What's changed on UKB-RAP: a guide for researchers

Since UKB-RAP closed earlier this year, we have made a number of changes to how the platform operates.

These changes have been introduced to strengthen the safety and security of participants’ data. 

Click the links below for more details on these changes, along with supporting resources.

The reopening and strengthening of UKB-RAP is an ongoing process. We will keep the below pages updated as we continue our work to improve the platform.

• In the process of strengthening the platform, all researchers who are not Account Holders have been disconnected from their projects. Your projects, and all the work within them, are safe and unaffected.

• You will need to re-add researchers to each of your projects. You will only be able to do this after a researcher has reactivated their account by logging in.
  
  Watch our explainer video here.
  
  If you can't find a researcher when trying to add them, they may not have logged in and reactivated their account yet. Ask them to log in to UKB-RAP, then try adding them again.

• You may wish to contact your project's Org Admin to confirm that they know they need to re-add you once you have logged in to reactivate your account.

• Changes to authentication mean that API tokens can no longer be used to log in to UKB-RAP via the command line interface (CLI). Researchers can still use the CLI with username and password authentication.
  
  You will also be logged out after 15 minutes of inactivity and will need to authenticate again using Two Factor Authentication (2FA).
  
  If you use DNAnexus commercial services with SSO, you may need to adjust the way you work to minimise time spent with the platform in the background.
  
  Jobs and analysis will continue to run, even if you are logged out unexpectedly.

• Initially, you will not be able to download results from the platform. Later this year, we will introduce a manual Output Checking System (OCS) with only limited capacity to allow results to be downloaded. By early 2027, we aim to have an automated OCS that allows researchers to take all of their results off the UKB-RAP.
  
  You can still create private applets, but public applets are no longer available. Code can be exported through Airlock.
  
  You will also no longer be able to build public applets, or share tools with researchers outside of your application. You can still create private applets, and you will be able to export code once the OCS is operational.

• It will not initially be possible to refresh or dispense data; researchers will only be able to work with data already dispensed to their project.
  
  We hope to re-enable this soon and will update accordingly.

• Interactive tools such as RStudio and Jupyter are now available through isolated browsing.
  
  This provides an additional layer of security by separating the interactive session from your local browser. It may look similar to screen sharing, and researchers outside the UK may experience some additional latency.
  
  Interactive jobs will not have general internet access. Access to specific websites may be permitted where they have been whitelisted.
  
  Copying and pasting are also restricted: you cannot copy text from an interactive job, and pasted text is limited to 300 characters.

• The Preview tools are currently disabled. To view the contents of files or notebooks, you will need to launch a new compute instance.
  
  We are working to restore Preview functionality.

• You can no longer SSH into jobs, meaning you can no longer log in to a running job or view its logs from outside UKB-RAP, whether through your browser or the command line interface (CLI).
  
  You can still access jobs from within the job itself.

• The way participant-level data are displayed in Cohort Browser has changed.
  
  You can no longer view a table of participant data or copy individual encrypted identifiers (EIDs) directly from Cohort Browser.
  
  You can still save your cohort and use the table exporter to export the filtered data as a CSV file.

• The command line interface (CLI) can no longer be used to directly navigate participant data in a tabular format. The relevant commands can still be used from within jobs running on UKB-RAP, such as via ttyd.

• Whole Genome Sequencing (WGS) CRAM files will not be available for any projects.
  
  We hope to re-enable these data soon and will update accordingly.