Research Environment Training Session: Introduction to the Research Environment

The Genomics England Research Environment provides access to Genomics England data, including genomes, variants and phenotypic data from rare disease and cancer patients from the 100,000 Genomes project and NHS Genomic Medicine Service. Due to the sensitive nature of the data, all analyses on these data must be carried out within the Research Environment and only non-identifiable aggregate data can be exported. To enable this, a variety of tools are available within the Research Environment to segment and analyse the data.

This training session is aimed at newcomers to the Genomics England Research Environment and will introduce what is in the Research Environment, both in terms of data and tools. The basic functionality of the tools will be covered, along with how you can export data and the restrictions on doing this.

The demos in this training session be pre-recorded videos with sensitive data censored out, so anyone can join this session. We recommend joining this session if you are thinking about registering to access the RE, if you have started the application process for accessing the RE or have recently gotten access to the RE.

Timetable

13.30 Welcome and introduction
13.35 Sources and type of data in the Research Environment
13.50 Tools in the Research Environment
14.10 Programmatic access to Genomics England data
14.20 Running command line tools and pipelines using our HPC cluster
14.30 The Airlock, restricted import and export of data
14.45 Questions

Learning objectives

After this training you will know:

• what data can be accessed in the Genomics England Research Environment
• the functions of the Participant Explorer, LabKey, IVA and IGV
• what APIs are available for exploring the data
• the kinds of jobs you can run on the HPC cluster and when you might use it
• how to import and export data from the Genomics England Research Environment using Airlock
• how to use the documentation to learn more

Target audience

This training is aimed at researchers who:

• Are new to working in the Genomics England RE
• Would like to get an overview of what is possible and available in the RE