Registry of Open Data on AWS

Allen Cell Imaging Collections

Tutorials

Tools & Applications

Publications

4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics by Jessica S. Yu, Blair Lyons, Susanne Rafelski, Julie A. Theriot, Neda Bagheri & Graham T. Johnson
A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes by Tanya Grancharova*, Kaytlyn A. Gerbin*, Alexander B. Rosenberg, Charles M. Roco, Joy E.Arakaki , Colette M. DeLizo, Stephanie Q. Dinh, Rory M. Donovan-Maiye, Matthew Hirano, Angelique M. Nelson, Joyce Tang, Julie A. Theriot, Calysta Yan, Vilas Menon, Sean P. Palecek, Georg Seelig & Ruwanthi N. Gunawardane
A deep generative model of 3D single-cell organization by Rory M. Donovan-Maiye, Jackson M. Brown, Caleb K. Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg & Gregory R. Johnson
A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs) by Caroline Hookway*, Antoine Borensztejn*, Leigh K. Harris*, Sara Carlson, Gokhan Dalgin, Suraj Mishra, Nivedita Nivedita, Ellen M. Adams, Tiffany Barszczewski, Julie C. Dixon, Jacqueline H. Edmonds, Erik A. Ehlers, Alexandra J. Ferrante, Margaret A. Fuqua, Philip Garrison, Janani Gopalan, Benjamin W. Gregor, Maxwell J. Hedayati, Kyle N. Klein, Chantelle L. Leveille, Sean L. Meharry, Haley S. Morris, Gouthamrajan Nadarajan, Sandra A. Oluoch, Serge E. Parent, Amber Phan, Brock Roberts, Emmanuel E. Sanchez, M. Filip Sluzewski, Lev S. Snyder, Derek J. Thirstrup, John Paul Thottam, Julia R. Torvi, Gaea Turman, Matheus P. Viana, Lyndsay Wilhelm, Chamari S. Wijesooriya, Jie Yao, Julie A. Theriot, Susanne M. Rafelski & Ruwanthi N. Gunawardane
Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy by Benjamin W. Gregor*, Mackenzie E. Coston*, Ellen M. Adams, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Aditya Nath, Angelique M. Nelson, Susanne M. Rafelski, Emmanuel E. Sanchez, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Brian P. Whitney, Calysta Yan, Ruwanthi N. Gunawardane & Nathalie Gaudreault
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes by Kaytlyn A. Gerbin*, Tanya Grancharova*, Rory M. Donovan-Maiye*, Melissa C. Hendershott*, Helen G. Anderson, Jackson M. Brown, Jianxu Chen, Stephanie Q. Dinh, Jamie L. Gehring, Gregory R. Johnson, HyeonWoo Lee, Aditya Nath, Angelique M. Nelson, M. Filip Sluzewski, Matheus P. Viana, Calysta Yan, Rebecca J. Zaunbrecher, Kimberly R. Cordes Metzler, Nathalie Gaudreault, Theo A. Knijnenburg, Susanne M. Rafelski, Julie A. Theriot & Ruwanthi N. Gunawardane
Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories by Julie C. Dixon*, Christopher L. Frick*, Chantelle L. Leveille*, Philip Garrison, Peyton A. Lee, Saurabh S. Mogre, Benjamin Morris, Nivedita Nivedita, Ritvik Vasan, Jianxu Chen, Cameron L. Fraser, Clare R. Gamlin, Leigh K. Harris, Melissa C. Hendershott, Graham T. Johnson, Kyle N. Klein, Sandra A. Oluoch, Derek J. Thirstrup, M. Filip Sluzewski, Lyndsay Wilhelm, Ruian Yang, Daniel M. Toloudis, Matheus P. Viana, Julie A. Theriot & Susanne M. Rafelski
Integrated intracellular organization and its variations in human iPS cells 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
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds by Ritvik Vasan, Alexandra J. Ferrante, Antoine Borensztejn, Christopher L. Frick, Nathalie Gaudreault, Saurabh S. Mogre, Benjamin Morris, Guilherme G. Pires, Susanne M. Rafelski, Julie A. Theriot & Matheus P. Viana
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
Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization by Brock Roberts*, Amanda Haupt*, Andrew Tucker, Tanya Grancharova, Joy Arakaki, Margaret A. Fuqua, Angelique Nelson, Caroline Hookway, Susan A. Ludmann, Irina A. Mueller, Ruian Yang, Rick Horwitz, Susanne M. Rafelski & Ruwanthi N. Gunawardane

1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5, 3.7, 4.0, 4.2, and 4.4

Tutorials

Tools & Applications

Publications

Accurate and efficient calling of small and large variants from popgen datasets using the DRAGEN Bio-IT Platform by Illumina Inc. (2021)
Data solution empowering population genomics by Illumina Inc. (2021)
Demystifying the versions of GRCh38/hg38 reference genomes, how they are used in DRAGEN and their impact on accuracy by Illumina Inc. (2021)
DRAGEN Sets New Standard for Data Accuracy in PrecisionFDA Benchmark Data. Optimizing Variant Calling Performance with Illumina Machine Learning and DRAGEN Graph by Illumina Inc. (2022)
DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes by Illumina Inc. (2020)
Genotyping variants at population scale using DRAGEN gVCF Genotyper by Illumina Inc. (2023)
Overcoming high homology to detect variation in *CYP21A2* with whole-genome sequencing in DRAGEN by Illumina Inc. (2023)
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions by Olson et al (2020)
Unveiling Illumina Connected Annotations: A breakthrough in genomic annotation by Illumina Inc. (2024)

Cell Painting Gallery

Tutorials

Tools & Applications

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

Distributed Archives for Neurophysiology Data Integration (DANDI)

Tutorials

Tools & Applications

DANDI API by DANDI Project
DANDI CLI and Python API by DANDI Project
DANDI JupyterHub by DANDI Project
DANDI Web Interface by DANDI Project
ITK/VTK Viewer for OME-Zarr by Kitware
Neuroglancer by Google
Neurosift - Interactive NWB Viewer by Flatiron Institute
NWB Explorer by Open Source Brain

Publications

A comparison of neuroelectrophysiology databases by Subash P, Gray A, Bhattacharyya B, et al.
Facilitating analysis of open neurophysiology data on the DANDI Archive using large language model tools by Magland JF, Ly R, Rübel O, Dichter B
Neurosift: DANDI exploration and NWB visualization in the browser by Magland J, Soules J, Baker C, Dichter B

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
AWS LambdaAWS AppSyncAmazon DynamoDBAWS Step 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

Open Targets

Tutorials

Tools & Applications

Publications

Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery by Annalisa Buniello

The Cancer Dependency Map (DepMap) Cancer Cell Line Encyclopedia (CCLE) Dataset

Tutorials

DepMap Omics CCLE data on the AWS Open Data Registry by Devin McCabe

Tools & Applications

Cancer Cell Line Encyclopedia (CCLE) by Ghandi, Huang, Jané-Valbuena et al.
The Cancer Dependency Map (DepMap) by Arafeh, Shibue, Dempster et al.

Publications

Bridging the gap between cancer cell line models and tumours using gene expression data by Noorbakhsh, Vazquez & McFarland
Genetic dependencies associated with transcription factor activities in human cancer cell lines by Thatikonda, Supper, Wachter et al.
Integrated cross-study datasets of genetic dependencies in cancer by Pacini, Dempster, Boyle et al.
Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors by Sanders, Chandra, Zebarjadi et al.
Next-generation characterization of the Cancer Cell Line Encyclopedia by Ghandi, Huang, Jané-Valbuena et al.
Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal by Krill-Burger, Dempster, Borah et al.
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks by Ben Guebila, Wang, Lopes-Ramos et al.
The present and future of the Cancer Dependency Map by Arafeh, Shibue, Dempster et al.

Alliance of Genome Resources

Tutorials

Alliance of Genome Resources AWS Data Access Tutorials by Alliance of Genome Resources Consortium

Tools & Applications

Publications

Alliance of Genome Resources Portal - unified model organism research platform by Alliance of Genome Resources Consortium

NHGRI AnVIL Project

Publications

A complete reference genome improves analysis of human genetic variation by Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael E. G. Sauria, Mitchell R. Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey A. Rosenfeld, Benedict Paten, Ryan Layer, Chen-Shan Chin, Fritz J. Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. Schatz
A draft human pangenome reference by Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten
Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing by Sam Kovaka, Shujun Ou, Katharine M. Jenike, Michael C. Schatz
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References by Dylan J. Taylor, Jordan M. Eizenga, Qiuhui Li, Arun Das, Katharine M. Jenike, Eimear E. Kenny, Karen H. Miga, Jean Monlong, Rajiv C. McCoy, Benedict Paten, and Michael C. Schatz
CNPI: Rapid Analyses of Human Copy Number Data by Jack Ustanik, Tychele N. Turner
Deciphering the impact of genomic variation on function by IGVF Consortium
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) by Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L. Grossman, Ira M. Hall, Kasper D. Hansen, Jonathan Lawson, Jeffrey T. Leek, Anne O’Donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D. O’Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J. Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet, AnVIL Team
Jasmine and Iris: population-scale structural variant comparison and analysis by Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, Alexis Battle, Sergey Aganezov, Michael C. Schatz
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation by Mikhail Kolmogorov, Kimberley J. Billingsley, Mira Mastoras, Melissa Meredith, Jean Monlong, Ryan Lorig-Roach, Mobin Asri, Pilar Alvarez Jerez, Laksh Malik, Ramita Dewan, Xylena Reed, Rylee M. Genner, Kensuke Daida, Sairam Behera, Kishwar Shafin, Trevor Pesout, Jeshuwin Prabakaran, Paolo Carnevali, Jianzhi Yang, Arang Rhie, Sonja W. Scholz, Bryan J. Traynor, Karen H. Miga, Miten Jain, Winston Timp, Adam M. Phillippy, Mark Chaisson, Fritz J. Sedlazeck, Cornelis Blauwendraat, Benedict Paten
The complete sequence and comparative analysis of ape sex chromosomes by Kateryna D. Makova, Brandon D. Pickett, Robert S. Harris, Gabrielle A. Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C. McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G. Bouffard, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E. Cook, Sarah J. C. Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage H. Garcia, Patrick G. S. Grady, Richard E. Green, Diana Haddad, Pille Hallast, William T. Harvey, Glenn Hickey, David A. Hillis, Savannah J. Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L. Kosakovsky Pond, Troy M. LaPolice, Charles Lee, Alexandra P. Lewis, Yong-Hwee E. Loh, Patrick Masterson, Kelly M. McGarvey, Rajiv C. McCoy, Paul Medvedev, Karen H. Miga, Katherine M. Munson, Evgenia Pak, Benedict Paten, Brendan J. Pinto, Tamara Potapova, Arang Rhie, Joana L. Rocha, Fedor Ryabov, Oliver A. Ryder, Samuel Sacco, Kishwar Shafin, Valery A. Shepelev, Viviane Slon, Steven J. Solar, Jessica M. Storer, Peter H. Sudmant, Sweetalana, Alex Sweeten, Michael G. Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A. Wilson, Alice C. Young, Huiqing Zeng, Xinru Zhang, Zachary A. Szpiech, Christian D. Huber, Jennifer L. Gerton, Soojin V. Yi, Michael C. Schatz, Ivan A. Alexandrov, Sergey Koren, Rachel J. O’Neill, Evan E. Eichler, Adam M. Phillippy
The complete sequence of a human Y chromosome by Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik Garrison, Ariel Gershman, Jennifer L. Gerton, Patrick G. S. Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. McCoy, Jennifer McDaniel, Brandy M. McNulty, Paul Medvedev, Alla Mikheenko, Katherine M. Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. Salzberg, Michael E. G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha Surapaneni, Angela M. Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. Wilson, Samantha Zarate, Yiming Zhu, Justin M. Zook, Evan E. Eichler, Rachel J. O’Neill, Michael C. Schatz, Karen H. Miga, Kateryna D. Makova, Adam M. Phillippy
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update by The Galaxy Community
The Human Pangenome Project: a global resource to map genomic diversity by Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. Lawson, Julian K. Lucas, Adam M. Phillippy, Alice B. Popejoy, Mobin Asri, Caryn Carson, Mark J. P. Chaisson, Xian Chang, Robert Cook-Deegan, Adam L. Felsenfeld, Robert S. Fulton, Erik P. Garrison, Nanibaa’ A. Garrison, Tina A. Graves-Lindsay, Hanlee Ji, Eimear E. Kenny, Barbara A. Koenig, Daofeng Li, Tobias Marschall, Joshua F. McMichael, Adam M. Novak, Deepak Purushotham, Valerie A. Schneider, Baergen I. Schultz, Michael W. Smith, Heidi J. Sofia, Tsachy Weissman, Paul Flicek, Heng Li, Karen H. Miga, Benedict Paten, Erich D. Jarvis, Ira M. Hall, Evan E. Eichler, David Haussler, the Human Pangenome Reference Consortium

Open NeuroData

Tutorials

Tools & Applications

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

Tools & Applications

Publications

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

CHAMMI-75

Tutorials

Get To Know A Dataset: CHAMMI-75 by Vidit Agrawal, Juan Caicedo
Running CHAMMI-75 Evaluation Benchmarks by Vidit Agrawal, Juan Caicedo

Tools & Applications

CHAMMI Benchmarking Source Code by Chau Pham
CHAMMI-75 Source Code by Vidit Agrawal
CHAMMI-75 Website by Vidit Agrawal, Juan Caicedo
MorphEm Model (Trained on CHAMMI-75) by Vidit Agrawal, John Peters, Juan Caicedo

Publications

CHAMMI-75: pre-training multi-channel models with heterogeneous microscopy images by Vidit Agrawal, John Peters, Tyler N. Thompson, Mohammad Vali Sanian, Chau Pham, Nikita Moshkov, Arshad Kazi, Aditya Pillai, Jack Freeman, Byunguk Kang, Samouil L. Farhi, Ernest Fraenkel, Ron Stewart, Lassi Paavolainen, Bryan A. Plummer, Juan C. Caicedo
CHAMMI: A benchmark for channel-adaptive models in microscopy imaging by Zitong Sam Chen, Chau Pham, Siqi Wang, Michael Doron, Nikita Moshkov, Bryan Plummer, Juan C. Caicedo

NIH Roadmap Epigenomics

Tutorials

Publications

Chromatin architecture reorganization during stem cell differentiation by GJesse R. Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E. Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie, Yarui Diao, Jing Liang, Huimin Zhao, Victor V. Lobanenkov, Joseph R. Ecker, James A. Thomson & Bing Ren
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease. by Elizabeta Gjoneska, Andreas R. Pfenning, Hansruedi Mathys, Gerald Quon, Anshul Kundaje, Li-Huei Tsai & Manolis Kellis.
Human body epigenome maps reveal noncanonical DNA methylation variation by Matthew D. Schultz, Yupeng He, John W. Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D. Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J. Sejnowski, Wei Wang & Joseph R. Ecker
Integrative analysis of 111 reference human epigenomes by Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour etc.al, Ting Wang, Manolis Kellis
The epigenomic landscape of transposable elements across normal human development and anatomy by Erica C. Pehrsson, Mayank N. K. Choudhary, Vasavi Sundaram & Ting Wang
WashU Epigenome Browser update 2019 by Daofeng Li, Silas Hsu, Deepak Purushotham, Renee L Sears and Ting Wang

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

DynaCell

Tutorials

Get to know DynaCell v1 — loading and exploring the dataset by Computational Imaging Group at Biohub

Tools & Applications

Publications

DynaCell: an Evaluation Framework for Dynamic 3D Virtual Staining of Live Cells by Kalinin, Zheng, Theodoro, Ivanov, Hirata-Miyasaki, Lee, Liu, Varra, Chandler, Pradeep, Liu, Leonetti, Arias, Huang, Mehta

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

OME-Zarr Open SciVis Datasets

Tutorials

Tools & Applications

A list of tools and libraries with OME-Zarr support by NGFF community

Publications

OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies by Josh Moore, Chris Allan, Sébastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer & Jason R. Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support by Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva M. Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E. Diel, David Gault, Satrajit S. Ghosh, Ilan Gold, Yaroslav O. Halchenko, Matthew Hartley, Dave Horsfall, Mark S. Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Koji Kyoda, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Dominik Lindner, Melissa Linkert, Joel Lüthi, Jeremy Maitin-Shepard, Trevor Manz, Luca Marconato, Matthew McCormick, Merlin Lange, Khaled Mohamed, William Moore, Nils Norlin, Wei Ouyang, Bugra Özdemir, Giovanni Palla, Constantin Pape, Lucas Pelkmans, Tobias Pietzsch, Stephan Preibisch, Martin Prete, Norman Rzepka, Sameeul Samee, Nicholas Schaub, Hythem Sidky, Ahmet Can Solak, David R. Stirling, Jonathan Striebel, Christian Tischer, Daniel Toloudis, Isaac Virshup, Petr Walczysko, Alan M. Watson, Erin Weisbart, Frances Wong, Kevin A. Yamauchi, Omer Bayraktar, Beth A. Cimini, Nils Gehlenborg, Muzlifah Haniffa, Nathan Hotaling, Shuichi Onami, Loic A. Royer, Stephan Saalfeld, Oliver Stegle, Fabian J. Theis & Jason R. Swedlow
Open SciVis Datasets by Pavol Klacansky

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)

Automated Segmentation of Intracellular Substructures in Electron Microscopy (ASEM) on AWS

Tutorials

Tools & Applications

Publications

Deep neural network automated segmentation of cellular structures in volume electron microscopy by Benjamin Gallusser, Giorgio Maltese, Giuseppe Di Caprio, Tegy John Vadakkan, Anwesha Sanyal, Elliott Somerville, Mihir Sahasrabudhe, Justin O’Connor, Martin Weigert, Tom Kirchhausen

Caenorabditis Diversity Natural Resource

Tutorials

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

Publications

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

The Human Connectome Project

Tutorials

Exploring the Human Connectom by The Human Connectome Project

Tools & Applications

The Human Connectome Workbench by 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.
The minimal preprocessing pipelines for the Human Connectome Project by Glasser MF, Sotiropoulos SN, Wilson JA, Coalson TS, Fischl B, Andersson JL, Xu J, Jbabdi S, et al.
The WU-Minn Human Connectome Project: an overview. by Van Essen DC, Smith SM, Barch DM, Behrens TEJ, Yacoub E, Ugurbil, K, and the WU-Minn HCP Consortium.

Basic Local Alignment Sequences Tool (BLAST) Databases

Tools & Applications

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

Publications

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

Encyclopedia of DNA Elements (ENCODE)

Tutorials

Publications

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

Epigenomes of the Human Pangenome Reference Consortium (HPRC) Release 2

Tutorials

"Get To Know A Dataset: HPRC Epigenome" by HPRC Epigenome Browser

Publications

"Modbed track: Visualization of modified bases in single-molecule sequencing" by Daofeng Li, Xiaoyu Zhuo, Jessica K. Harrison, Shane Liu, Ting Wang
A draft human pangenome reference by Liao, WW., Asri, M., Ebler, J. et al.
WashU Epigenome Browser update 2025 by Chanrung Seng, Shane Liu, Wenjin Zhang, Xiaoyu Zhuo, Daofeng Li, Ting Wang

International Skin Imaging Collaboration (ISIC) Archive

Tutorials

ISIC Archive Data Dictionary by International Skin Imaging Collaboration (ISIC)

Tools & Applications

ISIC Archive Gallery by International Skin Imaging Collaboration (ISIC)
isic-cli - The official command line tool for interacting with the ISIC Archive by International Skin Imaging Collaboration (ISIC)

Publications

A patient-centric dataset of images and metadata for identifying melanomas using clinical context by Rotemberg V, Kurtansky N, Betz-Stablein B, Caffery L, Chousakos E, Codella N, et al
Human surface anatomy terminology for dermatology: a Delphi consensus from the International Skin Imaging Collaboration by Navarrete-Dechent C, Liopyris K, Molenda M, Braun R, Curiel-Lewandrowski C, Dusza S, et al
International Skin Imaging Collaboration - Designated Diagnoses (ISIC-DX): Consensus terminology for lesion diagnostic labeling by Scope A, Liopyris K, Weber J, Barnhill R, Braun R, Curiel-Lewandrowski C, et al
The SLICE-3D dataset: 400,000 skin lesion image crops extracted from 3D TBP for skin cancer detection by Kurtansky N, D'Alessandro B, Gillis M, Betz-Stablein B, Cerminara S, Garcia R, et al

Mouse Brain Anatomy: MouseLight Imagery

Tools & Applications

HortaCloud by David Schauder, Donald J. Olbris, Jody Clements, Cristian Goina, Robert R. Svirskas, Konrad Rokicki
MouseLight NeuronBrowser by Tiago A. Ferreira, Jayaram Chandrashekar
MouseLight Project Website by Tiago A. Ferreira, Jayaram Chandrashekar

Publications

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain by Johan Winnubst, Erhan Bas, Tiago A. Ferreira, Zhuhao Wu, Michael N. Economo, Patrick Edson, Ben J. Arthur, Christopher Bruns, Konrad Rokicki, David Schauder, Donald J. Olbris, Sean D. Murphy, David G. Ackerman, Cameron Arshadi, Perry Baldwin, Regina Blake, Ahmad Elsayed, Mashtura Hasan, Daniel Ramirez, Bruno Dos Santos, Monet Weldon, Amina Zafar, Joshua T. Dudman, Charles R. Gerfen, Adam W. Hantman, Wyatt Korff, Scott M. Sternson, Nelson Spruston, Karel Svoboda, Jayaram Chandrashekar

OpenCell on AWS

Tools & Applications

Publications

Refgenie reference genome assets

Tutorials

Basic Refgenie tutorial by Nathan Sheffield

Tools & Applications

Publications

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

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

Tutorials

Sample search query on all images files for cumulus 92, using Alfresco. by Carolina Acosta
Amazon S3
Sample search query on november audio files for cumulus 92, using Alfresco. by Carolina Acosta
Amazon S3
Sample search query on november video files for cumulus 92, using Alfresco. by Carolina Acosta
Amazon S3

Publications

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

The Impact of Variation on Function Consortium (IGVF)

Tutorials

Tools & Applications

The IGVF Catalog by The IGVF Consortium

Publications

Deciphering the impact of genomic variation on function by Jesse M. Engreitz and The IGVF Consortium

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.

Human and Mammalian Brain Atlas

Tutorials

Tools & Applications

HMBA Basal Ganglia resources in Brain Knowledge Platform's Data Catalog by Allen Institute for Brain Science

Imaging MIT Licensed data and models

Tutorials

Publications

CELL-Diff: Unified diffusion modeling for protein sequences and microscopy images by Zheng Dihan, Bo Huang
SubCell: Vision foundation models for microscopy capture single-cell biology by Ankit Gupta, Zoe Wefers, Konstantin Kahnert, Jan N Hansen, William D. Leineweber, Anthony Cesnik, Dan Lu, Ulrika Axelsson, Frederic Ballllosera Navarro, Theofanis Karaletsos, Emma Lundberg

NASA Space Biology Open Science Data Repository (OSDR)

Publications

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

National Herbarium of NSW

Tutorials

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

Publications

Open Human Genome Library

Tutorials

Using OpenHGL data by Heng Li

Publications

AGC: compact representation of assembled genomes with fast queries and updates by Sebastian Deorowicz, Agnieszka Danek, Heng Li
BWT construction and search at the terabase scale by Heng Li

ProteinGym

Tutorials

Scoring ProteinGym assays with TranceptEVE by Daniel Ritter

Tools & Applications

ProteinGym website by Pascal Notin & Daniel Ritter

Publications

ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design by Pascal Notin, et al.

QIIME 2 Tutorial Data

Tutorials

Transcriptomic MIT Licensed data and models

Tutorials

Publications

A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model by Pearce, J. D., et. al.
scGenePT: Is language all you need for modeling single-cell perturbations? by Ana-Maria Istrate, Donghui Li, Theofanis Karaletsos

4D Nucleome (4DN)

Tutorials

Animal Tracking - Acoustic Telemetry - Quality controlled detections

Tutorials

BrainGlobe Atlases

Tutorials

Interacting with cloud atlas data through Python by Alessandro Felder

Publications

BrainGlobe Atlas API: a common interface for neuroanatomical atlases by Federico Claudi, Luigi Petrucco, Adam L. Tyson et al.

Broad Genome References

Tutorials

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

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 Data Lake

Tutorials

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

Tools & Applications

Cell Painting Image Collection

Tools & Applications

Accelerating Drug Discovery with high-throughput Cell Painting on AWS by Chris Kaspar

Publications

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

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)

E11bio PRISM

Tutorials

E11.Bio PRISM OpenData by Arlo Sheridan & Johan Winnubst

Tools & Applications

Volara by Arlo Sheridan & Will Patton

EMory BrEast Imaging Dataset (EMBED)

Tutorials

Screening Label Assignment Example by Emory-HITI

Publications

The EMory BrEast imaging Dataset (EMBED): A Racially Diverse, Granular Dataset of 3.4M Screening and Diagnostic Mammograms by Jiwoong J. Jeong, Brianna L. Vey, Ananth Reddy, Thomas Kim, Thiago Santos, Ramon Correa, Raman Dutt, Marina Mosunjac, Gabriela Oprea-Ilies, Geoffrey Smith, Minjae Woo, Christopher R. McAdams, Mary S. Newell, Imon Banerjee, Judy Gichoya, Hari Trivedi

Emory Knee Radiograph (MRKR) dataset

Tutorials

Example Notebook by Emory-HITI

Publications

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

GATK Structural Variation (SV) Data

Tutorials

AWS Setup & Execution by Goldfinch Bio and Loka Inc.

Tools & Applications

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

Human Cell Atlas

Publications

The Human Cell Atlas from a cell census to a unified foundation model by Jennifer E. Rood, Samantha Wynne, Lucia Robson, Anna Hupalowska, John Randell, Sarah A. Teichmann & Aviv Regev
The Human Cell Atlas White Paper by Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, Gary Bader, Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau, Peter Campbell, Mary Carmichael, Piero Carninci, Leslie Castelo-Soccio, Menna Clatworthy, Hans Clevers, Christian Conrad, Roland Eils, Jeremy Freeman, Lars Fugger, Berthold Goettgens, Daniel Graham, Anna Greka, Nir Hacohen, Muzlifah Haniffa, Ingo Helbig, Robert Heuckeroth, Sekar Kathiresan, Seung Kim, Allon Klein, Bartha Knoppers, Arnold Kriegstein, Eric Lander, Jane Lee, Ed Lein, Sten Linnarsson, Evan Macosko, Sonya MacParland, Robert Majovski, Partha Majumder, John Marioni, Ian McGilvray, Miriam Merad, Musa Mhlanga, Shalin Naik, Martijn Nawijn, Garry Nolan, Benedict Paten, Dana Pe'er, Anthony Philippakis, Chris Ponting, Steve Quake, Jayaraj Rajagopal, Nikolaus Rajewsky, Wolf Reik, Jennifer Rood, Kourosh Saeb-Parsy, Herbert Schiller, Steve Scott, Alex Shalek, Ehud Shapiro, Jay Shin, Kenneth Skeldon, Michael Stratton, Jenna Streicher, Henk Stunnenberg, Kai Tan, Deanne Taylor, Adrian Thorogood, Ludovic Vallier, Alexander van Oudenaarden, Fiona Watt, Wilko Weicher, Jonathan Weissman, Andrew Wells, Barbara Wold, Ramnik Xavier, Xiaowei Zhuang, Human Cell Atlas Organizing Committee
The Human Cell Atlas: towards a first draft atlas by Various authors
The Human Cell Atlas: towards a first draft atlas by Various authors
The network effect: studying COVID-19 pathology with the Human Cell Atlas by Sarah Teichmann, Aviv Regev

Indexes for Kaiju

Tutorials

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

Publications

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

Somatic Mosaicism across Human Tissues (SMaHT)

Tools & Applications

Somatic Mosaicism across Human Tissues Data Portal by SMaHT Data Analysis Center (DAC)

Publications

The Somatic Mosaicism across Human Tissues Network by Coorens T, Oh J, Choi Y, Lim N, Zhao B, Voshall A et al.

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

Tabula Sapiens

Publications

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues by The Tabula Sapiens Consortium, Stephen R Quake
The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans by The Tabula Sapiens Consortium

UniProt

Tutorials

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

COVID-19 Genome Sequence Dataset

Tools & Applications

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

NYUMets Brain Dataset

Publications

Longitudinal deep neural networks for assessing metastatic brain cancer on a massive open benchmark. by Link et al (2023)

National Herbarium of Israel

Tutorials

How to use AWS S3 bucket to explore our public images dataset by Eyal Ben-Hur

OceanOmics

Tutorials

Case-studies on using OceanOmics genomes and eDNA data by Philipp Bayer

OpenNeuro

Tutorials

Accessing UCLA Consortium for Neuropsychiatric Phenomics from OpenNeuro with Scigantic by Scigantic

Orcasound - bioacoustic data for marine conservation

Tools & Applications

Github for our open source projects by Orcasound open source community

Oxford Nanopore Technologies Benchmark Datasets

Tutorials

ONT Dataset Tutorials by EPI2MELabs

Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD)

Tools & Applications

Seattle Alzheimer’s Disease Brain Cell Atlas by Lein, E et al.

Tabula Muris

Publications

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

Tabula Muris Senis

Tutorials

Fast queries of scRNAseq datasets with Amazon Athena by Andrew Ang, James Golden, Lisa McFerrin, and Lee Pang
Amazon AthenaAWS Glue

VitalDB

Publications

VitalDB, a high-fidelity multi-parameter vital signs database in surgical patients by Hyung-Chul Lee, Yoonsang Park, Soo Bin Yoon, Seong Mi Yang, Dongnyeok Park, and Chul-Woo Jung

ZINC Database

Publications

ZINC Database by John Irwin

recount3

Tutorials

recount3 quick start guide by Leonardo Collado-Torres

Imaging BSD licensed data and models

Tutorials

Publications

Cytoland: robust virtual staining of landmark organelles by Liu, Hirata-Miyasaki, et al.

MetaGraph Sequence Indexes

Tutorials

Usage within AWS by Oleksandr Kulkov
AWS CloudFormationAWS Step FunctionsAWS LambdaAWS BatchAmazon S3Amazon SNS

Tools & Applications

CloudFormation stack with a Step Function for dataset queries via AWS Batch by Oleksandr Kulkov

Publications

A global metagenomic map of urban microbiomes and antimicrobial resistance by Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KE, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, et al.