Accessing the Research Analysis Platform

Learn how to create a Research Analysis Platform account, access the Platform, and connect your account to the UK Biobank Access Management System.

Before You Begin

Before you can use the Research Analysis Platform, you need to:

1. Create a UK Biobank Access Management System (AMS) account, via the AMS signup page.

2. Ensure that you’ve received UK Biobank access approval from the UK Biobank Access Management Team (AMT). If you haven’t, log into the AMS and follow the directions to complete your registration and get AMT approval.

3. Ensure that you are listed as a collaborator on a UK Biobank-approved access application by that application's Principal Investigator (PI).

See the AMS user guide for more on creating and managing an AMS account.

Accessing the Research Analysis Platform

If you already have a DNAnexus account, log into the Research Analysis Platform using your existing username and password. Then skip to Connecting Your Account to UK Biobank below.

If your organization uses SSO with DNAnexus, follow your organization's login procedures to access the Research Analysis Platform. Note that your AMS and DNAnexus accounts do not need to use the same email address.

If you need to create an account, follow the instructions in the next section.

Creating a Research Analysis Platform Account

If you don’t already have a Research Analysis Platform account, you’ll need to create one. Here’s how:

1. Navigate to the Research Analysis Platform. Click Create an Account.

2. Fill out the Create New Account form, then click Create Account. Note that in selecting a username, you don’t need to use the same username you use on the UK Biobank AMS.

3. You'll receive an email with a link to click, to activate your account. Click the link.

4. Log into the Platform.

5. Complete your profile, then click Access Platform.

Connecting Your Account to UK Biobank

Once you have a Research Analysis Platform account. you need to connect it to your AMS account. You need do this only once.

1. The first time you access the Research Analysis Platform, you’ll see a prompt to Connect Your Account to UK Biobank.

2. Read the Terms of Service, then click Accept & Continue.

3. You'll be redirected to the AMS. Log into the AMS.

4. Your AMS and Research Analysis Platform accounts are now connected.

5. You'll be redirected once again, this time back to the Research Analysis Platform. You can now use the Platform.

Authentication Tokens

Generating tokens

You can log in without having to provide a username and password for a certain amount of time by using authentication tokens (henceforth referred to as tokens). Broadly, authentication tokens are generated by providing your username and password to the platform and specifying a time period for which the token may be used to log in.

If you provide your token to a third party, they may access the Research Analysis Platform with your token, effectively impersonating you as a user. They will have the same access level as you for any projects to which the token has access, potentially allowing them to run jobs and incur charges to your account. Please keep your token safe and secure.

In order to generate a token:

1. After logging into the Research Analysis Platform, access your profile by clicking on your user icon in the top right side of the screen and click Profile.

2. Once you are on your profile page, click on the API Tokens tab.

3. The New Token modal will appear on screen. Fill out the required fields and then click Generate Token.

A pop-up will then appear saying “Your token has been generated. Please copy it for later use; for security purposes, this is the only time you will see it.” with a 32-character token comprised of letters and numbers in the line below. Copy down this token in a secure location and save it for later.

Some examples in which tokens might be used include the following:

• Writing a script: Tokens can be helpful when writing scripts that require logging in to the platform. However, if you incorporate a token into a script, the token should only be valid for as long as the script requires access to the platform; the "Expiration Date" field should be modified accordingly. Furthermore, the token should only be granted access to the projects required by the script. If your script uploads data to only one project, the "Token Scope" should reflect the limited access.

• Logging in to the command line for interactive use: If for some reason you don't wish to log in to the command line with your username and password, tokens are quite useful. This is the only scenario in which you should use a full-scope token, thereby allowing you to access all of your available projects.

Logging in with an authentication token

In order to use a token to log in on the command line, you must use dx login with the --token flag. See the example below of what a user would see after logging in:

$ dx login --token 

Note: Use "dx select --level VIEW" or "dx select --public" to select from
projects for which you only have VIEW permissions.

Available projects (CONTRIBUTE or higher):
0) SAM importer test (CONTRIBUTE)
1) Scratch Project (ADMINISTER)
2) Mouse (ADMINISTER)

Pick a numbered choice [2]: 1
Setting current project to: Scratch Project

Revoking authentication tokens

You must navigate to the API tokens tab of your profile in order to revoke a token.

Once in the API tokens tab, select which token you wish to revoke and then click the Revoke button:

Once you confirm that you wish to revoke the token, the token will be revoked.

Some examples in which tokens might be revoked include the following:

• Token accidentally shared too widely: If more people have access to your token than you would like, revocation of the token will cut off access to your account by unwanted parties.

• Token no longer needed: For example, if the script utilizing the token is no longer in use; or if the group granted access to the platform using the token no longer exist; or in any other instance in which the token is no longer necessary, you should revoke it to restrict access to your account.

Troubleshooting

I entered valid credentials on the AMS, but got an error message saying I’m not yet registered.

‌See Step 3 in the Before You Begin section above. You must complete the AMS registration process, and get the approval of the AMT.

For additional information, see the Creating an Account and Registration sections of the AMS Getting Started guide.

‌I tried creating a Research Analysis Platform account and got the error message "Email Already Registered."

‌‌You already have a DNAnexus account. Use your existing username and password to log in.

I previously completed my account setup, but now I am being asked to accept Terms of Service and enter AMS credentials again.

Occasionally the platform may ask you to refresh your account association, due to security reasons. Among others, this can happen if your state on the AMS changes for any reason - if you update your contact details on the AMS, for example.

I updated my AMS account information and am having issues accessing the AMS via the Research Analysis Platform

If you update your AMS account information, you may experience access issues until UK Biobank reviews and re-approves your account.

I lost access to a project

One of two issues is likely the reason why you've lost access to a project.

You were removed from the access application

You may have been removed from the UK Biobank-approved access application. In this case, you will not be able to regain access to projects linked to that application.

To check the access applications in which you're included, log onto the AMS.

The access application has been temporarily suspended

UK Biobank may have temporarily suspending the access application to which the project is linked. If this is the case, you can be added back to the project when the suspension is lifted.

If you are the admin of the wallet to which the project is billed, follow these steps to add yourself back to the project:

1. Select Org Admin from the main Platform menu, then select the org wallet in question.

2. Open the Projects tab

3. Select the project to which you need to regain access

4. Click Grant Permission

If you are not the wallet admin, but the admin is also in the access application to which the project is linked, have the wallet admin:

1. If he or she is not in the project in question, follow the steps above, to add himself or herself to the project

2. Share the project with you

3. Optionally, remove himself or herself from the project

If you are not the wallet admin, and the wallet admin is not in the access application to which the project is linked, have the wallet admin transfer project ownership to you.

Working with Multiple Accounts

Note that:

• ‌An AMS account may be associated to exactly one Research Analysis Platform account

• A Research Analysis Platform account may be associated to exactly one AMS account

‌