Full day hands-on training, November 2024¶
Description¶
This course will provide you with the knowledge and skills to work with the Genomics England Research Environment. Covering the data available and tools you can use to access and analyse it, this course will take you through the processes for cohort building for rare disease and cancer, working on the HPC (High Performance Cluster), using containers, and exporting your results from the Research Environment.
As part of this course, you will hear lectures on our data, watch demonstrations using our tools and take part in hands-on practicals and exercises. We invite you to bring your own problems and receive help from our expert bioinformaticians to achieve your research goals.
This course will last one day, held at our offices at One Canada Square in London, however, if you cannot attend in person, it will also be possible to join the sessions virtually, please indicate how you would like to attend when you register.
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. Please register with the email address you used to register for Research Environment access and include your username in your registration.
Course content¶
This course will cover:
- The genome data available in the Research Environment and how to find it for your participants of interest
- The clinical data collected as part of the 100,000 Genomes Project and NHS Genomic Medicine Service and how this can be accessed in the Research Environment
- Using tools, such as Participant Explorer, LabKey and IVA, in the Research Environment
- Building cohorts of participants based on cancer, rare disease, or common disease phenotypes, or on genotypes
- Working on the Genomics England High Performance Cluster, including accessing existing software and bringing in software with containers
- Data security in the Research Environment, exporting and publishing your results and using the Airlock export tool
Learning objectives¶
At the end of this training, you should be able to:
- Work within the data security framework and guidelines of the Research Environment
- Know what applications are available and what use-cases they can support
- Understand the types of clinical and genomic data we have for rare disease and cancer for both the 100,000 Genomes Project and NHS Genomic Medicine Service
- Plan a project end-to-end, including exporting the data Find help and documentation
Target audience¶
This course is aimed at researchers working with the Genomics England Research Environment who can program in python and/or R, wishing to become more familiar with Genomics England tools and data, to further their research goals.
Date and time¶
20th November 2024, 9am-5pm.
Materials¶
You can access the redacted slides and video below. Workbooks can be found in the RE. All sensitive data has been censored.
Slides¶
Video¶
Workbooks¶
gel_data_resources/example_scripts/workshop_scripts/all_day_training_Nov_2024
Here you will find:
- A worksheet with instructions for demos and tasks
- Jupyter and R notebooks for API access
- Example files