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DATA COMMONS USER MANUAL
Maintenance: Tues, Jan 28, 2020

ACCESS TO OR USAGE OF THE FOLLOWING SERVICES WILL BE UNAVAILABLE OR DISRUPTED:

Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
 
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
 
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
 
User Portal                   8:00am to 5:00pm MST
The User Portal, http://user.cyverse.org, will be unavailable while we perform maintenance and updates.
 
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
 
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
 
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA

Keep up to date with our maintenance schedules on the CyVerse public calendar
http://www.cyverse.org/maintenance-calendar
Check your local timezone here https://bit.ly/36iVOkX 
 
Please contact support@cyverse.org for any questions, or concerns.

 

 

 

 

 

 

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The Data Commons publishes data to our own repository at  datacommons.cyverse.org as well as external repositories. All data published to Data Commons Curated Data receive a permanent identifier (PID) in the form of a DOI (Digital Object Identifier) or ARK (Archival Resource Key) and are expected to be stable and permanent. Data published to the Cyverse Community Contributed folder do not have PIDs, and may change or be removed at any time. The sections below provide more information on each kind of data publication available through CyVerse. For more details on the range of data sharing options in CyVerse, see the CyVerse Data Policy.

Publishing Data Commons Curated Data

Data publication to Data Commons Curated Data a service offered for datasets that are intended to be stable and permanent. For Curated Data, the Data Commons provides landing pages, permanent DOIs or ARKs and the requirement to include an open data license. Permanent identifiers allow data to have a stable location on the web so that other users can always find them, along with the information that makes them understandable, citable, and reusable.  An open data license is important to allow others to reuse your data, but it does not exclude users from the obligation to correctly cite your data.

For more information about whether or not a Data Commons Curated Data is right for your dataset, see the Permanent Identifier FAQs page and the Data Commons Policy.

When you are ready to publish, see Requesting a Permanent Identifier in the Data Commons.

Publishing CyVerse Community Contributed Data

Community Contributed Data folders are available for evolving datasets that individuals or communities want to make available as quickly as possible for research and reuse. Community Contributed Data are intended for datasets that are growing or changing frequently or that may not need long-term preservation. Data can transition from Community Contributed Data to Data Commons Curated Data by requesting a DOI or ARK.

Publishing to external repositories

SRA pipeline: Data Commons enables CyVerse users to make submissions to the NCBI Sequence Read Archive directly. Submissions instructions include compressed sequenced files (FASTQ.gz, SFF.gz, and BAM.gz) and an XML metadata file, organized into a submission package.

WGS pipeline and TSA: Coming soon 

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