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

September 2017

20
Executive Masters in Management of Research Infrastructures
University of Milano-Bicocca - Piazza dell'Ateneo Nuovo, 20126,  Milan,  MI, Italy
20th Sep - 15th Mar

This Masters development programme is aimed at current Research Infrastructures managers and leaders who wish to develop the competencies required to meet the needs of Research Infrastructures in the planning, construction and operation phases.

Open application with selection

Course
Project management

February 2018

2
EMBL Webinar Series: Lifelong Learning in the Biomedical Sciences
2nd Feb - 18th May

Competent professionals, who are committed to staying at the leading edge of developments in their field and developing their personal skills, are the underlying foundation of successful research. This webinar series explores how your organisation and indeed YOU can be ‘fit for the future’ in this environment.

First come, first served

Webinar
Lifelong learning

April 2018

23
Ensembl programmatic access with Perl, April 2018
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
23rd - 26th Apr

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

First come, first served

Course
Genomics
Bioinformatics
25
Ensembl Browser workshop, EBI April 2018
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
25th Apr

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

Course
Bioinformatics
Genomics
26
Ensembl browser workshop, Austrian Institute of Technology, Vienna, Austria, 26 April 2018
Austrian Institute of Technology - Giefinggasse 4, 1210,  Vienna, Austria
26th Apr

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

Course
Bioinformatics
Genomics
27
How to prepare and incentivise research scientists and healthcare professionals for collaborative innovation
27th Apr

Michel Goldman and Hilde Stevens will describe an innovative educational program that aims at preparing the next generation of healthcare professionals and fostering collaboration between public and private stakeholders.

First come, first served

Webinar
Lifelong learning

May 2018

8
Automatic annotation systems in UniProt
8th May

UniProt is a high quality, comprehensive protein resource. Next to expert curation, one of the core activities at UniProt is to develop computational methods for the functional annotation of protein sequences. In this webinar we will introduce two rule-based annotation systems, UniRule and the Statistical Automatic Annotation System (SAAS), and explain how they complement each other to automatically annotate the unreviewed records in the UniProt Knowledgebase (UniProtKB/TrEMBL) with a high coverage and a high degree of accuracy. We will also give you an early peek at the formats and systems we plan to make available to enable researchers to annotate their own protein sequences.

First come, first served

Webinar
Protein properties
11
Hands-on on Protein Function Prediction with Machine Learning and Interactive Analytics
11th May

Understanding protein functions is crucial to unlocking the value of genomic data for biomedical research and innovation. Delivering personalized health and precision medicine requires a detailed understanding of the consequences of sequence variants in proteins and their impact on phenotype. This tutorial will help you understanding how to use Spark and Interactive Analytics to make sense of protein data and build Machine Learning models to infer their functions.

First come, first served

Webinar
Modelling
Protein properties
14
Networks and Pathways
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
14th - 18th May

This course will provide life scientists training on exploring and using protein interaction bioinformatics resources. The content examines the data repositories, resources and tools available to explore and analyse large datasets and introduce the principles of biological network and pathway analysis.

Open application with selection

Course
Molecular interactions, pathways and networks
Protein interactions
16
Sequence similarity searching using HMMER
16th May

This webinar is currently under development and full details about the webinar are not yet available. Once the details have been confirmed we will post them here. Please register to confirm your place and to receive updates.

First come, first served

Webinar
sequence similarity searching
18
Science, technology and innovation for upskilling knowledge-based economies in Africa
18th May

This three-part will be presented by Kevin March, Trudie Lang and Allan Pamba will discuss career development for African researchers.

First come, first served

Webinar
Lifelong learning
24
EMBL-EBI Workshop: Tools for functional genomics data
Conrad Hotel, Seoul, South Korea - 10 Gukjegeumyung-ro, Yeoeuido-dong, Yeongdeungpo-gu, Seoul, Seoul,  07326, South Korea
24th May

This course will provide participants with an introduction to functional genomics resources at EMBL-EBI, in particular to ArrayExpress and the submission tool Annotare.

First come, first served

Course
Transcriptomics
Functional genomics
Data curation and annotation
28
Ensembl Browser workshop, Seoul, 28th May 2018
Conrad Hotel, Seoul, South Korea - 10 Gukjegeumyung-ro, Yeoeuido-dong, Yeongdeungpo-gu, Seoul, Seoul,  07326, South Korea
28th May

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

Course
Genomics
Bioinformatics
29
Ensembl Browser workshop, Seoul, 29th May 2018
Conrad Hotel, Seoul, South Korea - 10 Gukjegeumyung-ro, Yeoeuido-dong, Yeongdeungpo-gu, Seoul, Seoul,  07326, South Korea
29th May

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

Course
Genomics
Bioinformatics
30
Effective Literature Research with Europe PMC
30th May

This webinar is currently under development and full details about the webinar are not yet available.  Once the details have been confirmed we will post them here.  Please register to confirm your place and to receive updates.

First come, first served

Webinar
Literature and reference
31
Ensembl Browser workshop, The George Washington University, Washington, DC, 31 May 2018
31st May

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

Course
Bioinformatics
Genomics

June 2018

3
In Silico Systems Biology
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
3rd - 8th Jun

Run jointly with the Wellcome Trust, this course will provide participants with an introduction to network analysis and an in-depth training in the main modelling approaches used in systems biology.

Open application with selection

Course
Systems biology
Modelling
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

Course
Immunology
Molecular interactions, pathways and networks
5
Ensembl Browser workshop, UNC Chapel Hill, NC, 5 June 2018
5th Jun

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

Course
Bioinformatics
Genomics
6
Ensembl Browser workshop, National Institute of Environmental Health Sciences, Durham, NC, 6 June 2018
6th Jun

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.

Course
Bioinformatics
Genomics
6
PhenoMeNal Gateway: Portal to metabolomics data analysis in the cloud
Tennis Court Suite, Wellcome Genome Campus - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
6th - 8th Jun

This course will provide an introduction to metabolomics data analysis in a cloud computing environment, using infrastructure developed by the PhenoMeNal project.

Open application with selection

Course
Metabolomics
8
Ensembl Browser workshop, Duke University, Durham, NC, 8 June 2018
8th Jun

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

Course
Bioinformatics
Genomics
11
Ensembl Browser workshop, NC State University, Raleigh, 11 June 2018
NC State University - 1000 Harris Hall, Raleigh, , NC,  27695, United States
11th Jun

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

Course
Bioinformatics
Genomics
12
Bioinformatics for Principal Investigators
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
12th - 14th Jun

The aim of this course is to provide principal investigators with an introduction to the challenges of working with biological data as a research leader. This course will not provide a platform for teaching hands-on bioinformatics analysis.

Open application with selection

Course
Data search, query and retrieval
Data management
Computational biology
12
Bioinformatics for Core Facility Managers
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
12th - 14th Jun

Bioinformatics core facilities play an essential role in enabling research in the molecular life sciences. This is an opportunity for managers of core facilities to learn directly from EMBL-EBI’s service teams, from each other and from potential users.

Open application with selection

Course
Bioinformatics
Data management
17
BioExcel Summer School on Biomolecular Simulations
17th - 22nd Jun

The summer school will include lectures and hands-on sessions on the following topics: Molecular Dynamics simulations Biomolecular Docking QM/MM Free energy calculations Advanced sampling methods (metadynamics) During the hands-on computer practicals you will work on a use case integrating the various topics above making use, among others, of the BioExcel flagship software (Gromacs, HADDOCK, PMX, CPMD).

Open application with selection

Course
Molecular dynamics
Molecular docking
Molecular modelling
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

Course
Genomics
Transcriptomics
Oncology
Gene expression
25
Summer School in Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
25th - 29th Jun

This popular computational course is run jointly with Wellcome Trust Advanced Courses and Scientific Conferences and will provide an introduction to the use of bioinformatics in biological research using publicly available data resources and tools.

Open application with selection

Course
Data search, query and retrieval
Critical thinking
Sequence analysis

July 2018

10
Exploring Human Genetic Variation
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
10th - 11th 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

Course
Genomics
Genotype and phenotype
Genetic variation
Functional genomics
15
Proteomics Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
15th - 20th Jul

This course provides hands-on training in the basics of mass spectrometry and proteomics bioinformatics.

Open application with selection

Course
Proteomics
Molecular interactions, pathways and networks
Mass spectrometry
NMR spectroscopy
17
Metagenomics Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
17th - 20th Jul

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

Course
Metagenomics
Sequence analysis
Function analysis

September 2018

3
Structural Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
3rd - 7th Sep

This course explores bioinformatics data resources and tools for the interpretation and exploitation of bio-macromolecular structures.

Open application with selection

Course
Structural biology
Protein structure analysis

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

Course
Genomics
Transcriptomics
9
ENA Sequencing Retrieval
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
9th - 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

Course
Nucleic acid sequence analysis
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

Course
Sequence analysis
Genomics
Genetic variation
Gene annotation

November 2018

5
Bioinformatics for Plant Biology
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
5th - 9th Nov

A course aimed at introducing those working in plant biology to a range of bioinformatics resources and approaches applicable to their research.

Open application with selection

Course
Plants
Data search, query and retrieval
Bioinformatics
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

Course
Sequence alignment
Sequence analysis

Online courses

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10th Anniversary Treasure Hunt

Author(s): David Armstrong, Melissa Burke, Laura Huerta, Maria Levchenko, Alex Mitchell, Sarah Morgan, Grace Mugumbate, Prudence Mutowo, Sandra Orchard, Emily Perry, Sangya Pundir, Lorna Richardson, Amy Tang

In 2017 the EMBL-EBI Training Programme is celebrating 10 amazing years of providing onsite, offsite and online training in bioinformatics. To help celebrate this anniversary, we designed a treasure hunt to give you a taster of the free resources...

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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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Biocuration: An introduction

Author(s): Claire ODonovan

Claire O'Donovan, leader of the Protein Function Content team at EMBL-EBI, gives an introduction into biocuration and talks about what it is like to work as a biocurator and the skill sets you need. This webinar was recorded on 2 March 2016 and is...

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Bioinformatics for the terrified

Author(s): Cath Brooksbank

This course will give you a broad overview of how bioinformatics can enable bench-based research. It is aimed at experimental researchers in the molecular life sciences who have little or no previous experience of using bioinformatics databases or...

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Biomacromolecular structures: An introduction to EMBL-EBI resources

Author(s): Joanna Argasinska

Introduction to structural biology and related resources at EMBL-EBI.

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Biomedical data: Ethical, legal and social implications

Author(s): Sarah Morgan

This course explores the ethical, legal and social implications (ELSI) of biomedical data sharing. The material will introduce the reasons why we want to share data, the benefits it can bring, and the challenges of doing so. It will present ideas...

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BioModels: Quick tour

Author(s): Vijayalakshmi Chelliah

This quick tour provides a brief introduction to EMBL-EBI’s resource of mathematical models of biological/biomedical systems: BioModels .

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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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Cellular Microscopy Phenotype Ontology (CMPO): Quick tour

Author(s): Gabry Rustici

This quick tour provides a brief introduction to the Cellular Microscopy Phenotype Ontology (CMPO). It covers the scientific principles that led to the creation of this ontology and how it can be used.

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ChEBI: Quick tour

Author(s): Gareth Owen

This quick tour provides a brief introduction to ChEBI, the EBI's Chemical Entities of Biological Interest database, which focuses on 'small' chemical compounds. For a more detailed walthrough of ChEBI, have a look at our ChEBI: the online...

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ChEBI: The online chemical dictionary for small molecules

Author(s): Namrata Kale

Chemical Entities of Biological Interest (ChEBI) is a user-friendly online chemical dictionary that focuses on the nomenclature, structure, and biological properties of 'small' molecules that may be encountered by anyone working in (or merely with...

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ChEMBL walkthrough: webinar

Author(s): Prudence Mutowo

Prudence Mutowo presents this webinar on ChEMBL - a manually curated chemical database of bioactive molecules with drug-like properties. This webinar took place on 6th February 2017 and is an update to a webinar recorded by Louisa Bellis in 2015. It...

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ChEMBL: Exploring bioactive drug-like molecules

Author(s): Louisa Bellis

This course will show you the content and search facilities for the ChEMBL database . ChEMBL is a database of bioactive drug-like molecules, and contains 2D structures, calculated properties and associated bioactivities. Some basic understanding of...

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ChEMBL: Quick tour

Author(s): Louisa Bellis

This quick tour provides a brief introduction to ChEMBL, the EBI's chemogenomics resource. For a more detailed walthrough of ChEMBL, have a look at our ChEMBL: Exploring bioactive drug-like molecules tutorial.

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Complex Portal: Quick tour

Author(s): Birgit Meldal

This quick tour provides a brief introduction to EMBL-EBI's Complex Portal: a manually curated, encyclopedic resource of macromolecular complexes from a number of key model organisms.

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Complex Portal: webinar

Author(s): Birgit Meldal

Birgit Meldal gives an introduction to the Complex Portal . The Complex Portal provides manually curated summaries about macromolecular complexes, including lists of participants, function and property information as well as cross-references. This...

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Computational chemistry in drug discovery

Darren Green, Director of Computational Chemistry at GSK, presents a talk on using computational chemistry approaches for drug discovery. The talk explains how informatics can aid many steps in the discovery and development process, to elucidate...

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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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Drug repurposing

Author(s): John Overington

John Overington, Director of Bioinformatics at Stratified Medical, and former group leader at EMBL-EBI, presents a talk on the repurposing of drugs for novel therapeutic applications. The talk explores how computational approaches can be used to...

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Druggability and the druggable genome

Author(s): Anna Gaulton

Anna Gaulton presents this webinar on the druggable genome and the concept of druggability. She discusses why druggability is so important in drug discovery and what methods and databases you can used to determine the druggability of your targets...

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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 resources: An introduction

Author(s): Tom Hancocks, Jennifer Cham

The EMBL-EBI is the home of the world's most comprehensive range of freely available molecular databases and resources. Our resources help researchers share and analyse data and perform complex queries in many different ways. Join Tom Hancocks in...

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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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EMPIAR: Quick tour

Author(s): Andrii Iudin, Ardan Patwardhan

This quick tour provides a brief introduction to the Electron Microscopy Pilot Image Archive (EMPIAR), a public resource for raw, 2D electron microscopy images.

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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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Enzyme Portal: Quick tour

Author(s): Sangya Pundir

This quick tour provides a brief introduction to the Enzyme Portal - a data resource that provides access to information from several enzyme-related databases, both at EMBL-EBI and the Swiss Institute of Bioinformatics (SIB).

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Enzymes in UniProt

Author(s): Rossana Zaru

This webinar provides a practical walkthrough of the UniProt website for enzyme data. It highlights features that will help researchers find the information they need on their enzymes of interest, demonstrating how to get the data they’re looking...

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Europe PMC: get the most from literature searches

Author(s): Michael Parkin

With Europe PMC, a free biomedical repository and partner in PubMed Central International, you can search worldwide, life-sciences literature, including articles, books, patents, and clinical guidelines. In this webinar we will show how to use...

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Europe PMC: Quick tour

Author(s): Michael Parkin

This quick tour gives a brief introduction to Europe PMC , an open and free-access literature resource for biomedical and life sciences researchers. Course updated in June 2017.

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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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Exploring models for human disease with UniProt

Author(s): Sangya Pundir

UniProt is the Universal Protein Resource covering human variants and their disease association, in addition to general protein function and sequence data. This webinar will illustrate how to explore models for human disease variants to support...

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Exploring protein interactions with UniProt

Author(s): Klemens Pichler

UniProt is the Universal Protein Resource covering human variants and their disease association, in addition to general protein function and sequence data. This webinar will illustrate how to explore protein interactions with the UniProt website...

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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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Global Alliance for Genomics and Health (ELSI): Quick tour

Author(s): Sarion Bowers

This quick tour provides a brief introduction to The Global Alliance for Genomics and Health (Global Alliance), which was formed to help accelerate the potential of genomic medicine to advance human health. This Quick tour focuses on the Ethical,...

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GO: Quick tour

Author(s): Rebecca Foulger

This quick tour provides a brief introduction to the EBI's Gene Ontology resource. For information about gene ontology annotation, see the UniProt-GOA quick tour .

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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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HipSci: a UK national iPS cell resource webinar

Author(s): Ian Streeter

The Human Induced Pluripotent Stem Cell Initiative (HipSci) is establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their...

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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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IMPC: Using the mouse phenotyping portal

Author(s): Terry Meehan

The International Mouse Phenotyping Consortium (IMPC) portal allows you to search for phenotypes, disease models and knockout mouse strains for your gene of interest. This course will show you how to use the IMPC portal and what data is available.

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IntAct: Molecular interactions at EMBL-EBI

Author(s): Pablo Porras Millan

This course will show you what kind of information you can find in IntAct (one of the EBI's molecular interactions databases), how to access it, the different tools that can be used to access data and some practical examples on how to search and use...

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IntAct: Quick tour

Author(s): Sandra Orchard

This quick tour provides a brief introduction to the EBI's molecular interactions database, IntAct.

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IntAct: The molecular interactions database at EMBL-EBI: webinar

Author(s): Pablo Porras Millan

This two-part webinar from Pablo Porras Millan provides you with an introduction to protein-protein interactions and the molecular interaction database IntAct (recorded on 30th September 2015). IntAct is a central, public repository where molecular...

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InterPro: Functional and structural analysis of protein sequences

Author(s): Alex Mitchell

InterPro is a classification database that provides predictive information about protein sequences. This course will show you what kind of information is available in InterPro, how to access it, and how to search the database..

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InterPro: Quick tour

Author(s): Alex Mitchell

This quick tour provides a brief introduction to InterPro, the EBI's database of protein families, domains and functional sites. For a more detailed walkthrough of InterPro have a look at our InterPro tutorial .

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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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Introduction to training with EMBL-EBI

Author(s): Cath Brooksbank

This year is the tenth anniversary of the EMBL-EBI Training Programme! Join Cath Brooksbank to learn about the types of training that EMBL-EBI offers and how you can benefit from it. We welcome students, postdocs, academics, industrial scientists (...

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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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MetaboLights: Quick tour

Author(s): Kenneth Haug

This quick tour provides a brief introduction to the EBI's metabolomics resource: MetaboLights .

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Metabolomics: An introduction

Author(s): Reza Salek, Laura Emery, Stephan Beisken

This course provides a basic introduction into the rapidly emerging field of metabolomics and its importance and applications.

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Metabolomics: molecules of life, an introduction

Author(s): Reza Salek

Join Reza Salek on an introductory tour of metabolomics. This webinar will help you understand what metabolomics is and how it can be used to inform biological research. It will also introduce the basics of the analytical technologies and data...

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myChEMBL: webinar

Author(s): George Papadatos

George Papadatos takes you through myChEMBL - the ChEMBL virtual machine. This video is best viewed in full screen, using Google Chrome. See upcoming webinars from this series.

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Network analysis of protein interaction data: an introduction

Author(s): Pablo Porras Millan

This course provides an introduction to the theory and concepts of network analysis. It explores some of the features of protein-protein interaction networks and their implications for biology. Finally, the course discusses the tools and strategies...

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Ontology Lookup Service (OLS)

Author(s): Simon Jupp

The Ontology Lookup Service (OLS) provides access to over 150 public biomedical ontologies. You can use OLS to search and visualise ontologies, and an API is also provided for programmatic access. Ontologies provide standard terminology for...

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PDBe: Exploring a Protein Data Bank (PDB) entry

Author(s): Sanchayita Sen

This course will show you how to explore the structural information in a PDB entry using the Protein Data Bank in Europe (PDBe) - EMBL-EBI's resource for the collection, organisation and dissemination of data on biological macromolecular structures...

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PDBe: Quick tour

Author(s): Sameer Velankar

This quick tour provides a brief introduction to the Protein Data Bank in Europe (PDBe), EMBL-EBI's resource for the collection, organisation and dissemination of data on biological macromolecular structures.

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PDBe: Searching for biological macromolecular structures

Author(s): David Armstrong

The Protein Data Bank in Europe (PDBe) is a free and easily accessible resource for biological macromolecular structures. We collect, organise and disseminate data in both the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB)...

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PDBe: Searching the Protein Data Bank

Author(s): Sanchayita Sen

This course will show you how to search the Protein Data Bank in Europe (PDBe) - EMBL-EBI's resource for the collection, organisation and dissemination of data on biological macromolecular structures. The course contains the following mini-tutorials...

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PDBeChem: Searching for small molecules and small molecule fragments

Author(s): Gary Battle

PDBeChem allows you to search for chemical components (ligands, small molecules and monomers) that appear in PDB entries, and discover which protein structures bind a particular ligand. This course will show you how to use PDBeChem and what you can...

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PDBeFold: Searching for structural homologues of a protein

Author(s): Gary Battle

PDBeFold can be used to identify structural homologues in the PDB. PDBe's Secondary Structure Matching service (SSM) allows you to interactively compare, align and superimpose protein structures in 3D. This course will show you how to use PDBeFold...

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PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure

Author(s): Gary Battle

PDBePISA allows you to explore macromolecular (protein, DNA/RNA and ligand) interfaces and predict the quaternary structure of your protein. This course will show you how to use PDBePISA and what you can do with it. An undergraduate degree in a life...

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Pfam: Quick tour

Author(s): Sara El-Gebali, Lorna Richardson, Rob Finn

This quick tour provides a brief introduction to the protein families database Pfam, based at EMBL-EBI. Each protein family is represented by multiple sequence alignments and a profile hidden Markov model, which is used to create a probabilistic...

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PhenoMeNal: accessing metabolomics workflows in Galaxy

Author(s): Namrata Kale, Sijin He, Pablo Moreno

PhenoMeNal ( Phe nome and Me tabolome a Nal ysis) is a standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications. This course will give you an overview...

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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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PRIDE and ProteomeXchange: webinar

Author(s): Juan Antonio Vizcaino

Juan Antonio Vizcaino presents this webinar on PRIDE and ProteomeXchange. PRIDE is a resource that stores mass spectrometry-based protein expression data (including e.g. mass spectra, peptide and protein identifications, among other data types)...

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PRIDE: Quick tour

Author(s): Juan Antonio Vizcaino

This quick tour provides a brief introduction to the EMBL-EBI's PRoteomics IDEntifications database, PRIDE.

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Protein classification: An introduction to EMBL-EBI resources

Author(s): Amaia Sangrador

This course will provide an introduction to protein classification and basic concepts, such as proteins families, domains and sequence features.

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Protein interactions and their importance

Author(s): Pablo Porras Millan

This course will provide an introduction to molecular interactions, their importance and the methodologies use to generate and capture interaction data.

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ProteomeXchange submissions via PRIDE

Author(s): Juan Antonio Vizcaino

How to submit MS/MS data to ProteomeXchange via PRIDE. This course is aimed at proteomics researchers with data that they want to make available through public-domain databases of proteomics experiments.

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Proteomics: An introduction to EMBL-EBI resources

Author(s): Sandra Orchard

This course will provide an overview of proteomics. We will then introduce resources provided by the EBI related to proteomics.

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QuickGO - Gene ontology annotation

Author(s): George Georghiou

The Gene Ontology Annotation (GOA) project provides high-quality functional annotations to gene products, such as proteins, protein complexes and non-coding RNAs. Currently our database contains over 390 million annotations to 60 million distinct...

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Reactome: Exploring biological pathways

Author(s): Steve Jupe

This course provides an overview to the Reactome pathway database web interface and the database content. For a short introduction to Reactome, please visit the Reactome quick tour .

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Reactome: Exploring biological pathways: webinar

Author(s): Steve Jupe

This two-part webinar from Steve Jupe provides you with an introduction to Reactome and how you can use it to explore biological pathways (recorded on 22 June 2016). Part 1 gives an overview of what Reactome is and why it is important. Part 2...

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Reactome: Quick tour

Author(s): Steve Jupe

This quick tour provides a brief introduction to Reactome, the biological pathway database.

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Reactome: Tools for analysis of biological pathways

Author(s): Steve Jupe

This course introduces the tools available via the Reactome pathway database web interface. For a short introduction to Reactome, please visit the Reactome quick tour . For an intruduction to the Reactome web interface including the Pathway Browser...

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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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Structural volume data

Author(s): Martyn Winn

This course provides a basic introduction of volume matching techniques in the field of structural bioinformatics. It explains the use of electron microscopy (EM) and electron tomography (ET) data in creating 3D volume maps of proteins, and the...

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SureChEMBL: Accessing chemical patent data: webinar

This two-part webinar from George Papadatos provides you with an introduction to the chemical patent database SureChEMBL (recorded on 11th March 2015). Part 1 gives an overview of what SureChEMBL is and why it is important. Part 2 provides a demo of...

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Text mining: Key concepts and applications

Author(s): Jee-Hyub Kim, Senay Kafkas

Jee-Hyub Kim and Senay Kafkas from the Literature Services team at EMBL-EBI present this talk on an introduction to text mining and its applications in service provision. The 1st part of this talk focuses on what text mining is and some of the...

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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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UniChem: EMBL-EBI’s mapping tool for small molecule database identifiers: webinar

Author(s): Jon Chambers, Anne Hersey

Jon Chambers and Anne Hersey present this webinar on UniChem a simple system developed to cross-reference compounds across databases both internal to EMBL-EBI and externally. UniChem currently has cross-references to 140 million compounds in 30...

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UniChem: Quick tour

Author(s): Jon Chambers

This quick tour provides a brief introduction to UniChem , a compound identifier mapping service. It covers the scientific principles behind the tool, and outlines the use of UniChem and UniChem 'Connectivity Search' to directly locate identical and...

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UniProt peptide search and publications view: webinar

Author(s): Klemens Pichler

UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. This webinar will guide you through the main updates and features on the UniProt website. It...

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UniProt-GOA: Quick tour

Author(s): Rachael Huntley

This quick tour provides a brief introduction to UniProt-GOA, the Gene Ontology Annotation resource. For information about the Gene Ontology, see the GO quick tour .

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UniProt: Exploring protein sequence and functional information

Author(s): Michele Magrane, Sangya Pundir

This course is a guide to the UniProt resource, including what kinds of information it provides and how to access the data using the UniProt website. Some knowledge of biology and proteins is required. Some bioinformatics knowledge is useful but not...

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UniProt: Exploring protein sequence and functional information - webinar

Author(s): Sangya Pundir

In the first webinar , Sangya Pundir shows us how we can use UniProt to explore protein sequence and functional information. The second webinar showcases the latests updates to the UniProt website (webinar recorded on 9th Dec 2015). The third...

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UniProt: Programmatic access to UniProtKB: webinar

Author(s): Klemens Pichler

Klemens Pichler presents this webinar on accessing UniProtKB programmatically. This webinar was recorded on 3rd June 2015. This video is best viewed in full screen using Google Chrome. See upcoming webinars .

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UniProt: Quick tour

Author(s): Michele Magrane

This quick tour provides a brief introduction to the Universal Protein Resource (UniProt). A full tutorial of UniProt can be found here .

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User experience design

Author(s): Tom Hancocks

This course introduces user experience design (UXD) in the context of bioinformatics tools and service development. It provides an overview of basic concepts and links to external resources on UXD where you can learn more.

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User experience design for more user-friendly applications

Author(s): Michele Ide-Smith, Nikiforos Karamanis

Interested in learning how User Experience (UX) design can help you meet your goals? What are the quick wins for knowing your users, designing with your team and getting feedback on your designs? This webinar is for you if you are involved in...

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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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Visualising protein structures online

Author(s): David Armstrong

Litemol is a new, online macromolecular structure viewer at the PDBe, offering users the chance to easily view PDB and EMDB data in their browser and even on mobile devices. This webinar will introduce users to this fantastic new viewer and explain...

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