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ArrayExpress in BioStudies

ArrayExpress is a collection in the BioStudies database for functional genomics data. This quick tour will walk you through how datasets are stored in ArrayExpress and will teach you how to effectively search for and retrieve data.

Scientific topics: Functional genomics, Genomics

Resource type: e-learning

Biostatistics

This collection will introduce you to common principles of statistical methods, and give you hands-on experience of user-friendly tools for data visualisation and testing. It is tailored to the properties of biological data, and uses biological examples. In the interactive online tutorials...

Scientific topics: Statistics and probability

Keywords: Biostatistics, R

Resource type: e-learning

Genetic variation

Genetic variation is the difference in DNA sequences between individuals within a population. This collection of online tutorials, videos and materials covers a variety of topics, EMBL-EBI data resources and tools related to genetic variation.

Scientific topics: Genetic variation

Keywords: GWAS, Variation, VEP, EVA

Resource type: e-learning

Nextflow

Nextflow is an open-source workflow orchestrator that simplifies writing and deploying data-intensive computational pipelines on any infrastructure. Discover what Nextflow is and how you can use it to develop and deploy your own workflows.

Scientific topics: Workflows

Keywords: Nextflow, Cloud, Pipelines, Containers

Resource type: e-learning

Methods in bioinformatics

This tutorial introduces a variety of methods used in bioinformatics, including Gene Ontology, building biological networks, genomic variant calling, mass spectrometry-based proteomics, and bioimage analysis, through videos presented by experts from EMBL-EBI and worldwide.

Resource type: e-learning

Biocuration

Biocuration involves the collection, curation and integration of information related to the biological sciences into databases or resources. In this collection, we bring together online tutorials and videos introducing knowledge and skills pivotal to biocuration, including ontologies, programming...

Scientific topics: Database management, Ontology and terminology, Natural language processing

Keywords: Programmatic access, Programming, Text mining, Biocuration, Biocurators, User experience, UX

Resource type: e-learning

Workflows

Computational workflows allow for automation of multi-step analyses and support the reproducibility of analyses. This tutorial provides a short introduction to workflows for the analysis of life sciences data, providing examples of platforms for creating workflows and the considerations required...

Scientific topics: Workflows

Keywords: Galaxy, NextFlow, SnakeMake

Resource type: e-learning

Finding and using publicly available data

Sharing knowledge and data in the life sciences allows us to learn from each other and built on what others have discovered. This collection of online courses brings together a variety of training, covering topics such as biocuration, open data, restricted access data and finding publicly...

Resource type: e-learning

Using publicly available data

Publicly available data, generated by scientists from around the world, across all areas of the life sciences, is made available through openly accessible data resources. Discover more about what publicly available data is, with examples from the life sciences and details on how you can use...

Keywords: Publicly available data, Open data, Licences, Programmatic access, Data management

Resource type: e-learning

Chemical biology

This curated pathway brings together a number of online tutorials and recorded webinars to provide an introduction to chemical biology, a brief tour of the related informatics resources available from EMBL-EBI, including ChEMBL, Reactome and Metabolights.

Scientific topics: Chemical biology, Drug discovery

Resource type: e-learning

Introduction to CATH database

This quick tour will introduce you to CATH, a resource that provides structural classification of protein domains, allowing you to explore the structure and function of your own proteins of interest.

Scientific topics: Protein structure analysis, Structure analysis

Keywords: Protein superfamily, Structural classification, CATH domain

Resource type: e-learning

2022 highlights

In 2022, we continued to develop a huge range of online training from trainers across EMBL-EBI and beyond, from a series of webinars discussing the impact of the protein structure database, AlphaFold, to a collection on biocuration and the skills required to be a biocurator. To celebrate this...

Scientific topics: Bioinformatics

Keywords: Introduction

Resource type: e-learning

Open Targets informatics tools

This quick tour provides a brief introduction to Open Targets, an industry-academia collaboration, and the informatics tools it maintains.

Scientific topics: Drug development, Drug discovery

Resource type: e-learning

EMBL-EBI Tools

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.

Scientific topics: Bioinformatics, Genetic variation, Protein structure analysis, Sequence analysis

Keywords: Introduction, Tools

Resource type: e-learning

A guide to...

Bioinformatics brings together concepts from biology, computer science and mathematics to build resources for analysing complex and big data in life sciences. This online tutorial will help you explore some concepts and resources in bioinformatics with videos presented by experts from EMBL-EBI...

Resource type: e-learning

MGnify portal

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 MGnify resource.

Scientific topics: Metagenomic sequencing, Metatranscriptomics, Sequencing

Resource type: e-learning

COVID-19 Data Portal

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.

Scientific topics: Bioinformatics, Virology

Keywords: COVID-19, SARS-CoV-2, Corona virus

Resource type: e-learning

Machine learning in drug discovery

What is machine learning and how can it be applied in drug discovery to identify or prioritise new drug targets? Find out more with this introduction to machine learning applications in drug discovery using WEKA.

Resource type: e-learning

Introductory bioinformatics

This curated collection brings together a number of online tutorials and recorded webinars to provide an introduction to bioinformatics, a brief tour of the resources available from EMBL-EBI and more details about some of those resources, including Ensembl, UniProt and Expression Atlas.

Scientific topics: Bioinformatics

Keywords: Introduction

Resource type: e-learning

Biomedical data

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...

Scientific topics: Biomedical science, Data acquisition

Keywords: ELSI, Biomedical data, Ethics, Biobanking, Medical data

Resource type: e-learning

PRIDE

This quick tour provides a short introduction to EMBL-EBI's repository for mass spectrometry-based proteomics data, PRIDE.

Scientific topics: Protein modifications, Proteomics experiment

Keywords: Proteomics identifications, ProteomeXchange, Peptide identifications, Post-translational modifications, PTMs

Resource type: e-learning

European Genome-phenome Archive

This quick tour provides a brief introduction to the European Genome-phenome Archive (EGA), a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects.

Scientific topics: Genotype and phenotype

Keywords: EGA, Biomedical data, Phenotype, Genetic data

Resource type: e-learning

ResOps

This course will provide an introduction to cloud computing and some practical experience in building, deploying and running applications in cloud platforms - OpenStack, Google, Amazon and Azure.

Scientific topics: Computer science, Data architecture, analysis and design, Software engineering

Resource type: e-learning

BioModels

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

Scientific topics: Systems biology

Keywords: Systems modelling, Mathematical modelling, Modelling

Resource type: e-learning

EMBL-EBI, programmatically

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...

Scientific topics: Chemical biology, Genetics, Proteins

Keywords: Introduction, API, Programmatic access, REST, PDBe, EVA, Open Targets

Resource type: e-learning

Reactome

This course introduces the analysis tools available via the Reactome pathway database web interface. For a short introduction to Reactome, please visit the Reactome quick tour.

Keywords: Pathway database, Systems biology, Network analysis

Resource type: e-learning

User experience design

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.

Scientific topics: Bioinformatics

Keywords: UX design

Resource type: e-learning

Structural volume data

This course provides a basic introduction to 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 approaches that can be used to compare volumes. It...

Scientific topics: Electron microscopy, Protein structure analysis, Structural biology

Keywords: Structural bioinformatics, Segmentation, Volume matching

Resource type: e-learning

IntAct

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

Scientific topics: Molecular interactions, pathways and networks

Keywords: Molecular interaction data

Resource type: e-learning

Cellular Microscopy Phenotype Ontology

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.

Scientific topics: Ontology and terminology

Keywords: CMPO, Microscopy, Imaging, Controlled vocabulary

Resource type: e-learning