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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 CyVerse Data Commons manages all public data in the Data Store that is stored under the /iplant/home/shared directory and supports data publication to external repositories. “Public data” on CyVerse is defined as any data that is visible to the public via datacommons.cyverse.org, whether or not the viewer has a CyVerse user account. Public data on CyVerse is also available to registered users via all methods described under Downloading and Uploading Data.

Publishing in the Data Commons Repository

CyVerse provides a landing page for each public dataset. Such landing page is populated with the metadata provided by the user.

DOIs are assigned upon request of the project lead. A DOI is a type of global identifier that allows a digital object to be persistently referenced on the Internet even if the item is moved to another online repository. DOIs use the DataCite metadata schema for purposes of citation. However, for data to be reused, more descriptive information is required so we encourage users to further document their datasets. Please see ……

What about data that has been published already elsewhere

If an upload involves data that has been published elsewhere and or has an existing DOI, project leads have the opportunity to reference those datasets using the External URL box. The existing DOI and/or a link can be added to the dataset information.

Upon publication data creators can request to retrieve their data from the repository. To do so, a User must contact the repository curator and provide a justification. A record stating that the dataset was available and including an abstract and an explanation about why the data was removed will be in place. It has to be reminded that the dataset will have a DOI and that DOI will remain active so that when people use it from a citation they can verify that the data is no longer there.

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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