Training

EMBL-EBI Training

We train scientists at all levels to get the most out of publicly available biological data.

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Training events

November 2017

27
Ensembl REST API course – 27th-28th November 2017
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
27th 28th Nov

Work with the Ensembl developers to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments.

First come, first served

28
Ensembl Browser Workshop, DKFZ, 28th November 2017
Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) - Deutsches Krebsforschungszentrum (DKFZ)Im Neuenheimer Feld 280, 69120,  Heidelberg, Germany
28th Nov

Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart.

First come, first served

29
Ensembl Bite-Sized November 2017
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
29th Nov

Work with the Ensembl team to get to grips with fungal, protist and bacterial species in the Ensembl Genomes browser and data.

First come, first served

30
Ensembl Browser workshop, DKFZ, 30th November 2017
Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) - Deutsches Krebsforschungszentrum (DKFZ)Im Neuenheimer Feld 280, 69120,  Heidelberg, Germany
30th Nov

Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart.

First come, first served

December 2017

4
EMBL-EBI resources and tools for genomics and proteomics
National Veterinary Research Institute - Państwowy Instytut Weterynaryjny, Państwowy Instytut Badawczy, Aleja Partyzantów 57, 24-100,  Puławy, Poland
4th 8th Dec

In this course participants will explore EMBL-EBI data and resources for genomes, functional genomics, sequences, protein structure and function, and protein-ligand interactions.

By invitation

13
Ensembl release 91 webinar
13th Dec

Ensembl is a genome browser, offering gene, variation, comparative genomics and regulation data integrated together onto vertebrate genomes. Ensembl is updated on a regular basis, integrating new data and interfaces. Release 91 is Ensembl's biggest yet, featuring 12 new primate genomes, as well as updates to 6 existing genomes in Ensembl. What does this mean for you? Come to our release webinar to learn more about Ensembl and what's new.

First come, first served

February 2018

6
EMBL-EBI workshop: The European Nucleotide Sequence Archive
University of Cambridge - Downing Site, Cambridge,  CB2 3AR, United Kingdom
6th Feb

The European Nucleotide Sequence Archive (ENA) is a global database for storing experimental nucleotide data and also interpreted data (alignment files, variant calling, analysis results).

First come, first served

15
EMBL-EBI workshop: European Variation Archive
University of Cambridge - Downing Site, Cambridge,  CB2 3AR, United Kingdom
15th Feb

This interactive module offers participants hands-on experience in the use of the European Variation Archive.

First come, first served

15
EMBL-EBI Workshop: Ensembl VEP
University of Cambridge - Downing Site, Cambridge,  CB2 3AR, United Kingdom
15th Feb

This interactive module offers participants hands-on experience in the use of the Ensembl VEP to annotate genetic variants with the effects they have on Ensembl genes.

First come, first served

20
Introduction to Multiomics Data Integration
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
20th 23rd Feb

This course will provide participants with biological examples of data integration, and the challenges that researchers face. The course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation.

Open application with selection

April 2018

9
Introduction to Next Generation Sequencing
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
9th 12th Apr

This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data.

Open application with selection

16
Advanced RNA-Seq Analysis
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
16th 20th Apr

The aim of this course is to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches.

Open application with selection

June 2018

4
Bioinformatics Resources for Immunologists
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
4th 8th Jun

This course will introduce and explore a number of key bioinformatics tools and resources that can be applied to immunological research.

Open application with selection

18
Cancer Genomics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
18th 21st Jun

This course will focus on the analysis of data from genomic studies of Cancer.

Open application with selection

July 2018

10
Exploring Human Genetic Variation
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
10th 12th Jul

A short workshop to introduce you to data resources and tools developed by EMBL-EBI and the Sanger Institute, that can help you better understand human genetic variation.

First come, first served

16
Metagenomics Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
16th 20th Jul

This course is aimed at life scientists who are working in the field of metagenomics, in the early stages of their data analysis, and who already have some prior experience in using bioinformatics in their research.

Open application with selection

October 2018

2
Introduction to Next Generation Sequencing
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
2nd 5th Oct

This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data.

Open application with selection

22
Analysis of High Throughput Sequencing Data
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
22nd 26th Oct

The aim of this course is to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches.

Open application with selection

November 2018

27
Exploring Biological Sequences
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
27th 29th Nov

This course will introduce you to approaches used for finding, analysing and using biological sequences.

First come, first served

Online courses

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ArrayExpress: why and how to submit your data

Author(s): Melissa Burke

Join Melissa Burke, a former curator with ArrayExpress, for a webinar on why and how to submit your functional genomics data to ArrayExpress using Annotare, our online submissions tool. ArrayExpress is a database of functional genomics experiments...

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BioSamples Database RDF: webinar

Author(s): Marco Brandizi

This webinar is presented by Marco Brandizi and covers the BioSamples database resource description framework (RDF). This video is best viewed using Google Chrome and in full screen mode.

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BioSamples: Quick tour

Author(s): Luca Cherubin

This quick tour provides a brief introduction to the EBI's BioSamples data resource. Undergraduate-level understanding of biology would be an advantage.

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DGVa: Quick tour

Author(s): Lisa Skipper

This quick tour provides a brief introduction to the DGVa, the EBI's Database of Genomic Variants archive.

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EBI Metagenomics portal: Quick tour

Author(s): Hubert Denise

This quick tour provides a brief introduction to EBI Metagenomics - a free resource for archiving, analysing, visualising, discovering and comparing metagenomic and metatranscriptomic datasets. If you want to submit your metagenomics data to EBI...

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EBI Metagenomics portal: Submitting metagenomics data to the European Nucleotide Archive

Author(s): Hubert Denise

This tutorial provides you with a step-by-step guide for submitting metagenomics data to the European Nucleotide Archive (ENA) in order for it to be analysed by the EBI Metagenomics resource.

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EBI Metagenomics: analysing and exploring metagenomics data

Author(s): Alex Mitchell

EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as...

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EBI: Next Generation Sequencing Practical Course

Author(s): Emily Perry

Here you will find a collection of video lectures from the 'Hands on training in Next-Generation Sequencing' course that took place at EMBL-EBI on 12-14 March 2012, available for you to watch in your own time. The workshop provides an introduction...

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EGA: Quick tour

Author(s): Gary Saunders

This Quick tour provides a brief introduction to the European Genome-phenome archive (EGA).

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EMBL-EBI, programmatically: take a REST from manual searches

Author(s): David Armstrong, Melissa Burke, Andrew Cowley, Anna Foix, Joon Lee, Maria Levchenko, Matthew Laird, Michal Nowotka, Klemens Pichler

From BLAST searches to literature services, gene annotation and information on protein structure and function, large amounts of biological data can be accessed online with the click of a button. When it comes to repeated tasks with large volumes of...

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Ensembl browser webinar series

Author(s): Emily Perry, Ben Moore, Helen Sparrow, Denise Carvalho-Silva, Victoria Newman

Between the 6th April and 18th May 2017, we will be holding a series of live Ensembl webinars which come together to provide a complete browser course. This course includes an introduction to Ensembl, what kind of data Ensembl has, and how to browse...

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Ensembl Genomes (non-chordates): Quick tour

Author(s): Paul Kersey

This quick tour provides a brief introduction to Ensembl Genomes , the non-chordate genome browser.

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Ensembl tools: webinar

Author(s): Emily Perry

Taught by Emily from the Ensembl Outreach team, this webinar will show you what tools are available in Ensembl and how you can use them in your work, taking you through the processes step-by-step. We'll look at Data Slicer, Assembly Converter, File...

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Ensembl Variant Effect Predictor (VEP): webinar

Author(s): Ben Moore

Want easy analysis of your own variant calls? The Ensembl Variant Effect Predictor (VEP) allows you to annotate variants with the genes and regulatory features they hit and what effect they have on them. It can also tell you if your variant is known...

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Ensembl: Browsing genomes

Author(s): Emily Perry, Giulietta M. Spudich, Ben Moore, Helen Sparrow

This course focuses on genomes on the Ensembl website at www.ensembl.org. It provides a quick beginner's guide to the overall structure of the Ensembl genome browser.

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Ensembl: Filmed API workshop

Author(s): Emily Perry

Ensembl runs API workshops worldwide, and for the first time we make one available online. Here you will find a collection of video lectures from the 'Ensembl API workshop' that took place at EMBL-EBI 22nd-24th May 2013, using Ensembl version 71...

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Ensembl: Filmed browser workshop

Author(s): Emily Perry

UPDATE: The new browser webinar series is here. This new course consisted of live webinars over 7 weeks, which were recorded and the videos posted online, along with exercises to let you practice using Ensembl. The new course has replaced this one...

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Ensembl: Genomic features that regulate genes

Author(s): Emily Perry

This webinar was held on the 6th July 2016 and takes you through the Ensembl regulatory build, which is used to predict the location of promoters, enhancers and other regulatory features in the human and mouse genomes, using experimental data from...

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Ensembl: Quick tour

Author(s): Emily Perry

This course provides a very short introduction to the Ensembl website for browsing chordate genomes. This is a quick overview to the browser, designed to give you an idea of what is possible, and will not give you a full tutorial on how to do...

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European Nucleotide Archive (ENA): An introduction: webinar

Author(s): Marc Rossello

In this webinar, Marc Rossello gives an introduction the European Nucleotide Archive (ENA). This webinar took place on 8 April 2015. NB: This video works best using Google Chrome and when viewed in full screen. Find out about upcoming webinars .

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European Nucleotide Archive: Quick tour

Author(s): Clara Amid

This quick tour provides a brief introduction to the European Nucleotide Archive, the EBI's repository for nucleotide sequence data.

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European Nucleotide Archive: Using the primary nucleotide sequence resource

Author(s): Clara Amid

This course will show you how to search and retrieve nucleotide sequence data from the European Nucleotide Archive (ENA). The ENA provides sequence assembly details and biological annotation, and uses versioning to track sequence changes.

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European Variation Archive at EMBL-EBI: webinar

Author(s): Gary Saunders

There are a number of open-access variation datasets available for the genomics community. These are found on numerous FTP servers, various literature resources and probably one or two thousand hard-drives that are floating across the globe. We can...

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European Variation Archive: Quick tour

Author(s): Gary Saunders

This quick tour provides a brief introduction to the European Variation Archive - an open-access repository for genetic variation datasets that are submitted directly from the community, or are loaded to the resource by internal staff members.

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Genomics resources: webinar

Author(s): Laura Emery

This 25 minute webinar from Dr Laura Emery provides you with an introduction to EMBL-EBI and the data resources available (recorded on 25th February 2015). The webinar focuses in particular on three core resources - Ensembl, ENA and the Metagenomics...

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Genomics: An introduction to EMBL-EBI resources

Author(s): Giulietta M. Spudich

This course will introduce the field of genomics and provide an overview of the different resources at the EBI which are related to this field. The course is aimed at graduates in the life sciences or related subjects, with an interest in using...

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GWAS Catalog: Exploring SNP-trait associations

Author(s): Laura Emery, Jackie MacArthur

The NHGRI-EBI GWAS Catalog is a publically available resource of Genome Wide Association Studies (GWAS) and their results. This course provides an introduction of how to browse SNP-trait associations using the NHGRI-EBI GWAS Catalog.

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Human genetic variation (I): an introduction

Author(s): David Armstrong, Melissa Burke, Laura Emery, Jackie MacArthur, Andrew Nightingale, Emily Perry, Sangya Pundir, Gary Saunders

Genetic variation is fundamental to the evolution of all species and is what makes us individuals. Our genes have a large influence on our lives. They affect what we look like, our personalities and preferences and our susceptibility to disease. By...

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Human genetic variation (II): exploring publicly available data

Author(s): David Armstrong, Melissa Burke, Laura Emery, Jackie MacArthur, Andrew Nightingale, Emily Perry, Sangya Pundir, Gary Saunders

Genetic variation is fundamental to the evolution of all species and is what makes us individuals. Our genes have a large influence on our lives. They affect what we look like, our personalities and preferences and our susceptibility to disease. By...

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Introduction to 1000 Genomes Project and IGSR data resources

The 1000 Genomes Project set out to catalogue common human genetic variation, publishing a set of variations based on sequencing of 2504 individuals from 26 populations. Variant calls, sequence data, high-density genotyping chip calls and cell lines...

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Large Scale Gene Function Discovery to Support Human Health: The International Mouse Phenotyping Consortium (IMPC)

Author(s): Terry Meehan

The International Mouse Phenotyping Consortium (IMPC) is a G7- recognised global research infrastructure that is coordinating the global production of a knockout mouse gene for every protein coding gene. The mice are characterised in a standardised...

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Locus Reference Genomic (LRG) resource: webinar

Author(s): Joannella Morales

This webinar provides you with an overview and demo of the Locus Reference Genomic (LRG) resource - a manually curated reference resource for the reporting of clinically relevant variants. NB: This video works best using Google Chrome and when...

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Phylogenetics: An introduction

Author(s): Laura Emery

This course provides a basic introduction to the field of phylogenetics, with an emphasis on how to read and interpret phylogenetic trees. An undergraduate-level understanding of biology would be an advantage.

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Rfam: Quick tour

Author(s): Sarah Burge

This quick tour provides a brief introduction to Rfam, the EBI's database of RNA families.

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RNAcentral: Exploring non-coding RNA sequences

Author(s): Anton Petrov

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from multiple specialised resources and provides a single entry point for accessing ncRNA sequences of all types from all organisms. This course provides a brief...

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RNAcentral: webinar

Author(s): Anton Petrov

This webinar provides you with an overview and demo of RNAcentral - an international database of non-coding RNA (ncRNA) sequences that aggregates data from multiple specialised ncRNA resources. This webinar took place on 28th October 2015. NB: This...

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The NHGRI-EBI GWAS Catalog, a curated resource of SNP-trait associations

Author(s): Joannella Morales

The GWAS Catalog is a manually curated summary resource of human genotype-phenotype associations from GWAS publications. The Catalog contains a vast amount of data, encompassing over 38,000 SNP-trait associations from more than 2,800 publications as...

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Using sequence similarity searching tools at EMBL-EBI: webinar

Author(s): Andrew Cowley

This webinar focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, including tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages...

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