Genomics England’s CloudOS Training Centre

CloudOS is an end-to-end solution for large-scale clinico-genomic analyses using AWS Cloud infrastructure. CloudOS serves a wide range of users, including clinicians, researchers, and bioinformaticians.

Become a CloudOS pioneer with hands-on training courses led by Lifebit’s expert bioinformaticians. Register to join the next virtual training sessions below.

1-Data_Training title images-1
 

Course date: Monday 19th June, 10-11am
Deadline to register: Wednesday 14th June, 5pm

About this course 

This course provides CloudOS users with an understanding of what public data is available on CloudOS, how to bring in data and how to export via Airlock. 

Course Objectives

After completing this course, you should know:
    • The differences between cloud and cluster/local computing
    • How to find or upload all the data you need
    • How to export results through Airlock
Register
2-CB_Training title images (1)-1
 

Course date: Monday 19th June, 11:30am-1pm
Deadline to register: Wednesday 14th June, 5pm

About this course

This course will introduce cohort building using the Cohort Browser in CloudOS, and includes browsing Genomics England clinical and omic datasets, creating phenotypic and genomic queries and using the SQL editor.

Course Objectives

After completing this course, you should know:
    • How to create a phenotypic query using different querying modalities (i.e. standard, table and SQL modes)
    • How to create an omic query with openCGA data
    • How to create a joint phenotypic and genotypic query
    • Exporting cohorts for downstream analysis
Register
3-int_Training title images (2)
 

Course date: Tuesday 20th June, 10am-12pm
Deadline to register: Wednesday 14th June, 5pm

About this course

This course is intended for technical users and will share how to set up and code within a command line interface in CloudOS using Jupyter notebooks or RStudio. Includes programmatic data querying from an interactive session.

Course Objectives

After completing this course, you should know:
    • How to set up the interactive session of your choice, load data, install software, save results and create snapshots for easy access for your next session
    • How to programmatically query data from SQL databases in a Jupyter notebook
Register
4-Batch_Training title images (3)
 

Course date: Wednesday 21st June, 10am-1pm
Deadline to register: Wednesday 14th June, 5pm

About this course

This course will provide a comprehensive overview of running Nextflow with AWS Batch in CloudOS. Follow the journey of linking a repository, setting up configurations, running and monitoring jobs. It is intended for users who run their own or their collaborator’s already built pipelines. Running WDL workflows will also be introduced. As an optional add-on, this course includes how to launch jobs using CloudOS CLI

Course Objectives

After completing this course, you should know:
    • How to bring in your tools into CloudOS and launch jobs using cloud computing resources
    • How to monitor, troubleshoot and rerun jobs
    • How to find outputs and results of your job
    • How to use the CloudOS CLI for programmatic launching of jobs
Register
5-Admin_Training title images (4)
 

Course date: Wednesday 21st June, 3-4pm
Deadline to register: Wednesday 14th June, 5pm

About this course

This course will provide Admin users with the knowledge how to manage the workspace and control cost and data access.

Course Objectives

After completing this course, you should know:
    • How to manage user and data access of your workspace
    • How to monitor cost and compute usage of your workspace
    • How to control compute resources of your workspace

Register