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

January 2019

7
Ensembl Browser Workshop, University of Rwanda, 7th January 2019
University of Rwanda - University of Rwanda, KN 7 Ave, Kigali, Rwanda
7th Jan

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

8
Ensembl Browser Workshop, University of Rwanda, 8th January 2019
University of Rwanda - University of Rwanda, KN 7 Ave, Kigali, Rwanda
8th Jan

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

10
Ensembl Browser Workshop, INES Ruhengeri, 10th January 2019
INES Ruhengeri - INES Ruhengeri, 155 Ruhengeri, Ruhengeri, Rwanda
10th Jan

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

13
PAG 2019 Workshop: Browsing Genes and Genomes with Ensembl and Ensembl Genomes
Town and Country Hotel - 500 Hotel Circle North, San Diego, , CA,  92108, United States
13th Jan

'Browsing Genes and Genomes with Ensembl and Ensembl Genomes' will include an introduction to the Ensembl browsers, demonstrate key views in browsing genomes, and show you how to use tools for accessing genomic data and analysing your own, BioMart and the VEP.

First come, first served

14
PAG 2019 Workshop: Exploring your data in Ensembl (Digital tools and resources)
Town and Country Hotel - 500 Hotel Circle North, San Diego, , CA,  92108, United States
14th Jan

The 'Exploring your data in Ensembl' session will introduce how to upload and display your own data files in the Ensembl genome browser. We will introduce tools for direct upload by URL.

First come, first served

16
Ensembl release 95 webinar
16th Jan

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 95 features genome annotation for 9 new vertebrate species, as well as genome assembly and annotation updates for 3 agriculturally important species. What does this mean for you? Come to our release webinar to learn more about Ensembl and what's new.

First come, first served

17
Ensembl Browser Workshop, Royal Marsden Hospital, 17th January 2019
The Royal Marsden Hospital (Surrey) - The Royal Marsden Hospital, Downs Road, Sutton, Surrey,  SM2 5PT, United Kingdom
17th Jan

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

18
Ensembl Browser Workshop, UCSD, 18th January 2019
University of California, San Diego - UC San Diego, Medical Education and Telemedicine Building, San Diego, , CA,  92161, United States
18th Jan

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 Browser Workshop, DKFZ Heidelberg, 29 January 2019
Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) - Deutsches Krebsforschungszentrum (DKFZ)Im Neuenheimer Feld 280, 69120,  Heidelberg, Germany
29th Jan

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 Browser workshop, University of Nottingham, 29th January 2019
University of Nottingham - University Park, Nottingham,  NG7 2RD, United Kingdom
29th Jan

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

30
Ensembl Browser Workshop, DKFZ Heidelberg, 30 January 2019
Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) - Deutsches Krebsforschungszentrum (DKFZ)Im Neuenheimer Feld 280, 69120,  Heidelberg, Germany
30th Jan

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.

February 2019

7
Ensembl Browser Workshop, Cartagena, 7 February 2019
Universidad de Cartagena - Claustro San Agustín, centro cra. 6, Calle de la Universidad No. 36 - 100, 130001,  Cartagena, Colombia
7th Feb

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

8
Ensembl REST API Workshop, Cartagena, 8 February 2019
Universidad de Cartagena - Claustro San Agustín, centro cra. 6, Calle de la Universidad No. 36 - 100, 130001,  Cartagena, Colombia
8th Feb

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

First come, first served

11
Ensembl Browser Workshop, Bogota, 11 February 2019
Universidad de los Andes - UniAndes - Cra 1 Nº 18A - 12, 111711,  Bogota,  CUN, Colombia
11th Feb

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

12
Ensembl REST API Workshop, Bogota, 12 February 2019
Universidad de los Andes - UniAndes - Cra 1 Nº 18A - 12, 111711,  Bogota,  CUN, Colombia
12th Feb

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

First come, first served

March 2019

18
Introduction to Next-generation Sequencing
LANGEBIO, Cinvestav - LANGEBIO, Cinvestav, Libramiento Norte Carretera Leon Km 9.6, Irapuato,  GUA,  36821, Mexico
18th 20th Mar

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

Open application with selection

19
Exploring Human Genetic Variation
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
19th 20th Mar

This two-day workshop will data resources and bioinformatics tools available at EMBL-EBI and the Sanger Institute that will aid understanding of human genetic variation.

First come, first served

26
Introduction to RNA-Seq and Functional Interpretation
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
26th 29th Mar

This course will provide an introduction to the technology, data analysis, tools and resources used in RNA sequencing and transcriptomics.

Open application with selection

April 2019

1
Livestock Genomics
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
1st 5th Apr

This course will introduce participants to methods and approaches for analysing genomic data from common livestock species.

Open application with selection

8
RNA-Sequence Analysis
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
8th 12th Apr

This course will familiarise participants with advanced data analysis methodologies in the field of transcriptomics and to provide practical training in the latest analytical approaches.

First come, first served

9
Exploring Biodiversity through Bioinformatics
International Potato Center (CIP) - Avenida La Molina 1895, 1558,  LIM,  La Molina, Peru
9th 12th Apr

This course aims to provide knowledge on available approaches, methods and tools to perform studies on biodiversity employing modern high-throughput sequencing approaches.

By invitation

May 2019

13
Computational Molecular Evolution
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
13th 24th May

This course provides theoretical knowledge and practical experience in conducting molecular evolutionary analyses on sequence data.

June 2019

10
Metagenomics Bioinformatics 2019
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
10th 13th Jun

This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including marker gene, whole gene shotgun (WGS) and assembly-based approaches.

Open application with selection

November 2019

11
Bioinformatics & Functional Genomics in Zebrafish
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
11th 15th Nov

This course has been designed specifically for researchers working within the Zebrafish community, providing an introduction and practical knowledge of tools and resources for working with functional genomics data.

Online courses

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ArrayExpress: Discover functional genomics data quickly and easily

Author(s): Anja Füllgrabe

ArrayExpress is a database of functional genomics data. This course will give you an overview of how these data are stored in ArrayExpress and will teach you how to effectively search and retrieve data from the ArrayExpress website . Course...

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ArrayExpress: Quick tour

Author(s): Melissa Burke

This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress. This course was updated in December 2015. An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional...

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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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diXa data warehouse: Exploring data from toxicogenomics studies

Author(s): Vera Matser

The diXa data warehouse is a curated collection of toxicogenomics experiments, accessible through the diXa website . This course will show you how to use the diXa warehouse and what data is available.

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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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EMBO Practical Course on Analysis of High-Throughput Sequencing Data

Author(s): Gabry Rustici

Here you will find a collection of materials including videos of lectures from the 'EMBO Practical Course on Analysis of High-Throughput Sequencing Data' that took place at EMBL-EBI on 23-29 October 2011. This course was aimed at advanced PhD...

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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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Expression Atlas: Quick tour

Author(s): Maria Keays

This extended quick tour provides a brief introduction to the Expression Atlas (“Atlas”). Expression Atlas provides information on gene expression patterns under different biological conditions. An undergraduate-level understanding of biology is an...

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Functional genomics (I): Introduction and designing experiments

Author(s): Melissa Burke, Laura Huerta

This is the first part of our functional genomics course. This course will give you an introduction to functional genomics. We will introduce you to different types of functional genomics studies and discuss best practices when designing your own...

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Functional genomics (II): Common technologies and data analysis methods

Author(s): Laura Huerta, Melissa Burke

This is the second part of our functional genomics course. This course will introduce you to common technologies in functional genomics studies, including microarrays and next generation sequencing (NGS), with a special focus on RNA-sequencing (RNA-...

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Functional genomics (III): Submitting your data and functional genomics databases

Author(s): Melissa Burke, Laura Huerta

This is the third and final part of our functional genomics course. In this course, we will look at why, when, where to submit your functional genomics data. We recommend that you look at Functional genomics (I): Introduction and designing...

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Functional genomics: An introduction to EMBL-EBI resources

Author(s): Amy Tang

This course will introduce the field of functional genomics and provide an overview of the major resources for this field at EMBL-EBI. Updated in August 2014. For a more in depth look at functional genomics, we have just launched three new courses (...

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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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