General

Learn about how to access UKB data and get started working on the UKB-RAP.

Introduction to UKB data & UKB-RAP

About data & how to apply for access

Learn about the mission of the UK Biobank, the new 500k whole exome sequencing data release and how to become an approved researcher.

Topics included:

  • Who is the UK Biobank?

  • What data is available to researchers?

  • Recently released data: 500K WGS

  • Other types of data: imaging, COVID, healthcare records

  • Data roadmap

  • The process for applying to become an approved researcher and submitting a research proposal

  • Tips on speeding up your application and approvals

  • Accessing the data on the Research Analysis platform

Video chapters

  • 00:00 Introduction

  • 01:25 Overview of UK Biobank and the Data

  • 15:03 300k Whole Exome Data: Overview and Best Practices

  • 25:29 Access and How to Apply to Use the Resource

  • 38:35 Getting on to RAP

General platform functionality

UKB-RAP overview

Video chapters

  • 00:00 Introduction

  • 01:16 Getting Started on UKB RAP

  • 03:48 Data available only on UKB-RAP

  • 04:10 How to Join and Start Analysis on UKB-RAP

  • 06:22 RAP Projects

  • 08:03 Troubleshooting Data Dispensal

  • 08:42 How to update data on UKB-RAP

  • 09:27 Managing project access for users

  • 10:10 File operations available

  • 10:45 Dataset vs Bulk Data

  • 11:30 How to add data to your project

  • 12:44 Bulk Files

  • 16:18 Structure of UKB Data on UKB-RAP

  • 18:54 Datasets & Cohorts

  • 19:41 Introduction to the Cohort Browser

  • 20:34 Cohort Browser components

  • 21:07 Exploring data on the Cohort Browser

  • 22:56 Creating cohorts with filters on the Cohort Browser

  • 23:50 Creating cohorts with comparisons on the Cohort Browser

  • 25:30 Data preview tab for cohort data

  • 25:44 Extracting cohort data

  • 25:50 View Genomics cohort data

  • 27:51 Working with and extracting phenotype data

  • 28:28 Ways to extract phenotype data on UKB-RAP

  • 29:45 Table Exporter app info for extracting phenotype data

  • 29:59 Demo of using dx extract_dataset with R for extracting phenotype data

  • 34:15 Demo of using dx extract_dataset with JupyterLab for extracting phenotype data

  • 34:45 Decode categorical values results

  • 35:30 Intro to using Apps via UI

  • 37:47 Example of using an app: swiss-army-knife (SAK)

  • 40:53 Options for working with UKB data on UKB-RAP

  • 41:34 Local analysis vs Cloud analysis

  • 43:34 Where Next?

How to run tools available on UKB-RAP

DNAnexus experts give you an introduction to the applet and workflow development process by building a simple project that works on Bulk files on RAP.

The webinar covers:

  • An introduction to the Applet and Workflow Development Process

  • How to build & run your own Applet using CLI

  • How to build & run using Command Line Interface and Platform UI

  • Customizing the software environment of your applet -Building applets and deploying them in a RAP project

Video chapters

  • 00:00 Introductions to Apps/Applets & Workflows

  • 06:13 Running App/Applet Using UI

  • 12:34 Monitoring Jobs Using UI

  • 18:43 Running App/Applet Using CLI

  • 27:30 Batch Execution and Monitoring

  • 42:04 Running and Monitoring Workflows

  • 50:18 Q&A

How to create an app/workflow & bring your own tools

DNAnexus experts give you an introduction to the applet and workflow development process by building a simple project that works on Bulk files on RAP.

The webinar covers:

  • An introduction to the Applet and Workflow Development Process

  • How to build & run your own Applet using CLI

  • How to build & run using Command Line Interface and Platform UI

  • Customizing the software environment of your applet

  • Building applets and deploying them in a RAP project

Video chapters

  • 00:00 Introduction to Applets and Workflows

  • 04:41 Applets from the User Perspective

  • 06:00 Applet Development Concepts

  • 09:27 Basic Applet Building Workflow

  • 12:57 Let's Build an Applet

  • 21:25 Part B: Executable Scripts in your App

  • 27:07 Part C: Building the Applet

  • 42:40 Building Our First DNAnexus Workflow (UI and CLI)

Accelerating time to discovery with WES

Mark Effingham, Deputy CEO at UK Biobank, Tim Harkins, Product Manager, Genomics at NVIDIA, Will Salerno, Senior Director of Genome & Sequencing Informatics at Regeneron Genetics Center, Ben Busby, Director, Solutions Science at DNAnexus, and Harry Clifford, Senior Product Architect, Genomics at NVIDIA review the exact analysis pipeline used to quickly generate the 450,000 reference data set, and are offering UK Biobank researchers a free 6 month trial license to NVIDIA Clara Parabricks to help them replicate this accelerated workflow. The webinar provides an overview of this analysis pipeline to enable all UK Biobank researchers the opportunity to fully harmonize their own data, at any scale, with the UK Biobank exome data.

Video chapters

  • 00:00 Introduction

  • 03:10 UK Biobank Overview & Mission

  • 17:56 UK Biobank Exome Informatics

  • 35:42 Accelerated Framework: NVIDIA Clara Parabricks

  • 42:16 How to Re-Run RGC Pipeline on RAP

  • 53:54 Q&A

Slides are available here

Moving to a cloud platform

Starting cloud analysis

This webinar covers:

  • Identifying similarities & differences between HPC and Cloud

  • Running any script (BASH, R, Python) on RAP using equivalent commands via the command line interface

  • Running single and distributed jobs via the Platform UI

Video chapters

  • 00:00 Learning Objectives

  • 01:10 Options for Working with UK Biobank Data on RAP

  • 02:50 Basic Terminology & Concepts

  • 06:42 Mental Models of Computing

  • 14:34 Learning Challenges of Cloud Computing

  • 20:55 Running Apps on Files

  • 33:08 Instance Types & Use Cases

Cloud computing for HPC users

Coming from high performance computing? Learn equivalent cloud-based methods for running bioinformatics jobs quickly on the Research Analysis Platform.

New to Cloud Computing? This introductory session covers basic Cloud Computing concepts that will set you up for success on the Research Analysis Platform. Topics discuss include basic cloud computing concepts, selecting instance types, and the basics of running apps on files in your RAP project.

Video chapters

  • 00:00 Introduction

  • 01:47 Refresh Data in your Project

  • 02:14 HPC vs UKB RAP

  • 04:46 Mental Models of Computing

  • 11:20 Running Apps in the Cloud

  • 20:15 Single Job: Use dx run on Command Line Directly

  • 29:26 Single Job: Use dx run in a Script

  • 32:24 Batch Processing: Use dx run in a Shell Script on Multiple Files

  • 42:37 Batch Processing: Working with Files Using dxFUSE

  • 48:05 Useful Links

  • 49:46 Q&A

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