Learning and Using the Research Analysis Platform

Learning to Use the Research Analysis Platform
‌The UK Biobank Research Analysis Platform is built on the DNAnexus Platform, and using the two is largely the same experience. See the DNAnexus Platform documentation for detailed information on Platform features and how to use them. Of particular note: 
​Key Concepts - Learn about projects, organizations, apps, and workflows, and how to create and use each.
​User Interface Quickstart - Learn to access and use Platform features via the web user interface (UI).
​Command Line Quickstart - Learn to access and use Platform features via the command-line interface (CLI), using dx command-line client, available for download as part of the DNAnexus SDK.
​Cohort Browser - Learn to explore related genomic and phenotypic datasets, and easily create subject cohorts for analysis. 
​Introduction to Building Apps - Learn to build and deploy custom analysis applications.
​Introduction to Building Workflows - Learn to build and deploy custom workflows for processing and analyzing data.
Uploading and Sharing Files - Learn to upload files to use in analyses, via either the dx client or, for multiple or large files, the Upload Agent. See also this step-by-step walkthrough on uploading data to a project, then sharing the project with other project members. Note that to access a project on the Research Analysis Platform, a user needs to be listed on the linked access application.
​Running Apps and Workflows - Learn to configure and run apps and workflows, monitor progress, and view results, both from the UI and the CLI. 
​Platform API - Learn to access Platform features and capabilities programmatically.
​JupyterLab - Learn to use Jupyter notebooks to create, hone, and run sophisticated custom analyses, in your preferred programming language. 
​Stata - Learn how to access and use Stata, a popular statistical software package for data science.
​Integrated Genomics Viewer - Learn to use the Integrated Genomics Viewer (IGV) with genomic data files stored on the Platform.  
Initial Usage Credit
The first time you access the Research Analysis Platform, the system will create for you a "wallet" (i.e. a "personal billing account"), funded in the amount of £40, courtesy of DNAnexus. Note that this wallet is separate and unrelated to the "Trial Subscription" mentioned in section 2.8 of the DNAnexus Terms of Service.
Specifics of Using the Research Analysis Platform
This section describes functionality and limitations specific to the Research Analysis Platform.  
Note that as a rule, Research Analysis Platform access and sharing restrictions are related to UK Biobank access applications.  All Research Analysis Platform projects are linked to a UK Biobank-approved access application. To access a project, a user must be named as a Principal Investigator or collaborator, on the linked access application. 
For more detail on UK Biobank access applications, see Creating a Project.
Creating Projects
On the Research Analysis Platform, projects can only be created via the UI. A project cannot be created via the CLI.
Sharing Projects
You can collaborate on the DNAnexus Platform by giving project access to other users.  For details, refer to the Platform documentation sections covering Project Sharing and Project Access.
On the Research Analysis Platform, you can only share a project with another user, if he or she is named on the linked UK Biobank access application, and has Research Analysis Platform access.
Copying Files Between Projects
On the DNAnexus Platform, you can easily copy files from one project to another. 
On the Research Analysis Platform, you can only copy files from one project to another, if both projects are linked to the same UK Biobank access application.  
Enabling Group Billing
To enable shared billing for a group of users, follow these instructions. 
Platform Endpoints
When accessing the Research Analysis Platform, note the following default settings:
For logging in via the command line (with 'dx login'): auth.dnanexus.com:443 
For interacting with the Platform API to perform uploads: api.dnanexus.com:443 
For the actual data transfer that the client will perform to S3: dnanexus-eu-west-2-platform-upload-ukb-prod.s3-eu-west-2.amazonaws.com:443 
For connecting to the Platform Thrift server, follow these instructions, substituting this JDBC URL: jdbc:hive2://query.eu-west-2.apollo.dnanexus.com:10000/\;ssl=true
Transferring Project Ownership
On the DNAnexus Platform, you can easily transfer project ownership to another user.
On the Research Analysis Platform, project ownership can only be transferred to a user who is listed on the UK Biobank access application linked to the project. 
Participant Withdrawals
​Participants are free to withdraw from UK Biobank at any time and request that their data no longer be used. When participants withdraw, their data is removed from the UK Biobank, and from all datasets on the Research Analysis Platform. These participants' data will no longer be accessible to you, or be able to be used in future analyses. 
If a participant’s withdrawal affects your dispensed data, you will receive an email from UK Biobank containing the anonymized IDs of these participants and any others who have withdrawn previously. It is possible that this list will contain IDs which you have never received as they may have withdrawn before your datasets were generated. 
For any data, files, objects generate on the platform through usage, you are responsible for removing the records corresponding to all withdrawn participants from further analyses. Any files you download or manipulate (ex. results file from a GWAS, a CSV file created using Table Exporter) will not be changed by the withdrawal of participant data.
AWS Region
The Research Analysis Platform is hosted in the AWS "aws:eu-west-2" or "Europe (London)" region. 

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Outline

Learning to Use the Research Analysis Platform

Initial Usage Credit

Specifics of Using the Research Analysis Platform

Creating Projects

Sharing Projects

Copying Files Between Projects

Enabling Group Billing

Platform Endpoints

Transferring Project Ownership

Participant Withdrawals

AWS Region