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‎datasets/depmap-omics-ccle.yaml‎

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Name: The Cancer Dependency Map (DepMap) Cancer Cell Line Encyclopedia (CCLE) Dataset
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Description: This dataset consists of whole genome sequencing (WGS), whole exome sequencing (WES), and RNA sequencing files generated from ~1000 cancer cell lines described in Ghandi et al., 2019.
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Documentation: https://github.com/broadinstitute/depmap-omics-ccle
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Contact: https://forum.depmap.org
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ManagedBy: "[Cancer Data Science](https://cancerdatascience.org/), [Broad Institute](https://www.broadinstitute.org/)"
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UpdateFrequency: occasionally (as additional sequencings are generated for publicly-releasible CCLE models)
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Tags:
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- aws-pds
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- bam
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- biology
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- bioinformatics
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- cancer
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- genetic
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- genomic
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- Homo sapiens
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- life sciences
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- short read sequencing
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- transcriptomics
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- whole exome sequencing
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- whole genome sequencing
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License: https://grants.nih.gov/policy-and-compliance/policy-topics/sharing-policies/accessing-data/using-genomic-data
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Citation: Ghandi, Huang, Jané-Valbuena et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019). https://doi.org/10.1038/s41586-019-1186-3
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Resources:
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- Description: CRAM/BAM files (and their corresponding CRAI/BAI indexes) for RNA, WES, and WGS samples released by The Cancer Dependency Map (DepMap) as part of the Cancer Cell Line Encyclopedia (CCLE) project
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ARN: arn:aws:s3:::depmap-omics-ccle
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Region: us-east-1
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Type: S3 Bucket
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- Description: Notifications for new depmap-omics-ccle data
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ARN: arn:aws:sns:us-east-1:019511184952:depmap-omics-ccle-object_created
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Region: us-east-1
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Type: SNS Topic
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DataAtWork:
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Tutorials:
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- Title: DepMap Omics CCLE data on the AWS Open Data Registry
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URL: https://github.com/broadinstitute/depmap-omics-ccle
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AuthorName: Devin McCabe
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Tools & Applications:
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- Title: The Cancer Dependency Map (DepMap)
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URL: https://depmap.org
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AuthorName: Arafeh, Shibue, Dempster et al.
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- Title: Cancer Cell Line Encyclopedia (CCLE)
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URL: https://sites.broadinstitute.org/ccle
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AuthorName: Ghandi, Huang, Jané-Valbuena et al.
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Publications:
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- Title: Next-generation characterization of the Cancer Cell Line Encyclopedia
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URL: https://www.nature.com/articles/s41586-019-1186-3
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AuthorName: Ghandi, Huang, Jané-Valbuena et al.
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- Title: The present and future of the Cancer Dependency Map
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URL: https://www.nature.com/articles/s41568-024-00763-x
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AuthorName: Arafeh, Shibue, Dempster et al.
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AuthorURL: https://depmap.org
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- Title: Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal
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URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03020-w
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AuthorName: Krill-Burger, Dempster, Borah et al.
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- Title: Genetic dependencies associated with transcription factor activities in human cancer cell lines
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URL: https://www.sciencedirect.com/science/article/pii/S2211124724005035
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AuthorName: Thatikonda, Supper, Wachter et al.
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- Title: Bridging the gap between cancer cell line models and tumours using gene expression data
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URL: https://www.nature.com/articles/s41416-021-01359-0
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AuthorName: Noorbakhsh, Vazquez & McFarland
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- Title: Integrated cross-study datasets of genetic dependencies in cancer
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URL: https://www.nature.com/articles/s41467-021-21898-7
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AuthorName: Pacini, Dempster, Boyle et al.
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- Title: Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors
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URL: https://www.nature.com/articles/s42003-022-04075-4
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AuthorName: Sanders, Chandra, Zebarjadi et al.
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- Title: "The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks"
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URL: https://link.springer.com/article/10.1186/s13059-023-02877-1
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AuthorName: Ben Guebila, Wang, Lopes-Ramos et al.
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ADXCategories:
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- Healthcare & Life Sciences Data

‎datasets/fvcom_gom3.yaml‎

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Name: UMASSD-FVCOM-GOM3-Hindcast
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Description: The Finite Volume Community Ocean Model (FVCOM) was used to simulate ocean water levels, velocity, temperature and salinity over a multi-decadal period (1984-present) in the waters of the Northeast US including the Gulf of Maine. The model was configured and run by the Dr. Changshen Chen, Director of the Marine Ecosystems Dynamics Modeling Laboratory in the School for Marine Science & Technology at the University of Massachusetts Dartmouth. The triangular mesh has a varying horizontal resolution from several hundred meters inshore to several kilometers offshore, and 45 terrain-following vertical layers. The model output was saved at hourly intervals from 2009-08-21 to 2022-06-17.
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Documentation: https://en.wikipedia.org/wiki/Finite_Volume_Community_Ocean_Model
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Contact: [email protected]
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ManagedBy: Open Science Computing, LLC
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UpdateFrequency: None
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Citation: https://web.archive.org/web/20161229211546id_/http://fvcom.smast.umassd.edu/wp-content/uploads/2013/11/MITSG_12-25.pdf
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Tags:
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- aws-pds
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- oceans
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License: CC0
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Resources:
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- Description: A collection of NetCDF files, kerchunk-generated Parquet reference files, and an Intake catalog
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ARN: arn:aws:s3:::fvcom-gom3
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Region: us-east-1
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Type: S3 Bucket
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DataAtWork:
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Tutorials:
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- Title: FVCOM Explorer Notebook
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URL: https://github.com/opensciencecomputing/fvcom
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NotebookURL: https://github.com/opensciencecomputing/umassd-fvcom/blob/main/fvcom_gom3_explore.ipynb
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AuthorName: Rich Signell
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AuthorURL: https://about.me/rich.signell
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Services:
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Publications:
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- Title: An Unstructured Grid, Finite Volume, Three Dimensional, Primitive Equations Ocean Model with Application to Coastal Ocean and Estuaries
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URL: https://doi.org/10.1175/1520-0426(2003)020%3C0159:AUGFVT%3E2.0.CO;2
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AuthorName: Changsheng Chen, Hedong Liu, and Robert C. Beardsley

‎datasets/noaa-nexrad.yaml‎

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ARN: arn:aws:sns:us-east-1:684042711724:NewNEXRADLevel3Object
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Region: us-east-1
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Type: SNS Topic
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- Description: "*OLD NEXRAD Level II archive bucket* which is now <b>Deprecated</b>. It is recommended to move to the new bucket: unidata-nexrad-level2 and SNS topic: arn:aws:sns:us-east-1:684042711724:NewNEXRADLevel2Archive"
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ARN: arn:aws:s3:::noaa-nexrad-level2
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Region: us-east-1
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Type: S3 Bucket
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- Description: "Notifications for the *OLD Level II archival bucket* which is now <b>Deprecated</b>. It is recommended to move to the new bucket: unidata-nexrad-level2 and SNS topic: arn:aws:sns:us-east-1:684042711724:NewNEXRADLevel2Archive"
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ARN: arn:aws:sns:us-east-1:811054952067:NewNEXRADLevel2Archive
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Region: us-east-1
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Type: SNS Topic
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DataAtWork:
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Tutorials:
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- Title: Using Python to Access NCEI Archived NEXRAD Level 2 Data (Jupyter notebook)

‎datasets/noaa-wod.yaml‎

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The World Ocean Database (WOD) is the largest uniformly formatted, quality-controlled, publicly available historical subsurface ocean profile database. From Captain Cook's second voyage in 1772 to today's automated Argo floats, global aggregation of ocean variable information including temperature, salinity, oxygen, nutrients, and others vs. depth allow for study and understanding of the changing physical, chemical, and to some extent biological state of the World's Oceans. Browse the bucket via the AWS S3 explorer: https://noaa-wod-pds.s3.amazonaws.com/index.html
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Documentation: https://www.nodc.noaa.gov/OC5/WOD/pr_wod.html
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Contact: |
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For any questions regarding data delivery not associated with this platform or any general questions regarding the NOAA Big Data Program, email noaa.bdp@noaa.gov.
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<br /> We also seek to identify case studies on how NOAA data is being used and will be featuring those stories in joint publications and in upcoming events. If you are interested in seeing your story highlighted, please share it with the NOAA BDP team here: noaa.bdp@noaa.gov
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For any questions regarding data delivery not associated with this platform or any general questions regarding the NOAA Open Data Dissemination (NODD) Program, email the NODD Team at nodd@noaa.gov.
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We also seek to identify case studies on how NOAA data is being used and will be featuring those stories in joint publications and in upcoming events. If you are interested in seeing your story highlighted, please share it with the NODD team by emailing nodd@noaa.gov
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ManagedBy: "[NOAA](http://www.noaa.gov/)"
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UpdateFrequency: Data is update on a quarterly basis
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Collabs:
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- Title: The World Ocean Database User's Manual
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URL: https://data.nodc.noaa.gov/woa/WOD/DOC/wodreadme.pdf
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AuthorName: Hernan E. Garcia, Tim P. Boyer, Ricardo A. Locarnini, Olga K. Baranova, Melissa M. Zweng
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