Service packages

This FAQ addresses what's included with Standard Support on UKB-RAP, what's included with purchases of a UKB-RAP Service Package and how DNAnexus handles more complex queries.

What is already included with the UKB-RAP standard support team?

Email support ([e-mail]) is available for users to submit questions for billing, administration issues, to report platform performance issues, or to report bugs in the DNAnexus provided tools. You can also learn more in our blog post announcing the new model.

UK Biobank’s Community is also there to answer any questions you might have about accessing data, using it, navigating and working on the UK Biobank Research Analysis Platform (UKB-RAP).

This free site contains articles, guides, webinars, and videos to help you – along with a Forum where you and other researchers can ask and answer questions. The search function gathers answers from all these sources to help you.

Additionally, all of DNAnexus tutorials & webinars on YouTube, documentation will remain available for users to access.

Who should I contact for support?

When should I contact the DNAnexus support?

Standard Support: Technical platform issues, service or administrative requests on UKB-RAP. Examples include:

• Job failed due to platform technical issue or error in native application

• Login issues

• Worker limit increase

• Billing issues ([e-mail])

Service Packages: Anything that is not a technical platform issue, service or administrative request on UKB-RAP. Examples include:

• Job failed due to issue in customer code, wrong instance type, spot instance interruption

• Help with issues described in documentation

• User code debugging

• App building and other development questions

When should I contact the UKB access team?

Issues associated with UK Biobank data or AMS. They can be reached at [e-mail].

Examples include:

• UKB-RAP Project: Your data were dispensed but you see 0 participants in your cohort

• Error message: AMS application is not enabled for UKB-RAP

• Error message: Application id XYZ does not belong to this user or is not an approved application

• Error message: You entered the wrong username/password or you do not have approved researcher status. Please ensure your AMS profile includes your date of birth

• UKB Data: Suspicion of UKB files incompatibilities or corruption

• UKB Data: Missing data. Please provide your application ID and field IDs you are missing in your project

• UKB Data: How to apply for data access

• UKB Data: Data from papers and where to find it

• UKB Data: Explanation of data content/structure

What is included with the new Service Packages?

Users can now purchase service packages that will provide you with 1:1 expert guidance from DNAnexus to answer questions ranging from troubleshooting custom applets to asking for scientific guidance when using the UKB-RAP. Note that complex questions may require more than one ticket and tickets expire within 12 months from purchase. The DNAnexus team will assess the complexity of your question(s) and advise how many tickets will be required to help.

It should also be noted that some requests, for example where you wish DNAnexus to run an analytical pipeline on your behalf, would require DNAnexus to become a Third-Party Processor[1] on your research application. DNAnexus would be open to supporting you in this capacity and, if this is of interest, please get in touch with us directly at [e-mail]. DNAnexus will work together to ensure compliance with UK Biobank policies.

With the new service package, the DNAnexus team will walk you through solving your more complex bioinformatics queries in the UKB-RAP, equipping you with the right understanding to succeed.

What are the benefits of using a Service Package?

• Our DNAnexus team will work directly with users, to understand their objectives and develop a plan to achieve early wins ensuring their success using UKB-RAP.

• Learn first-hand from our team’s deep experience working with UKB data. Learn best practices for working with large multi-omics sets and complex data structures.

• Receive answers to your specific questions on research topics such as genetic association, clinical data, imaging analysis, multimodal data analysis, integrated analysis or machine learning.

What Falls Under Standard Support vs. Service Packages?

Examples of Standard Support Questions	Examples of Questions that Require Service Packages
“We need help setting up a purchase order.” “I am having trouble logging into the platform” “I have opened a new RStudio session but I get an error message when I try to open it.” “I would like to request access to the whole exome and whole genome sequence data through the RAP” “What happens when my initial credit expires?.”	“My team is trying to implement a pipeline analyzing rare variants in exome data but need some guidance setting it up efficiently” “We want to query WES genotypes across a large selection of UKB samples. Can you provide recommendations on the best way to do this?” “What’s the best way to merge genomic & proteomic data?”

What is the process of obtaining a service package?

Please fill in the form here. You will be then contacted by our DNAnexus team with order forms to complete your purchase. Once this is completed and submitted our DNAnexus support team will be able to answer your questions.

What are the prices for each Service Package?

You can find the pricing documentation here.

How do I know which service package I should purchase?

Service packages come in different bundles of service tickets: 1, 5, 20, 50 and 100. You can choose a smaller bundle if you’re unsure of how many service tickets you will actually need or purchase a larger one and save the service tickets for future inquiries. Service Packages are valid for 12 months after purchase.

For most inquiries, 1 service ticket will be redeemed for each support question outside the scope of standard support. Note that complex questions may require more than one ticket and tickets expire within 12 months from purchase. The DNAnexus team will assess the complexity of your question(s) and advise how many tickets will be required to help.

Do I need to name you as a 3rd Party Processor?

If your support inquiry requires DNAnexus to run a pipeline or test a pipeline within your workspace, then you will be required to name us as a 3rd Party Data Processor in your annual report

Examples of questions that require DNAnexus to be a 3rd Party Processor:

• Set up, optimization or executing of the pipelines where access to the data is required

• Running of scripts to convert standards or provide mapping

• Set up and hands on training of tooling/pipelines within the customers’ project

Can DNAnexus help me complete my research?

Yes. DNAnexus can advise on the best way to approach analysis in the UKB-RAP, help build pipelines or help users optimize their current workflow processes. Note that if you are interested in having DNAnexus experts directly access and/or process UK Biobank data, please reach out to [e-mail].

What happens if DNAnexus is unable to help after I have purchased my bundle?

DNAnexus will ensure that your inquiry is resolved satisfactorily and in a timely fashion.

[1] For more information on guidelines for Third Party Processors, please reference the UK Biobank MTA.