RADx® Data Hub

Workbench Tutorial
Approved Data
General

My Approved Data allows you to access data files based on your Database of Genotypes and Phenotypes (dbGaP) approvals. This page will group files into one table per study. Within each study table, the files are organized by bundles, which is a set of files including a data file, metadata file, and data dictionary (along with any SAS file equivalents if available).

After accessing My Approved Data, you can:

Note: My Approved Data will be empty until you are approved to access to at least one RADx Data Hub study in dbGaP.

Figure 1: My Approved Data Link in Navigation Bar
Figure 1: My Approved Data Link in Navigation Bar
Download Files

To download files, select them using one of three techniques:

  • Option 1 - Select a Bundle: To select a bundle, check the box next to a harmonized or non-harmonized data file. This will select the high-level data file and its supporting files (i.e., metadata and data dictionary files).
  • Option 2 - Select an Individual File: This process varies for supporting files (e.g., metadata and data dictionary files) and data files. To select a metadata or data dictionary file, check the box next to the file name. To select an individual harmonized or non-harmonized file, first check the box next to the file name. This will select the entire bundle. Then, deselect the metadata and data dictionary files.
  • Option 2 - Select All Files: Click the “Select All” button. This will select all study table files.

After selecting the desired files, you can click “Zip & Download,” and the files will appear in your browser’s download center as a zip file, which you can save or open.

Figure 2: Selection Functionality and Zip & Download Button
Figure 2: Selection Functionality and "Zip &Download" Button
Apply for Add-ons

After registering, you will automatically have the default Workbench access, which includes JupyterLab and RStudio but does not include Data Wrangler or SAS Viya. To access those tools, you must apply for a Workbench Add-on. To apply:

  1. Press “Apply for Add-on” (Figure 3). The system will direct you to a separate page displaying the request form.
    2. Figure 3: Apply for Add-on Button
    Figure 3: "Apply for Add-on" Button
  2. Fill out the required fields.
    3. Figure 4: Add-on Application Form
    Figure 4: Add-on Application Form
  3. Download and read the Terms of Service. You should type your name in the “Agree to the Terms of Service” field if you agree.
  4. Press “Submit.” The RADx Data Hub team will review the request and email you if you are approved for a Workbench Add-on.
Note: There are a limited number of licenses available for SAS and Data Wrangler. The licenses are distributed on a first-come, first-serve basis. You may only hold one license at a time.
Create a Workbench

To create a workbench, press “Create Workbench.” In the future, press “Launch Workbench” to access an existing workbench.

Figure 5: Create Workbench Button
Figure 5: "Create Workbench" Button
Add Files to Workbench

To add approved files to a workbench, select the file or files to transfer. Then, click “Add to Workbench” in the top right of the study table (Figure 6).

Figure 6: Add to Workbench Button
Figure 6: Add to Workbench Button