This is the third and last part of a webinar series on ...
This is the third and last part of a webinar series on InterPro which is held between May 6th 2020 and May 20th 2020.
InterPro is a database that helps users to understand the possible functions of proteins sequence by identifying what family it belongs to or what domains and motifs it contains. To deal with the growing volume of protein sequence data and an increasing demand to retrieve subsets of the data, often via programmatic access, the InterPro website has been entirely redesigned. It provides additional features and more flexibility in querying, presenting and retrieving data. The website relies on an Application Programming Interface (API) which can also be utilised by users for direct access to the data.
This webinar describes how the InterPro data is structured in the API, and how it could be accessed programmatically for further bioinformatics analyses.
You can access the slides via GitHub.
Who is this course for? This webinar is aimed at scientists and bioinformaticians, with basic programming knowledge, who are interested in accessing the InterPro database programmatically.
The Ensembl project offers integrated genome, variation, gene regulation and comparative genomics ...
The Ensembl project offers integrated genome, variation, gene regulation and comparative genomics data of mainly vertebrate genomes on an open access web browser platform.
This webinar will introduce you to the analysis of Linkage Disequilibrium (LD) between variants with Ensembl. We will look at different ways to explore and visualise LD in the Ensembl genome browser website. We will discuss the new LD Calculator tool which has been released with Ensembl 91 and show how to use it.
Who is this course for? This webinar is aimed at individuals who wish to learn more about analysing LD with Ensembl. No prior knowledge of bioinformatics is required, but an understanding of undergraduate level genetics would be useful.
Outcomes By the end of the webinar you will be able to:
Analyse linkage disequilibrium between variants in Ensembl Visualise linkage disequilibrium using the Ensembl Genome Browser
UniProt is a high quality, comprehensive protein resource. Next to expert curation, ...
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 be introducing our functional annotation system UniFire that can be used by the community to share and run rule-based automatic annotation systems to add functional information to proteins.
Who is this course for? No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.
Outcomes By the end of the webinar you will be able to:
Outline the types of data available in UniProt Describe the automatic annotation systems used in UniProt Describe the UniFire platform for sharing and utilising UniProt’s automatic annotation systems
The Ensembl VEP is a powerful tool that allows you to input ...
The Ensembl VEP is a powerful tool that allows you to input a list of genetic variants and determines which genes are affected and how. In this webinar, you’ll learn how to use the online VEP tool, which is suitable for analysing short lists of genetic variants, and the offline tool, which allows you to annotate whole genome variant calls.
Who is this course for? This webinar is suitable to any clinical or research scientists who are interested in exploring genetic variants and their effect. In this webinar we will use examples from human clinical data but the VEP tool is available for other species too.
Outcomes By the end of the webinar you will be able to:
Describe the application of VEP Analyse short lists of genetic variants using VEP Annotate variation data
UniProt is a high quality, comprehensive protein resource in which the core ...
UniProt is a high quality, comprehensive protein resource in which the core activity is the expert review and annotation of proteins where the function has been experimentally investigated. At the same time the UniProt database contains large numbers of proteins which are predicted to exist from gene models, but which do not have associated experimental evidence indicating their function. UniProt commits significant resources to developing computational methods for functional annotation of these predicted proteins based on the data in entries that have gone through the expert review process.
We will describe the two main automated annotation systems currently in use. First, UniRule, which is an established UniProt system in which curators manually develop rules for annotation. Second ARBA (Association-Rule-Based Annotator), which has recently been introduced as a significant improvement in fully automated functional annotation. ARBA is a multiclass learning system which uses rule mining techniques to generate concise annotation models. ARBA employs a data exclusion set that censors data not suitable for computational annotation, and generates human-readable rules for each UniProt release.
We will also briefly touch on the mechanism UniProt has set up to enable researchers to run these automated annotation systems on their own protein datasets.
Who is this course for? This webinar is for scientists and bioinformaticians with an interest in functional annotation of protein sequences.
Outcomes By the end of the webinar you will be able to:
Recall the role of UniProt's two main automated annotation systems Describe how UniRule and ARBA work Get started using these automated annotation systems
This quick tour provides a brief introduction to EMBL-EBI’s resource of mathematical ...
This quick tour provides a brief introduction to EMBL-EBI’s resource of mathematical models of biological/biomedical systems.
By the end of the course you will be able to: Identify how mathematical models are used in investigating the mechanism underlying biological systems and why do we need them. Explore the content, features, functionality and use of BioModels Determine where to find out more about BioModels Database
This quick tour provides a brief introduction to BioSamples data resource, the ...
This quick tour provides a brief introduction to BioSamples data resource, the EMBL-EBI resource that stores and supplies descriptions and metadata about biological samples.
By the end of the course you will be able to: Describe the role of BioSamples Navigate the BioSamples website Describe where to find out more about BioSamples
BioSamples is the EMBL-EBI archive which records and supplies metadata about biological ...
BioSamples is the EMBL-EBI archive which records and supplies metadata about biological samples and connects sample records across EBI databases to the corresponding experimental data. BioSamples aims to improve metadata quality through ontology annotation, metadata curation, data validation and certification.
In this webinar, we will briefly introduce BioSamples and highlight specific use cases from current collaborations and features deployed to increase FAIRness (Findability, Accessibility, Interoperability, Reusability) of the data.
Ongoing collaboration with major consortia rely on and drive addition of new features to BioSamples:
Ability to walk an ontology hierarchy such as disease for the Global Alliance for Genomics and Health (GA4GH) Synthetic dataset and linking to human controlled access data for the Common Infrastructure for National Cohorts in Europe, Canada, and Africa (CINECA) Metrics and automated processes for FAIRplus Who is this course for? Biologists and bioinformaticians who are interested in sample metadata and FAIR practices.
Outcomes By the end of the webinar you will be able to:
Describe the role of BioSamples Recall use cases that increase FAIRness of data
The goal of the BioStudies database is to facilitate transparency and reproducibility ...
The goal of the BioStudies database is to facilitate transparency and reproducibility of research by aggregating all the outputs of a study (a ‘data package’) in a single place. A data package consists of the overall biological study description (metadata), links to data generated in this study in key community databases at EMBL-EBI and elsewhere, as well as “orphan data” such as supplemental data. The database can accept a wide range of types of studies described via a simple format and does not impose minimum requirements outside those agreed by the respective community.
In this webinar we will introduce the basic principles of BioStudies, explore data access and data deposition interfaces, as well as briefly consider some more advanced topics such as use of BioStudies for data sharing in an ongoing project.
Who is this course for? No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.
What is bioinformatics and where does it fit with bench-based life science ...
What is bioinformatics and where does it fit with bench-based life science research? Find out more about bioinformatics tools and resources that are available and how you can start to apply them in your research.
By the end of the course you will be able to: Assess the role of bioinformatics in molecular science. Describe the key features of primary and secondary databases. List strategies for describing data consistently. Identify some of the different types of data analysis that can be applied to solving biological problems.
The EMBL-EBI Job Dispatcher framework (https://www.ebi.ac.uk/services) provides free access to several core ...
The EMBL-EBI Job Dispatcher framework (https://www.ebi.ac.uk/services) provides free access to several core Bioinformatics tools and related data, via the web or programmatically via Web Services APIs. In this webinar, we will give an overview of the Web Interface and RESTful API. We will then explore how to use our Sample Clients to perform various bioinformatics analysis, and how we can leverage CWL to run analysis workflows.
Who is this course for? This webinar is aimed at individuals at all levels of expertise, particularly those interested in learning how to use our Web Services programmatically.
This course provides an introduction to structural biology and related resources at ...
This course provides an introduction to structural biology and related resources at EMBL-EBI.
By the end of the course you will be able to: Describe what biomacromolecular structures are List common methods for obtaining biomacromolecular structure data Identify the protein structure resources which are available at the EBI
This course explores the ethical, legal and social implications (ELSI) of biomedical ...
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 for best practice and cover resources that provide guidance and advice for sharing data.
By the end of the course you will be able to: Explain the benefits of sharing data Explain the challenges of sharing data Describe some best practices around data sharing
Most researchers know that data management is essential for getting the most ...
Most researchers know that data management is essential for getting the most out of your data. But what exactly is it and how do you ensure that you’re managing your data well? This course, focused around a series of webinars, introduces key concepts in data management and how to apply them in your research.
By the end of the course you will be able to: Describe the data management cycle Discuss benefits and challenges of data sharing Explain what happens to data after it is shared Identify appropriate data repositories and their submission requirements Describe how ontologies and standards are used to annotate biological data Identify appropriate resources and tools for data management
The COVID-19 Data Portal was launched in April 2020 to bring together ...
The COVID-19 Data Portal was launched in April 2020 to bring together relevant datasets for sharing and analysis in an effort to accelerate coronavirus research. This course provides a short overview of what the COVID-19 Data Portal is, how to access it and how to submit data.
By the end of the course you will be able to: Explain the purpose of the COVID-19 Data Portal Describe what data is accessible through the COVID-19 Data Portal Know where to submit COVID-related data
This quick tour provides a brief introduction to the Cellular Microscopy Phenotype ...
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.
By the end of the course you will be able to: Describe the role of CMPO Search and browse the ontology and use it to annotate data
This quick tour provides a brief introduction to ChEBI, the EBI's Chemical ...
This quick tour provides a brief introduction to ChEBI, the EBI's Chemical Entities of Biological Interest database, which focuses on 'small' chemical compounds.
By the end of the course you will be able to: explain what the ChEBI Database is and how you can use it to access chemical compounds of interest demonstrate where to find out more about ChEBI
Chemical Entities of Biological Interest (ChEBI) is a user-friendly online chemical dictionary ...
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 molecular biology. This course will show you what kind of information is available in ChEBI and how to access and query the database.
By the end of the course you will be able to: Evaluate what ChEBI is and how it can be useful in your day-to-day research Know what data are stored and how ChEBI classifies molecules (understanding ChEBI ontology) Be able to carry out different types of search
This quick tour provides a brief introduction to ChEMBL, the EMBL-EBI's chemogenomics ...
This quick tour provides a brief introduction to ChEMBL, the EMBL-EBI's chemogenomics resource.
By the end of the course you will be able to: Describe what ChEMBL is and how it can help you to understand the interactions between drugs or drug-like molecules and their targets Recall where to find out more about ChEMBL
This quick tour provides a brief introduction to EMBL-EBI's Complex Portal: a ...
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.
By the end of the course you will be able to: Outline the scope of the available data in Complex Portal Describe how to search for macromolecular complexes of interest List manual and computational methods for downloading Complex data Outline how to submit curation requests for Complexes Identify sources of more information about Complex Portal
This webinar will present how the research community can contribute both literature ...
This webinar will present how the research community can contribute both literature references and annotation to the UniProt database of protein sequence and function (www.uniprot.org).
First, we will provide an overview of the resource and then we will focus on describing the functionality to add publications and knowledge to protein entries, including a demo.
In this webinar you will also learn how your domain knowledge contribution improves the resource for the general community, and how it can be used as an alternative metric of your research output given that UniProt uses ORCID, a unique identifier for each researcher, as a mechanism for user validation and credit for these contributions.
Who is this course for? This webinar is aimed at scientists, clinicians, biocurators and students interested in protein related research. No knowledge of programming is required.
Outcomes By the end of the webinar you will be able to:
explain how the research community can contribute to UniProt add publications and knowledge to protein entries describe how UniProt can be used as an alternative metric of research output
This webinar will demonstrate how to create more complex queries by combining ...
This webinar will demonstrate how to create more complex queries by combining the PDBe search API with numerous other calls. By introducing specific case studies, we will highlight the scope of PDBe programmatic access.
This webinar is part of a 6-part PDBe API webinar series, introducing different levels of programmatic access at PDBe.The series will range from basic data retrieval and search using the PDBe API to more advanced features, including access and reuse of PDBe data visualisation components.
Who is this course for? This webinar is open to anyone who is interested in learning about the programmatic access of PDBe.
Outcomes By the end of the webinar you will be able to:
Create complex queries by combining the PDBe search API with numerous other calls
In this webinar we will go through the basic principles of designing ...
In this webinar we will go through the basic principles of designing scientific figures to communicate our research findings. We will focus on how we can utilise colour effectively and help our audience make accurate quantitative judgements by taking advantage of fundamental principles of human perception. We will also discuss strategies for visualising complex datasets.
The webinar is based on the articles in data visualisation which were published in the Points of View column in Nature Methods with additional material from publications by Edward Tufte, Tamara Munzner and other leading researchers on data visualisation.
Who is this course for? This webinar is aimed at scientists who wish to learn more about the principles of data visualisation. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.
This webinar will introduce some of the data visualisations available from PDBe, ...
This webinar will introduce some of the data visualisations available from PDBe, how to add these to your own website and how to customise them for your own requirements. There will also be specific case studies that demonstrate how these visualisations can be used and implemented.
This webinar is part of a 6-part PDBe API webinar series, introducing different levels of programmatic access at PDBe.The series will range from basic data retrieval and search using the PDBe API to more advanced features, including access and reuse of PDBe data visualisation components.
Who is this course for? This webinar is open to anyone who is interested in learning about the programmatic access of PDBe.
Outcomes By the end of the webinar you will be able to:
Explore the function of data visualisation tools available at PDBe Customise data visualisation tools according to your own requirements
For readers of life sciences journal articles, annotations make it easier to ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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
The Ensembl REST API provides language-agnostic programmatic access to genomic data in ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 – ...
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.
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