Study creation

About studies and Terra workspaces

Studies in Single Cell Portal can serve as visualization portals, data repositories, or both.

Creating a study makes a space in the portal for others to download and/or interact with your data. This is a great way to support the exploration of a publication for others, as well as to create a web presence for your science (a URL is created you can reference in your publication). Data can be added to the study allowing others to download and reproduce the analysis.

Every study created in the portal also comes with a workspace in Terra, which has an attached Google Cloud Storage bucket. This is where uploaded data files are stored. When you create a study, you will receive an invitation email from Terra asking you to complete your registration. While you can still interact with your study & data through the portal, you will not be able to view your Terra workspace or associated Google storage bucket until you complete the registration.

How to create a study

Start at the portal home page

Visit the site here

Step 1. Log in or sign up

If you are creating an account for the first time check out the documentation around creating an account, otherwise log in to the Portal Log in with your Google account credentials.

Step 2. Accept terms of service (if you haven't already)

If you haven't done so already please read and accept the SCP Terms of Service. You will not be able to complete the login process until you do so. 

Step 3. Click "Create a study"

After logging in, you will be able to view your studies and add new ones. To add a new one click the "Create a study" button located in the upper right corner of the site. 

Step 4. Set study info and access levels

The Portal will navigate to a form where you will be prompted to fill in information about your study.

The form fields are as follows:

1. Name - choose a study name, this will be how people refer to and identify your study in the portal. 
2. Terra billing project - the Single Cell Portal provides a default billing project that all users of the Portal can utilize at no cost. However, public studies using the default billing project are restricted to 0.5T daily download quota. For large data sets, consider providing your own billing project to facilitate the dissemination of your data set.
3. (optional) Data release date - This is not a required step. If your study is still under peer review, and you do not want users to be able to access your data until the review is completed, you can set an embargo date to prevent downloads until the specified date. Select a time in the calendar after when data associated with the study can be downloaded. This only affects public data and private data is always private, no matter embargo status. Any collaborators you share this study with will always be able to access the data, regardless of any embargo. For more information please consult Study Permissions.
4. Public - Indicate if the study is private (only seen by the study owner and collaborators with permission) or public (seen by all). Read more about study permissions in the Study and data permissions.
5. Use an existing workspace - Choose "Yes" if you would like to utilize an existing Terra workspace. This might be useful if you have already set up a Terra workspace and populated it with the data you would like to have in your study in the Portal. You could then use the Sync feature to bring that data over. Otherwise you can choose "No" and a new workspace will be created for your study.
6. Existing Terra workspace - This field will be disabled if you chose "No" to the previous prompt. If you chose "Yes" then this is where you can supply the name of your Terra workspace.
7. Description - The description will be the main way to communicate to others the context and design of your study. The full description you provide here will be displayed in your study in the Overview tab. You are welcome to add your abstract, links, or other items to create a rich description of your science. Consider providing commonly requested study details.

Step 5. Sharing

You can add collaborators for your study at this point. Alternatively you can add collaborators later through your study settings page. If your study is private the following three permission levels for collaborators are available:

1. Edit - This user will have read/write access to both this study and Terra workspace
2. View - This user will have read access to both this study and Terra workspace (cannot edit)
3. Reviewer - This user will only have read access to this study (cannot download data or view Terra workspace)

If your study is public you can set these same permissions but only the Edit access will have an effect.

Step 6. Publication/Resource Links

Here you can add links to webpages or URLs that will be displayed in your study summary page.

Step 7. Save

After you are satisfied with the information and settings you have chosen for you study you can click the "Save study" button at the bottom of the page and your study will be created.