UKB-RAP resources and documentation

The UK Biobank Research Analysis Platform (UKB-RAP), which can be accessed here, is an informatics platform which allows its registered users access to UK Biobank data. It is hosted by our partners at DNAnexus, meaning that whilst there is plenty of documentation to get you started on the UKB-RAP, these resources are spread over different platforms. This article will walk you through where to find some of these essential resources, and where you can find the information you need to begin your data analysis.

UKB-RAP essential information

You will have already watched the researcher training courses when you applied for access to the UKB-RAP. However, the Researcher Induction Course 2 is a great resource to look back to if you need help with the basics of operating the UKB-RAP. This involves creating a UKB-RAP account, setting up a billing account, creating a project and dispensing data, as well as adding collaborators. The video additionally walks you through the cohort browser, and will direct you to different areas of the UKB-RAP, including where to find your tabular and bulk files, the data dictionary in the Showcase metadata folder, and the tools library. If you wish to know about how to scale and monitor jobs, including what the priority, instance types and nodes settings mean, the video will also cover each of these points.

UK Biobank GitHub notebooks

To help researchers understand how to use the UKB-RAP, UK Biobank has created the UKB GitHub to offer code examples and insights for data analysis on the platform. This involves looking at how to access, extract and analyse data covering a range of data types, using Jupyter notebooks for both python and R, as well as Rstudio notebooks. More specifically, the A-series (Accessing Data) notebooks focus on how to access and examine UKB phenotypic data, and the G-series (Genomics) notebooks focus on performing genomics analytics workflows. Additionally, there are notebooks which allow individual SNPs to be filtered from the UKB genotyping data, as well as notebooks for researchers interested in executing complex, multi-stage workflows on the UKB-RAP via apps, applets and Workflow Description Language (WDL). To learn more about these notebooks and how to access them, please see our UK Biobank GitHub notebooks article on the community forum which explains what there is on offer.

On a related note, DNAnexus also operates a a GitHub which offers some notebooks that you may find useful. For example, the basic data extraction notebook guides you on how to extract phenotypic data, and the dx data notebook can help you to load, access and retrieve metadata within datasets and cohorts.

Main UKB-RAP documentation Gitbook

The UKB-RAP gitbook contains information on a lot of the main components of working on the UKB-RAP, including but not limited to:

After watching the training courses, this website is a great place to refer back to for information on key ways of working on the UKB-RAP, and for information on specific approaches to data analysis on the platform.

UKB-RAP help centre

The UKB-RAP help centre provides a page which links to various UKB-RAP support resources. For example, the page provides links to the UKB-RAP status, UKB webpages, and the UKB-RAP newsletter. Additionally, it will walk you through some of the main gitbook pages (mentioned above), for additional guidance on where you can find relevant content, and point you to the training resources page (more below).

Training resources

The UKB-RAP training resources page allows you to specifically navigate to different video tutorials of the UKB-RAP. Some particular videos of note include the overview training videos. Part 3 covers the cohort browser and how to explore and extract data, part 4 talks about how to extract phenotype data using both table exporter and dx extract_dataset, whilst part 5 talks about the tools library with a focus on using Swiss Army Knife. Additionally, a particularly notable webinar video (found here) guides you through data dispensal, project creation, data refreshing, dataset types and structures, basic file operations, apps in the UI and the considerations of cloud based analysis.

DNAnexus documentation

The DNAnexus documentation page provides detailed information on how to perform operations in the UKB-RAP using both the command line interface (CLI) and the user interface (UI), including how to run apps and workflows, as well as operate the cohort browser. A particularly essential resource for users of the CLI is the index of dx commands page, which you can use to search for commands to perform operations like deleting, uploading and downloading data. If you have questions about what data you can download, please see the following community forum post.

UKB-RAP costs

For guidance on how much money you can expect to spend for computation and data storage on the UKB-RAP, please see the UKB-RAP Rate Card where you will find information on the cost per hour of using different instance types. You may also want to see our costs and billing page and the costs & financial support webpage. To help reduce costs, remember to maintain good file management.

Find support

If you have further questions about using the UKB-RAP, the UK Biobank community forum is a great place to browse previously asked questions and to post your own inquiries to help out the wider research community. Alternatively, you can submit a ticket to get help from UK Biobank or contact DNAnexus support at ukbiobank-support@dnanexus.com for assistance with any technical issues you may be facing.

If you are interested in looking through the metadata for fields in the UKB-RAP, you may also be interested in looking at the Showcase website. Please see this article for more details.

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