panda, S. Trahan, and C. R. Alexander
  
• Status of NOAA's Next Generation Convection-Allowing Ensemble: The Rapid Refresh Forecast System by Carley J.R., C.R. Alexander, J.K. Wolff, J. Beck, L. Wicker, E. Rogers, J.A Abeles, E. Aligo, J.A. Aravequia, B. Blake, L. Dawson, C.-H. Jeon, D. Jovic, T. Lei, J. Purser, M.E. Pyle, P. Shafran, R. Vasic, W.-S. Wu, Y. Wu, X. Zhang, D.T. Kleist, and J.-W. Bao
  

Normalized Difference Urban Index (NDUI)

Tutorials

• An example of using ndui data with AWS sagemaker tools by Yifang Wang
  EC2
• Automated extraction of urban built-up areas with NDUI using Python and Google Earth Engine by Yifang Wang
  EC2

Tools & Applications

• Global DMSP images Correction by Yifang Wang
  

Publications

• A Robust Method to Generate a Consistent Time Series From DMSP/OLS Nighttime Light Data by Qingling Zhang and Bhartendu Pandey and Keren C.Seto
  
• Building a Better Urban Picture:Combining Day and Night Remote Sensing Imagery by Qingling Zhang and Bin Li and David Thau & Rebecca Moore
  

OpenStreetMap on AWS

Tutorials

• Develop and Extract Value from Open Data by Daniel Bernao
  
• Querying OpenStreetMap Changesets with Amazon Athena by Jennings Anderson
  Athena
• 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
  

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
  

RarePlanes

Tutorials

• Announcing YOLTv4: Improved Satellite Imagery Object Detection by Adam Van Etten
  
• Getting Started with YOLTv4 for Object Detection in Imagery: Getting Training Data by Sophia Parafina
  
• Notebook for training and testing YOLYv4 by Adam Van Etten
  

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
  

Sea Around Us Global Fisheries Catch Data

Tutorials

• Tutorial for analyzing Sea Around Us Global Fisheries Catch Data using Jupyter Notebook by Shelumiel Ortiz
  

Tools & Applications

• Sea Around Us Global Fisheries Catch Data by Sea Around Us, CIC
  
• Sea Around Us Tools & Data by Sea Around Us
  

Publications

• Global Atlas of Marine Fisheries: A critical appraisal of catches and ecosystem impacts. Island Press, Washington D.C. (2016) by Pauly, D.; Zeller, D. (eds)
  
• List of the Sea Around Us publications by Sea Around Us
  

SondeHub Radiosonde Telemetry

Tutorials

• Loading example notebooks into SageMaker by Michaela Wheeler
  SageMaker
• Using Athena to read radiosonde data by Michaela Wheeler
  Athena
• Using pysondehub to read radiosonde data by Michaela Wheeler
  S3

Tools & Applications

• pysondehub by Sondehub
  

Publications

• STM32 Development Boards (literally) Falling From The Sky (How to submit data) by Mark Jessop & Michaela Wheeler
  

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
  

Boreas Autonomous Driving Dataset

Tutorials

• Introduction to Visualizing Sensor Types (Jupyter notebook) by Keenan Burnett
  SageMaker
• Project Lidar onto Camera Frames (Jupyter notebook) by Keenan Burnett
  SageMaker

Publications

• Do we need to compensate for motion distortion and doppler effects in spinning radar navigation? by K. Burnett, A. P. Schoellig, T. D. Barfoot
  
• Radar odometry combining probabilistic estimation and unsupervised feature learning by K. Burnett, D. J. Yoon, A. P. Schoellig, T. D. Barfoot
  

CMAS Data Warehouse

Tutorials

• AMET Documentation by USEPA
  
• CMAQ Installation and Benchmarking Tutorial by USEPA
  
• Documentation for CMAQ on AWS ParallelCluster by CMAS Center
  ParallelCluster
• EQUATES Benchmark by Liz Adams
  

Community Earth System Model v2 Large Ensemble (CESM2 LENS)

Tools & Applications

• Jupyter Notebook and other documentation and tools for CESM2-LE on AWS by NCAR Science at Scale team
  
• Rendered (static) version of Jupyter Notebook by Maxwell Grover, NCAR
  
• Urban Climate Explorer by Zhonghua Zheng
  

Publications

• Ubiquity of human-induced changes in climate variability by Rodgers et al. (2021), Earth Syst. Dynam., 12, 1–19, 2021
  

Earth Radio Occultation

Tutorials

• Tutorial Demonstrations for Working with GNSS Radio Occultation Data in AWS Open Data Registry archive by Stephen Leroy, Amy McVey, Hailing Zhang, Chi Ao
  S3EC2Batch

Tools & Applications

• Utilities for Handling Data in the AWS Open Data Registry archive of GNSS Radio Occultation Data by Stephen Leroy, Amy McVey
  

Publications

• A technical description of atmospheric sounding by GPS occultation by Hajj, G.A. et al.
  
• Observing Earth's atmosphere with radio occultation measurements using the Global Positioning System by Kursinski, E.R. et al.
  

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
  

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)
  

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
  
• Himawari-8: Enabling access to key weather data by Manan Dalal, Jena Kent
  
• Introduction of Himawari-8/9 (pdf file) by JMA
  

NA-CORDEX - North American component of the Coordinated Regional Downscaling Experiment

Tools & Applications

• Intake-ESM Catalog by Brian Bonnlander (NCAR)
  
• Jupyter Notebook and other documentation and tools by Brian Bonnlander, Seth McGinnis (NCAR)
  
• Rendered (static) version of Jupyter Notebook by Brian Bonnlander (NCAR)
  

Publications

• The NA-CORDEX dataset, version 1.0. NCAR Climate Data Gateway, Boulder CO (2017) by Mearns, Linda O., 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
  
• Explainable deep learning for insights in El Nino and river flows by Yumin Liu, Kate Duffy, Jennifer G. Dy, and Auroop R. Ganguly
  

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

• Physics-guided machine learning for improved accuracy of the National Solar Radiation Database by Grant Buster, Mike Bannister, Aron Habte, Dylan Hettinger, Galen Maclaurin, Michael Rossol, Manajit Sengupta, Yu Xie
  
• The National Solar Radiation Data Base (NSRDB) by Manajit Sengupta, Yu Xe, Anthony Lopez, Aron Habte, Galen Maclaurin, James Shelby
  

OpenCell on AWS

Tools & Applications

• cytoself (an unsupervised ML model to quantify localization patterns) by Hirofumi Kobayashi, Keith C. Cheveralls, Manuel D. Leonetti, Loic A. Royer
  
• OpenCell web portal by OpenCell team
  

Publications

• OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization by Nathan H. Cho, Keith C. Cheveralls, Andreas-David Brunner, Kibeom Kim, André C. Michaelis, Preethi Raghavan, et al.
  
• Self-Supervised Deep-Learning Encodes High-Resolution Features of Protein Subcellular Localization by Hirofumi Kobayashi, Keith C. Cheveralls, Manuel D. Leonetti, Loic A. Royer
  

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
  

SILO climate data on AWS

Tutorials

• Using relative humidity grids with xarray from s3 by Richard Scott
  

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
  

Sea Surface Temperature Daily Analysis: European Space Agency Climate Change Initiative product version 2.1

Tutorials

• Working with surftemp-sst data - Tutorial 1 - Getting started by Niall McCarroll
  
• Working with surftemp-sst data - Tutorial 2 - Analysing Marine Heatwaves by Niall McCarroll
  

Publications

• Adjusting for desert-dust-related biases in a climate data record of sea surface temperature (2020). by Merchant, C.J. and Embury, O.
  
• Satellite-based time-series of sea-surface temperature since 1981 for climate applications (2019). by Merchant, C.J., Embury, O., Bulgin, C.E., Block, T., Corlett, G.K., Fiedler, E., Good, S.A., Mittaz, J., Rayner, N.A., Berry, D., Eastwood, S., Taylor, M., Tsushima, Y., Waterfall, A., Wilson, R. and Donlon, C.
  

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-2 L2A 120m Mosaic

Tutorials

• How to Make the Perfect Time-Lapse of the Earth by Matic Lubej
  

Tools & Applications

• Digital Twin Sandbox by Sentinel Hub
  
• Sentinel Hub WMS/WMTS/WCS Service and Process API by Sinergise
  

Publications

• Digital Twin Sandbox Sentinel-2 collection available to everyone by Grega Milcinski & Matic Lubej
  

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
  

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
  

Publications

• Towards a More Realistic and Detailed Deep-Learning-Based Radar Echo Extrapolation Method by Yuan Hu, Lei Chen, Zhibin Wang, Xiang Pan and Hao Li
  

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
  

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
  

iSDAsoil

Tutorials

• iSDAsoil Python tutorial by Matt Miller
  CloudFormationSageMaker

Tools & Applications

• iSDAsoil homepage - view soil property maps online by iSDA
  
• iSDAsoil liming demo app on Observable by Jamie Collinson
  

Publications

• African soil properties and nutrients mapped at 30 m spatial resolution using two-scale ensemble machine learning by Tomislav Hengl, Matthew A. E. Miller, Josip Križan, Keith D. Shepherd, Andrew Sila, Milan Kilibarda, Ognjen Antonijević, Luka Glušica, Achim Dobermann, Stephan M. Haefele, Steve P. McGrath, Gifty E. Acquah, Jamie Collinson, Leandro Parente, Mohammadreza Sheykhmousa, Kazuki Saito, Jean-Martial Johnson, Jordan Chamberlin, Francis B. T. Silatsa, Martin Yemefack, John Wendt, Robert A. MacMillan, Ichsani Wheeler & Jonathan Crouch
  

Allen Ivy Glioblastoma Atlas

Tutorials

• Accessing Ivy Glioblastoma Atlas Project data by Allen Institute for Brain Science
  

Tools & Applications

• Ivy Glioblastoma Atlas Project by Allen Institute for Brain Science
  

Publications

• An anatomic transcriptional atlas of human glioblastoma by Ralph Puchalski, et al.
  

Allen Mouse Brain Atlas

Tutorials

• Accessing Allen Mouse Brain Atlas data 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.
  

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.
  

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
  

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)
  

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
  

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. Hoffman, 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.
  
• Whole-cell organelle segmentation in volume electron microscopy by Lisa Heinrich, Davis Bennett, David Ackerman, Woohyun Park, Jon Bogovic, Nils Eckstein, et al.
  

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.
  

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
  

IBL Neuropixels Brainwide Map on AWS

Tutorials

• Accessing the public data via ONE by IBL Data Architecture Working Group
  
• Exploring the public IBL data with ONE by IBL Data Architecture Working Group
  

Tools & Applications

• ONE-api on pypi.python.org - python API to query and download neurophysiology data by IBL Data Architecture Working Group
  

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
  

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
  GlueHealthLakeSageMaker
• 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
  

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
  

Multiview Extended Video with Activities (MEVA)

Publications

• ActEV: Activities in Extended Video by National Institute of Standards and Technology (NIST)
  
• MEVA: A Large-Scale Multiview, Multimodal Video Dataset for Activity Detection by Kellie Corona, Katie Osterdahl, Roderic Collins, Anthony Hoogs
  
• TinyAction Challenge: Recognizing Real-world Low-resolution Activities in Videos by Praveen Tirupattur, Aayush J Rana, Tushar Sangam, Shruti Vyas, Yogesh S Rawat, Mubarak Shah
  

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
  AthenaCloudFormationGlue
• 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
  AthenaGlue

NOAA High-Resolution Rapid Refresh (HRRR) Model

Tutorials

• HRRR-B Python package: download and read HRRR grib2 files by Brian Blaylock
  
• The HRRR Zarr Archive Managed by MesoWest by Taylor Gowan
  

Publications

• Using Cloud Computing to Analyze Model Output Archived in Zarr Format by Taylor A. Gowan, John D. Horel, Alexander A. Jacques, and Adair Kovac
  

NapierOne Mixed File Dataset

Tutorials

• napierOne use examples by s.davies
  

Publications

• Exploring the Need For an Updated Mixed File Research Data Set by Simon R.Davies, Richard Macfarlane, William J.Buchanan.
  
• NapierOne - A modern mixed file data set alternative to Govdocs1 by Simon R.Davies, Richard Macfarlane, William J.Buchanan
  

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
  

Open City Model (OCM)

Tutorials

• Investigating environmental characteristics of US cities using publicly available ASDI datasets by Darren Ko
  SageMaker Studio Lab
• Running queries on Open City Model using AWS Athena by Allen Gilliland
  
• Using Open City Model with the 3dCityDB by Allen Gilliland
  

OpenAlex dataset

Tutorials

• Download snapshot by OurResearch
  
• Getting citation data from OpenAlex by DOI (Jupyter notebook) by Jens Peter Anderson
  

Publications

• OpenAlex: A fully-open index of scholarly works, authors, venues, institutions, and concepts by Jason Priem, Heather Piwowar, Richard Orr
  

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
  

Serratus: Ultra-deep Search for Novel Viruses - Versioned Data Release

Tools & Applications

• Serratus Explorer by Serratus Team
  
• Tantalus: An R Package for exploration of Serratus data by Serratus Team
  

Publications

• coronaSPAdes. From biosynthetic gene clusters to RNA viral assemblies by Meleshko D., Hajirasouliha I., and Korobeynikov A. (2021)
  
• Diversification of mammalian deltaviruses by host shifting by Bergner L.M., Orton R.J., et al (2021)
  
• Petabase-scale sequence alignment catalyses viral discovery by Edgar R., Taylor J., Lin V., et al (2021)
  
• Ribovirus classification by a polymerase barcode sequence by Babaian A., and Edgar R. (2021)
  

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
  

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
  

1940 Census Population Schedules, Enumeration District Maps, and Enumeration District Descriptions

Tutorials

• 1940 Census on the AWS Registry of Open Data by National Archives and Records Administration
  

Tools & Applications

• National Archives 1940 Census by National Archives and Records Administration
  

1950 Census Population Schedules, Enumeration District Maps, and Enumeration District Descriptions

Tutorials

• 1950 Census on the AWS Registry of Open Data by National Archives and Records Administration
  

Tools & Applications

• National Archives 1950 Census by National Archives and Records Administration
  

4D Nucleome (4DN)

Tutorials

• Finding and Downloading 4DN Data files by 4DN-DCIC
  
• Using jupyterhub on the 4DN data portal by 4DN-DCIC
  

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
  

Atmospheric Models from Météo-France

Tools & Applications

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

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
  AthenaGlueS3CloudFormation

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
  

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.
  

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)
  

ComStock

Tutorials

• Downloading individual building data files from ComStock results by Carlo Bianchi, Andrew Parker
  
• Running queries on ComStock using AWS Athena by Carlo Bianchi, Andrew Parker, Henry Horsey
  

Consented Activities of People

Tools & Applications

• OpenFAD - Open Fine Grained Activity Detection Challenge by Visym Labs & NIST
  
• Visym Collector by Visym Labs & Systems & Technology Research
  

Copernicus Digital Elevation Model (DEM)

Tools & Applications

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

DNAStack COVID19 SRA Data

Tutorials

• Viral lineage assignment by Heather Ward
  BatchEC2S3

Tools & Applications

• Viral AI by DNAstack
  

DigitalCorpora

Publications

• Bringing Science to Digital Forensics with Standardized Forensic Corpora by Garfinkel, Farrell, Roussev and Dinolt
  
• Creating Realistic Corpora for Forensic and Security Education by Woods, K., Christopher Lee, Simson Garfinkel, David Dittrich, Adam Russel, Kris Kearton
  

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.
  

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
  

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
  

NAIP on AWS

Tools & Applications

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

NOAA Climate Forecast System (CFS)

Publications

• The NCEP Climate Forecast System Reanalysis by Saha, Suranjana, and Coauthors
  
• The NCEP Climate Forecast System Version 2 by Saha, Suranjana, and Coauthors
  

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 Archives Catalog

Tutorials

• National Archives Catalog on the AWS Registry of Open Data by National Archives and Records Administration
  

Tools & Applications

• National Archives Catalog by National Archives and Records Administration
  

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.
  

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.
  

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
  

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
  

REDASA COVID-19 Open Data

Tools & Applications

• Curadr - Curation Platform by REDASA Consortium, Imperial College London
  

Publications

• Using a Secure, Continually Updating, Web Source Processing Pipeline to Support the Real-Time Data Synthesis and Analysis of Scientific Literature: Development and Validation Study by Uddhav Vaghela, Simon Rabinowicz, Paris Bratsos, Guy Martin, Epameinondas Fritzilas, et al.
  

STOIC2021 Training

Tools & Applications

• STOIC2021 Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

Publications

• Study of Thoracic CT in COVID-19: The STOIC Project by Revel, Marie-Pierre, et al.
  

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
  

Sounds of Central African landscapes

Publications

• Listen to the rainforest chorus that's helping scientists protect African elephants by Amazon Staff
  
• You can now hear rainforest sounds worldwide-here's why that matters by Rachel Fobar
  

Speedtest by Ookla Global Fixed and Mobile Network Performance Maps

Tutorials

• How to deliver performant GIS desktop applications with Amazon AppStream 2.0 by Ethan Fahy and Spencer DeBrosse
  AppStreamRDS
• New Year, Great Data: The Best Ookla Open Data Projects We’ve Seen So Far by Katie Jolly
  

TIGER Training

Tools & Applications

• TIGER Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  
• Whole slide data - python package for working with wholeslide images and annotations files by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

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
  

UniProt

Tutorials

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

1000 Genomes

Publications

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

A2D2: Audi Autonomous Driving Dataset

Tutorials

• Data Service for ADAS and ADS Development by Ajay Vohra
  EKS

AI2 Diagram Dataset (AI2D)

Publications

• A Diagram is Worth a Dozen Images by Aniruddha Kembhavi, Michael Salvato, Eric Kolve, Minjoon Seo, Hannaneh Hajishirzi, Ali Farhadi
  

AI2 Meaningful Citations Data Set

Publications

• Identifying Meaningful Citations by Marco Valenzuela, Vu A. Ha, Oren Etzioni
  

AI2 Reasoning Challenge (ARC) 2018

Publications

• Think you have Solved Question Answering? Try ARC, the AI2 Reasoning Challengg by Peter Clark, Isaac Cowhey, Oren Etzioni, Tushar Khot, Ashish Sabharwal, Carissa Schoenick, Oyvind Tafjord
  

ARPA-E PERFORM Forecast data

Tools & Applications

• ARPA-E PERFORM by ARPA-E
  

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
  

Analysis Ready Sentinel-1 Backscatter Imagery

Tutorials

• Compare Cloud-Optimized Geotiffs from Amazon Sustainability Data Initiative (ASDI) hosted on S3 using SageMaker Studio Lab (SMSL) by Gianfranco Rapino
  

CIViC (Clinical Interpretation of Variants in Cancer)

Publications

• CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer by Malachi Griffith
  

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
  

Conformational Space of Short Peptides

Tutorials

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

Coupled Model Intercomparison Project Phase 5 (CMIP5) University of Wisconsin-Madison Probabilistic Downscaling Dataset

Publications

• Assessment Report: Analysis of Impact of Nonstationary Climate on NOAA Atlas 14 Estimates by NOAA
  

CoversBR

Tutorials

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

Crowdsourced Bathymetry

Tutorials

• Crowdsourced Bathymetry Data (CSB) Visualization by David Neufeld
  

Daylight Map Distribution of OpenStreetMap

Tutorials

• Loading the Daylight Map Distribution OpenStreetMap Features into AWS Athena by Jennings Anderson
  Athena

Defense Meterology Satellite Program (DMSP) Auroral Particle Flux

Tools & Applications

• ssj_latbin: Create and read ML-ready DMSP particle precipitation data by Liam Kilcommons
  

Discrete Reasoning Over the content of Paragraphs (DROP)

Publications

• DROP: A Reading Comprehension Benchmark Requiring Discrete Reasoning Over Paragraphs by Dheeru Dua, Yizhong Wang, Pradeep Dasigi, Gabriel Stanovsky, Sameer Singh, Matt Gardner
  

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
  

High Resolution Population Density Maps + Demographic Estimates by CIESIN and Meta

Tutorials

• Investigating environmental characteristics of US cities using publicly available ASDI datasets by Darren Ko
  SageMaker Studio Lab

High-Order Accurate Direct Numerical Simulation of Flow over a MTU-T161 Low Pressure Turbine Blade

Publications

• High-Order Accurate Direct Numerical Simulation of Flow over a MTU-T161 Low Pressure Turbine Blade by A. S. Iyer, Y. Abe, B. C. Vermeire, P. Bechlars, R. D. Baier, A. Jameson, F. D. Witherden, and P. E. Vincent
  

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
  

Image classification - fast.ai datasets

Tools & Applications

• Oxford-IIIT Pet Image Classification on Amazon SageMaker by AWS
  

LOFAR ELAIS-N1 cycle 2 observations on AWS

Publications

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

Legal Entity Identifier (LEI) and Legal Entity Reference Data (LE-RD)

Publications

• AWS hosts new open dataset to help businesses identify climate finance risks and investments by AWS Public Sector Blog Team
  

NIH NCBI PMC Article Datasets - Full-Text Biomedical and Life Sciences Journal Articles on AWS

Tutorials

• PMC Article Datasets in the AWS Cloud by NCBI PMC
  

NOAA Emergency Response Imagery

Publications

• Open data helps recovery in the aftermath of devastating weather events by Jena Kent
  

NOAA Global Forecast System (GFS)

Publications

• GFS Warm Restart Files Additional Information by Fanglin Yang
  

NOAA Integrated Surface Database (ISD)

Tutorials

• NOAA Integrated Surface Database (ISD) Example Notebook by Zac Flamig
  AthenaCloudFormationGlueSageMaker

NOAA National Digital Forecast Database (NDFD)

Publications

• NDFD Product Spreadsheet (excel file) by NOAA MDL
  

NOAA S-111 Surface Water Currents Data

Tutorials

• NOAA Precision Marine Navigation Program: Developing Next-Gen Data Svcs for the Maritime Community by NOAA
  

NOAA Wave Ensemble Reforecast

Tutorials

• Examples and scripts to support users to download, visualize, and process the WAVEWATCH III output files by Ricardo Campos
  

NOAA/PMEL Ocean Climate Stations Moorings

Publications

• OCS publications - All OCS-relevant publications are updated at the URL below. by PMEL
  

Natural Earth

Publications

• Natural Earth Vector (2009) by Nathaniel Vaughn Kelso, Tom Patterson
  

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
  

OpenSurfaces

Publications

• OpenSurfaces: A Richly Annotated Catalog of Surface Appearance by Sean Bell, Paul Upchurch, Noah Snavely, Kavita Bala
  

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
  

Quoref

Publications

• Quoref: A Reading Comprehension Dataset with Questions Requiring Coreferential Reasoning by Pradeep Dasigi, Nelson F. Liu, Ana Marasović, Noah A. Smith, Matt Gardner
  

Reasoning Over Paragraph Effects in Situations (ROPES)

Publications

• Reasoning Over Paragraph Effects in Situations by Kevin Lin, Oyvind Tafjord, Peter Clark, Matt Gardner
  

SILAM Air Quality

Tutorials

• Simple examples by Roope Tervo
  

Safecast

Tools & Applications

• Safecast Map by Nick Dolezal
  

SiPeCaM (Sitios Permanentes de la Calibración y Monitoreo de la Biodiversidad)

Publications

• Sitios Permanente de la Calibración y Monitoreo de la Biodiversidad by Michael Schmidt et. al.
  

Tabula Muris

Publications

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

The Human Connectome Project

Publications

• The Human Connectome Project: A retrospective by Elam JS, Glasser MF, Harms MP, Sotiropoulos SN, Andersson JL, Burgess GC, Curtiss SW, et al.
  

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
  

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)
  

MultiCoNER Dataset

Publications

• Dynamic Gazetteer Integration in Multilingual Models for Cross-Lingual and Cross-Domain Named Entity Recognition by Besnik Fetahu, Anjie Fang, Oleg Rokhlenko and Shervin Malmasi
  
• Gazetteer Enhanced Named Entity Recognition for Code-Mixed Web Queries by Besnik Fetahu, Anjie Fang, Oleg Rokhlenko and Shervin Malmasi
  
• GEMNET: Effective Gated Gazetteer Representations for Recognizing Complex Entities in Low-context Input by Tao Meng, Anjie Fang, Oleg Rokhlenko and Shervin Malmasi
  

2021 Amazon Last Mile Routing Research Challenge Dataset

Tools & Applications

• AWS Last Mile Route Sequence Optimization by Chen Wu, Yin Song, Verdi March, Eden Duthi
  
• Code repository used for the 2021 Amazon Routing Research Challenge (this repository is included for reference and documentation purposes only, you do not need to install it to access the data) by CAVE Lab, MIT Center for Transportation and Logistics
  

AgricultureVision

Publications

• Agriculture-Vision: A Large Aerial Image Database for Agricultural Pattern Analysis by Mang Tik Chiu, Xingqian Xu, Yunchao Wei, Zilong Huang, Alexander Schwing, Robert Brunner, Hrant Khachatrian, Hovnatan Karapetyan, Ivan Dozier, Greg Rose, David Wilson, Adrian Tudor, Naira Hovakimyan, Thomas S. Huang, Honghui Shi
  
• The 2nd International Workshop and Prize Challenge on Agriculture-Vision, Challenges & Opportunities for Computer Vision in Agricutlure by Humphrey Shi, Naira Hovakimyan, Jennifer Hobbs, Ed Delp, Melba Crawford, Zhen Li, David Clifford, Jim Yuan, Mang Tik Chiu, Xingqian Xu
  

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
  

Binding DB - Data Lakehouse Ready

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
  

ChEMBL - Data Lakehouse Ready

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
  

ClinVar - Data Lakehouse Ready

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 - Data Lakehouse Ready

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
  

YouTube 8 Million - Data Lakehouse Ready

Tutorials

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

Publications

• YouTube 8 Million by Google Research
  

1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5 - Data Lakehouse Ready

Tutorials

• Sample Queries on the 1000 Genomes, gnomAD and ClinVar data Lake by Sujaya Srinivasan
  AthenaGlue

Amazon-PQA

Publications

• Answering Product-Questions by Utilizing Questions from Other Contextually Similar Products by Ohad Rozen, David Carmel, Avihai Mejer, Vitaly Mirkis, and Yftah Ziser
  

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
  

COVID-19 Open Research Dataset (CORD-19)

Tools & Applications

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

Corn Kernel Counting Dataset

Publications

• Broad Dataset and Methods for Counting and Localization of On-Ear Corn Kernels by Jennifer Hobbs, Vachik Khachatryan, Barathwaj Anandan, Harutyun Hovhannisyan, David Wilson
  

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
  

Genome Aggregation Database (gnomAD) - Data Lakehouse Ready

Tutorials

• Sample Queries on the 1000 Genomes, gnomAD and ClinVar data Lake by Sujaya Srinivasan
  AthenaGlue

Google Brain Genomics Sequencing Dataset for Benchmarking and Development

Publications

• An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development by Baid G., Nattestad M., Kolesnikov A., Goel S., Yang H., Chang P., and Carroll A (2020)
  

Helpful Sentences from Reviews

Publications

• Identifying Helpful Sentences in Product Reviews by Iftah Gamzu et al (2021)
  

Humor Detection from Product Question Answering Systems

Publications

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

Humor patterns used for querying Alexa traffic

Publications

• “Alexa, Do You Want to Build a Snowman?” Characterizing Playful Requests to Conversational Agents by Shani C., Libov A., Tolmach S., Lewin-Eytan L., Maarek Y., and Shahaf D.
  

Learning to Rank and Filter - community question answering

Publications

• IR Evaluation and Learning in the Presence of Forbidden Documents by David Carmel, Nachshon Cohen, Amir Ingber & Elad Kravi
  

Longitudinal Nutrient Deficiency

Publications

• Detection and Prediction of Nutrient Deficiency Stress using Longitudinal Aerial Imagery by Saba Dadsetan, Gisele Rose, Naira Hovakimyan, Jennifer Hobbs
  

Low Context Name Entity Recognition (NER) Datasets with Gazetteer

Publications

• GEMNET: Effective Gated Gazetteer Representations for Recognizing Complex Entities in Low-context Input by Tao Meng, Anjie Fang, Oleg Rokhlenko and Shervin Malmasi
  

MODIS MYD13A1, MOD13A1, MYD11A1, MOD11A1, MCD43A4

Tools & Applications

• Astraea Earth OnDemand by Astraea, Inc.
  

Multilingual Name Entity Recognition (NER) Datasets with Gazetteer

Publications

• Gazetteer Enhanced Named Entity Recognition for Code-Mixed Web Queries by Besnik Fetahu, Anjie Fang, Oleg Rokhlenko and Shervin Malmasi
  

Orcasound - bioacoustic data for marine conservation

Tools & Applications

• Github for our open source projects by Orcasound open source community
  

PASS: Perturb-and-Select Summarizer for Product Reviews

Publications

• PASS: Perturb-and-Select Summarizer for Product Reviews by Nadav Oved and Ran Levy (2021)
  

Pre- and post-purchase product questions

Publications

• "Did you buy it already?", Detecting Users Purchase-State From Their Product-Related Questions by Lital Kuchy, David Carmel, Thomas Huet & Elad Kravi
  

Swiss Public Transport Stops

Tools & Applications

• Map Viewer by Swiss Geoportal
  

The Multilingual Amazon Reviews Corpus

Publications

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

VoiSeR

Publications

• VoiSeR: A New Benchmark for Voice-Based Search Refinement by Simone Filice, Giuseppe Castellucci, Marcus Collins, Eugene Agichtein & Oleg Rokhlenko
  

WikiSum: Coherent Summarization Dataset for Efficient Human-Evaluation

Publications

• WikiSum: Coherent Summarization Dataset for Efficient Human-Evaluation by Nachshon Cohen, Oren Kalinsky, Yftah Ziser & Alessandro Moschitti