To access ATLAS data from Workbench, you need to first generate an API key.

From the portal, go to your profile page. You can then follow the instructions on the top right corner of the screen to generate an API key.

Entering your password and hitting the check mark will copy an API key into to your clipboard. We recommend that you store that API key in a secure location, e.g. a password manager.

Afterwards, set the API key in your R session in one of the following ways:

• [Recommended on Code Ocean] Set it as a user secret, attach it to your capsule, and use the environment editor to change the name of the env var to EMDB_API_KEY. See our Guide to User Secrets on Code Ocean for guidance with this process! Any of the other options will require you to repeat those steps each time you start a new cloud workstation on Code Ocean.
• [Recommended elsewhere] Run emconnect::initialize_SDA_connection. This will prompt you for your API key and save it to your ~/.Renviron file.
• Alternatively, add a line EMDB_API_KEY="<Paste results here from previous step>" to your ~/.Renviron and restart your R session.
• If you want to temporarily use a different API key, you can also set the EMDB_API_KEY directly in a session: Sys.setenv(EMDB_API_KEY="<Paste results here from previous step>")