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

August 2018

27
VEPTC 2018 Practical Session: The Ensembl Genome Browser
Newcastle University Medicine Malaysia - 1 JALAN SARJANA, Iskandar Puteri,  Johor,  79200, Malaysia
27th 30th Aug

Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing variation data, and annotating variants with the Variant Effect Predictor (VEP).

First come, first served

September 2018

4
Ensembl Browser workshop, Universiti Putra Malaysia, 4th September 2018
University of Putra Malaysia - Jalan Upm, Serdang,  Selangor,  43400, Malaysia
4th Sep

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

5
Ensembl REST API workshop, Universiti Putra Malaysia, 5th September 2018
University of Putra Malaysia - Jalan Upm, Serdang,  Selangor,  43400, Malaysia
5th Sep

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

5
European Variation Archive (EVA): A database of all types of genetic variation data from all species
5th Sep

The European Variation Archive (EVA) is a primary open repository for archiving, accessioning, and distributing genomic variation in any species. This webinar will include an overview on how to access data via the website and API, requirements for submission and the latest information on the EVA’s responsibility for issuing and maintaining variant identifiers (rs#) for non-human species and the progress of importing data from dbSNP. 

First come, first served

6
Ensembl Browser workshop, IMR Malaysia, 6th September 2018
Institute for Medical Research, Kuala Lumpur - Institute for Medical Research, Jalan Pahang, Kuala Lumpur,  Kuala Lumpur,  50588, Malaysia
6th Sep

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

7
Ensembl REST API workshop, IMR Malaysia, 7th September 2018
Institute for Medical Research, Kuala Lumpur - Institute for Medical Research, Jalan Pahang, Kuala Lumpur,  Kuala Lumpur,  50588, Malaysia
7th Sep

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

9
Ensembl Browser workshop, Sunway University, 9th September 2018
Sunway University - 5 Jalan Universiti, Bandar Sunway, Subang Jaya,  Selangor,  47500, Malaysia
9th Sep

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 REST API workshop, Sunway University, 10th September 2018
Sunway University - 5 Jalan Universiti, Bandar Sunway, Subang Jaya,  Selangor,  47500, Malaysia
10th Sep

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

12
Ensembl Train the Trainer Workshop, Sunway University, 12th September 2018
Sunway University - 5 Jalan Universiti, Bandar Sunway, Subang Jaya,  Selangor,  47500, Malaysia
12th Sep

Work with the Ensembl outreach team to develop teaching skills and practice delivering Ensembl Browser workshops.

By invitation

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

3
Ensembl Browser Workshop, NABDA- Abuja, 3rd October 2018
National Biotechnology Development Agency (NABDA) - Umaru Musa Yar'Adua Road, Abuja, Nigeria
3rd Oct

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.

Open application with selection

4
Ensembl REST API workshop, NABDA- Abuja, 4th October 2018
National Biotechnology Development Agency (NABDA) - Umaru Musa Yar'Adua Road, Abuja, Nigeria
4th Oct

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

Open application with selection

5
Ensembl Train the Trainer Workshop, NABDA- Abuja, 5th October 2018
National Biotechnology Development Agency (NABDA) - Umaru Musa Yar'Adua Road, Abuja, Nigeria
5th Oct

Work with the Ensembl outreach team to develop teaching skills and practice delivering Ensembl Browser workshops.

Open application with selection

8
Ensembl Browser Workshop, Kwame Nkrumah University of Science and Technology, 8th October 2018
Kwame Nkrumah University of Science and Technology (KNUST) - Kwame Nkrumah University of Science and Technology, Accra Road, Kumasi, Ghana
8th Oct

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

9
Ensembl REST API workshop, Kwame Nkrumah University of Science and Technology, 9th October 2018
Kwame Nkrumah University of Science and Technology (KNUST) - Kwame Nkrumah University of Science and Technology, Accra Road, Kumasi, Ghana
9th Oct

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

Open application with selection

10
Ensembl Train the Trainer Workshop, Kwame Nkrumah University of Science and Technology, 10th October 2018
Kwame Nkrumah University of Science and Technology (KNUST) - Kwame Nkrumah University of Science and Technology, Accra Road, Kumasi, Ghana
10th Oct

Work with the Ensembl outreach team to develop teaching skills and practice delivering Ensembl Browser workshops.

By invitation

10
ENA Sequence Retrieval
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
10th Oct

This training will introduce ENA (European Nucleotide Archive) users to powerful search and retrieval methods available for annotated sequences, genomes, raw data and metadata, as well as download options from the ENA browser and an introduction to the various ENA browser tools. There will also be a section on cross references and how to retrieve accessions for other resources linked to the primary data in ENA. There will be time for users to present their own use cases or request specific help with their own queries.

First come, first served

12
Ensembl Browser Workshop, University of Ibadan, 12th October 2018
University of Ibadan - University of Ibadan, Oduduwa Road, Ibadan, Nigeria
12th Oct

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.

Open application with selection

15
Ensembl Browser Workshop, Nigerian Institute of Medical Research- Lagos, 15th October 2018
Nigerian Institute of Medical Research (NIMR) - Nigerian Institute of Medical Research, 6 Edmund Crescent, Lagos, Nigeria
15th Oct

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

15
Bioinformatics & Functional Genomics in Zebrafish
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
15th 18th Oct

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.

Open application with selection

16
Ensembl Train the Trainer Workshop, Nigerian Institute of Medical Research - Lagos, 16th October 2018
Nigerian Institute of Medical Research (NIMR) - Nigerian Institute of Medical Research, 6 Edmund Crescent, Lagos, Nigeria
16th Oct

Work with the Ensembl outreach team to develop teaching skills and practice delivering Ensembl Browser workshops.

Open application with selection

17
Ensembl browser workshop, EMBL-EBI, 17 October 2018
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
17th Oct

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
CABANA Workshop: Functional genomics, Variation and Genomics resources and tools for plant research
Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA) - INTA-Castelar, Calle Repetto y De Los Reseros, Hurlingham, C.P. 1686,  Buenos Aires,  Buenos Aires, Argentina
18th 19th Oct

In this workshop participants will explore EMBL-EBI resources for genomics, genetic variation and transcriptomics applications. The sessions focus on browsing, searching and retrieving genomics and functional genomics data.

Open application with selection

23
Analysis of High Throughput Sequencing Data
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
23rd 26th Oct

This course will familiarise participants with methodologies for bioinformatics analysis on next generation sequencing (NGS) data.

Open application with selection

26
Ensembl Browser Workshop, BioCity Turku, 26 October 2018
Turku Centre for Biotechnology - Tykistökatu 6 A 5th floor, 20520,  Turku, Finland
26th Oct

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.

Open application with selection

November 2018

13
Exploring Biological Sequences
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
13th 15th Nov

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

First come, first served

19
EMBL-EBI Workshop: Analysis of genome scale data from bulk and single-cell sequencing
National Institute of Biomedical Genomics (NIBMG) - Kalyani Silpanchal Station Road, Kalyani, West Bengal, India,  741251, United Kingdom
19th 23rd Nov

This course will provide practical training to researchers in India who are engaged in research or applications that involve analyses of data generated by massively-parallel DNA sequencers using DNA isolated from bulk cells or a single-cell.

Open application with selection

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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