This material briefly reintroduces the DNA double Helix structure, explains SNP and INDEL mutations in genes and describes FASTA, FASTQ, BAM and VCF file formats. It also explains the index creation, alignment, sorting, marking duplicates and variant calling steps of a simple preprocessing workflow and how to write a Perl script to automate the execution of these steps on a Virtual Machine Image.

This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.

For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find evidence in scientific literature.

Who is this course for?
This webinar is suitable for scientists, database curators or anyone who wishes to learn more about how to use annotations.

Outcomes
By the end of the webinar you will be able to:

Explore Europe PubMed Central
Use text mining for scientific literature searches

EMBL-EBI provides a comprehensive range of tools to access and analyse life sciences data. This online tutorial will help you discover the variety of tools that are available, as well as providing video introductions to a selection of them.

By the end of the course you will be able to:
Know where to search the complete list of EMBL-EBI tools
List some examples of EMBL-EBI's tools
Recall where to find more information on EMBL-EBI's tools

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 data, the best way to get quick and automated access is to do it programmatically.

By the end of the course you will be able to:
List available EMBL-EBI webservices
Describe processes that can be performed using EMBL-EBI RESTful APIs
Know where to find help, documentation and get support
Access example scripts

A brief introduction to the Electron Microscopy Public Image Archive (EMPIAR), a public resource for raw electron microscopy images.

By the end of the course you will be able to:
Search and access raw electron microscopy images in EMPIAR
Deposit electron microscopy data in EMPIAR
Know how to access further support when using EMPIAR

Ensembl offers integrated genome, variation, gene regulation and comparative genomics data on an open access web browser platform. This course includes an introduction to Ensembl, what kind of data Ensembl has, and how to browse and export the data.

By the end of the course you will be able to:
Navigate Ensembl using the web browser platform
Access main data types in Ensembl: genomes, genes, genetic variation, regulatory features and comparative genomics
Annotate your own variant data with the VEP
Mine Ensembl data using BioMart
Display your own data in Ensembl

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.

By the end of the course you will be able to:
Explain what Ensembl is and where the data come from
Access and navigate the Ensembl homepage
Search the Ensembl browser with a gene, location (a region of a genome), or variant of interest
Explore a region on a genome, a gene and a transcript
Determine where to view gene trees, sequence variation, and regions involved in gene regulation in Ensembl
View a sequence for a gene, protein, or a genome of interest
Determine how genes are annotated
Assess the different ways the data are presented in Ensembl (including the gene, location, transcript and variation tabs)
Export Ensembl data quickly and easily with the browser and BioMart

Ensembl runs API workshops worldwide, and here we have made one available online. 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. The exercises associated with the workshop are included to carry out at your leisure.

By the end of the course you will be able to:
Describe how data are organised in the Ensembl database
Describe how Ensembl assigns objects and methods
Navigate the API Doxygen documentation
Write Perl scripts that query the Ensembl database for various different kinds of data

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

By the end of the course you will be able to:
Describe what Ensembl Genomes is and how it can help you to access and analyse genome-scale data
Recall where to find out more about the Ensembl Genomes resource

This course provides a very short introduction to the Ensembl website for browsing chordate genomes.

By the end of the course you will be able to:
Outline Ensembl and what you can do with the resource
Know where to find out more about Ensembl

The Ensembl REST API provides language-agnostic programmatic access to genomic data in the Ensembl database. This course uses Jupyter Notebooks hosted by Google Colab to walk you through the APIs and practise writing scripts to access these data. A video provides a brief overview of the REST API, endpoints and instructions on working with the Jupyter notebooks.

By the end of the course you will be able to:
Describe the data types accessible through the Ensembl REST API
Describe the methods in the Ensembl REST API
Navigate the Ensembl REST API documentation to find available methods
Write scripts to access data via the Ensembl REST API

This webinar will introduce you to the data available in the Ensembl Rapid Release site, a new, lightweight genome browser designed to allow quick release of the latest genome annotation for a large number of vertebrate and non-vertebrate species.

Who is this course for?
This webinar is suitable for any wet-lab scientists and bioinformaticians who are interested in studying genomes.

Outcomes
By the end of the webinar you will be able to:

Describe the data available in Ensembl Rapid Release
Navigate Ensembl Rapid Release

Ensembl provides the GENCODE gene annotation that is used by major sequencing projects, such as gnomAD, GTEx and ENCODE. In this webinar you will learn about how the GENCODE genes are annotated and how you can best use them to report the locations of clinically relevant variants. We will also cover our latest project, collaborating with RefSeq to create the MANE (Matched Annotation from NCBI and EBI) transcript set, to ensure consistent variant reporting across databases.

Who is this course for?
This webinar is individuals working on clinical genomics who wish to learn more about the annotating and reporting variants. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of genetic variation would be useful.

Enzyme Portal is a freely available resource to find and explore enzyme-related information. It integrates relevant enzyme data for a wide range of species from various resources such as UniProt, PDB, Reactome or CHEMBL.

This webinar will provide a practical overview of the type of information that the Enzyme Portal provides for enzymes. We will show, using various examples, how to search the Portal for specific enzymes according to the reactions they catalyse, the pathways or the diseases they are involved in.

Who is this course for?
This webinar is aimed at individuals who wish to learn more about enzymes. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

This quick tour provides a brief introduction to Enzyme Portal - a data resource that provides access to information from several enzyme-related databases, many of which are based at EMBL-EBI.

By the end of the course you will be able to:
Navigate Enzyme Portal to access enzyme-related data
Identify the various possibilities to search Enzyme Portal
Describe what type of enzyme-related data Enzyme Portal provides

This webinar will provide a practical overview of the type of information the protein database UniProt offers for enzymes and how to access it. We will introduce the new enhanced enzyme annotation based on Rhea, a comprehensive expert-curated database of biochemical reactions that uses the ChEBI ontology to describe reaction participants, their chemical structures, and chemical transformations.

In this webinar, we will show how this new feature forms the basis of a new search. Ultimately, this information will help users to integrate and analyse metabolomic data, annotate metabolic networks and models, or mine reaction data to study enzyme evolution and predict new pathways for drug production or bioremediation.

Who is this course for?
This webinar is aimed at individuals who wish to learn more about enzymes in Uniprot. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

The FAIR principles – standing for Findability, Accessibility, Interoperability, and Reusability – have become the guiding principles for the wider sharing of research data in the life sciences. While FAIR provides guidance for the management of data as well as tools and workflows, the institutional conditions and organizational challenges associated with data sharing need to be taken into account to ensure responsible and fair data practices. This requires considering the context of legal requirements, for instance the principle of fairness and transparency in GDPR, expectations of research participants/data subjects, societal aspects and the “ethics work” that is an integral part of data flows, as well as fairness, equity and benefit sharing within transnational collaborations, which is of utmost importance. This webinar will, from the perspective of ethical, legal and societal implications (ELSI), discuss this broader context of responsible and fair data sharing associated with FAIR.

The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.

Who is this course for?
People involved in research in the life sciences and interested in fair data sharing.

The new EurOPDX Research Infrastructure (RI), funded by the European Union Horizon 2020 programme, aims to improve cancer drug development success rates through the enablement of collaborative cancer research using patient-derived xenograft (PDX) models. In particular, we are developing efficient and user-friendly IT tools to optimise access to, and data searching of the collection of PDX models and their clinical, molecular and pharmacological annotations. We will be presenting the EurOPDX RI and the possibilities of access to PDX models, as well as the functionalities of the EurOPDX Data Portal, with the objective to support future applicants to our PDX access grant programme.

Who is this course for?
This webinar is for individuals who are working with patient-derived xenograft models in the context of cancer drug discovery. No prior knowledge of bioinformatics is required but an undergraduate-level knowledge of biology is recommended. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

The new EurOPDX Research Infrastructure (RI), funded by the European Union Horizon 2020 programme, aims to improve cancer drug development success rates through the enablement of collaborative cancer research using patient-derived xenograft (PDX) models. In particular, we are developing efficient and user-friendly IT tools to optimise access to, and data searching of the collection of PDX models and their clinical, molecular and pharmacological annotations.

Following a first webinar in October 2019 introducing the new EurOPDX Data Portal, we will present the latest data and functionalities added to the repository, and associated IT tools to browse molecular data associated with the models: the EurOPDX instance of the well-known cBioPortal, and the GenomeCruzer for 3D interrogation of data.

The webinar will in particular support the last applicants to our PDX access grant programme (last deadline on 18th September 2020, https://www.europdx.eu/europdxri-ta).

Who is this course for?
This webinar is for individuals who are working with patient-derived xenograft models in the context of cancer drug discovery. No prior knowledge of bioinformatics is required but an undergraduate-level knowledge of biology is recommended.