Creating your workspace

You will only need to complete this step once per course. If you are having issues with your workspace or if it goes into UNKNOWN status, contact your TAs.

The first time you log in in Service Workbench; you will see that there are no research workspaces (i.e., you cannot run any code yet). To set up your Research Workspace, Click on the Studies symbol on the left panel.

Studies are subfolders linked to Amazon S3 storage. You should have access to 2-4 studies: the course specific READ-only study, a LIB folder, and your personal study folder. Some courses may also have an additional project folder. Navigate to the “Organization” tab on the Studies page to see them. You will need to link all of these studies to the research workspace you create. Do this by checking the boxes next to both studies and clicking next. The data in the READ-Only folder must NEVER be downloaded, copied, or changed, as it can contain patient-level information.

Now is the time to choose which kind of research workspace we want to create. Depending on the course, you will select either HMS SRCE Rstudio Server or HMS SRCE SageMaker Notebook. If there are multiple versions available, select the most recent one (higher v number). We will add some information to our research workspace, such as the Name and the Project ID.

• For the Name, we will use: <firstname><lastname><coursecode><year>

  • For example: AlbaGutierrezAISC2023

• For the Project ID, we will select: DBMI-teaching

The next thing we need to select is Configuration. We can choose between different RStudio configurations. For this course, we will select the RStudio-small. (For Sagemaker workspaces, select sagemaker-small).

To finish creating our research workspace, we need to add a Description. You can fill this box with something like: "Research workspace for ..." followed by your first and last name. Now we are ready to click the Create Research Workspace button on the bottom right corner of the screen.

In the Workspace tab, we will now see the new research workspace we have just created, and a message like this will pop up for some seconds on the right corner of your screen.

In the Research Workspace we have created, note that it will be in Pending status for around 5 minutes, the time required to create the workspace for the first time.

When Available it will turn out Green.

You will only have to complete these steps once for this course. You will use this research workspace for the rest of the semester. Once you create your workspace you cannot add additional studies to it.

After the workspace is created and we have checked that everything looks correct and that the workspace is still as AVAILABLE we will just need to click on Connections. Then we click on Connect in the bottom right corner of the box, and a new page will automatically open on your browser.