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Welcome!

Welcome to the Genomics England Research Environment User Guide.

In this documentation, we will provide you with the knowledge and training materials that you will need to navigate and analyse the wealth of data available to you.

We suggest that you go through this documentation step-by-step so that you become familiar with the data and the analysis tools within the Research Environment. 

Table of Contents

What is the Research Environment? 

All analysis on the Genomics England dataset will be done within a secure workspace called the Research Environment. This avoids any potential security breaches that may occur when using data, but does require the environment to be somewhat restrictive to enforce such protection. You will always have access to the most up-to-date research dataset available to you in the Research Environemnt and will be able to run your analyses on the Genomics England high-performance compute cluster. 


Important Points

Tip
titleFollow these points to help you on your research journey!
  1. The Research Environment contains the most up-to-date research dataset that you are entitled to.
  2. The latest genomic and clinical data are released into the Research Environment on a three monthly cycle .
  3. The Research Environment is a linux virtual desktop environment hosted by Inuvika.
  4. There is no inbound or outbound internet access internet access inside the Research Environment; though some websites are whitelisted.
  5. You can't copy out of the Research Environment, but you can paste in using the clipboard application.
  6. If you want to bring data in or take your results out of the Research Environment, you have to use the File Transfer application.
  7. You will have access to the Genomics England high-performance compute cluster free of charge.
  8. Command-line tools are available for you to perform analysis and new software can be installed on request.
  9. You will be able install your own R and Bioconductor packages.
  10. You will have a working space of several petabytes in size within your shared working folder.


Research Environment Useful Links

Link

URL

Research Environmenthttps://re.extge.co.uk/ovd/
Staging Environmenthttp://re-staging.extge.co.uk/
File Transfer Applicationhttps://airlock-staging.extge.co.uk/
Genomics England Service Deskhttp://bit.ly/ge-servicedesk



Data in the Research Environment

Below is a summary of the latest Main Programme data release for October February 2018  (Version 5.16). 


Getting Help


Tip

If you should encounter a problem or need assistance while using the Research Environment, please feel free to submit a ticket to the Genomics England Service Desk and we will get back to you.