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DATA COMMONS USER MANUAL
Maintenance Notification

CyVerse systems will be unavailable on Tuesday, September 18th, from 7:00am to 5:00pm MST.
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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.

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

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Atmosphere instances will continue to run.
Commonly-used images will be available for launching instances, but users will be unable to create new images, or launch instances from rarely-used images, while we perform Atmosphere and DataStore maintenance.

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

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There are several steps to properly organizing your dataset. These include determining what data to include, how many identifiers to request, how to organize the data into folders, and creating the ReadMe file and data inventory.

Step 2.1. Determine what to include

A data collection may be composed of multiple files and different datasets. In preparing your data for publication:

  1. Identify the data and other materials that you consider useful for validation and reuse of your research:
    • Data associated to a research project may include multiple files with different roles.
    • If there are components of your dataset that belong in a public repository such as NCBI (e.g., fastq files), submit them to the repository, rather than to CyVerse Curated Data.
  2. Beyond data, you will include the ReadMe file (see Step 4), and you may include scripts or links to scripts to run your analysis.

Step 2.2. Determine how many permanent identifiers to request

To determine how many DOIs to request for a given data collection, consider the following:

  • Think about its size and components.
  • How many studies or publications does it represent?
  • Is your data collection formed by different datasets and are those likely to be used separately?
  • Do you want to create a data collection with one DOI for the entire project and additional related DOIs for distinct datasets so that they are cited individually?

If you are uncertain about how many DOIs to request, contact us at doi@cyverse.org.

Step 2.3. Organize your data into folder(s)

  1. Organize your data so that there is one folder for each DOI (see CyVerse Curated Data folder-naming guidelines for naming conventions).
  2. Within a folder, include all files in your data package plus the ReadMe file and the inventory.
    • You may have subfolders within a data package.
    • You may include compressed files in a package, as described on the Permanent Identifier FAQs, but do not compress the entire folder/package.

Step 2.4. Name your top level folder according to the guideline

The folder containing your dataset should be named using the $Creator_$subject_$date format.

For more details on folder naming, see the CyVerse Curated Data Folder-Naming Guidelines.

 Step 2.5. Create a ReadMe file

Create a text file labeled "readMe" with the following information:

Step 2.6. Create an inventory

2.7 Supporting documents on data management and organization

Here is a useful guide to data organization: Research Data Management: File Organization (PDF).

 

 

 

 

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