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
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
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.
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
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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