Note
Please note: the Research Environment documentation has been moved to Research Environment User Guide. Please visit this space to find instructions for using the environment.

All analysis on the Genomics England dataset will be done within a secure workspace called the Research EnvironmentBecause of the sensitivity of the data within the Genomics England Research Environment, we have provided an environment within which all analysis will be done. This avoids any potential security breaches that might may occur when downloading using data, but does require the environment to be quite somewhat restrictive to enforce those protections. However, by providing a secure environment it allows us to make a far broader set of row-level data available for research; you have access to data that would not otherwise be available to researchers. It also means you such protection. You will always have access to the most up-to-date research dataset and can available to you in the Research Environment and will be able to run your analyses on a the Genomics England high-performance compute cluster for no charge.On these pages you'll find training materials for the Genomics England Research Environment, and helpful information on understanding the data you will have access to. If there is something we've missed, doesn't make sense, or is just plain wrong then please add a comment at the appropriate place and we'll look into it..

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title	The important pointsImportant points for GeCIP members using the Research Environment

The Research Environment is preloaded with the data you are entitled to, but there are some hoops to jump through when you first get access.
Although all of GeCIP see all of the same data, some of it is protected by a Publication Moratorium.
There is no internet access inside the Research Environment; however, some websites are available (called 'whitelisted websites').
If your program requires access to the internet to run, it will not work unless you apply to get the service whitelisted.
You can't copy out of the Research Environment, but you can paste in using the intermediate clipboard. Read instructions for doing so here.
If you want to bring data or information in, or take your results out, you have to go through the Airlock.
There are commandline tools available, we are calling them 'modules', you need to load them up as and when you need them.
If you've got lots of data to analyse, it'll happen far quicker if you submit it to the cluster.
When your initial thoughts and analyses start to coalesce into When you start work on a research project, you need to register it on the Research Registry: see Using the Research Registry.
You cannot install your own tools and applications - you have to submit a request to the Genomics England Service Desk.

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Please note: the Research Environment documentation has been moved to Research Environment User Guide. Please visit this space to find instructions for using the environment.

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