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DATA COMMONS USER MANUAL
Maintenance Notice 23 Oct 2018

CyVerse systems will be unavailable on Tuesday, October 23rd, from 7:00am to 5:00pm MST.
Check your local timezone here https://goo.gl/iLJg6R

Keep up to date with our maintenance schedules on the CyVerse public calendar
http://www.cyverse.org/maintenance-calendar

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

Discovery Environment:        7:00am 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.

DataS
tore                    
7:00am to 5:00pm MST
The DataStore will be unavailable during the maintenance period.

Atmosphere                   
7:00am to 5:00pm MST
Atmosphere instances will be operational; however, you will not be able to use the Data Store within your instance.

User Portal                   7:00am to 5:00pm MST
The User Portal, http://user.cyverse.org, will be unavailable while we perform maintenance and updates.

Agave/Science API             7:00am to 5:00pm MST

The Agave/Science API will be unavailable during this maintenance period.


Please contact suppport@cyverse.org for any questions, or concerns.

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This page is updated approximately once per quarter.

Projects under development 

Data Commons Website - datacommons.cyverse.org and dc.cyverse.org

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  • Project creation (timeline uknown)
    • Step 1:
      • Ability to create a project
      • Ability to add metadata to a project
      • Ability to manage people, data, apps, tools, analyses, and allocations within a project
    • Step 2:
      • Ability to create datasets within a project
      • Ability to publish datasets from within a project, to DCR or external repositories

Submission to NCBI TSA (Transcriptome Assembly) 

Status: Planning

Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are generally being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. We are adapting the CyVerse SRA submission pipeline (see below) to submit sequences to WGS.

  •   Similar to SRA submission features. Users must create a BioProject and BioSample and apply appropriate metadata before submission

Ontology-based Metadata Management (OMM)

Image Modified

First available: Q2 2016

A big hurdle to using adequate metadata is that scientists often have to supply different sets of metadata for different uses of the same file such as getting a DOI, submitting to NCBI, or publishing to Dryad. Often the different fields contain the same information, but with slightly different labels, meaning that researchers have to enter the same data multiple times, fuss with formatting, and often end up getting frustrated and giving up. Another hurdle for getting scientist to use metadata is the large amount of effort required for limited value in return.

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  • On hold until after site visit.
  • See JIRA epic DS-114

Re-organization of Community Data

 

Policies

Completed projects

These features are operational and under maintenance. As new user needs arise, further development of these features may take place.

CyVerse Data Policies

  • A new  Data Commons User Agreement and Data Policy were released 04/2017.
  • Data policy was updated 08/2017 at the request of the Science team. Users can now request up to 10 TB without executive team review. 

 

Submission to external repositories

Submission to NCBI SRA repository

First available: Q2 2015

CyVerse users can now submit data to SRA through the DE. The process is documented on the NCBI Sequence Read Archive (SRA) Submission (Workflow Tutorial) wiki page.

 

Submission to NCBI WGS repository

 

Status: In First available: Q2 2017, in beta testing

 

Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are generally being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. We are adapting the CyVerse SRA submission pipeline (see below) to submit sequences to WGS.

  •  

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  •   Similar to SRA submission features. Users must create a BioProject and BioSample and apply appropriate metadata before submission

 

Submission to NCBI TSA (Transcriptome Assembly) 

 

Status: Planning


Future projects

Improved data discovery and reporting

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