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Overview

The Research Environment has a number of applications on the desktop that will aid you in your analysis of the Genomics England dataset. These applications are accessible via desktop icons or through the Applications icon on the taskbar at the bottom of the screen.

Similarly, the Research Environment also has a number of whitelisted websites that will be accessible once inside the environment. You can request additional desktop applications or for websites to be whitelisted within the Research Environment by contacting the Genomics England Service DeskPlease be aware that we will not install desktop applications that are redundant with existing applications and we will not whitelist websites that may put the security of the Research Environment at risk.

Below, you will see the most up-to-date list of desktop applications and whitelisted websites within the Research Environment. 

Desktop Applications

Inuvika Desktop Applications

Home

Desktop file manager to navigate and access the files and folders that are available to you.

LabKey

A software suite to access, integrate, and analyse the Genomics England clinical dataset.

FirefoxInternet browser for whitelisted website.
LibreOfficeA Microsoft Office-like suite of applications for data manipulation and presentation.
TerminalThe Linux command line interface.

R

A powerful and flexible programming language for statistical computing and graphics.

RStudio

An integrated development environment (IDE) for R.

AtomA source code editor that can be used as an integrated development environment (IDE) for Python.

SciTE

Text editor.

GVim

Text editor.

PDF Viewer

Portable Document Format (PDF) viewer.

IGV Genome Browser

A high-performance visualisation tool for interactive exploration of large, integrated genomic datasets.

GalaxyA scientific workflow, data integration, and data and analysis persistence and publishing platform.
PanelAppA crowdsourcing tool to allow gene panels to shared, viewed and evaluated by the scientific community.

Rocket Chat

Rocket Chat is a chat facility that is available within the Research Environment to help you collaborate and communicate with other users.

File Transfer

An electronic form for you to request data transfer in and out of the Research Environment.

Research Environment Documentation

A link to the Research Environment documentation.

Whitelisted Sites

WebsiteWhitelisted urlsHomepage
ClinVarwww.ncbi.nlm.nih.gov/clinvar/*www.ncbi.nlm.nih.gov/clinvar/
Compbio HPO Browsercompbio.charite.de/hpoweb/*http://compbio.charite.de/hpoweb/
Consensus CDS Projectwww.ncbi.nlm.nih.gov/CCDS/*www.ncbi.nlm.nih.gov/CCDS/
COSMIC    cancer.sanger.ac.uk/wgs/*http://cancer.sanger.ac.uk/cosmic/    
cancer.sanger.ac.uk/_asset/*
cancer.sanger.ac.uk/cancergenome/*
cancer.sanger.ac.uk/javascripts/*
cancer.sanger.ac.uk/cosmic/*
DBsnpwww.ncbi.nlm.nih.gov/snp/*www.ncbi.nlm.nih.gov/snp/
DECIPHERdecipher.sanger.ac.uk/*http://decipher.sanger.ac.uk/
EMBL EBI  www.ebi.ac.uk/*www.ebi.ac.uk/  
www.ebi.ac.uk/interpro/*
www.ebi.ac.uk/wen_guidelines/*
Ensembl Human     ensembl.org/*http://ensembl.org/Homo_sapiens/     
ensembl.org/Homo_sapiens/Gene/*
ensembl.org/Homo_sapiens/*
static.ensembl.org/*
static.ensembl.org/minified/*
www.ensembl.org/id/*
exAC Browser betahttp://exac.broadinstitute.org http://exac.broadinstitute.org
Genetics Home Reference Gene Browser  ghr.nlm.nih.gov/*http://ghr.nlm.nih.gov/gene  

ghr.nlm.nih.gov/gene/*

ghr.nlm.nih.gov/images/*
Genomics Plc Misc..incoming01.genomicsplc.com
gnomAD Browser betahttp://gnomad.broadinstitute.orghttp://gnomad.broadinistitute.org
Google Misc.www.gstatic.com/charts/* 
HUGO Gene Nomenclature Committee     www.genenames.org/*http://www.genenames.org/     
www.genenames.org/data/*
www.genenames.org/sites/*
www.genenames.org/css/*
www.genenames.org/js/*
rest.genenames.org/*
Human Phenotype Ontology  www.human-phenotype-ontology.org/hpoweb/*http://compbio.charite.de/hpoweb/showterm  
www.human-phenotype-ontology.org/*
human-phenotype-ontology.github.io/*
IGV Browser igv.broadinstitute.org/* 
igvdata.broadinstitute.org/* 
Local LabKeylabkey.embassy.local/* 
NCBI Genewww.ncbi.nlm.nih.gov/gene*www.ncbi.nlm.nih.gov/gene
NCBI Nucleotidewww.ncbi.nlm.nih.gov/nuccore/*www.ncbi.nlm.nih.gov/nuccore/
NCBI     www.ncbi.nlm.nih.gov/portal*www.ncbi.nlm.nih.gov/portal     
www.nlm.nih.gov/core/*
.nlm.nih.gov/*
www.ncbi.nlm.nih.gov/gtr/tests/*
www.ncbi.nlm.nih.gov/core/*
www.ncbi.nlm.nih.gov/project/*
OMIM    omim.org/*http://omim.org    
omim.org/entry/*
omim.org/static/*
omim.org/search/*
api.europe.omim.org/api/*
Xfam (Pfam, Rfam, Dfam, Treefam, iPfam, Antifam)  pfam.sanger.ac.uk/family/*http://xfam.org  
pfam.sanger.ac.uk/*
xfam.org/*
Panelapphttps://panelapp.genomicsengland.co.uk/https://panelapp.genomicsengland.co.uk/
Pubmed  static.pubmed.gov/*www.ncbi.nlm.nih.gov/pubmed/  
www.ncbi.nlm.nih.gov/pubmed/*
dev-static.pubmed.gov/*
SMART (a Simple Modular Architecture Research Tool)smart.embl-heidelberg.de/*http://smart.embl-heidelberg.de
The Human Gene Mutation Database www.hgmd.cf.ac.uk/ac/*www.hgmd.cf.ac.uk 
www.hgmd.cf.ac.uk/*
The Sequence Ontology     www.sequenceontology.org/miso/current_release/term/*www.sequenceontology.org/     
www.sequenceontology.org/css/*
www.sequenceontology.org/js/*
www.sequenceontology.org/img/*
www.sequenceontology.org/browser/*
www.sequenceontology.org/*
UCSC Genome Browserwww.genome.ucsc.edu/* 
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