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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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This page provides guidance for labs or projects that are considering using CyVerse to share data and analyses. 

Getting started

Any project members who will be using CyVerse should take a look at the wiki page Getting Started with CyVerse Home. Be sure that all project members have CyVerse accounts.

Sharing data with project members

For projects that are part of a single lab, we recommend that the PI create a CyVerse account and share it with lab members. Specific sub-directories can be shared with specific lab members as desired.

The sharing functionality the CyVerse Data Store can be used to share data among project members. This can be done through the Discovery Environment or on the command line using iCommands. Project members also can upload and download data using the desktop application Cyberduck, but not for setting sharing permissions.

According to our allocation policy, all users receive a default allocation of 100GB. Shared data is counted as part of the allocation of whoever owns it (uploaded it). To request an increase to your allocation, should that become necessary, use this form. We expect that users hosting shared directories will need to request larger data allocations.

If your project needs a shared folder for data that will be made public, you can request community data hosting.

Managing data in a shared project

We strongly recommend that a single person be in charge of data management. There should also be a single person (generally the PI) who has ownership of the project folders and who sets read and write permissions for others. This ensures continuity when people move on. The PI can give ownership to a data manager for setting lab permissions, but should maintain their ownership as well.

The owner of a folder has the ability to delete or rename the folder and any of its contents. If project members are given write permission to the project folder, they will be able to create their own sub-folders which they will own.

For more general data management tips, see Using CyVerse to make your data FAIR.

Sharing tools and analyses with project members

Projects can use CyVerse analysis platforms to develop and share analysis tools and workflows.

The Discovery Environment contains hundreds of application that can be used by projects. Apps can be chained together to form workflows in the DE. It is now possible for CyVerse users to integrate their own applications or any open source application into the DE, using Docker containers.

Atmosphere can be used to set up a virtual machine (VM) with project software, which can then be used by all project members. The VM can later be imaged (made permanent) and published along with the project.

If your project includes a lot of computationally intensive analyses, you should consider requesting an XSEDE allocation (for the U.S. national super-computer infrastructure) and setting up HPC workflows using tools such as Pegasus.

has been moved to the CyVerse Learning Center at https://learning.cyverse.org/projects/cyverse-group-project-quickstart/en/latest/index.html.