Introduction to the Research Environment, March 2022¶
There is a more up-to-date version of this tutorial from January 2023.
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. 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.
You are only allowed to attend this session if you are eligible for data access. This means that you are a Research Network or Discovery Forum member that has met the necessary verification checks and passed our Information Governance training course. If you do not meet this criteria by 14th March 2022, you will be unregistered for this session.
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.
14.00 Welcome and introduction
14.05 Sources and type of data in the Research Environment
14.20 Tools in the Research Environment
14.40 Programmatic access to Genomics England data
14.50 Running command line tools and pipelines using our HPC cluster
15.00 The Airlock, restricted import and export of data
15.10 Getting help
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
This training is aimed at researchers:
- new to the Genomics England Research Environment
Mar 15, 2022 02:00 PM in London
You can access the redacted slides and video below. All sensitive data has been censored.