> For the complete documentation index, see [llms.txt](https://dnanexus.gitbook.io/uk-biobank-rap/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/quickstart.md). # Quickstart Get started using the Research Analysis Platform. ## 1. Create a UKB-RAP account [Follow these instructions](/uk-biobank-rap/getting-started/quickstart/creating-an-account.md) to create an account on the platform. You will first create a UK Biobank Access Management System account, then create a Research Analysis Platform account and finally you will connect your two accounts. ## **2. Create a project and dispense data** On the UKB-RAP, you'll be able to work with UK Biobank data from data-fields associated with your approved access application. To access this data, [start by creating a project and having the data dispensed to this project](/uk-biobank-rap/getting-started/quickstart/creating-a-project.md). {% hint style="info" %} Due to the large size of the UK Biobank data, data dispensal can take over an hour, or even longer, in some cases. You can monitor the process by going back to the project list, where you can see the project status including what percentage of the data has been populated. {% endhint %} ### **Collaboration** To collaborate with colleagues who are named on the same approved access application, add them as members to the project associated with this application. ## **3. Getting started using UKB-RAP** Get started exploring the UKB-RAP using your initial credit of £40. A guide detailing all of the key functionality and setup of UKB-RAP can be found [here](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/ukb-rap). You can also [watch our overview series of short tutorial videos](https://www.youtube.com/watch?v=53lFjPiWAyQ\&list=PLRkZ0Fz-n3Z71Pt9h8-0AEweopm0SVlTr) to gain an understanding of the platform or watch the [overview webinar](https://youtu.be/uT_jD1Ey3Fk?si=XZRCGzGb2mzPt5_m) going into more details. ### Overview #### *An introduction to how the UKB-RAP platform is organized* {% embed url="" %} ### Data A [guide on how the data is organized on the platform](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/working-with-ukb-data). In general there are 2 data types available on the platform: Phenotype data and Bulk data. Phenotype data include things like patient diagnosis and gender. #### *How data is structured on the UKB-RAP* {% embed url="" %} An example of phenotype data include fields ids like 21022 which captures participant age. This data can be found in the dataset of the root directory of your project. To learn more about how to extract this type of data see the guide [here](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-phenotypic-data-as-a-file). #### *Ways to extract phenotype data* {% embed url="" %} Bulk data includes quantitative measurements like VCF files. An example of bulk data include filed id 22418 which is associated with genotype array calls. This data can be found in the /Bulk folder within your project. A guide for working with bulk data can be found [here](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/working-with-bulk-data-files). #### *How to work with bulk data on UKB-RAP* {% embed url="" %} ### Learning path: Coming from a local computer | Resource | Type | Why its useful | | ----------------------------------------------------------------------------------------------------------------------------- | ------------ | --------------------------------------------------------------------- | | [Cloud computing for scientists](https://www.youtube.com/watch?v=9I78As5uRfw) | Webinar | Introduction to cloud computing concepts | | [Bash for bioinformatics: Cloud computing](https://laderast.github.io/bash_for_bioinformatics/03-cloud-computing-basics.html) | Book chapter | Learn essential cloud computing concepts (storage, projects) | | [UKB overview](https://www.youtube.com/watch?v=uT_jD1Ey3Fk) | Webinar | Understand the basic UKB RAP project structure and work with it | | [Introduction to cohort browser](https://www.youtube.com/watch?v=foB7y2ZJHF4) | Tutorial | Learn how to access UKB data through Cohort Browser and build cohorts | ### Learning path: Coming from HPC | Resource | Type | Why its useful | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------ | ---------------------------------------------------------------------------------------------- | | [Cloud computing for HPC users](https://www.youtube.com/watch?v=lGxna-ZVYUg) | Webinar | Translate HPC skills to the UKB RAP | | [Bash for bioinformatics](https://laderast.github.io/bash_for_bioinformatics/) | Online book | Contains recipes for automating processes on UKB RAP using bash and the CLI | | [Running apps](https://www.youtube.com/watch?v=U8QZAGwnUm0) | Webinar | Details how to run common bioinformatics apps (Plink, samtools) using the Swiss Army Knife app | | [Building apps](https://www.youtube.com/watch?v=A_iki_50Ig0) | Webinar | Run other executables (such as GATK) by building a UKB-RAP compatible version | | [Using docker](https://www.youtube.com/watch?v=aOP_iSZpR6g) | Webinar | Learn how to use custom environments | | [GWAS guide](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/gwas-ex) | Online guide | Learn to use the already built Regenie app on the platform for GWAS | | [End to end target discovery](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/genomic-target-discovery-for-ischaemic-heart-disease-using-gwas-ld-clumping-and-phewas) | Webinar | Going through the genomic target discovery use case on UKB-RAP | ## 4. Billing and Costs Each account has an initial credit of £40 toward usage charges. Before depleting this credit, [follow these instructions to set up billing for the account](/uk-biobank-rap/administrator/billing-and-costs.md), in order to continue using the platform. If you have grants credits [follow the instructions in the FAQs](https://dnanexus.gitbook.io/uk-biobank-rap/master/frequently-asked-questions/general-faqs#aws-credits-program) for setting up a *grant org instead of a billing account* ## Getting Help ### **UKB Community Site** The [UK Biobank Community site](https://community.ukbiobank.ac.uk) gives platform users a forum to share what you've learned and done on the platform, and learn from one another. ### Support See the table below for who to contact for help with accessing and using the Platform. For additional support options, visit the [Support FAQ page](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/support-model-and-service-packages-faq)
Types of questionsWho to contact

(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
Email ukbiobank-support@dnanexus.com

Alternatively, in the menu at the top of the UI, click Help, then select Contact Support from the dropdown menu. A contact form will open in a modal window. Fill out the form and click Send.

After you submit a request, you'll receive an automated reply, confirming that your request has been logged in the Research Analysis Platform Support tracking system
Billing issuesEmail billing@dnanexus.com

Issues associated with UK Biobank data or AMS. 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
Email access@ukbiobank.ac.uk

(Service package) 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
Learn more about if a service package is right for you