27 September - 1 October 2021

Mathematics of life: Modelling molecular mechanisms

This course will provide participants with an introduction and hands-on training on modelling approaches, tools and resources used in systems biology as well as touch on network analysis. Computer models are increasingly used to understand the essential processes of biology. Researchers in academic institutions as well as the pharmaceutical industry use mathematical models to generate hypotheses on how complex biomolecular systems work. Modelling of biochemical pathways deregulated in disease conditions can offer mechanistic insights into the pathology, help to elucidate mechanisms behind drug action, and predict the dose required for treatment thus facilitating fundamental research and drug discovery. This course will provide a helpful introduction to tools and resources used in this scientific field. The course will involve participants learning via pre-recorded lectures, live presentations, trainer Q&A sessions and hands-on tutorials. The content will be delivered over Zoom, with additional text communication over Slack.  In order to make the most out of the course, you should make sure to have a stable internet connection throughout the week. Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Trainers will be available to provide support, answer questions, and further explain the analysis during these practicals. Selected participants will be sent materials prior to the course. These might include pre-recorded talks and required reading that will be essential to fully understand the course. Participants will need to be available between the hours of 09:30-17:15 BST each day of the course.

Jane Reynolds

27 September - 1 October 2021

Bioinformatics for Immunologists

Run jointly with Wellcome Connecting Science, this course will provide participants with an introduction to a range of bioinformatics resources and approaches applicable to immunological research. The resources introduced during the course will cover a variety of data types, from genomic and proteomic data to computational models, biological pathways, and reaction information. Participants will gain experience of the analysis pipelines for NGS experiments relevant to immunology and will be led through an exploration of this data to identify information of interest. Additionally, participants will be introduced to how data from several sources can be integrated to provide a wider view of their research, thereby enabling them to be more confident users of their own data and that from public sources. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, trainer Q&A sessions and hands-on training. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants before the start of the course. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their machines. Participants will need to be available between the hours of 09:00-17:30 BST each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis during these times.

Wellcome Connecting Science

27 September - 4 October 2021

Genome Engineering: CRISPR/Cas from Cells to Mice

This course will provide hands-on training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR/Cas9 system. Participants will learn design of CRISPR targets using bioinformatics tools, generation of gene knock-outs/knock-ins, and target validation using the most current technologies. The course will be split into two groups (mammalian cells OR mice) based on participants' expertise.

Neil Humphreys, Birgit Koch, Premnath Rajakannu, Elisabeth Zielonka

23 September 2021

The future of preprint peer review

Public review of preprints is rapidly gaining momentum, with expert reviews, commentary and recommendations shared on various preprint platforms. In this webinar we look at the current state of preprint peer review and share our thoughts on the future of the preprint review process. Our first speaker, Tatiana Giraud, a CNRS senior scientist at the University Paris Saclay, Professor at the Ecole Polytechnque and College de France, member of the French Academy of Science and the Peer Community In (PCI) association, will present the PCI initiative, and share her experience reviewing and recommending preprints, her involvement with the PCI initiative, and her outlook on preprint peer review. Next we will hear from Nonia Pariente, the Editor-in-Chief of PLOS Biology, will discuss how editors interact with preprints across PLOS (with some emphasis on PLOS Biology), summarising the results of the PLOS preprint commenting pilot, in which editors looked at preprint comments during the peer-review process, as well as PLOS’es interactions with preprint review initiatives such as Review Commons and Peer Community In. Following on, Thomas Lemberger, Deputy Head of Scientific Publications at EMBO, will present some of the data obtained from running the preprint peer review platform Review Commons. These results will be discussed in the broader context of a cultural shift in the practice of peer review and the role of refereed preprints in the early dissemination of peer reviewed research. Next, Paul Shannon, Head of Technology at eLife, will introduce Sciety, a new web-based tool to enable scholars to discover preprint content via a network of curation and evaluation output. Paul will talk about how Sciety brings peer review, highlights, automated screening and recommendation of preprints together from 16 diverse groups of scientists, while allowing individuals to curate and share lists of preprints to help others navigate the preprint landscape. Finally, Maria Levchenko, Europe PMC Community Manager, will talk about Europe PMC as a unified platform to discover preprints and linked preprint resources, such as community peer reviews. Maria will also look at ways to filter preprints in the absence of journal titles and the role that aggregators like Europe PMC can play to prevent information overload. About the speakers Tatiana Giraud is a CNRS senior scientist at the University Paris Saclay, Professor at the Ecole Polytechnque and College de France, and member of the French Academy of Science. Tatiana Giraud is an evolutionary biologist with broad scientific interests. She has contributed to the understanding of speciation, pathogen virulence, host-pathogen coevolution, biological invasions, evolution of cooperation by kin selection, mating systems, apple-tree and cheese fungi domestication, using theory, experiments, population genetics and genomics. Tatiana Giraud is also a member of the Peer Community In (PCI) association and recommender for PCI Evolutionary Biology, PCI Genomics and PCI Ecology. Nonia Pariente is Editor-in-Chief of the not-for-profit, open access journal PLOS Biology. Nonia trained as a virologist, receiving a PhD from the Autonoma University of Madrid followed by postdoctoral research at the University of California in Los Angeles. In 2007, Nonia joined the EMBO reports editorial team and over 8 years held various editorial roles, joining the launch team of Nature Microbiology in 2015. After handling microbiology on and off at Nature for two years, Nonia became Chief Editor of Nature Microbiology in 2019 and joined PLOS as PLOS Biology Editor-in-Chief in early 2020.  Thomas Lemberger is Deputy Head of Scientific Publications at EMBO (embo.org) in Heidelberg, Germany. Trained as a molecular biologist, Thomas received his PhD at the University of Lausanne, Switzerland. He joined EMBO as scientific editor to launch the open access journal Molecular Systems Biology (msb.embopress.org). He was Chief Editor of the journal for more than 10 years. Thomas is currently responsible for data and technology at EMBO Press. He heads the SourceData project (sourcedata.embo.org), developed the Early Evidence Base site (eeb.embo.org) and leads the development of the peer-review platform Review Commons (reviewcommons.org) at EMBO. Paul Shannon is the Head of Technology at eLife, responsible for technology strategy and delivery, ensuring the team are committed to openness in the products they produce to encourage broad change across the research communication landscape. He is currently leading the development of Sciety, a new web-based tool to enable scholars to discover preprint content via a network of curation and evaluation output. Maria Levchenko is a Community Manager for Europe PMC, an open literature database for life sciences developed by the European Bioinformatics Institute (EMBL-EBI). Europe PMC indexes over 300,000 preprints abstracts and full text COVID-19 preprints from 20 life sciences preprint servers alongside published journal articles. Before joining Europe PMC, Maria obtained a PhD in Biochemistry from Georg-August University in Goettingen, Germany, and has worked with the European Research Council (ERC) Executive Agency. Maria is passionate about innovative solutions in scholarly communications that help the research community to advance scientific knowledge.  

Nonia Pariente, Tatiana Giraud, Maria Levchenko, Paul Shannon, Thomas Lemberger

22 September 2021

Retrieving biological data from EMBL-EBI resources using Dbfetch

Dbfetch provides a single point of access to retrieve biological data entries from various databases at EMBL-EBI. This webinar will provide a brief overview of the Dbfetch service and illustrate various output formats of data retrievable via Dbfetch. In addition to the web browser-based applications of Dbfetch, we will also demonstrate accessing Dbfetch using the API.

Nandana Madhusoodanan, Fabio Madeira

16 September 2021

Exascale-ready cell-level simulations for European Personalised Medicine

Personalised Medicine (PerMed) opens unexplored frontiers to treat diseases at the individual level combining clinical and omics information. However, the performances of the current simulation software are still insufficient to tackle medical problems such as tumour evolution or patient-specific treatments. The challenge is to develop a sustainable roadmap to scale-up the essential software for the cell-level simulation to the new European HPC/Exascale systems. Simulation of cellular mechanistic models are essential for the translation of omic data to medical relevant actions and these should be accessible to the end-users in the appropriate environment of the PerMed-specific big confidential data. The goal of PerMedCoE is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance. It will accomplish so by: Optimising four core applications for cell-level simulations to the new pre-exascale platforms; Integrating PerMed into the new European HPC/Exascale ecosystem, by offering access to HPC/Exascale-adapted and optimised software; Running a comprehensive set of PerMed use cases including simulations of tumour evolution and drug combinations for cancer treatment; & Building the basis for the sustainability of the PerMedCoE by coordinating PerMed and HPC communities, and reaching out to industrial and academic end-users, with use cases, training, expertise, and best practices. The PerMedCoE cell-level simulations will fill the gap between the molecular- and organ-level simulations from the other CoEs with which this project is aligned at different levels. It will connect method developers with HPC, HTC and HPDA experts. Finally, PerMedCoE will work with biomedical consortia and pre-exascale infrastructures, including a substantial co-design effort. About the speaker Alfonso Valencia is a Spanish biologist, ICREA Professor, current director of the Life Sciences department at Barcelona Supercomputing Center (BSC) and of Spanish National Bioinformatics Institute (INB-ISCIII). He received his PhD in molecular biology in 1988 from the Autonomous University of Madrid. From 1989 to 1994 he was a Postdoctoral Fellow in the laboratory of Chris Sander at the European Molecular Biology Laboratory (EMBL) in Heidelberg, studying the evolution of protein function using sequence- and structure-based approaches. In 1994 Valencia formed the Protein Design Group at the Spanish National Center for Biotechnology (CNB). He was leader of the Structural and Computational Biology Group at Spanish National Cancer Research Center (CNIO). From 2015-2018, he was President of the International Society for Computational Biology (ISCB). As computational biologist, the focus of his work is the mechanistic understanding of biological systems, including cancer and other diseases, with a combination of Bioinformatics, Network Biology and Machine Learning approaches. His group has developed systems in the areas of protein structure prediction, protein interactions and protein networks, systems biology, text and data mining, with applications in epigenetic, cancer genomics and disease comorbidity. All these activities converge into the general topic of Personalised Medicine, with particular interest in the interface with Artificial intelligence and High Performance Computing.

Alfonso Valencia

15 September 2021

Getting started with the Open Targets Platform GraphQL API

The Open Targets Platform is a comprehensive research tool that supports systematic identification and prioritisation of potential therapeutic drug targets.‌ By integrating publicly available datasets along with data generated by the Open Targets consortium, the Platform builds and scores target-disease associations. Users can also explore relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships. This webinar will provide an overview of the GraphQL API that powers the Open Targets Platform. The API provides multiple endpoints that support language-agnostic queries for a single entity or target-disease association. Users can also browse the schema to see available API fields and run sample queries using the API playground. During the webinar, participants will have access to interactive walkthroughs and API queries that can be run directly in their browser. There will also be sample Python and R scripts that they can run to test different endpoints.

Andrew Hercules, Helena Cornu

15 September - 17 September 2021

Multiomics to Mechanisms: Challenges in Data Integration

The current speed at which high-throughput data are produced and the growing number of studies that use not only one but multiple omics technologies on the same samples offers tremendous opportunities for enhancing our molecular understanding of biological systems. One of the biggest challenges in the era of multiomics is the integration and interpretation of the diverse large-scale omics data in a way that provides biological insights. This requires the development of statistical, mathematical and computational tools and - equally important - experimental strategies to follow up on hypotheses generated by large-scale data. Together, these computational and experimental tools will enable us to address novel questions and identify biological mechanisms.

Nevan Krogan, Uwe Sauer, Judith Zaugg

14 September - 16 September 2021

Virtual Ensembl REST-API Workshop, 14th-16th Sept

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

Ben Moore

8 September 2021

How to interpret AlphaFold structures

This webinar will introduce AlphaFold system for prediction and interpretation of protein structures. This webinar is designed for experimental biologists who wish to understand the strengths and limitations of AlphaFold and use the models to guide their experimental studies. In this webinar we will provide an overview for the AlphaFold method and statistics that can be used to understand the reliability of the models. We will also introduce the AlphaFold Database, which provides hundreds of thousands of ready-made models across the tree of life, as well as highlight the AlphaFold Open Source and Colab notebooks that can be used to generate structures of sequences not yet available within the AlphaFold Database.  We will conclude by demonstrating a range of use cases followed by a question and answer session with all the presenters.

Alex Bateman, Sameer Velankar, Kathryn Tunyasuvakool, Sergey Ovchinnikov, Pedro Beltrao, Bálint Mészáros

7 September - 9 September 2021

Virtual Ensembl Browser Workshop, 7th-9th Sept

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.

Michal Szpak

7 September - 10 September 2021

Protein Synthesis and Translational Control

The regulation of mRNA translation is a process required to maintain cell homeostasis, and its malfunction can lead to disease. In recent years, advances in high-throughput and microscopy methods have revealed findings that challenge hitherto established dogmas, such as extensive translation in “untranslated” regions of a transcript, pervasive initiation from non-AUG codons, heterogeneity and specialization of the ribosome or specialized roles for 'general' translation factors. The influence of epitranscriptomics and physical transitions in translation, or the molecular mechanisms underlying ribosome quality control are just examples where rapid progress is impacting our view of translation.

Fátima Gebauer, Matthias W. Hentze, Jerry Pelletier, Christian Spahn

6 September - 10 September 2021

In-situ CLEM at Room Temperature and in cryo

Correlative Light and Electron Microscopy (CLEM) allows precise localisation of an event of interest within cells and tissues. During this course, we will focus on a specific method that has been developed at EMBL that enables the location of fluorescent proteins with high accuracy at the ultrastructural level. The course will cover both the theory and practicals of high precision CLEM, as well as opportunities to discuss their research with CLEM experts and receive practical and troubleshooting advice.

Ori Avinoam, Rachel Mellwig, Paolo Ronchi, Martin Schorb

30 August - 2 September 2021

Gene Expression at Spatial Resolution

This course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics. The Visium Spatial Gene Expression Solution incorporates unbiased, high-throughput total mRNA analysis for intact tissue sections with morphological context, offering a previously inaccessible view of tissue biology. These two complementary methods to study tissue come together on Visium Spatial Gene Expression slides. Through both theoretical sessions as well as extensive hands-on practical work the participants will learn the entire workflow of sample preparation of fresh-frozen tissue samples, fixation and optimisation of tissue permeabilisation and sequencing library preparation. Utilising the 10x Genomics Loupe Browser pipeline, the participants will also have hands-on training of spatial transcriptomics data analysis.

V. Benes, K. Danielski, E. Zielonka

29 August - 1 September 2021

The Mobile Genome: Genetic and Physiological Impacts of Transposable Elements

Although often disparaged as “junk” DNA, it is now undeniable that transposable element (TE) activity has significantly shaped the structure and function of all genomes, ranging from bacteria to humans. TEs are major drivers of genetic diversity and contribute to human disease. Remarkably, recent research has shown that TE-derived sequences also can be co-opted by the host to play important roles in gene expression, early development, immunity, neuronal diversification, and, perhaps, aging. The goal of this conference is to assemble world-leading experts from diverse fields including genomics, epigenetics, structural biology, developmental biology, immunology, cancer biology and neurobiology, to discuss the broad impacts of TEs on organismal biology. It will provide a venue for cross-disciplinary discussions, with the goal of catalysing inter-disciplinary collaborations to address emerging questions in these scientific fields.

Orsolya Barabas, Julius F. Brennecke, Jose L. Garcia-Perez, John V. Moran

23 August - 27 August 2021

Advanced Fluorescence Imaging Techniques

This practical course will cover advanced light microscopy techniques and participants will learn how to derive qualitative and quantitative insights on molecular mechanisms in cells and developing organisms.

P. Barthelemy, J. Delgado, A. Halavatyi, S. Marawske, S. Reither

2 August - 10 August 2021

CABANA Workshop: Genomic and transcriptomic resources for eukaryotic species

This course is intended to be a gentle introduction to the computational resources available for analysis of omics data in eukaryotic species. Specifically, we will cover: 1) an optional Linux crash course; 2) file formats commonly used in NGS data analysis; 3) web resources available for the analysis of eukaryotic omics data; 4) common bioinformatics pipelines used to analyse genomic/transcriptomic data from eukaryotic species (sequence alignment, phylogenetic tree reconstruction, variant detection, RNA-Seq and data visualization in genome browsers). Live components of the course will run around 09:00-12:00 BRT and you are encouraged to use the afternoon to practice, using a specified forum or communication method to ask for support. Support will end around 17:00 BRT each day.

Francisco Lobo

26 July - 30 July 2021

FISHing for RNAs: Classical to Single Molecule Approaches

This course aims to highlight three powerful RNA visualisation techniques in histological tissue samples. During this course, the participants will learn to validate the cellular localisation of candidate genes from transcriptome studies through conventional ISH and, the more recent cutting-edge, smFISH (Single Molecule Fluorescent ISH) and HCR-ISH (Hybridization Chain Reaction), based RNA ISH hybridisation methods. Additionally, the course will also cover essential tissue embedding protocols that are adapted for use in visually interrogating RNA transcripts in mammalian tissues.

I. Gaspar, E. Perlas, E. Zielonka

19 July - 30 July 2021

Basics to Advanced Genome Annotations at Ensembl and REST Application Programming Interfaces (APIs)

We are organising this high quality workshop for the participants interested in the genomics, bioinformatics, and genome annotations. In this workshop, one of the trainers from European Bioinformatics Institute (EMBL-EBI), United Kingdom, will provide the hands-on training sessions of 'Ensembl Genome browser, and Ensembl REST Application Programming Interfaces (APIs)'. This workshop will cover the topics from basics to advanced techniques of genome annotations. This workshop will be equally useful for the researchers working with any domain of life (e.g. microbes, animals, fungus, and plants). At the successful completion of this workshop, participants will be become expert of all the modules of Ensembl Genome browser, and Ensembl REST Application Programming Interfaces (APIs) for their research.  

NextGenHelper

12 July - 16 July 2021

Proteomics bioinformatics

Hands-on training in the basics of mass spectrometry, proteomics bioinformatics, and related methods and resources Run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences, this popular course provides hands-on training in the basics of mass spectrometry (MS) and proteomics bioinformatics approaches, search engines and post-processing software, quantitative proteomics approaches and related statistical concepts, MS proteomics data repositories and public data re-use, how to employ existing databases for protein analysis, perform the annotation of subsequent protein lists and the incorporation of information from molecular interaction and pathway databases. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and two weeks before the course, there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 09:00-17:30 BST each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis during these times.

Advanced courses

12 July - 16 July 2021

Microscopy data analysis: Machine learning and the BioImage Archive

Develop programmatic skills for the analysis of bioimage data. This course will introduce programmatic approaches used in the analysis of bioimage data via the BioImage Archive. The content will explore a variety of data types including electron microscopy, cell and tissue microscopy, and miscellaneous or multi-modal imaging data. Participants will cover contemporary biological image analysis with an emphasis on machine learning and advanced image analysis. Further instruction will be offered using applications such as ZeroCostDL4Mic, ilastik, the BioImage Model Zoo, and CellProfiler. The organisers welcome applications from scientists who have specific research questions that look to use publicly available data held in the BioImage Archive and can demonstrate use cases for the resource. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.  Pre-recorded material may be provided before the course starts that participants will need to watch, read or work through to gain the most out of the actual training event. In the week before the course, there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 09:30-17:30 BST each day of the course. Trainers will be available to assist, answer questions, and provide further explanations during these times.

Marina Pujol

12 July - 16 July 2021

Super-Resolution Microscopy: Time-Resolved STED Nanoscopy

This five day advanced course on fluorescence super-resolution microscopy will cover the theory and practical application of current super-resolution microscopy techniques to biological questions.

M. Lampe, R. Pepperkok, U. Schwarz

7 July 2021

A guide to EBI Search

This webinar will introduce the EBI Search service. EBI Search is a text search engine that provides easy and uniform access to the biological data resources hosted at EMBL-EBI. It provides up-to-date search results across all of the stored datasets, as well as simple intra-domain navigation via internal cross-references. In addition to the web front-end, there is a RESTful API interface, allowing the search engine to be queried programmatically. The webinar will illustrate both the web application, and take a brief look at the RESTful interface.

Matt Pearce

7 July - 9 July 2021

New Approaches and Concepts in Microbiology

This symposium will cover a broad range of topics in microbiology, including antibiotic-related research, bacterial communities and microbiome, cell biology, regulation & signalling, pathogenesis and evolution. Emphasis will be placed on novel approaches and technologies (from systems-based to single-cell) that drive each field or have the potential to revolutionise future research in microbiology.

30 June 2021

A guide to analysing binding sites in protein structures

This webinar gives an introduction to the information required to effectively interpret ligand binding sites in protein structures. It will highlight tools available at the Protein Data Bank in Europe (PDBe) and PDBe Knowledge Base (PDBe-KB) to analyse ligand binding pockets and interactions. It will also highlight how this information can be used for the design of new inhibitors, through a specific case study.

David Armstrong, James Tolchard

28 June - 2 July 2021

Summer school in bioinformatics

This virtual course, organised in association with Wellcome Genome Campus, Scientific Conferences and Advanced Courses, provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research. Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management and reproducibility. To enable specific exploration of resources in their particular field of interest, participants will be divided into focused groups to work on a small project set by EMBL-EBI resource and research staff, ending in a presentation from each group on the final day of the course to bring together learnings from all participants. The course includes training and mentoring by experts from EMBL-EBI and external institutes. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 09:30-17:30 BST each day of the course. Trainers will be available to assist, answer questions and further explain the analysis during these times. Group projects Genome variation across human populations Natural variation between individuals or between different human populations is a result of genome mutations throughout evolutionary history. Some mutations may become fixed because of their beneficial effect while most drift among individuals. During this project, you will investigate genomic variation between two separate human populations of European and Asian descent. Using sequence data from a number of individuals from each population, you will use a range of bioinformatics tools to discover variants that exist between them. In the second section of the project, you will attempt to analyse the functional consequences of the variants you have identified, linking them to phenotypes. Modelling cell signalling pathways Curating models of biological processes is an effective training in computational systems biology, where the curators gain an integrative knowledge of biological systems, modelling and bioinformatics. You will learn to encode and simulate ordinary differential equation models of signalling pathways from a recent publication using user-friendly software such as COPASI even without extensive mathematical background. You will learn to perform in silco experiments, new predictions and develop hypotheses. Furthermore, you will learn how to annotate models and re-use pre-existing models from open repositories such as BioModels. Interpreting functional information from large scale protein structure data This project will introduce you to the wealth of publicly available data in the Protein Data Bank (PDB) and give you the opportunity to investigate how large subsets of structure data can be used to analyse protein features and determine function. In the project you will learn how to: identify relevant protein structures, collate and interpret functional information, implement this process programmatically. Networks and pathways This project will cover typical bioinformatics analysis steps needed to put differentially expressed genes into a wider biological context. You will start with gene expression data (RNA-seq) to build an initial interaction network. Next, you will learn to combine public network datasets, identify key regulators of biological pathways and explore biological function through network analysis. You will get first-hand experience in integration and co-visualising with additional data and functional enrichment analysis. All this helps to put the initial results into a previously known context and provide hypotheses for potential follow up experiments. We will use Cytoscape, Expression Atlas, g:Profiler, StringDb, among other tools. We also may give a few R packages a try. Multiomics analysis of human disease In this project, you will explore the benefits of multiomics data integration to investigate the onset and progression of human disease. You will analyse plasma proteomics and metabolomics data from patients and healthy controls to identify immunological and physiological changes that are associated with disease severity. You will exploit differential analysis, dimensionality reduction methods and multiomics integration tools to identify features that distinguish different patient groups, perform functional enrichment analysis, and visualise metabolomics and proteomics correlation networks in Cytoscape. Finally, you will build basic machine learning models to predict the course of disease and to propose therapeutic interventions that are likely to be most effective at different disease stages Posters All participants are expected to provide a poster for the course. We expect the posters to provide other delegates and trainers with information on your research and to act as a talking point. They should give an idea of the work you are engaged in, what you are planning to do next, any challenges you have experienced in your research and anything of interest that might be useful for other delegates. Further information about posters will be provided following application selections.

Scientific conferences

28 June - 2 July 2021

Advanced Methods in Bioimage Analysis

The course focuses on the highly interdisciplinary topic of metagenomics. During the course, participants will receive an overview of state-of-the-art genomic technologies and bioinformatic tools. A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines.

R. Haase, A. Klemm, S. Nørrelykke, P. Paul-Gilloteaux, C. Tischer, C. Wahlby

23 June 2021

A guide to proteomics data analysis using UniProt and InterPro

This webinar will give a brief introduction to the UniProt and InterPro websites and highlight resources available that proteomic scientists or other users with protein datasets may find useful to analyse their data. This will encompass searching by protein sequence, identifying protein peptides, and retrieving sequence-specific features and functional information both curated and predicted. The UniProt database aims to provide a high quality, comprehensive, publicly available protein database, annotated by expert curators. It contains detailed information on protein function, interactions, pathways, protein sequences and isoforms, disease variants and post-translational modifications.  InterPro is a database that helps users to understand the possible functions of protein sequences by identifying what family it belongs to or what domains and motifs it contains. InterPro provides the world’s most comprehensive predictions by combining predictions from 13 member databases. Both databases are  freely available resources that are actively maintained with bi-monthly data updates, additionally all data is available through intuitive user interfaces, APIs, and data downloads.  

Typhaine Paysan-Lafosse, Emily Bowler-Barnett, Paul Denny

21 June 2021

Preprints 101 for authors

Joint webinar with ASAPbio, Sumeet Pal Singh and Europe PMC Preprints enable researchers to rapidly share their work publicly before the formal peer review process. In this webinar you will learn more about preprints and their benefits for the research community from ASAPbio (Accelerating Science and Publication in biology); will hear an author’s perspective on posting preprints from Sumeet Pal Singh, a group leader at IRIBHM, ULB; and will find out how to incorporate preprints in your literature search routine by using the preprint discovery tools developed by Europe PMC. ASAPbio is a scientist-driven nonprofit that promotes the productive use of preprints in the life sciences. ASAPbio coordinates a global community of researchers and stakeholders interested in preprints and develops resources to advance best practices and help researchers make informed decisions about communicating their work via preprints. Iratxe Puebla, Associate Director at ASAPbio, will provide an overview of preprints and their growth in the life sciences, and cover things researchers should consider before posting a preprint.  Sumeet Pal Singh is a group leader at IRIBHM, ULB and an ASAPbio fellow. Sumeet will describe the journey of publishing his first senior author paper from a preprint to a peer-reviewed article, as well as the details related to the timing of posting a preprint and its relationship to the peer-review process. He will outline a new path provided by Review Commons that allows the authors to receive peer reviews for their manuscript prior to a journal submission, as well as post the reviewer’s comments and the authors’ response on preprint server (bioRxiv). Europe PMC indexes over 300,000 preprints abstracts and full text COVID-19 preprints from 20 life sciences preprint servers alongside published journal articles. Preprints in Europe PMC are linked to citations, data, community peer reviews and more. In this part of the talk we will demonstrate how to find relevant preprints, cite and track preprint citations, claim preprints to ORCID, or discover relevant resources.

Iratxe Puebla, Sumeet Pal Singh, Maria Levchenko

21 June - 25 June 2021

Curso Internacional: Estrategias bioinformáticas para el estudio de enfermedades tropicales desatendidas (ETDs)

Este curso ofrecerá entrenamiento en herramientas y estrategias bioinformáticas para el estudio de enfermedades tropicales desde una perspectiva molecular. Las sesiones cubrirán el análisis de datos provenientes de múltiples repositorios ómicos con información relacionada sobre los patógenos causantes de las enfermedades. El objetivo principal es explorar metodologías para el descubrimiento de blancos moleculares e inhibidores que sirvan para modularlos, usando una perspectiva traslacional de los hallazgos computacionales. Información estructural de las proteínas y redes de interacción proteína-proteína serán cubiertas en detalle, además de otros recursos disponibles en la web.  El curso será transmitido via Zoom. Los participantes deben asegurar que tengán activo y funcionando el sistema de audio para escuchar y hablar durante el evento.

Rodrigo Ochoa

21 June - 25 June 2021

Systems biology: From large datasets to biological insight

This course, run with Wellcome Connecting Science, covers the use of multi-omics data and methodologies in systems biology. The content will explore a range of approaches - ranging from network inference to machine learning - that can be used to extract biological insights from varied data types. Together these techniques will provide participants with a useful toolkit for designing new strategies to extract relevant information and understanding from large-scale biological data. The motivation for running this course is a result of advances in computer science and high-performance computing that have led to groundbreaking developments in systems biology model inference. With the comparable increase of publicly-available, large-scale biological data, the challenge now lies in interpreting them in a biologically valuable manner. Likewise, machine learning approaches are making a significant impact in our analysis of large omics datasets and the extraction of useful biological knowledge. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines; however, a small app will need to be installed to access the compute infrastructure. Participants will need to be available between the hours of 09:30-17:30 BST each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis during these times.

Advanced Courses

16 June 2021

A guide to the maintenance of life science data by biocurators

The aim of this webinar is to introduce you to the principles of how biological data is archived, curated, maintained and updated by expert biocurators and how you can contribute.

Claire O’Donovan, Deborah Harrus, Birgit Meldal, Rossana Zaru

15 June - 17 June 2021

Open Virtual Ensembl API Workshop

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

Michal Szpak

15 June - 17 June 2021

Bioinformatics for principal investigators

This course has been designed to provide Principal Investigators (PI's) working in the life sciences with an introduction to the challenges of working with biological data as a research leader. Starting with a look at where bioinformatics and data science fits into their research teams, the course will enable PI’s to take a strategic look at the requirements for undertaking such work and how bioinformatics capacity can be developed from personnel through to computational needs.  It will additionally provide guidance on strategies for managing data and the importance of data sharing; how to work with computational collaborators and what resources are available across the life sciences to support such work. During this course we will not be teaching hands-on bioinformatics analysis, but we will be signposting appropriate training resources to upskill you and your team.

Jane Reynolds

14 June - 16 June 2021

Predicting Evolution

The conference will explore the evolution of biological systems at different levels: from genes and molecules to organism development and ecology. As such, we have invited leaders in their respective fields across various scales of evolution: molecular, network, microbial, developmental, and community. Particular emphasis for this conference will be placed on understanding evolution through mechanistic biology. We will explore recent advances in experimental and theoretical approaches to study how genetic and non-genetic changes drive and constrain evolution.

9 June 2021

A guide to sequence similarity search for biomolecular sequences

This webinar aims to provide an introduction to basic concepts in sequence similarity search with a focus on the similarity search tools and databases provided by EMBL-EBI. In this webinar, we will also provide useful tips on which tools and databases to use, and explore some examples of use cases using BLAST.  

Nandana Madhusoodanan

8 June - 10 June 2021

Open Virtual Ensembl Browser Workshop

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.

Michal Szpak

4 June - 11 June 2021

BioExcel Summer School on Biomolecular Simulations 2021

The summer school will include lectures and hands-on sessions on the following topics: Molecular Dynamics simulations Biomolecular Docking Free energy calculations Advanced sampling methods (Metadynamics) BioExcel Building Blocks (BioBB) Quantum mechanics/molecular mechanics (QM/MM) During the hands-on computer practicals you will make use of the BioExcel flagship software and tools: e.g. GROMACS, HADDOCK, PMX, BioBB, and CP2K. The trainers, developers and/or experts in the use of the software, will provide guidance and support.

Michelle Mendonca

2 June 2021

A guide to multiomics pathway analysis

In this webinar we will discuss how to perform comparative multi-omics pathway analyses using the ReactomeGSA pathway analysis system. We will be comparing independent studies that use different 'omics approaches, as well as different 'omics measurements from the same study. Additionally, we will be looking at simple to use methods to integrate public datasets into one's own analysis. Finally, we will use the ReactomeGSA R package to improve the annotations of single-cell RNAseq data. During the webinar we will use Reactome's web interface as well as the ReactomeGSA Bioconductor R package.

Johannes Griss

26 May 2021

A guide to molecular interactions

During this webinar, we will give you an introduction to molecular interactions and how to find these through the molecular interaction database IntAct. We will show you examples of how you can search for interaction data, how to create molecular interaction networks using our network viewer based on Cytoscape.js and how to download this data for further analysis. We will also have a quick look at two other resources, PSICQUIC and IMEx, that integrate molecular interactions from several sources.

Birgit Meldal, Kalpana Panneerselvam

25 May 2021

PsyArXiv preprints in Europe PMC

Psychological sciences preprints from PsyArXiv are now searchable in Europe PMC, an open database of life sciences literature. Join us for this live demo to learn how to find PsyArXiv preprints in Europe PMC, how to explore links to data, citations, comments or open peer reviews, how to claim preprints to your ORCID record, and more.

Maria Levchenko, Jack Arnal

25 May - 27 May 2021

Open Virtual Ensembl API Workshop

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

Emily Perry

25 May - 27 May 2021

BioMalPar XVII: Biology and Pathology of the Malaria Parasite

The 17th BioMalPar conference will address fundamental questions on the biology of the malaria parasite, its vector, the immune response of the host, the disease that it causes and the latest technological approaches. The conference will emphasise training and networking, with a focus on allowing speaking opportunities for early career researchers.

19 May 2021

A guide to identifying and prioritising drug targets with the Open Targets Platform

The Open Targets Platform - https://platform.opentargets.org/ - is a comprehensive research tool that supports systematic identification and prioritisation of potential therapeutic drug targets.‌ By integrating publicly available datasets along with data generated by the Open Targets consortium, the Platform builds and scores target-disease associations. Users can also explore relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships. This webinar will provide an overview of the Open Targets Platform which is a freely available resource that is actively maintained with bi-monthly data updates. All data is available through an intuitive user interface, a GraphQL API, and data downloads. Likewise, the pipeline and infrastructure codebases are open-source and can be used to create a self-hosted private instance of the Platform with custom data.

Helena Cornu, Andrew Hercules

19 May - 20 May 2021

Ri.Logistica

The RI.Logistica conference is an online event designed for research infrastructures (RIs), their users and collaborators, companies in the supply chain management and governmental authorities to discuss all aspects of logistics critical for research facilities and laboratories.

18 May - 20 May 2021

Open Virtual Ensembl Browser Workshop

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.

Michal Szpak

18 May - 20 May 2021

Managing a bioinformatics core facility

This virtual knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL-EBI’s service teams, from each other, and from potential users of their services. These facilities play an essential role in enabling research in the molecular life sciences. The landscape is constantly evolving as new research tools emerge, as experiments become increasingly data intensive, and as their clients – experimental researchers – become more exposed to the power of data-driven biology. Virtual workshop The workshop will involve participants learning via pre-recorded lectures, live presentations, and trainer Q&A sessions. The content will be delivered over Zoom, with additional text communication over Slack.  Live sessions will include both group and individual activities, alongside optional social and networking opportunities. Participants will need to be available between the hours of 08:45 - 15:30 BST each day. Programme may be subject to slight changes before registration.

Marina Pujol

17 May - 21 May 2021

Cancer genomics

This course will focus on the analysis of data from genomic studies of cancer.  Lectures and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data, whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the lecturers. Virtual course The course will involve participants learning via pre-recorded lectures, live presentations, and trainer Q&A sessions. The content will be delivered over Zoom, with additional text communication over Slack. Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Trainers will be available to provide support, answer questions, and further explain the analysis during these practicals. Participants will need to be available between the hours of 09:30-18:00 BST each day of the course.

Jane Reynolds

17 May - 25 May 2021

Measuring Translational Dynamics by Ribosome Profiling

Regulation of translation is a key layer in the control of gene expression, playing a critical role in many biological and pathophysiological settings. In the last decade, methodological advances have provided comprehensive insights into cellular transcriptomes and proteomes, however, the systems-wide analysis of translation has remained an unsolved experimental challenge. The recent advent of ‘ribosome-profiling’ has provided the methodological basis for comprehensive transcriptome-wide analyses of translation at sub-codon resolution by the precise and high-throughput determination of ribosomal positions on mRNA. Its application in a variety of organisms yielded novel insights into protein synthesis and its dynamic regulation, significantly advancing our understanding of the post-transcriptional regulation of gene expression. This practical course will combine theoretical sessions with hands-on experimentation and computation emphasising the key steps of the protocol and computational quality control.

17 May - 20 May 2021

Chromatin and Epigenetics

Epigenetics refers to heritable changes in gene expression that do not involve changes to the underlying DNA sequence. At least three systems including DNA methylation, histone modifications and non-coding RNAs (ncRNA) are considered to play fundamental roles in epigenetic regulation. Research over the last two decades has uncovered the role of epigenetics in a variety of human disorders and fatal diseases. Moreover influence of age, environment, lifestyle, and disease state on epigenetic states is being increasingly appreciated and actively studied. This conference provides an international forum for cutting edge research in chromatin and epigenetics. It provides the “focal hub” for people to present their research and exchange ideas in a virtual format. Renowned speakers will cover the latest advances in the field.

13 May - 13 May 2021

EMBL-EBI workshop: The Open University, 2021 (Virtual)

This workshop will introduce participants to the publicly-available data resources provided by EMBL-EBI. It will serve to introduce the organisation, the role it plays in the wider life science data landscape, and provide a high-level overview of the data, resources and basic tools available to researchers. Participants will have the opportunity to ask questions, spend time exploring data of interest, and providing feedback that will help plan for future workshops that will offer a more in-depth explanation of key resources.

Tom Hancocks

12 May 2021

A guide to exploring drug-like compounds and their biological targets using ChEMBL

ChEMBL is a widely-used database of bioactivity data that links drug-like compounds to their biological targets and has applications in drug discovery. This webinar will provide an overview of the ChEMBL web interface, data types within ChEMBL and how ChEMBL can be used to answer questions relevant to medicinal chemistry and drug discovery.

Emma Manners, Fiona Hunter

10 May - 12 May 2021

AQUA-FAANG: Bioinformatic analysis of regulatory elements

This course will provide training on two bioinformatic pipeline core assays defined by the FAANG initiative for the study of regulatory elements in fish genomes. The content will cover the use of ChIP-seq (chromatin immunoprecipitation sequencing) and ATAC-seq (assay for transposase-accessible chromatin sequencing). Participants will be introduced to key bioinformatic steps involved in data analysis and interpretation, from raw sequence data through to peak calling, interpretation of data quality, and data integration including by use of genome segmentation methods. The concept of software containers and their use for reproducible pipeline deployment will also be explored. Please visit the AQUA-FAANG website for more information on the project.

Juanita Riveros

6 May 2021

Contributing to the UniProt Knowledgebase: how you can help

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.  

Cecilia Arighi

5 May 2021

A guide to organising data associated to a publication using BioStudies

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 may include links to parts of data deposited into specialised community databases at EMBL-EBI and elsewhere, as well as data that have no other natural home such as supplemental data. In this webinar we will look at a range of examples for data submission and access, including large image datasets.

Ugis Sarkans

4 May - 7 May 2021

The Identity and Evolution of Cell Types

Cell types are the fundamental units of multicellular life, which have diversified during animal evolution. Single-cell genomics/transcriptomics technologies and new insights into the molecular mechanisms specifying cell type identity allow us to explore this process in unprecedented detail. Our second EMBO | EMBL Symposium on the identity and evolution of cell types will re-assemble the growing community of scientists pushing forward the limits of this exciting new field. Based on the very positive feedback on the first symposium, we will keep session topics such as the cell type tree of life, and genetic and epigenetic mechanisms of cell type differentiation in development. We have also identified exciting new areas in our rapidly growing field – such as molecular mechanisms of cell type origination in evolution; the evolutionary assembly of cellular modules; different aspects of neuronal identity; and sensory cell type diversification in vertebrates. For this meeting, we will also provide extended discussion time within and between sessions and organize a final discussion.

D. Arendt, C. Baker, M.A. Tosches, G. Wagner

3 May - 7 May 2021

Quantitative Proteomics: Strategies and Tools to Probe Biology

This course will provide both theoretical and practical training in the use of quantitative proteomics approaches.  Participants will learn the principles of current methodologies including label-free, SILAC and TMT as well as targeted proteomics, and they will be trained in the use of bioinformatic tools for data analysis.

27 April - 28 April 2021

EIROforum Conference: Grand Challenges in AI and Data Science

OverviewOrganisers Overview

J. Korbel, J. McEntyre

27 April 2021

Emerging Infectious Diseases and Related Environmental, Clinical and Translational Challenges

This international conference will bring together leading international experts in molecular biology of viruses, infectious diseases and immunology to showcase the progress that the scientific community has achieved in tackling the SARS-CoV-2 pandemic. Particular focus will be given the progress made in vaccine development: from the success story linked to new technological advances in the field to safety aspects and the importance of gaining public trust for the vaccines to be effective, in addition to the lessons learnt and future planning for preparedness in case of emergence of unknown infectious diseases.

26 April - 30 April 2021

Single-cell RNA-seq & network analysis using Galaxy and Cytoscape

This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to cell cluster comparisons. In addition to running a basic pipeline, participants will explore single cell networks using Cytoscape. Please note that although participants will not be able to use their own data during the course practicals, there will be ample time to discuss their research and ideas with both course participants and trainers.  As part of this, participants will present lightning talks on their research topics. Near the end of the course, participants will engage in small group discussion about their research challenges and problems with each other and the trainers at the ‘Talk with Trainers’. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI’s virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 08:00-17:30 GMT each day of the course. Trainers will be available to assist, answer questions and further explain the analysis during these times.

Meredith Willmott

22 April 2021

UniProtKB: Increasing our understanding of neurodegenerative disorders through data curation

This webinar will give an overview on how molecular data of proteins associated with neurodegenerative diseases is provided in UniProtKB, including information on molecular protein function, protein-protein interactions, sequence variants, pathways, and drug candidates.

Yvonne Lussi

21 April 2021

A guide to RNA families

Rfam is a database of RNA families that currently contains almost 4,000 families. Together with the Infernal software, Rfam is commonly used to annotate non-coding RNAs in newly sequenced genomes. In this webinar, we will give an overview of the data available in Rfam and give a live demo of annotating a genome with non-coding RNAs using Rfam and the Infernal software. We will be joined by a guest speaker, Prof Sam Griffiths-Jones (University of Manchester), who founded Rfam in 2002 and is now responsible for miRBase, the microRNA registry. We will discuss the ongoing efforts to synchronise the microRNA families between Rfam and miRBase.

Anton Petrov, Sam Griffiths-Jones, Nancy Ontiveros-Palacios, Eric Nawrocki

15 April 2021

Ethics/ELSI considerations - From FAIR to fair data sharing

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.

Melanie Goisauf

14 April 2021

A guide to exploring genes and genomes with Ensembl

Ensembl is a genome browser that provides a single point access to annotated gene and genomes. This webinar will provide a brief overview to the Ensembl browser and demonstrate how you can access information about genes or genomes of your interest. We will also showcase the data types and tools available at Ensembl which can help your research. 

Aleena Mushtaq

12 April - 19 April 2021

Microbial Metagenomics: A 360º Approach

Organisers: V. Benes, G. D'Auria, J. E. González-Pastor, E. Zielonka The course focuses on the highly interdisciplinary topic of metagenomics. During the course, participants will receive an overview of state-of-the-art genomic technologies and bioinformatic tools. A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines.

31 March 2021

Submitting your genome wide association study data to the GWAS Catalog

The GWAS Catalog is a comprehensive and highly accessed resource for GWAS data, including full summary statistics. We encourage authors to submit their data to us, to make them accessible and reusable by the wider GWAS community. This webinar provides a step-by-step guide to the submission process, including setting up your account, converting your summary statistics to our standard format, providing metadata and receiving accession numbers to cite in publications.    

Elliot Sollis

31 March - 12 May 2021

SAXS (Small Angle X-Ray Scattering) for Biomolecules

Small angle X-ray scattering (SAXS) is a powerful method to obtain information on size and shape of macromolecules in solution. In this introductory course we will cover basics of SAXS, instrumentation, sample preparation, modelling techniques and complementary use with other methods. The course is aimed at students/researchers interested in structural biology methods. Time will be spent in understanding how to read/interpret SAXS sections of integrated structural biology research papers.

29 March - 30 March 2021

Strategy for Future EMBL Research Infrastructures in the Life Sciences in Hamburg

The workshop's main aim is to consult with leading experts and stakeholders about the synergistic use of the future X-ray infrastructures with complementary structural and computational methods. It is planned to review possible future needs and strategies for EMBL infrastructures at and around PETRA IV and to discuss how the interests of the research communities worldwide and in particular those in the EMBL member states could be best taken into account.

25 March 2021

Integrating knowledge of proteins and small molecules with UniProtKB

A complete understanding of biological systems requires integration of knowledge of the regulation and function of small molecule metabolites – the metabolome – with that of genes, transcripts, and proteins (the genome, transcriptome, and metabolome). The UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive, high quality and freely accessible resource of protein sequences and functional information. UniProtKB integrates, interprets and standardizes data from a range of sources including the scientific literature, tools for protein sequence analysis, other knowledge resources and databases, and automatic annotation systems, to provide a detailed overview of the available protein knowledge. This webinar will provide an introduction into how UniProtKB captures and represents knowledge of small molecule metabolites using the Rhea knowledgebase of biochemical reactions, based on the chemical ontology ChEBI, and how UniProt users can access and exploit that knowledge.

Alan Bridge

24 March 2021

Mol*: Improved molecular visualisation at PDBe

This webinar will focus on the use of the online molecular visualisation tool, Mol* at PDBe. We will show basic usage, observation of electron density maps and EM volumes, interrogation of ligand structures, and the visualisation of sequence annotations. We will also highlight the advantages to using Mol* in comparison to other tools and show the different ways the Mol* viewer is presented and accessed on PDBe's pages.

James Tolchard

23 March - 25 March 2021

VIZBI 2021: Visualizing Biological Data

The conference will feature talks from 21 world-leading researchers showcasing visualizations transforming how life scientists view data, and driving key advances in molecular biology, systems biology, biomedical science and ecology.

23 March - 25 March 2021

Ensembl API virtual workshop, 23rd-25th March 2021

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

22 March - 26 March 2021

Introduction to metabolomics analysis

EMBL-EBI plans to deliver the majority of its 2021 events face-to-face with a small number of virtual events. Please note that some events that are currently listed as ‘on-site’ might need to be delivered virtually, depending on the prevailing status of the pandemic at the time. More courses will be added to this programme as our plans develop further.

18 March 2021

How to make training FAIR

There is a wealth of training content developed and delivered across the globe each year, there will be many similar sessions on similar topics all delivered to similar audiences. At the same time, there will be trainers looking for inspiration and ideas on how to approach new topics or on new ways to teach old topics; as well as trainees looking for materials to further their own knowledge. Many trainers (or lecturers/educators etc) do not share their materials, or if materials are shared they are not easily found or re-used by others. During this webinar, we will give you some tips and suggestions on how you can make more of the training materials you produce and encourage others to do the same. FAIR is not just for data - we can make our training materials FAIR too. Join us to find out the benefits of sharing your FAIR materials and some simple ways you can make it easy for others to use your materials in their teaching, or as aids for individuals to learn more. 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.

Anna Swan, Sarah Morgan

17 March 2021

BioSamples: a FAIR sample metadata archive

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

Fuqi Xu

16 March - 18 March 2021

Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture

Synthetic morphogenesis is a novel and exciting field that requires collaboration among traditionally distinct scientific communities, from developmental biologists, to chemists, theoreticians and computational modellers. This symposium will bring together scientists from these different disciplines to discuss the extent to which cells/tissues/organs can be built de novo starting from isolated components.

16 March - 19 March 2021

Introduction to RNA-seq and functional interpretation

Gain an introduction to the technology, data analysis, tools, and resources used in RNA sequencing and transcriptomics. The content will provide a broad overview of the subject area, and introduce participants to basic analysis of transcriptomics data using the command line. It will also highlight key public data repositories and methodologies that can be used to start the biological interpretation of expression data. Topics will be delivered using a mixture of lectures, practical exercises, and open discussions. Computational work during the course will use small, example data-sets; and there will be no opportunity to analyse personal data. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course, there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 09:30-17:30 GMT each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis during these times.

Meredith Wilmott

16 March - 18 March 2021

Virtual Ensembl Browser workshop, 16th-18th March

Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, mine these data with BioMart and visualising your own data in Ensembl.

Michal Szpak

10 March 2021

Introduction to exploring genome-phenome data with EGA

European Genome-phenome Archive (EGA) is a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects. This webinar aims to cover a quick introduction to EGA by exploring topics ranging from searching and accessing data in EGA to interpreting Data Use Ontology (DUO) codes. We will also demonstrate downloading data with an EGA test account. 

Dona Shaju, Giselle Kerry

8 March - 11 March 2021

Friend or Foe: Transcription and RNA Meet DNA Replication and Repair

RNA biology is intimately interlinked with DNA metabolism on multiple levels, and the crosstalk between the two nucleic acids involves potential for both conflicts as well as cooperative relationships. On the one hand, gene expression poses a considerable risk for genome maintenance and vice versa. On the other hand, the machineries involved in RNA and DNA transactions are known to cooperate in several important aspects of nuclear biology. This symposium will bring together scientists studying genome maintenance and the DNA damage response with those investigating the biology of transcription and RNA biology in order to discuss these mutual interactions of DNA and RNA metabolism.

4 March 2021

Practically FAIR

This webinar will focus on practical applications of the FAIR data principles, particularly in the context of clinical bioinformatics. We will highlight several example projects that have put the FAIR principles in practice, and discuss the advantages and some of the challenges involved. ELIXIR Galaxy community (elixir-europe.org/communities/galaxy) promotes the use of Galaxy projects that enhance the FAIRness in data analysis. We will demonstrate the Galaxy services that deliver practical FAIR data analysis with “Single Sign-On” capability provided by ELIXIR-AAI. The aim is to provide (medical) researchers with the practicalities of implementing and using FAIR principles in the context of the CINECA project as applied to translational research at Erasmus University Medical Center. 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.  

Andrew Stubbs

3 March 2021

Annotating your own variation data with the Ensembl Variant Effect Predictor (VEP)

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.

Emily Perry (Pritchard)

1 March - 2 March 2021

Life at the Periphery: Mechanobiology of the Cell Surface

The cell surface – comprising the plasma membrane, the underlying cortical cytoskeleton and in many cell types a cell wall – is a central integrator of cell form and function. Its physico-chemical properties are rapidly modulated to accommodate or drive changes in shape or behaviour and to exchange matter and information with the environment. This symposium will bring together researchers from different communities interested in processes occurring at the cell surface across kingdoms. It will focus on new technologies that empower studies of cell wall, actin and membrane biology, such as advanced imaging in in vitro and in vivo systems, as well as approaches combining molecular biology with computational and biophysical approaches.

1 March - 5 March 2021

Data visualisation for biology: A practical workshop on design, techniques and tools

Please note this course is under review, and the dates are likely to change to later in 2021. Please email courses@ebi.ac.uk if you have any questions.

1 March - 11 March 2021

CABANA workshop: Analysis of crop genomics data

Please note this course was postponed in 2020 due to the COVID-19 pandemic and will take place virtually in 2021. This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping. During the course participants will learn about genotyping experimental design, variant calling, comparative genomics using Ensembl, analyse variation data with Ensembl Variant Effect Predictor and the European Variation Archive and explore concepts of genome wide association studies (GWAS).  The content will explain how to make use of existing public data, retrieve, submit and share your data with the community. It will also provide training on using R in genomics applications for crop genotyping. Trainers will cover the basics of diversity analysis using R, before analyzing various genomes to assess diversity. This will include hierarchical clustering, correlating genomic data with geographic and phenotypic information and investigating gene-phenotype relationships and microsatellites. This course will use genomic data of wheat, maize and potato as training datasets throughout the week. The course will be delivered through a combination of hands-on training sessions and lectures. Please note: The course will use genomic data from crop plant species throughout the week. It will not explore in detail methods for assembling genomes.

Marco Cristancho, Derrin Crawte, Marina Pujol

1 March - 4 March 2021

NEUcrest: "Big Data" workshop

This course will introduce participants to the concept of "big data" in relation to biology, bioinformatics, and life science data. It will explore data resources and bioinformatics tools from the European Bioinformatics Institute and the Wellcome Sanger Institute. The course content will also cover the fundamentals of bulk and single-cell sequencing of RNA samples and provide practical instruction in basic analytical approaches.

Tom Hancocks

28 February - 5 March 2021

Attacking Open Chromatin with ATAC Sequencing

V. Benes, U. Litzenburger, J. Zaugg

25 February - 25 February 2021

Integrating knowledge of proteins and small molecules with UniProtKB

This webinar will provide an introduction into how UniProtKB captures and represents knowledge of small molecule metabolites using the Rhea knowledgebase of biochemical reactions, based on the chemical ontology ChEBI, and how UniProt users can access and exploit that knowledge.

22 February - 26 February 2021

Introduction to multiomics data integration and visualisation

Identify the challenges, strategies and resources for multiomics data integration using biological examples.  The virtual course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation. Working with public domain data can provide added value to data derived through a researcher’s own work and additionally  inform experimental design. This course is highly relevant in the current research scenario, where an increased volume of data across the whole spectrum of biology has created both more opportunities and challenges to identifying novel perspectives and answering questions in the life sciences. This course will focus on issues around data integration, but will not include systems biology modelling or machine learning approaches. A major element of this course is a group project, where participants will be organised in small groups to work together on a challenge set by trainers from EMBL-EBI data resource and research teams. These will allow participants to explore the bioinformatics tools and resources introduced in the course and to apply these to a set problem, providing hands-on experience of relevance to their own research. The group work will culminate in a presentation session involving all participants on the final day of the course, giving an opportunity for wider discussion on the benefits and challenges of integrating data. Virtual course The course will involve participants learning via pre-recorded lectures, live presentations, and trainer Q&A sessions. The content will be delivered over Zoom, with additional text communication over Slack. Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Trainers will be available to provide support, answer questions, and further explain the analysis during these practicals. Participants will need to be available between the hours of 09:30-17:30 GMT each day of the course.

Jane Reynolds

16 February - 16 February 2021

Ensembl API workshop, University of Cambridge, 16.02.2021

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

15 February - 19 February 2021

Next generation sequencing bioinformatics

A guide to the technology, analysis workflows, tools, and resources for next generation sequencing data analysis. This virtual course will provide insights into how biological knowledge can be derived from genomics experiments and explain different approaches in analysing such data. The main focus will be on assembly, re-sequencing, and variant calling during the analysis of higher-eukaryotes, with a particular emphasis on human genetic research. Throughout the week, more advanced topics will introduce the creation of pipelines, automation, and the scaling-up of analysis experiments. Practical sessions will enable participants to process training datasets and apply appropriate statistical methods in their analyses. There will be no opportunity to work with personal research data during the course. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 09:30-17:30 GMT each day of the course. Trainers will be available to assist, answer questions and further explain the analysis during these times.

Marina Pujol

11 February - 11 February 2021

Ensembl Browser workshop, University of Cambridge, 11.02.2021

Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation and regulation data, and mine these data with BioMart.

10 February 2021

Exploring non‐coding RNAs in RNAcentral

RNAcentral is a database of non-coding RNA sequences that provides a unified view of >40 specialised databases. This webinar will give an overview of the data found in RNAcentral as well as the RNAcentral website. The team will share tips on how to efficiently explore the data using text and sequence similarity search, how to visualise RNA secondary structure, and how to access the bulk data in the FTP archive. More advanced functionality, including the programmatic data access and public Postgres database, will also be discussed. Join the webinar to also learn what's new in RNAcentral or ask any questions you may have.

Blake Sweeney, Carlos Ribas, Anton Petrov

8 February - 12 February 2021

Immune Profiling of Single Cells

V. Benes, K. Danielski, D. Ordonez, E. Zielonka

7 February - 11 February 2021

Deep Learning for Image Analysis

The advent of deep learning has brought a revolution in the field of computer vision, including most tasks and research questions concerned with microscopy image analysis. Neural networks have been successfully used for image restoration, classification and segmentation, for the detection of objects and characterisation of their morphology, for high-throughput imaging and large-scale processing in 3D. Despite these advances, training and deployment of such neural networks remains difficult for practitioners of image analysis. The aim of our course is to close this gap and teach the participants - in the most hands-on way possible - to apply deep learning-based methods to their own data and image analysis problems.

3 February 2021

UniProt for proteomics scientists

UniProt is a comprehensive, expert-led, publicly available database of protein sequence, function and variation information. This webinar will give a brief introduction to the UniProt website and then highlight resources available that proteomics scientists or users with large protein datasets may find useful in analysing their data. This will encompass our proteomes service, how to convert and retrieve ID mappings, and how to carry out a peptide search. The webinar will then go on to introduce the UniProt Proteins API which allows researchers to access and download UniProt data alongside large-scale genomic, proteomics and variation data without needing prior in-depth knowledge of programmatic languages. Data is available for download and querying in a range of formats; including XML, FASTA and PEFF. The API multi-query search functions will be demonstrated and useful features such as searching entries by peptide, and searching for proteomic peptides by protein entry will be explained. The UniProt Proteins API is available at //www.ebi.ac.uk/proteins/api/doc

Emily Bowler-Barnett

1 February - 5 February 2021

Single-cell RNA-seq analysis using R

This course covers the analysis of scRNA-seq data using R and command line tools. Participants will be guided through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. They will explore and interpret data using R as well as the Single Cell Expression Atlas. Finally participants will put their knowledge into practice through a group challenge on the final two days. Please note that participants will not analyse their own data as part of the course. There will, however, be ample opportunity to discuss their research and ideas with other course participants and trainers.

Meredith Willmott

1 February - 11 February 2021

EMBL-EBI workshop: University of Pavia, 2021 (Virtual)

This series of workshops will explore EMBL-EBI data resources for genomics, transcriptomics, protein sequences, structures and interactions, and chemical biology. Each half-day workshop will introduce participants to browsing, searching, retrieving, and conducting a basic analysis of a wide range of biological data types.  Two workshops will cover the Ensembl genome browser, where researchers can explore annotated genomes and features of interest including genes, transcripts, and variants. Participants will also be introduced to the Variant Effect Predictor (VEP) tool and BioMart for bulk data download. Functional genomics resources - Array Express, Expression Atlas - will introduce public data derived from transcriptomics experiments and provide instruction on how to begin investigating biological functions. Participants will also cover the Single-cell Expression Atlas and the expression data from individual cell sequencing. Three workshops will explore resources dedicated to protein data, covering UniProt, the PDBe, IntAct, the Complex Portal, and Reactome. These topics will provide overviews of protein sequence, structure, and interactions; allowing participants to gain a greater understanding of the role played by proteins in the cell. The final workshop will cover the EBI's chemical biology resources ChEBI and MetaboLights. Participants will learn how to access information on chemical entities of biological interest, and the myriad metabolites found in metabolomics experiements. Virtual workshop Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through trainer-led demonstrations and personal exercises on each resource. Live sessions will be delivered using Zoom with additional support and communication from the host, trainer and, resource specialists in the chat stream.

Claudia Binda

30 January - 5 February 2021

Analysis and Integration of Transcriptome and Proteome Data

V. Benes, R. Calogero, J. Krijgsveld, L. Martens

27 January 2021

Preprints discovery 101: Tips & tricks for authors

Preprints enable researchers to rapidly share their work publicly before the formal peer review process. This webinar will demonstrate how to incorporate preprints in your literature search routine by using the discovery tools developed by Europe PMC. Europe PMC indexes preprints abstracts and full text COVID-19 preprints from many life sciences preprint servers alongside published articles. Preprints in Europe PMC are linked to data and platforms that comment on or peer review preprints. We will demonstrate how to find the data behind preprints as well as comments and reviews associated with a given preprint. We will also share useful tips for posting your pre-prints, claiming a pre-print to your ORCID and tracking your pre-prints’ citations, revisions or recommendations by readers. To learn more about using Europe PMC in your research try our Europe PMC: Quick tour or our webinar Using Europe PMC for effective literature research.

Dayane Rodrigues Araujo

24 January - 28 January 2021

Exploratory Analysis of Biological Data: Data Carpentry

The missing step between data collection and research progress is a lack of training for researchers in crucial skills for effectively managing and analysing large amounts of data. This hands-on workshop teaches researchers the fundamental data skills they need to conduct their work and provides high-quality, domain-specific training covering the full lifecycle of data-driven research. The domain-specific approach allows participants to tailor the data, content, and tools to reflect the specific data and analysis needs of different areas.

20 January 2021

An introduction to EMBL-EBI resources

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 us for a tour of the core data resources at EMBL-EBI.

Sarah Morgan

14 January 2021

Automated annotation in UniProt

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.

Alistair MacDougall, Rabie Saidi

10 January - 14 January 2021

Drosophila Genetics and Genomics

The fruit fly Drosophila has played a leading role in the discovery and dissection of basic biological processes, uncovering general principles of development, evolution and disease. Almost a century of research has generated a powerful genetic toolbox that provides a unique arsenal of methods that can tackle almost any biological question. This, combined with exciting new technologies developed in recent years have changed the way Drosophila research is conducted, enabling biologists to address questions that were impossible to study before.

14 December - 17 December 2020

CAR-T Cells: The Leap from Basic Science to Medical Revolution - Cancelled

K. Schroeder, J. T. Lim, M. Paulsen

10 December 2020

Uncovering protein function with UniProt

This webinar will discuss what functional information is available in UniProt and where that information comes from. It will also describe how it the information is added to the resource and how to find it on the UniProt website.

Michele Magrane

7 December - 11 December 2020

CABANA: Genomic data for surveillance of communicable disease (Cancelled)

This course has been cancelled. We apologise for any inconvenience caused. This course will develop skills in the analysis of field-collected microbial genomes samples and how to use data this genomic in the surveillance of communicable diseases.

5 December - 8 December 2020

In situ Structural Biology: From Cryo-EM to Integrative Modelling - Virtual

M. Beck, J. Kosinski, J. Mahamid

3 December - 10 December 2020

Design Thinking: Approaches for Chronic Disease Management - Virtual

A. Jones, E-M Markutzik, K. Zeier, E. Zielonka

2 December 2020

Introduction to the Complex Portal

This webinar will introduce the Complex Portal, an encyclopaedic database for information on macromolecular complexes. In this webinar we will explain the coverage and curation priorities of the Complex Portal, show how to search for complexes using a variety of accession numbers, keywords and how to use the organism search. We will also demonstrate examples of complex details pages that include visualisation tools and link-outs to related database.

Birgit Meldal

1 December - 4 December 2020

CABANA workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 pandemic

This workshop will provide training on the use of bioinformatic tools for the design and analysis of research and diagnostic molecular assays. Trainees will receive training on viral genome assembly, comparative viral genomics and downstream applications of this data in research and applied contexts. Trainers will focus practical sessions on the analysis of Illumina SARS-CoV-2 sequences. This online workshop will be delivered on Zoom and comprise a blend of live lectures and hands-on practicals delivered by trainers across Latin America. Certificates will be provided to mark successful completion of this workshop. Sessions on Friday 4th December will be livestreamed on YouTube and made freely available on the platform thereafter. There will be an opportunity to deliver a short presentation about your work to other trainees.

Marina Pujol

30 November - 4 December 2020

CABANA: Bioinformatics for plant biology (Postponed until 2021)

Please note this course will be postponed to 2021, and as further information about the course becomes available we will update this page. By registering your interest using the button above, we will inform you applications open for the course. For details of previous courses hosted at EMBL-EBI please look at our 2019 onsite listing.

Marina Pujol

26 November - 28 November 2020

The Roaring 20s: A New Decade for Life Sciences - Virtual

PhD Students

26 November 2020

Sequence analysis tools in UniProt: BLAST and Align

BLAST and multiple sequence alignments are essential methods commonly used to find and compare protein or nucleotide sequences. In this webinar, we will demonstrate how you can access and run these sequence analysis tools in UniProt, a comprehensive resource of protein sequence and function. We will show you how to navigate the results and how you can exploit UniProt protein annotation to expand further the analysis of your results.

Rossana Zaru

25 November 2020

Discovering scientific evidence using Europe PMC SciLite annotation

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.

Dayane Rodrigues Araujo

24 November - 24 November 2020

Technologies for Extracellular Vesicles Research: Q&A

A. Hendrix, C. Lässer, E. Noltet Hoen, G. Van Niel

23 November - 27 November 2020

Structural bioinformatics (Virtual)

Structural biology, determining the three-dimensional shapes of biomacromolecules and their complexes, can tell us a lot about how these molecules function and the roles they play within a cell. Data derived from structure determination experiments enables life-science researchers to address a wide variety of questions. This course explores bioinformatics data resources and tools for the investigation, analysis, and interpretation of biomacromolecular structures. It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts. The course content will also cover predicting protein structure and function, and exploring interactions with other macromolecules as well as with low-MW compounds. This course will be a virtual event delivered via a mixture of live-streamed sessions, pre-recorded lectures, and tutorials with live support. We will be using Zoom to run the live stream sessions (all fully password protected) with support provided by Slack. In order to make the most out of the course, you should make sure to have a stable internet connection throughout the week. There will also be networking and short social activities throughout the course. Selected participants will be sent materials prior to the course. These might include pre-recorded talks and required reading or online training that will be essential to fully understand the course.

Meredith Willmott

18 November 2020

MGnify API: accessing microbiome data computationally

This webinar will provide an overview of the MGnify API. MGnify offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. The webinar will include how to utilise the API using a browser, where to find documentation, how to use filtering and pagination, available output formats, and scripting examples in Python.

Martin Beracochea

17 November - 20 November 2020

Basics to advanced genome annotation at Ensembl and REST Application Programming Interfaces (APIs)

Introduction to the Ensembl Genome Browser and REST API, in collaboration with NextGenHelper.

15 November - 19 November 2020

From Functional Genomics to Systems Biology - Virtual

A. Krebs, P. Liberali, D. Pe'er, M. Savitski

14 November - 21 November 2020

Single-Cell Omics - Postponed to 2021

Q. Deng, J. Korbel, A. Ståhlberg, E. Zielonka

12 November 2020

Understanding proteomes

A proteome is the set of proteins thought to be expressed by an organism. Through the Proteomes portal, UniProt provides a large collection of proteomes for organisms whose genomes have been sequenced and annotated. Currently, our database contains more than 300,000 proteomes spanning eukaryotes, bacteria, archea and viruses. This webinar will show you how to retrieve proteomes of interest and download the corresponding datasets. We will also cover where proteomes come from and the features available to help users find the right dataset for their work.

Ramona Britto

11 November 2020

MGnify today: analysing microbiome data

This webinar will describe how MGnify can assist you in your microbiome research by providing a broad overview of resources available in MGnify. MGnify offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. During this webinar, we will cover what types of microbiome data are included, improvements we have made to our analysis pipeline, as well as ways to search for data.

Varsha Kale

11 November - 12 November 2020

Transgenic Animals - Micromanipulation Techniques - Cancelled

I. Rollan, S. Stobrawa

11 November - 11 November 2020

CABANA train the trainer workshop for XMXP20

This highly interactive virtual workshop takes place within the X-meeting eXperience 2020, organized by AB3C. It will provide new trainers with knowledge, skills, guidance and tips for developing and delivering training. Trainees will explore a range of methods to enable and encourage learning, examine the requirements for a successful course and acquire appropriate feedback. The workshop itself will depend on trainee participation in group activities. The workshop will: provide guidance on general training techniques and appropriate use of methods based on learner needs, including some general 'DO's' and 'DO NOTs' for successful training provide a framework for successful curriculum design and further development, to enable trainers to build a course appropriate to their learners' needs The workshop will take place virtually via Zoom. 

Piraveen Gopalasingam, Mindy Stephania Miranda, Nicole Scherer

9 November - 10 November 2020

Ensembl Browser workshop, University of California San Francisco, 9-10 November 2020

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.

8 November - 11 November 2020

Biological Oscillators: Design, Mechanism, Function - Cancelled

A. Aulehla, H. Herzel, E. Marder, U. Schibler

4 November 2020

Variant submission and data access at the European Variation Archive

This webinar will cover how to access data using the EVA UI/API and the methodology of variant data submission to the EVA, specifically focusing on data transformation and formats. With a new version of the variant ID data release now available, this webinar will also cover what has been updated and what to expect from future releases.

Baron Koylass

3 November - 4 November 2020

Our House is Burning: Scientific and Societal Responses to Mass Extinction - Virtual

L. von Bredow

3 November 2020

Europe PMC: Programmatic access

Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, preprints, books, patents, and clinical guidelines. This webinar will introduce the Europe PMC Articles RESTful API and show how to programmatically access publications and related information, such as citations, references, data links, or text-mined terms.

Dayane Rodrigues Araujo

2 November - 5 November 2020

Protein Quality Control for Downstream Processes - Cancelled

K. Perez, K. Remans

2 November - 6 November 2020

Metagenomics bioinformatics (Virtual)

Gain knowledge of the tools, processes and analysis approaches used in the field of metagenomics. This course will cover the metagenomics data analysis workflow from the point of newly generated sequence data. Participants will explore the use of publicly available resources and tools to manage, share, analyse and interpret metagenomics data. The content will include issues of data quality control and how to submit to public repositories. While sessions will detail marker-gene and whole-genome shotgun (WGS) approaches; the primary focus will be on assembly-based approaches. Discussions will also explore considerations when assembling genome data, the analysis that can be carried out by MGnify on such datasets, and what downstream analysis options and tools are available. Virtual course The course content will involve participants learning via pre-recorded lectures, live presentations and trainer Q&A sessions. Practical experience will be developed through group activities and computational exercises. Sessions will be delivered over Zoom with additional text communication over Slack. Trainers will be available to assist, answer questions and further explain the analysis during these times. Computational practicals will be run in Docker containers operating on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Participants will need to be available between the hours of 09:00-17:00 GMT each day of the course.

Marina Pujol

29 October 2020

Introducing the new UniProt Disease Portal

This webinar will provide an interactive introduction to the new UniProt Disease Portal: a single centralised resource of UniProt disease-centric information which has been developed with the help of our users to better serve the needs of the research community and facilitate protein discoverability. The UniProt knowledgebase (UniProtKB) supports biomedical research by providing a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. To do this, UniProt integrates, interprets and standardises data from a range of sources including scientific literature, protein sequence analysis tools, other databases and automatic annotation systems to provide a detailed overview of the available protein knowledge. This webinar will introduce you to the UniProt Disease Portal which aims to help researchers explore and access current genomic disease-related data from the UniProtKB database, but in a single centralised resource. The portal incorporates UniProt functional annotations, protein network visualisations, genomic variant and drug-related data, and organises in a way that allows users to easily visualise and compare data to identify similarities using variants, protein interactions, diseases, and drug data. The Disease Portal is currently in its first beta release, so we hope that this interactive introduction will give you an understanding of how to access disease-centric protein data in UniProt and encourage your feedback to assist ongoing development of the Portal to further suit the requirements of our users.

Kate Warner, Emily Bowler-Barnett

28 October 2020

The PRIDE database: storing, disseminating and integrating proteomics data in the public domain

This webinar will provide an introduction to proteomics approaches and the PRIDE database, followed by more detailed examples of PRIDE public data re-use, including “big data” approaches.

Juan Antonio Vizcaino

27 October - 30 October 2020

Neuroepigenetics: From Cells to Behaviour and Disease - Virtual

R. Bonasio, C. Desplan, M. Götz, K. M. Noh

26 October - 2 November 2020

Solution Scattering from Biological Macromolecules - Postponed to 2021

M. Gräwert, A. Kikhney, D. Svergun

26 October - 2 November 2020

Microbial Metagenomics: A 360º Approach - Postponed to 2021

V. Benes, G. D'Auria, J. E. González-Pastor, E. Zielonka

23 October 2020

Open with purpose: How and why to make your data open

As part of EMBL-EBI’s celebration of Open Access week, this special one-off webinar will give you insight into the benefits of open access data, alongside guidance and tips on managing your data. Featuring four members of EMBL-EBI’s resource teams (from BioSamples, ENA, IntAct/Complex Portal & Europe PMC), you’ll get an overview of Open and FAIR data, insights into submission processes and support, the importance of open literature and some hints, tips and tricks for ensuring your data can easily be made available to others. You’ll also get an opportunity to ask live questions to all four of our speakers, and find out where you can learn more.

Fuqi Xu, Sam Holt , Birgit Meldal, Dayane Araujo

22 October - 23 October 2020

CABANA train the trainer workshop for ISCB-Latin America 2020

This virtual workshop takes place within the ISCB-LA SoIBio BioNetMX 2020 symposium. It will provide new trainers with knowledge, skills, guidance and tips for developing and delivering training. Participants will explore a range of methods to enable and encourage learning, examine the requirements for a successful course and acquire appropriate feedback.  The workshop will: provide guidance on general training techniques and appropriate use of methods based on learner needs, including some general 'DO's' and 'DO NOTs' for successful training provide a framework for successful curriculum design and further development, to enable trainers to build a course appropriate to their learners' needs The workshop will take place virtually via Zoom. 

Patricia Carvajal Lopez, Maria Trinidad Bernardi, Mindy Stephania Miranda

21 October 2020

Multiomics comparative pathway analysis with ReactomeGSA

The webinar will demonstrate how to perform multiomics comparative pathway analyses using ReactomeGSA. This will cover the web interface and R package. We will demonstrate how to use ReactomeGSA to quickly derive novel biological knowledge by combining multiple datasets. In addition, we will also cover the function of ReactomeGSA for investigating scRNA-seq cell clusters at the pathway level.

Johannes Griss

20 October - 24 October 2020

Organoids: Modelling Organ Development and Disease in 3D Culture - Virtual

H. Clevers, M. Huch, J. Knoblich, M. Lancaster, E. Schnapp

20 October 2020

Data visualisation at 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.

Mandar Deshpande

18 October - 23 October 2020

Computing Skills For Reproducible Research: Software Carpentry - Virtual

R.Alves, T. Hodges

14 October 2020

A guide to UniProt for students

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 ways in which students and researchers at all career stages may take a structured approach to access the data in the UniProtKB and Proteomes sections of the UniProt protein function database. The webinar will discuss the types of data that can be accessed, and using sequence analysis tools, how this data can be analysed to answer biological questions. We will demonstrate how to find the function of a protein, how the protein components of a pathway may be identified, features of proteins of interest can be compared, similar sections of sequence can be sought in other species and how whole data sets containing all the proteins expressed in an organism can be obtained. By accessing sequence, structural and functional data through UniProt, we want researchers to be part of data’s biological journey and support further work and adventures along the way! 

Hema Bye-A-Jee

14 October - 16 October 2020

Exploring biological sequences

We are currently developing the course programme for 2020, and as further information about the course becomes available we will update this page.

13 October 2020

PDBe tools in GitHub

This webinar will show you how to access some of the software packages created at PDBe, used to generate the data displayed on our website. This will include a walkthrough of our github repositories, highlighting the types of packages available, how to access them and some examples of how they can be used. 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.

Lukas Pravda

12 October - 14 October 2020

Gender Roles and their Impact in Academia - Virtual

E. Furlong, M. Garfinkel, C. Gross, H. Janssens, G. Wallon

12 October - 15 October 2020

FFPE/cfDNA NGS Library Prep for Genome and Methylome Analysis - Cancelled

V. Benes, B. Textor

12 October - 16 October 2020

Summer school in bioinformatics (Virtual)

This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research. Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management and reproducibility. To enable specific exploration of resources in their particular field of interest, participants will be divided into focused groups to work on a small project set by EMBL-EBI resource and research staff, ending in a presentation from each group on the final day of the course to bring together learnings from all participants. The course includes training and mentoring by experts from EMBL-EBI and external institutes. Group projects A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI. This allows people to explore the bioinformatics tools and resources available in their area of interest and apply them to a set problem, providing participants with hands-on experience relevant to their own research. The group work will culminate in a presentation session involving all participants on the final day of the course, giving an opportunity for wider discussion on the benefits and challenges of working with biological data. Groups are mentored and supported by the trainers who set the initial challenge, but the groups will be responsible for driving their projects forward, with all members expected to take an active role. Groups are pre-organised before the course, and all group members will be sent some short “homework” in preparation for their project work prior to the start of the course. Basic outlines of the projects on offer this year are given below. In your application you must indicate your first and second choice of project, based on which you think would benefit your research most. Not all projects may be offered, and final decisions on which projects will be run during the course will be made based on the number of applicants per project. This year’s projects are as follows: Networks and pathways This project will make use of gene expression data (RNA-seq) to build protein-protein interaction networks, which can be used to explore functional relationships between the (potentially) expressed protein products. You will use Cytoscape to visualise protein networks, identify key regulators of biological pathways and explore biological function through network analysis, integration and co-visualisation of additional data, and ontology/functional enrichment analysis - helping to build a better view of the wider biological context. Modelling cell signalling pathways Curating models of biological processes is an effective training in computational systems biology, where the curators gain an integrative knowledge of biological systems, modelling and bioinformatics. You will learn to encode computational models of signalling pathways from a recent publication using COPASI and how to reproduce the simulation results. Furthermore, you will learn how to annotate models and re-use pre-existing models from open repositories such as BioModels. Genome variation across human populations Natural variation between individuals or between different human populations is a result of genome mutations throughout evolutionary history. Some mutations may become fixed because of their beneficial effect while most drift among individuals. During this project, you will investigate genomic variation between two separate human populations of European and Asian descent. Using sequence data from a number of individuals from each population, you will use a range of bioinformatics tools to discover variants that exist between them. In the second section of the project, you will attempt to analyse the functional consequences of the variants you have identified, linking them to phenotypes. Metabolic network engineering using a systems model-based approach Metabolic pathway analysis helps to identify the structure and dynamics of a metabolic network and thereby also allow us to have an insight into cell physiology which is the foundation of metabolic engineering. You will work with a curated model related to a metabolism network chosen from BioModels, and learn how to carry out computational analyses to find common patterns in the networks. These might include computing feasible pathways through the network and minimal reactions to knock out specific metabolic functions, along with visualisation and exploration to gain a further insight into the results. Finding and interpreting publicly available structural data  This project will introduce you to the wealth of publicly available structural data and give you the opportunity to investigate how this data can be used to analyse macromolecular structures. You will firstly explore the search and entry pages at PDBe to identify the type of data available for analysis. Then using this knowledge, you will discover how to access this data programmatically and analyse a subset of your results to interpret biological relevance.  Functional annotation of proteins Functional annotation refers to discovering the functions of proteins. Participants will  annotate a protein of interest which has not been annotated previously, either manually or by any UniProt automatic system. Participants will use different ways to discover the function of their protein of interest from alignment to machine learning. You will learn the different annotation types in UniProtKB and how to use the UniProt resources for their investigation. You will also learn how to build machine learning models, from dataset construction to prediction.

Scientific conferences

7 October - 9 October 2020

Advancement Summit for Life Sciences

M. Hentze, M. Rayner

7 October 2020

The Ensembl Rapid Release genome browser

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.

Benjamin Moore

6 October - 9 October 2020

The Complex Life of RNA - Virtual

A. Ephrussi, W. Gilbert, K. Nagai, R. Pillai

6 October 2020

Using the PDBe graph API

This webinar will introduce the PDBe graph API, which is generated from the PDBe graph database and contains an even richer level of data than our standard API. We will highlight how this API supports our PDBe-KB aggregated views, with specific case studies that demonstrate the possibilities through this API. 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.

Sreenath Nair

5 October - 9 October 2020

CZI-CABANA Joint Workshop: Microbiome Bioinformatics with QIIME 2

Members of the QIIME 2 team will teach a five-day online workshop on bioinformatics tools for microbiome science. This workshop will provide attendees with the foundation needed to begin using QIIME 2 to advance their own microbiome research projects. This will be accomplished by providing detailed in-depth “theory” lectures, hands-on interactive tutorials, guided discussion, and general question-and-answer sessions The workshop will include lectures covering QIIME 2 usage and theory, and interactive work with QIIME 2 to perform microbiome analysis from raw sequence data through publication-quality statistics and visualizations. This workshop will also feature several opportunities for attendees to network with other researchers in the field, as well as with QIIME 2 developers and other experts.

Greg Caporaso, Matthew Ryan Dillon

3 October - 9 October 2020

Advanced Methods in Bioimage Analysis - Postponed to 2021

R. Haase, A. Klemm, S. Nørrelykke, P. Paul-Gilloteaux, C. Tischer, C. Wahlby

30 September 2020

Reproducibility in Systems Biology Modelling: BioModels' role

This webinar, will give an overview of BioModels, a popular repository of curated systems biology models. It will also provide a brief introduction to BioModels Parameters, a sub-resource within BioModels that provides model parts, followed by discussion of a study carried out to assess how reproducible systems biology models are, the reasons why mathematical models fail to reproduce simulation results and the solution we propose to tackle lack of reproducibility. 

Rahuman Sheriff

30 September - 2 October 2020

Molecular Mechanisms in Evolution and Ecology - Virtual

M. Dunham, J.-Y. Leu, G. Liti, S. Mitri, K. Patil

29 September 2020

Creating complex PDBe API queries

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.

Nurul Nadzirin

28 September - 2 October 2020

Whole Transcriptome Data Analysis - Cancelled

M. Beccuti, V. Benes, R. Calogero, F. Cordero

28 September - 2 October 2020

Mathematics of life: Modelling molecular mechanisms (Virtual)

Computer models are increasingly used to understand essential processes of biology. Researchers in academic institutions as well as the pharmaceutical industry use mathematical models to generate hypotheses on how complex biomolecular systems work. Modelling of biochemical pathways deregulated in disease conditions can offer mechanistic insights into the pathology, help to elucidate mechanisms behind drug action and predict the dose required for treatment thus facilitating fundamental research and drug discovery. This course will provide participants with an introduction to modelling resources, tools and approaches used in systems biology as well as touch on network analysis. This course will be a virtual event delivered via a mixture of live-streamed sessions, pre-recorded lectures and tutorials with live support. We will be using Zoom to run the live stream sessions (all fully password protected) with support provided by Slack. In order to make most out of the course you should make sure to have a stable internet connection throughout the week. Selected participants will be sent materials prior to the course. These might include pre-recorded talks and required reading that will be essential to fully understand the course.

Rebecca Nicholl

27 September - 5 October 2020

Genome Engineering: CRISPR/Cas from Cells to Mice - Virtual

V. Benes, N. Humphreys, B. Koch, E. Zielonka

25 September - 25 September 2020

Ensembl Browser workshop, IGMM, University of Edinburgh, 25 September 2020

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.

23 September 2020

Investigating genotype-phenotype data using the GWAS Catalog

This webinar will include a brief introduction to the GWAS Catalog, followed by hands-on demonstrations and exercises covering different methods for accessing GWAS Catalog data, focusing on the most common use-cases. This will include our web-based search interface, with a number of different tools for data access and visualisation, and download of filtered datasets. We will also briefly introduce and describe how to submit your own data. 

Laura Harris

22 September 2020

Searching with the PDBe API

This webinar will introduce the PDBe search API, a powerful Solr-based query system that underlies the PDBe search pages. The breadth of search options will be highlighted, along with specific case studies that demonstrate what is possible through the search API. 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.

John Berrisford

19 September - 22 September 2020

The Molecular Basis and Evolution of Sexual Dimorphism

D. Bachtrog, D. Charlesworth, H. Kaessmann

16 September 2020

The International Mouse Phenotyping Consortium (IMPC): a large-scale functional catalogue of mammalian genes

The IMPC is an international research infrastructure, comprised by 21 of the leading mouse genetics centres worldwide, that is systematically identifying the function of every protein-coding gene in the mouse genome. Despite having sequenced the entire genomes of many species, the exact function of most genes remains unknown. To address this, the IMPC is coordinating the production of a knockout mouse strain per protein-coding gene, which are then characterised using a standardised, broad-based phenotyping pipeline, giving insights into the function for genes for which very little is known. Our open-access database now includes phenotyping data for nearly 6,500 mouse genes. This webinar will discuss some of the exciting discoveries in genetic disease, development and sexual dimorphism that biologists and clinical researchers are making using IMPC resources. The IMPC strives to generate data that ultimately help understand human health and disease and identify new targets for therapeutic intervention. This data is also useful for research focusing on other mammalian species, including evolutionary research studies seeking to understand adaptation. All IMPC data is freely available to use and can be accessed at www.mousephenotype.org. The IMPC would like to encourage researchers to get in touch via the IMPC website if they are interested in using IMPC data and would like further guidance on how to use our data.

Violeta Munoz Fuentes, Hamed Haseli

15 September 2020

Introduction to PDBe programmatic access

This webinar will give an introduction to programmatic access at PDBe, highlighting the type of data that is available and how this can be utilised.  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.

David Armstrong

13 September - 16 September 2020

The Molecular Basis and Evolution of Sexual Dimorphism - Virtual

D. Bachtrog, D. Charlesworth, H. Kaessmann

13 September - 17 September 2020

The Neurovascular Interface - Cancelled

A. Acker-Palmer, R. Adams, C. Gu

11 September - 18 September 2020

Liquid Biopsies - Virtual

V. Benes, A. Stahlberg

8 September 2020

EurOPDX IT tools to support cancer research with patient-derived xenograft models

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).

Emilie Vinolo, Enzo Medico

7 September - 14 September 2020

Membrane Protein Expression, Purification and Characterisation (mPEPC2) - Postponed to 2021

M. Garcia Alai, E. Geertsma, C. Löw, K. Remans

2 September - 5 September 2020

Chemical Biology 2020 - Virtual

C. Deo, K. Johnsson, M. Köhn, C. Schultz

2 September - 2 September 2020

Ensembl API workshop, University of Cambridge (Virtual)

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write Python/Perl/R scripts to call them. Feedback from previous courses: "Wish I had taken the course long time ago. Didn't know before how good and powerful APIs are!" API workshop, EMBL-EBI, January 2016 "I really enjoyed the course, and the ENSEMBL API will become a very relevant part of my toolset." API workshop, Cambridge, December 2013   If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.

Michal Szpak

1 September - 1 September 2020

Ensembl Browser workshop, University of Cambridge (Virtual), 01.09.2020

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.

1 September - 4 September 2020

Gene Expression at Spatial Resolution - Virtual

V. Benes, K. Danielski, E. Zielonka

26 August - 29 August 2020

Transcription and Chromatin - Virtual

K. Adelman, E. Furlong, J. Müller, P. Verrijzer

18 August - 20 August 2020

Managing a bioinformatics core facility (Virtual)

This knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL-EBI’s service teams, from each other, and from potential users of their services. These facilities play an essential role in enabling research in the molecular life sciences. The landscape is constantly evolving as new research tools emerge, as experiments become increasingly data intensive, and as their clients – experimental researchers – become more exposed to the power of data-driven biology.

Marina Pujol

16 August - 28 August 2020

Cryo-Electron Microscopy and 3D Image Processing - Virtual

J. Briggs, J. Mahamid, L. Passmore, C. Sachse, H. Stahlberg

26 July - 31 July 2020

Proteomics bioinformatics (Cancelled)

EMBL-EBI has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are cancelling this course and apologise for the inconvenience.

19 July - 24 July 2020

Molecular Geobiology - Postponed to 2021

K. Patil, H. Sapers, E. Zielonka

19 July - 22 July 2020

Defining and Defeating Metastasis - Cancelled

J. Joyce, D. Klimmeck, J. Massague, C. Swanton

12 July - 15 July 2020

Microfluidics: Designing the Next Wave of Biological Inquiry - Virtual

A. Herr, C. Merten, A. Wu

6 July - 10 July 2020

Systems biology: From large datasets to biological insight (Cancelled)

EMBL-EBI has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are cancelling this course and apologise for the inconvenience.

6 July - 10 July 2020

Cancer genomics (Virtual)

This course will focus on the analysis of data from genomic studies of Cancer.  Lectures will give an insight into the bioinformatic concepts required to analyse such data, whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the lecturers and teaching assistants.

Rebecca Nicholl

5 July - 11 July 2020

Super-Resolution Microscopy - Postponed to 2021

M. Lampe, R. Pepperkok, U. Schwarz

2 July - 3 July 2020

SARS-CoV-2: Towards a New Era in Infection Research - Virtual

P. Beltrao, P. Cossart, D. Heinz, N. Typas

28 June - 1 July 2020

Innate Immunity in Host-Pathogen Interactions - Cancelled

B. Hube, J. Pfeiffer, F. Randow, F. Shao, C. Zipfel

28 June - 3 July 2020

Drosophila Genetics and Genomics - Postponed to 2021

C. Bergman, J. Crocker, E. Furlong, S. Hawley

24 June 2020

InterProScan

This webinar is about InterProScan, the underlying software application that scans both protein and nucleic acid sequences against InterPro's predictive models, which are provided by the InterPro’s member databases. InterPro is a freely available resource used to classify sequences into protein families and to predict the presence of important domains and sites.

Gift Nuka

23 June - 25 June 2020

Data Collection, Analysis and Interpretation for Genomic Medicine (Virtual)

The delivery of this course has changed from face-to-face to virtual. This workshop will introduce cloud technologies for creating bioinformatics pipelines relevant to clinical decision making in genomic medicine.

23 June - 25 June 2020

Data collection, analysis and interpretation for genomic medicine

This workshop will introduce cloud technologies for creating bioinformatics pipelines relevant to clinical decision making. The content will guide participants through the process of building data flows, using GA4GH standards and infrastructure available from ELIXIR nodes and the EMBL-EBI. Expertise and support will be available during the workshop from the trainers, allowing participants to tailor pipelines to suit their own needs, data types and analysis methods. The workshop content will cover aspects of data storage and collection with regards to standards and file formats; sharing data and metadata within the cloud community; visualisation and analysis of data with regards to end-point clinical decision making.   

Ajay Mishra

22 June - 26 June 2020

BioExcel summer school on biomolecular simulations 2020

 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).

Michelle Mendonca

21 June - 26 June 2020

Quantitative Proteomics: Strategies and Tools to Probe Biology - Postponed to 2021

J. Krijgsveld, C. Ludwig, M. Savitski

17 June - 19 June 2020

Bioinformatics for principal investigators (Cancelled)

EMBL-EBI has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are cancelling this course and apologise for the inconvenience.

16 June - 25 June 2020

Advanced Electron Microscopy for Cell Biology - Cancelled

G. Griffiths, R. Mellwig, P. Ronchi, Y. Schwab

10 June 2020

Exploring metabolite metabolism using the Enzyme Portal

This webinar will provide a practical overview of how to use the Enzyme Portal to find enzyme-related information about metabolites. The Enzyme Portal is a freely available resource to find and explore enzyme features. It integrates relevant enzyme data for a wide range of species from various resources including UniProt, PDB, Reactome and CHEMBL. We will demonstrate how to use the Enzyme Portal to find relevant enzymes involved in a specific metabolite biosynthesis or catabolism.

Rossana Zaru

10 June - 10 June 2020

Exploring metabolite metabolism using the Enzyme Portal

This webinar will provide a practical overview of how to use the Enzyme Portal to find enzyme-related information about metabolites.

7 June - 12 June 2020

Whole Transcriptome Data Analysis - Postponed

M. Beccuti, V. Benes, R. Calogero, F. Cordero

3 June - 4 June 2020

Protein function prediction with machine learning and interactive analytics (Cancelled)

EMBL-EBI has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are cancelling this course and apologise for the inconvenience.

3 June - 6 June 2020

Microtubules: From Atoms to Complex Systems - Virtual

A. Akhmanova, C. Janke, G. Ou, K. Verhey

1 June - 5 June 2020

Starting single cell RNA-seq analysis (Virtual)

The delivery of this course has changed from face-to-face to virtual. This course trains participants to analyse single cell RNA-seq data utilising Galaxy pipelines, an online open-access resource for the computer-phobic.

1 June - 5 June 2020

Starting single cell RNA-seq analysis

This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to cell cluster comparisons using data extracted from the Single Cell Expression Atlas. In addition to running a basic pipeline, participants will explore the variety of options within the Galaxy resource and individually analyse a given dataset. The results will be compared across the cohort to assess reproducibility and demonstrate the effect of analytical choice on research output. Finally, participants will learn about data submission, resources, and standards within the single cell field.  Please note that participants will not be able to use their own data during the course practicals. However, there will be plenty of time to discuss their research and exchange ideas with other participants and the trainers. Opportunities will include poster sessions, evening discussions and small group chats with the trainers.

Meredith Willmott

27 May 2020

PDBe Graph Database: A Neo4J-driven integrative knowledge graph for structural data

This webinar will introduce the concepts of a graph database and describe how we used a graph-approach for integrating the structural data of the Protein Data Bank. The presented PDBe knowledge graph combines annotations provided by PDBe-KB partners with the core PDB archive. Each PDB entry can be thought of as a tree, with the root being the PDB entry, connected to chains and entities, which are then connected to residues. Each of the more than 150 million PDB residues, the leaves of the tree representation, are linked to annotations that make it easier to answer scientific questions such as: Can we find small molecules which have the same scaffold, and interact with the same binding sites? Or, can we find macromolecular interaction interfaces which have highly conserved residues, and are annotated to be structurally flexible? The webinar will help the audience answer these, and other similar scientific questions and will provide a solid foundation for taking advantage of the PDBe knowledge graph and use it as an invaluable research tool.

Sreenath Nair

27 May - 27 May 2020

PDBe Graph Database: A Neo4J-driven integrative knowledge graph for structural data

This webinar will introduce the concepts of a graph database and describe how we used a graph-approach for integrating the structural data of the Protein Data Bank.

24 May - 28 May 2020

Hands-on Flow Cytometry - Learning by Doing! - Postponed

A. Filby, D. Ordonez, M. Paulsen, S. Schmitt

23 May - 29 May 2020

Advanced Fluorescence Imaging Techniques - Postponed to 2021

S. Marawske, R. Pepperkok, S. Terjung

21 May - 21 May 2020

Ensembl Browser Course (Cancelled)

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.

20 May 2020

Accessing InterPro programmatically

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.

Gustavo Salazar-Orejuela

19 May 2020

Finding the data behind research articles with Europe PMC

This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis. Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more.

Dayane Rodrigues Araujo

17 May - 19 May 2020

BioMalPar XVI: Biology and Pathology of the Malaria Parasite - Virtual

A. Cortes, S. Portugal, S. Wassmer

14 May - 14 May 2020

CABANA: Addressing UN Sustainable Goals in Latin America Through Data-driven Biology Symposium

The CABANA (www.cabana.online) project is a Global Challenge Research Fund project operating in Latin America. We will be hosting a one-day symposium at the Royal Society on Thursday 14th May 2020 entitled "Addressing UN Sustainable Goals in Latin America through data-driven biology".

13 May 2020

Using the InterPro website in your research

This is the second 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, the InterPro website has been entirely redesigned. It allows more flexibility and provides additional features to be used by the scientific community working on protein sequences. This webinar will guide you through searching and exploring the data available in the InterPro database and will show you how it can help finding data for your research.

Typhaine Paysan-Lafosse

11 May - 15 May 2020

Fundamentals of Widefield and Confocal Microscopy and Imaging - Postponed to 2021

S. Marawske, J. Marquardt, S. Terjung

10 May - 14 May 2020

Cellular Mechanisms Driven by Liquid Phase Separation - Postponed to 2022

S. Alberti, D. Dormann, E. Lemke, T. Mittag

6 May 2020

Contributing to the UniProt Knowledgebase: how you can help

The webinar will present how the research community can contribute both literature references and annotation to the UniProt database of protein sequence and function. We will provide an overview on UniProt and will focus on describing a new functionality which allows users to add publications and knowledge to protein entries. We will give a demo on how to link a publication to a UniProt entry, fill in the submission form and include functional annotation. UniProt uses ORCID, a unique identifier for each researcher, as a mechanism for user validation and credit for these contributions. 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.   This webinar will be presented by Cecilia Arighi from the Center of Bioinformatics and Computational Biology, University of Delaware.

6 May - 20 May 2020

InterPro webinar series

InterPro is a database that helps users to understand the possible functions of proteins sequence. Between 6-20 May 2020 we are running a webinar series that explores InterPro families, domains and functions; using InterPro in your research; and accessing InterPro programmatically.

6 May 2020

Understanding InterPro families, domains and functions

This is the first part of a webinar series on InterPro which is held between 6 May - 20 May 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. InterPro provides the world’s most comprehensive predictions by combining predictions from 13 member databases. This webinar defines the basic InterPro notions, concepts of protein classification and describes how InterPro ensures the accuracy of its data. This webinar also explains the different methodologies used by the InterPro member databases in their predictions and how we integrate them into the 5 different InterPro entry types: Homologous superfamily, family, domain, repeat and site. Finally, it presents some examples of different external resources using the InterPro database as an underlying resource.

Typhaine Paysan-Lafosse

6 May - 9 May 2020

Microglia 2020 - Postponed to 2021

S. Garel, F. Ginhoux, D. Schafer, A. Sierra

6 May - 6 May 2020

Ensembl REST API Workshop, DKFZ, 6 May 2020

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

5 May - 5 May 2020

Ensembl Browser Workshop, DKFZ, 5 May 2020

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.

5 May - 2 June 2020

Solution Scattering from Biological Macromolecules

M. Gräwert, A. Kikhney, D. Svergun

4 May - 8 May 2020

Ensembl Browser Workshop: ACEGID Bioinformatics Workshop, Redeemer's University, 4th-8th May 2020

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.

4 May - 8 May 2020

CABANA workshop: Exploring biological networks and its application in health and disease

This workshop will introduce open-source tools for creating, visualizing and analysing biological networks oriented towards the study of pathogens. Training will be provided on computational tools and databases such as Reactome, Cytoscape, Gephi for graph visualization and analyses, MetaFlux, Pathway Tools, BioCyc for reconstruction of pathway/genome databases using omics data, and Target Pathogen for the discovery of targets using integrative approaches. The main principles of network analysis will be covered as well as its applications to health and disease.

Maria Bernardi; Derrin Crawte

2 May - 9 May 2020

Measuring Translational Dynamics by Ribosome Profiling - Postponed

P. Baranov, J. Medenbach, S. Leidel, E. Zielonka

30 April - 30 April 2020

Ensembl Train the Trainer Workshop - Bingham University, 30th April 2020

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

29 April - 29 April 2020

Ensembl REST API Workshop - Bingham University, 29th April 2020

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

27 April - 28 April 2020

Ensembl Browser Workshop - Bingham University, 27th-28th April 2020

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.

23 April - 24 April 2020

Advanced Network Analysis and Visualisation in Cytoscape (Cancelled)

EMBL-EBI has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are cancelling this course and apologise for the inconvenience. This course will focus on advanced network analysis and visualisation functionalities of Cytoscape. The course will feature tutorials on advanced network data visualisation, integration of single cell data into network analysis, and computational access to Cytoscape functionalities. EMBL-EBI resources directly related to interaction and pathway information will also be highlighted.

22 April 2020

UniProtKB: Increasing our understanding of neurodegenerative disorders through data curation

The webinar will give an overview on our ongoing curation efforts at the Universal Protein database UniProtKB on proteins involved in neurodegenerative disorders, including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and others. By literature search and querying databases such as OMIM and Orphanet, we have identified over 200 neurodegenerative diseases with 165 associated proteins. We will focus our curation efforts on those proteins in order to help researchers to better understand the relationship between protein function and disease development. The webinar will cover how we provide experimental information on molecular data of proteins involved in neurodegenerative diseases through literature curation. Curation of molecular functions and interactions, as well as disease-associated variant positions, variant characterisation and their impact on protein structure and function will be outlined. Our efforts to supplement human protein information with data from protein orthologs, such as mouse, rat and the fruit fly Drosophila melanogaster, which provide excellent model organisms for studying disease, will be shown. By focusing our curation efforts on proteins involved in neurodegenerative diseases, we hope to provide the research community with a rich source of information on proteins involved in these debilitating diseases and enable research activities such as data-driven research, translational and personal medicine.  

22 April - 24 April 2020

The Epitranscriptome - Postponed to 2021

M. Frye, N. Kim, D. O'Carrol

21 April - 7 May 2020

Introduction to the Ensembl Genome Browser - Webinar Series

The Ensembl genome browser provides users with gene, variation, comparative genomics and regulation data integrated together onto vertebrate genomes. The Ensembl team presents an interactive, online version of their popular face-to-face browser course, delivered via webinar across three weeks.

20 April - 22 April 2020

2nd European Network Biology Conference: From Networks to Modelling

The conference will examine novel computational and experimental approaches for generating functional understanding from network modelling and review current trends in network mapping and analysis.

20 April - 24 April 2020

RNA-Sequence Analysis (Cancelled)

EMBL-EBI has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are cancelling this course and apologise for the inconvenience. This course will familiarise participants with advanced data analysis methodologies in the field of transcriptomics and to provide practical training in the latest analytical approaches.

8 April - 8 April 2020

UniProt for Proteomics Scientists

This webinar will give a brief introduction to the UniProt website and then highlight resources available that proteomics scientists or users with large protein datasets may find useful in analysing their data.

8 April 2020

Using Europe PMC for effective literature research

This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries. Europe PMC (https://europepmc.org/) is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more.

Dayane Rodrigues Araujo

7 April - 7 April 2020

Ensembl Train the Trainer Workshop - Uganda Medical Informatics Centre, MRC/UVRI & LSHTM, 7th April 2020

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

6 April - 6 April 2020

Ensembl Browser Workshop- Uganda Medical Informatics Centre, MRC/UVRI & LSHTM, 6th April 2020

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.

3 April - 3 April 2020

Ensembl Browser Workshop- University of Rwanda, 3rd April 2020

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.

2 April 2020

UniProt COVID-19 website

The new UniProt portal for the SARS-CoV-2 coronavirus and receptor protein entries provides the latest available pre-release UniProtKB data for the SARS-CoV-2 coronavirus and other entries relating to the COVID-19 outbreak. Please join us for a free webinar describing the use of the portal including data release and updates. 

Sangya Pundir

1 April 2020

Visualising your own data in the Ensembl genome browser

The Ensembl project (www.ensembl.org) 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 visualising your own datasets in the genome browser.

Michal Szpak

1 April - 1 April 2020

Ensembl Browser Workshop- KEMRI Centre for Global Health Research in Kisumu Kenya, 1st April 2020

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.

31 March - 2 April 2020

CABANA Workshop: Managing a bioinformatics core facility

This knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL-EBI’s service teams, from each other, and from potential users of their services. These facilities play an essential role in enabling research in the molecular life sciences. The landscape is constantly evolving as new research tools emerge, as experiments become increasingly data intensive, and as their clients – experimental researchers – become more exposed to the power of data-driven biology. The workshops will allow participants to share experiences, discuss challenges and solutions that they face, and plan ways to cope with the ever changing demands raised by the molecular life science field. It will include sessions to learn from data providers at EMBL-EBI, hear how others have tackled common problems, and work together to design core services. Please note this course will NOT provide bioinformatics training.   During this course you will learn about:  Core service design Technical aspects of bioinformatics core facility management Funding and financing your core facility Building your group HPC clusters, (secure) data needs

Derrin Crawte, Nicole Scherer, Thiago Parente

30 March - 2 April 2020

Introduction to Metabolomics Analysis

This course will provide an introduction to metabolomics data analysis.

29 March - 1 April 2020

Proteomics in Cell Biology and Disease Mechanisms - Virtual

A. Lamond, E. Lundberg, M. Mann, J.A. Vizcaino

29 March - 31 March 2020

The Four-Dimensional Genome - Virtual

W. Bickmore, J. Ellenberg, S. Gasser, C. Häring, B. van Steensel

27 March - 27 March 2020

EMBL-EBI Workshop: Interactions and pathways for endocrine biology

This course is aimed at giving life scientists and clinicians training on how to explore and use molecular interaction and pathway bioinformatics resources.

19 March - 23 April 2020

Engaging with your community through events and training

CORBEL and EOSC-Life are running a webinar series on communication and event organisation. In this series we will discuss about event management, course design and delivery, and effective scientific communication.

16 March - 20 March 2020

Data Visualisation for Biology: A Practical Workshop on Design, Techniques and Tools

This course will give insights into, and practical experience in data visualisation for exploring biological data.

14 March - 18 March 2020

Inter-Organ Communication in Physiology and Disease - Postponed to 2022

G. Karsenty, I. Miguel-Aliaga, M. Soares

14 March - 20 March 2020

FISHing for RNAs: Classical to Single Molecule Approaches - Cancelled

I. Gaspar, E. Perlas, E. Zielonka

11 March 2020

Exploring ChEMBL Data with the new ChEMBL Interface

ChEMBL is a manually curated open database of bioactivity data of molecules with drug-like properties. It enables users to identify data that relates chemical structural information to biological function and used to facilitate the discovery of new drugs. This webinar will highlight the data that is available in the ChEMBL database and how it can be accessed using the new ChEMBL web interface //www.ebi.ac.uk/chembl/. The webinar will include a walkthrough of several typical drug discovery use cases and will show how the data can be queried via the interface to identify this data.

Anne Hersey

10 March - 12 March 2020

Bioinformatics resources for protein biology

Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research? Do you want to know more about the sequence of your protein and its functions? Wondered whether a structure of your protein exists and how to explore it? Want to know more about the potential complexes and reaction pathways your protein of interest is involved in, giving you a better overview of its biological context? This three day workshop will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies. Each day will focus on a particular protein topic, with the aim of helping you get more from your data and also to explore publically-available data that can further support your research.

Charlotte Pearton

9 March - 12 March 2020

Circulating Tumour DNA in Clinical Applications - Cancelled

V. Benes, G. Obernosterer, E. Zielonka

8 March - 11 March 2020

Advances in Stem Cells and Regenerative Medicine - Cancelled

C. Nerlov, P. Neveu

4 March - 4 March 2020

Mol*: Improved molecular visualisation at PDBe

This webinar will focus on the use of the new online molecular visualisation tool, Mol* from PDBe. We will show basic usage, observation of electron density maps and EM volumes, interrogation of ligand structures, and the visualisation of sequence annotations.

2 March - 6 March 2020

Introduction to multiomics data integration and visualisation

With the increase in the volume of data across the whole spectrum of biology, more opportunities as well as challenges have been created to identify novel perspectives and answer questions in life sciences. This may also include public domain data, which can provide added value to data derived through researcher’s own work and inform experimental design. This introductory course will highlight the challenges that researchers face in integrating multiomics data sets using biological examples. The course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation. This course will not include systems biology modelling or machine learning. A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI data resource and research teams. This allows people to explore the bioinformatics tools and resources introduced in the course and to apply these to a set problem, providing hands-on experience of relevance to their own research. The group work will culminate in a presentation session involving all participants on the final day of the course, giving an opportunity for wider discussion on the benefits and challenges of integrating data.

Meredith Willmott

1 March - 6 March 2020

Techniques for Mammary Gland Research

M. Jechlinger, M. Smalley, M. Vivanco

29 February - 4 March 2020

The Organism and its Environment

E. Heard, M. Leptin

24 February - 25 February 2020

Ensembl Browser Workshop, Nottingham, 24/25 February 2020

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.

24 February - 4 March 2020

CABANA Workshop: NGS analysis applied to virome sequencing in agricultural systems

Virome sequencing is a high throughput method to identify and classify communities of viruses, not only in plants but also animals and humans. We will focus on the sequencing of small-interfering RNAs (siRNAs) to discover the virus population in plant samples. The resulting information analysis relies on viral databases that are constantly evolving, and software tools constantly being updated. Therefore, we will explore all of these aspects in this workshop. The workshop will consist of two modules: i) a wet bench workshop for training around the experimental design and DNA library preparation, and ii) a bioinformatics module overviewing multiple applications of Virome Sequencing, and its application in agricultural systems. People interested in this workshop may apply for both modules (limited to 10 participants) or only for the bioinformatics module (limited to 25 participants). Selection of participants will be based on application form.  The bioinformatics module includes a pipeline for detailed computational analysis of virome data; including genomic analysis tools such as Virus-DetectW, phylogenetic and recombination analysis with MegaX and RDP and network  analysis using the statistical package R. Also, publicly available resources for virus analysis and their application will be implemented during the workshop. The detection of pathogens is an essential task for people working on agricultural systems. In recent years the use of sequencing technologies has enabled the discovery and description of new viruses, even communities of pathogenic entities within crops, for example potato and sweet potato. This is relevant for surveillance and to develop strategies to control these pathogens across borders. 

CABANA UCR Costa Rica, Rebeca Campos-Sanchez, Jan Kreuze, Derrin Crawte

18 February - 20 February 2020

Mining PDBe and PDBe-KB using a graph database

This workshop covers the use of the PDBe graph database to extract data for solving complex structural biology queries. It will introduce the PDBe graph database and how to write Cypher queries to retrieve data of interest. Workshop participants will be able to use the graph database to explore data relevant to their own research with support and guidance from the development team at PDBe. The graph database integrates annotations provided by PDBe-KB partners and is implemented in Neo4J. In this graph each PDB entry is represented as a tree, with the root being the PDB entry, connected to chains and entities, which are then connected to residues. Each of the PDB residues (>150 million) are linked to available annotations (e.g. is the residue part of a catalytic site?, or is it on a macromolecular interaction interface?) and are also directly connected to their corresponding UniProt residues. Storing PDBe-KB data as a graph offers great benefits in particular by allowing straightforward transfer of annotations between PDB entries which map to the same UniProt accession, as well as to highly identical UniProt accession. Read the database schema here.

Meredith Willmott

12 February 2020

eQTL Catalogue: a compendium of uniformly processed human expression and splicing QTLs

The eQTL Catalogue is a new project aimed at accelerating the functional interpretation of human GWAS studies and the annotation of common variants through a comprehensive collection of gene expression and transcript splicing QTLs. Public datasets are thus collected then processed with a uniform pipeline to remove analysis artefacts and quality controlled, before being made freely available to all. In this webinar, we will describe the data and most importantly how to access it. Already, the results of the eQTL Catalogue can be accessed via bulk download, API access and browsed on the Open Targets Genetics platform.

Daniel Zerbino

12 February - 12 February 2020

Ensembl REST API workshop, Ben Gurion University, 12th February 2020

Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data for plants, such as genes, variants, homologues and alignments.

11 February - 11 February 2020

Ensembl Browser Workshop, Ben Gurion University, 11th February 2020

Work with the Ensembl Outreach team to get to grips with the Ensembl Plants genome browser, accessing gene, variation and comparative genomics data, and mine these data with BioMart.

11 February - 12 February 2020

Exploring human genetic variation

Do you want to understand more about genetic variation? Are you aware of the resources available for finding, viewing and exploring variant data? Are you trying to link variant data to phenotypes? This two-day workshop will demonstrate resources and bioinformatics tools available at EMBL-EBI and the Sanger Institute that will aid understanding of human genetic variation. 

Rebecca Nicholl

10 February - 10 February 2020

Ensembl Browser Workshop, Tel Aviv University, 10th February 2020

Work with the Ensembl Outreach team to get to grips with the Ensembl Plants genome browser, accessing gene, variation and comparative genomics data, and mine these data with BioMart.

9 February - 13 February 2020

Immune Profiling of Single Cells

V. Benes, K. Danielski, D. Ordonez, E. Zielonka

9 February - 12 February 2020

Engineering Multicellular Systems

M. Ebisuya, N. Montserrat, J. Samitier, J. Sharpe, X. Trepat, V. Trivedi

5 February 2020

Searching and browsing scientific publications with the new Europe PMC

Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant and most cited articles in a topic of interest. Also, learn how to find and explore the enhanced content available in Europe PMC.

Dayane Rodrigues Araujo

5 February - 7 February 2020

Expanding the Druggable Proteome with Chemical Biology

P. Aloy, A. Carter, A. Claude-Gavin, G. Drewes, S. Knapp, A. Müller-Fahrnow

5 February - 6 February 2020

Ensembl Browser Workshop, Erasmus MC Rotterdam, 5/6 February 2020

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.

4 February - 6 February 2020

Expanding the Druggable Proteome with Chemical Biology

OverviewSpeakersProgrammePractical information

2 February - 7 February 2020

Analysis and Integration of Transcriptome and Proteome Data

V. Benes, R. Calogero, J. Krijgsveld, L. Martens

27 January - 30 January 2020

Exploratory Analysis of Biological Data: Data Carpentry

T. Hodges

24 January - 24 January 2020

EMBL-EBI workshop in UC Davis: Transcriptomics data and resources

This is a one-day workshop to provide an overview of data management and ontology principles in addition to hands-on experience with functional genomics resources at the EBI which cover data submission, archive and visualisation. These resources are: Annotare, ArrayExpress and the transcriptomics knowledgebases Expression Atlases (bulk and single-cell). ArrayExpress: public database for functional genomics Expression Atlas: Gene expression across species and biological conditions

Nancy George, Monica Britton

23 January - 23 January 2020

Ensembl Browser Workshop, UC Davis, 23 January 2019

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.

23 January - 23 January 2020

Ensembl Train the Trainer Workshop, American University in Cairo, 23rd January 2020

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

22 January - 22 January 2020

Introduction to EMBL-EBI Resources

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 us for a tour of the core data resources at EMBL-EBI.

22 January - 22 January 2020

Ensembl REST API workshop, American University in Cairo, 22nd January 2020

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

21 January - 24 January 2020

Introduction to RNA-Seq and Functional Interpretation

This course is aimed at life science researchers wanting to learn more about processing RNA-Seq data and later downstream analysis.

21 January - 21 January 2020

EMBL-EBI Workshop in Stanford University: Transcriptomics data and resources

This is a one-day workshop to provide an overview of data management and ontology principles in addition to hands-on experience with functional genomics resources at the EBI which cover data submission, archive and visualisation. These resources are: Annotare, ArrayExpress and the transcriptomics knowledgebases Expression Atlases (bulk and single-cell). ArrayExpress: public database for functional genomics Expression Atlas: Gene expression across species and biological conditions

Michael Newman, Nancy George

21 January - 24 January 2020

Introduction to RNA-seq and functional interpretation

This course will provide an introduction to the technology, data analysis, tools and resources used in RNA sequencing and transcriptomics. The content is intended to provide a broad overview of the subject area, and to introduce participants to simple data analysis using  the command line and APIs. It will also highlight key resources, approaches and methodologies to begin the biological interpretation and analysis of transcriptomics data. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets - there will be no opportunity to  analyse personal data.

Marina Pujol

20 January - 24 January 2020

Deep Learning for Image Analysis

A. Kreshuk

19 January - 23 January 2020

Deep Learning for Image Analysis

OverviewSpeakers and TrainersProgrammePractical information

17 January - 17 January 2020

EMBL-EBI Workshop in UC San Diego: Transcriptomics data and resources

This is a one-day workshop to provide an overview of data management and ontology principles in addition to hands-on experience with functional genomics resources at the EBI which cover data submission, archive and visualisation. These resources are: Annotare, ArrayExpress and the transcriptomics knowledgebases Expression Atlases (bulk and single-cell). ArrayExpress: public database for functional genomics Expression Atlas: Gene expression across species and biological conditions

Jason Kreisberg, Nancy George

16 January - 16 January 2020

Ensembl Browser Workshop, UC San Diego, 16 January 2019

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.

13 December - 13 December 2019

EMBL Insight Lecture: Ageing and diseases – what is the link?

A free event for schools organised by EMBL, ELLS. Dame Janet Thornton will be discussing the link between ageing and diseases. Booking required.

11 December 2019

Single cell RNA-seq analysis using a Galaxy interface

In this webinar, we will look at a Galaxy interface for single cell analysis. Specifically, we will run Scanpy (which would otherwise require Python programming skills) to analyse a Drop-seq dataset located in EMBL-EBI's Single Cell Expression Atlas.

Wendi Bacon

7 December - 9 December 2019

Target Validation Using Genomics and Informatics

J. Barrett, S. John, G. Neubauer, O. Stegle

2 December - 5 December 2019

Enzymatic Methyl-Seq: Bisulfite-Free Methylation Analysis

V. Benes, B. Textor

2 December - 3 December 2019

Ensembl Browser Workshop, Universidad Icesi, 2nd-3rd December 2019

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.

2 December - 5 December 2019

IITM-EBI modelling workshop

Computer models are increasingly used by researchers as well as the pharmaceutical industry to investigate disease initiation, progression and therapy. Modelling of biochemical pathways deregulated in disease condition offers mechanistic insights into the pathology; helps to elucidate mechanisms behind dug action and predict dose required for treatment and thereby greatly facilitates fundamental research and drug discovery. Such modelling requires a background in both molecular biology and mathematics.  The four days workshop will train researchers from life science and mathematics to communicate and work together to learn to build and analyse computer models using user-friendly open-source software. The workshop will be jointly organised by EBI and Indian Institute of Technology Madras (IITM; https://www.iitm.ac.in/), more specifically, BioModels team from EBI along with  Initiative for Biological Systems Engineering (IBSE; https://ibse.iitm.ac.in/) and Robert Bosch Centre for Data Sciences and Artificial Intelligence (RBC-DSAI; https://rbcdsai.iitm.ac.in/) from IITM. This national-level workshop will be organised locally at IITM. Various modelling approaches and tools will be introduced to the participants. They will explore a few of the disease-specific computer models from a recent publication, freely available in BioModels repository (//www.ebi.ac.uk/biomodels/). Other EBI resources including Reactome, IntAct, OmicsDI, PRIDE, ExpressionAtlas will be introduced to the participants  BioModels team will lead the training on kinetic modelling of signalling pathways, curation and annotation of mathematical models as well as standards in modelling (SBML, SED-ML, etc). IITM/IBSE team will partner in the training on kinetic modelling approaches, and also introduce other paradigms such as constraint-based modelling (e.g. Flux Balance Analysis (FBA)) for the analysis of metabolic pathways.    An essential agenda in the meeting will be group projects where participants from both experimental and theoretical background would work to getter to curate mathematical models and submit them to the BioModels repository. This workshop will allow EBI to partner with IITM to share expertise on kinetic modelling and gain expertise on the curation of non-kinetic models in BioModels repository. Furthermore, this join workshop would be used as an opportunity for long term partnership with IITM to establish training for EBI resources in India, explore the possibility of joint data curation engagement and scientific collaboration.

IBSE Workshop Team

2 December - 6 December 2019

CABANA Workshop: Introduction to Metagenomics

In this course participants will learn the basics of metagenomics, covering experimental design and workflows, moving through to microbiome analysis via metabarcoding and shotgun metagenomics. The course theme will be the use of metagenomics oriented to biodiversity. The course will be delivered by experienced and dedicated world-renowned experts, including EMBL-EBI trainers, and will involve presentations, demonstrations and practical exercises to give participants hands-on experience.

Derrin Crawte, Maria Bernardi

28 November - 30 November 2019

Facing the Future: Perspectives and Challenges of Life Sciences in the 21st Century

PhD Students

27 November 2019

PDBe-KB Aggregated Views: Presenting PDB data in a different context

Our understanding of biological function can be advanced by the knowledge of biomolecular structures. Yet, it requires compiling data from individual entries in the Protein Data Bank (PDB), where each entry may represent only a segment of a complete system and may lack biological context. The Protein Data Bank in Europe - Knowledge Base (PDBe-KB) is a community-driven, integrated resource whose goal is to place macromolecular structures in their biological context and thus promote fundamental and translational research. PDBe-KB combines residue-level structural data with functional annotations and sequence information in a highly interconnected, complex graph database, on the scale of 1 billion nodes and 4 billion edges. PDBe-KB infrastructure allows compilation of data from multiple PDB entries into a context-specific view of the data that is made available via an extensive set of API endpoints and modular web components. This webinar presents an updated version of the first, protein-specific aggregated view that summarises all the data from the PDB and associated functional annotations from PDBe-KB partner resources in a user-friendly and accessible web-based view, providing a novel way to navigate structural data.

Lukas Pravda

27 November - 29 November 2019

Single cell RNA-seq analysis: From questions to clusters

This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to cell cluster comparisons using data extracted from the Single Cell Expression Atlas. In addition to running a basic pipeline, participants will explore the variety of options within the Galaxy resource and individually analyse a given dataset. The results will be compared across the cohort to assess reproducibility and demonstrate the effect of analytical choice on research output. Finally, participants will learn about data submission, resources, and standards within the single cell field. Please note that although participants will not be able to use their own data during the course practicals, there will be ample time to discuss their research and ideas with both course participants and trainers.

Marina Pujol

22 November - 22 November 2019

Dev Day 2019

Developers from all walks of life are welcome to the Wellcome Genome Campus for a day of tech talks, networking and workshops with a slight scientific twist. Whether your work involves science or not, there will be plenty of opportunities to learn from and catch up with peers from various fields who approach tech problem-solving in creative ways.

21 November 2019

Submitting metagenomic data to ENA

In order to have your metagenomic data analysed by MGnify your sequence data has to be captured by the European Nucleotide Archive (ENA). ENA is a comprehensive database of nucleotide sequences, providing information on raw sequencing data, sequence assemblies and functional annotation. This webinar will discuss how you can submit metagenomic studies to ENA, make sure they are well annotated, and help people understand your work. It will also cover Webin-CLI, the newly developed Webin Command Line Submission tool. The webinar is presented by Sam Holt who works for ENA.

Sam Holt

21 November - 22 November 2019

3D-BioInfo community annual meeting

ELIXIR Communities enable the participation of communities of practice in different areas of the life sciences in the activities of ELIXIR, which underpin the evolution of a data, tools, interoperability, compute and training infrastructure for European life science informatics (https://www.elixir-europe.org/use-cases). Structural bioinformatics has a broad impact across the life sciences and provides tools to archive, visualise, analyse, annotate, and predict the structure of biological macromolecules. Structural bioinformatics is traditionally very strong in Europe offering many software tools, methodologies, and databases, as well as community-wide prediction challenges. Its applications cover research activities from structural biology to drug discovery and personalised medicine that are all well represented within the national ELIXIR nodes. The 3D-BioInfo Community was approved by ELIXIR in May 2019. This meeting will be the first official meeting of the community to plan major activities and to identify research groups wishing to contribute to these activities.

Charlotte Pearton

18 November - 21 November 2019

Bioinformatics for Crop Plants

We are sorry to announce that this course is cancelled meaning that it will no longer run this year. 

17 November - 22 November 2019

Methods for Analysis of Circular RNAs: No Tautology

M.L. Baudet, V. Benes, I. Bozzoni, C. Dieterich

13 November 2019

Life cell by cell: Introduction to Single Cell Expression Atlas

Explore gene expression profiles across various species and conditions at single cell resolution. Single Cell Expression Atlas (SCEA) is an open resource committed to making the information from single cell sequencing datasets readily accessible to the research community and beyond. At SCEA we accumulate, curate and re-analyse available raw single-cell sequencing data from multiple species and across experimental conditions to make them cross-comparable and we present the analysis results in a user-friendly interface for public consumption. This allows researchers to gain a quick insight into the expression pattern of their gene of interest at the level of individual cells across different species from human to Saccharomyces. At SCEA we aim to keep pace with the rapidly growing single cell transcriptomics research and to make the knowledge thus obtained truly open and widely available so that it can serve as basis for further studies. The webinar will provide a quick overview of: Different single cell sequencing methods Various ways of searching SCEA How to filter and interpret the analysis results on the experiment page Additional features and resources available on the experiment page

Silvie Fexova

13 November - 16 November 2019

Precision Health: Molecular Basis, Technology and Digital Health

L. Steinmetz, J. Zaugg, M. Snyder

11 November - 14 November 2019

Bioinformatics & functional genomics in zebrafish

Zebrafish are widely used to study development, toxicity and disease, and functional genomics is used throughout the field to identify new pathways and mechanisms and for comparison to other model systems and humans. In this hands-on course, participants will learn how to design functional genomics experiments, manage and analyse RNA-seq datasets from zebrafish, and compare results to other species. The aim of the course is to equip researchers with tools to carry out functional analysis and data visualisation of RNA-seq data that has already been mapped to the genome and been analysed for differential gene expression. The course will be relevant to researchers working on a wide range of topics and will use real datasets from our lab for hands-on analysis.

Meredith Willmott

10 November - 15 November 2019

The Fundamentals of High-End Cell Sorting

D. Davies, A. Filby, D. Ordonez, M. Paulsen, S. Schmitt

6 November - 9 November 2019

CABANA workshop: Advanced RNAseq and network analysis in genomics

This course will provide training on RNAseq data production and interpretation. The course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. We will dedicate some time to analysing and constructing networks from expression data and using the Gene Ontology for gene set enrichment test. Finally, we will cover some aspects of Meta-metrics in networks (high-dimensional data).

Derrin Crawte

6 November - 8 November 2019

CABANA Workshop: Resources and tools for target identification and drug discovery

In this course, participants will learn the necessary theoretical background and basic tools of molecular target identification in pathogens and building of compound libraries for virtual screening. We also will introduce general concepts of molecular docking simulations.

Derrin Crawte, Maria Bernardi

3 November - 6 November 2019

Cancer Genomics

P. Campbell, J. Korbel, N. Lopez-Bigas, M. Meyerson

3 November - 9 November 2019

Practical Integrative Structural Biology

A. Jakobi, J. Kosinski, M. Wilmanns

2 November - 7 November 2019

Humanized Mice in Biomedicine: Challenges and Innovations

K-D. Bissig, C. Münz, Y. Petersen, J.J. Schuringa, L. Shultz, B. Soper, R. Stripecke

24 October - 25 October 2019

Science as Storytelling: From Facts to Fictions

H. Stefánsson

23 October 2019

EurOPDX Data Portal: a repository of patient-derived xenograft models

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.

Emilie Vinolo, Enzo Medico

22 October - 22 October 2019

Ensembl Browser Workshop, IGMM, Edinburgh, 22 October 2019

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.

20 October - 25 October 2019

Volume Electron Microscopy by Automated Serial SEM

C. Genoud, P. Machado, N. Schieber, Y. Schwab

16 October 2019

Explore the known protein space through UniProt Archive and Clusters

UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant, publicly accessible resources. To avoid redundancy, each unique sequence is stored only once with a stable protein identifier. As a result, performing a sequence search against UniParc is equivalent to performing the same search against all databases cross-referenced by UniParc. UniProt Reference Clusters (UniRef) provides clustered sets of sequences from the UniProt Knowledgebase (UniProtKB) and selected UniParc records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences. The reduced redundancy increases the speed of similarity searches and improves detection of distant relationships.

Hermann Zellner, Borisas Bursteinas

16 October - 16 October 2019

Ensembl REST API workshop

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. Our sister project Ensembl Genomes covers bacteria, plants, fungi, protists and (invertebrate) metazoa. This workshop is aimed at researchers and developers interested in exploring the data beyond the websites. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write Python/R/Perl scripts to call them.

Astrid Gall

15 October - 17 October 2019

Computing Skills For Reproducible Research: Software Carpentry

T. Hodges, M. Sharan, G. Zeller

15 October - 18 October 2019

The Non-Coding Genome

I. Bozzoni, N. Kim, J. Rinn, J. Vogel

15 October - 15 October 2019

Ensembl browser workshop

The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Our sister project at www.ensemblgenomes.org can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa. The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users. 

Astrid Gall

15 October - 18 October 2019

CABANA Workshop: Chemoinformatics in Drug Discovery

The aim of this workshop is to introduce researchers to the field of Chemoinformatics, especially in the areas of Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD). Trainees will cover the use of protein, ligand and drug databases, protein modelling, molecular docking and virtual screening for drug discovery applications. Managing and analysing virtual chemical libraries will also be covered, including the application of machine learning algorithms in drug discovery. The workshop will be instructed by trainers from the University of Antioquia in Colombia, from CINVESTAV Unit for Advanced Genomics (LANGEBIO) in Mexico, as well as local expert researchers from the School of Chemistry at the National Autonomous University of Mexico (UNAM).

Derrin Crawte

14 October - 15 October 2019

CABANA Train the Trainer Workshop in Lima, Peru

This course will provide new trainers with knowledge, skills, guidance and tips for developing and delivering training. Participants will explore a range of methods to enable and encourage learning, examine the requirements for a successful course and acquire appropriate feedback.  The workshop will: provide guidance on general training techniques and appropriate use of methods based on learner needs, including some general 'DO's' and 'DO NOTs' for successful training provide a framework for successful curriculum design and further development, to enable trainers to build a course appropriate to their learners' needs

Derrin Crawte

14 October - 15 October 2019

EMBL-EBI Workshop: Bioinformatics Resources for Chemical and Molecular Biology

This workshop will explore bioinformatics data resources related to the fields of biological and chemical physiology. Participants will be introduced to several databases and tool sets available through the EMBL-European Bioinformatics Institute website that can be used to identify useful scientific information and understanding of physiological processes. During the two days participants will learn about these resources through short lectures, work through practical examples and use cases of relevant databases and have time to discuss how best to make use of various tools in their own research.

Lucia Sironi

9 October - 12 October 2019

Seeing is Believing - Imaging the Molecular Processes of Life

J. Ellenberg, J. Lippincott-Schwartz, A. Miyawaki

8 October - 10 October 2019

Exploring biological sequences

This workshop will introduce basic bioinformatics approaches that are used to find, analyse and understand nucleotide or protein sequences. It will explore how to conduct searches across biological databases using both metadata and sequence data approaches. The course will explain how sequence searching techniques work, and how to use them effectively to find relevant results. Practical exercises will develop skills in searching for, accessing and aligning sequences; through the use of sample datasets participants will learn how to discover more about the biological context of nucleotide and protein sequences. The key areas covered by the workshop will include: Sequence data resources at EMBL-EBI Tools for sequence searching and alignments Using sequences to investigate families, function and structure If you would like to see details of similar course from previous years, please take a look at our course listings, using the filter boxes to refine your search by year and subject.

Meredith Willmott

7 October - 9 October 2019

Tools for Structural Biology of Membrane Proteins

F. Hagn, C. Löw, A. Ramamoorthy

3 October - 3 October 2019

Reproducible Research: Linking Publications to Curated Data Resources

Curation is an indicator of research quality. Linking back from the publications to the curated data resources is essential to make science more reproducible. Europe PMC (https://europepmc.org/), the database of life science publications, provides an External Links service that makes it easier to connect publications and the data behind them.

2 October 2019

Integrating publications into bioinformatics analysis

Research literature contains a wealth of information that can be extracted at scale using text-mining technologies. To make text-mining data available to a wider group of researchers, the publications database, Europe PMC, provides access to millions of text-mined annotations, such as genes and proteins, metabolites, species, mutations, phosphorylations, interactions, associations, and many more.  This webinar will demonstrate how to access text-mined literature evidence programmatically, and how to supplement it with bibliographic information for advanced use cases. Two of such use cases, mapping of tropical disease research by author affiliation geoparsing and comparison of applicability of analytical chemistry techniques, will be introduced by invited speaker, Dr. Magnus Palmblad.

Mariia Levchenko, Magnus Palmblad

2 October - 2 October 2019

Ensembl REST API Workshop, Reykjavik, 2 October 2019

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.

2 October - 2 October 2019

EMBL-EBI Workshop: Mathematics of life workshop: “Modelling molecular mechanisms: from basic science to drug discovery”

This workshop is open to postdocs in Cambridge, including candidates from University and affiliated institutions Computer models are increasingly used by researchers as well as pharmaceutical industry to investigate molecular mechanisms disease initiation, progression and therapy. Systems modelling of biochemical pathways deregulated in disease condition offers mechanistic insights into the pathology; helps to elucidate mechanisms behind dug action and predict dose required for treatment and thereby greatly facilitates fundamental research and drug discovery. Such modelling requires background in both molecular biology and mathematics. This workshop will train postdocs from life science and mathematics to communicate and work together to learn to build and analyse computational models using user-friendly open source software. Participant will explore selected computational models from a recent publication, freely available in BioModels repository (www.ebi.ac.uk/biomodels/).  The one-day workshop includes scientific talks from 3 distinguished speakers who will showcase how modelling is useful in fundamental research as well as pharmaceutical industry, a tutorial session on modelling of normal and disease pathways using simulation software, COPASI, and an extended afternoon hands-on training workshop / group project. Prior knowledge on systems biology modelling not essential. This course is free to attend and funded by the Office of Postdoctoral Affairs, University of Cambridge.

Rahuman Sheriff

1 October - 1 October 2019

Ensembl Browser Workshop, Reykjavik, 1 October 2019

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.

29 September - 4 October 2019

Whole Transcriptome Data Analysis

V. Benes, R. Calogero

29 September - 2 October 2019

Systems Genetics: From Genomes to Complex Traits

T. Lappalainen, B. Lehner, T. Lemberger, L. Steinmetz

24 September - 24 September 2019

A guide to UniProt for students

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 searching, exploring and analysing data with UniProt using case studies typically useful for students or early researchers beginning to use bioinformatics resources in their studies/research.

24 September - 26 September 2019

Ensembl Browser and REST API workshops: Multi-Omics data analysis using Ensembl resources, Big Data & Artificial Intelligence Course, Amity University

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. Optional second day to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments.

23 September - 27 September 2019

UNU-BIOLAC and CABANA: Latin American Workshop in Structural Bioinformatics of Proteins

This workshop will provide training on well-established resources to analyze protein structures using computational tools. The topics will involve the use of bioinformatics tools and databases, as well as background information on simulations using protein structures. The workshop will be instructed by trainers from the Protein Data Bank in Europe (PDBe), from CINVESTAV Unit for Advanced Genomics (LANGEBIO) in Mexico, as well as local expert researchers from the Max Planck Tandem Group of Biophysics of Tropical Diseases in Colombia working on protein simulations. Some of the examples used during the sessions will fall under the UN's sustainable development goal of communicable diseases prevention and treatment.

Rodrigo Ochoa, Piraveen Gopalasingam

23 September - 26 September 2019

Next generation sequencing bioinformatics

This course will provide an introduction to the technology, analysis workflows, tools and resources for next generation sequencing data analysis. The content will provide insights into how biological knowledge can be derived from genomics experiments and explain different approaches to analysing such data. The main focus of the course will look at the assembly, re-sequencing, and variant calling undertaken during the analysis of higher-eukaryotes, with a particular emphasis on human genetic research. Practical sessions will allow participants to process training datasets and apply appropriate statistical methods in their analyses. There will be no opportunity to work with your own data during the course.

Rebecca Nicholl

22 September - 27 September 2019

Liquid Biopsies

V. Benes, A. Ståhlberg

21 September - 24 September 2019

Creating is Understanding: Synthetic Biology Masters Complexity

A. Becker, J. Crocker, V. de Lorenzo, J.-L. Faulon

18 September 2019

Ensembl gene annotation for clinical genomics

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.

Emily Perry, Joannella Morales

16 September - 20 September 2019

Structural bioinformatics

Structural biology, determining the three-dimensional shapes of biomacromolecules and their complexes, can tell us a lot about how these molecules function and the roles they play within a cell. Bioinformatics data derived from structure determination experiments enables life-science researchers to address a wide variety of questions. For example, it aids the understanding of how mutations in a gene might alter a protein’s shape, disrupt a catalytic site, or alter the binding affinity of a pharmaceutical compound. This course explores bioinformatics data resources and tools for the interpretation and exploitation of biomacromolecular structures. It will focus on how best to analyse available structural data to gain useful information given specific research contexts. The course content will investigate the impact of genetic variation on structure, predicting protein structure and function, and exploring interactions with other macromolecules as well as with low-MW compounds. Participants will also have an opportunity to explore protein docking using HADDOCK.

Marina Pujol

15 September - 22 September 2019

Synthetic Biology in Action: Bridging Natural/Non-Natural

C. Arraiano, V. de Lorenzo, S. Panke, E. Zielonka

11 September 2019

Genome3D annotations in InterPro

Genome3D provides consensus structural annotations and 3D models for sequences from ten model organisms, including human. These data are generated by several UK-based resources that together form the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, pDomTHREADER and PHYRE. InterPro, meanwhile, provides functional analysis of proteins by classifying them into homologous superfamilies and families, and by predicting domains, repeats and important sites, based on data from 14 member databases. This webinar presents the new InterPro entry type, Homologous superfamily, as well as describing domain and structure predictions from Genome3D annotations, and how they are integrated in InterPro.

Typhaine Paysan-Lafosse

11 September - 12 September 2019

Analysing non-coding RNA with RNAcentral and Rfam

This workshop, organised in conjunction with the RNA Informatics conference, provides an overview of RNAcentral and Rfam, two databases for non-coding RNA analysis. Non-coding RNAs (ncRNAs) are RNA molecules that are not translated into proteins and are found in every living organism. Many ncRNAs are responsible for important biological functions. For example, rRNA is a key component of the ribosome, and microRNAs regulate gene expression. Researchers from different fields of biology may need to find what is known about specific ncRNA or identify ncRNA in their data, but may not have the required expertise.

Rebecca Nicholl

10 September - 12 September 2019

Multiomics to Mechanisms - Challenges in Data Integration

P. Cramer, N. Krogan, U. Sauer, J. Zaugg

10 September - 11 September 2019

Finding evidence in research publications

This workshop introduces tools and approaches used to discover biologically relevant data in the research literature. Participants will be introduced to the basics of programmatic analysis of scientific literature and explore the principles of dictionary-based text-mining, explained using relevant case studies. The workshop has a strong focus on practical exercises and group project work to give participants hands-on experience, tackling biologically relevant problems based on what they have learnt in this workshop. Do you want to identify publicly available datasets cited in research literature to use them in your future analyses? Do you want to develop basic skills to programmatically access and analyse scientific literature? Do you want to learn about the basics of text analytics to make the most of literature review? Published research contains a wealth of new data and evidence. Automating literature review and text analysis can help extract valuable knowledge from millions of research publications. Modern tools for literature analysis can help you identify potential drug targets, predict host-pathogen interactions, or infer growth regulators for crops, based on published findings.

Meredith Willmott

7 September - 17 September 2019

Current Methods in Cell Biology

A. Diz-Muñoz, S. Cuylen

4 September 2019

Variant submission and accessioning at the European Variation Archive

The European Variation Archive (EVA) is a primary open repository for archiving, accessioning, and distributing genome variation including single nucleotide variants, short insertions and deletions (indels), and larger structural variants (SVs) in any species. The EVA is in the process of releasing the first dbSNP data release which consists of RS ID-containing VCF files for each non-human species available in dbSNP. This webinar will provide an overview of the European Variation Archive including data ingestion, consumption, and how you can access and utilise dbSNP RS release batch files.

Baron Koylass

3 September - 7 September 2019

Protein Synthesis and Translational Control

F. Gebauer, W. Gilbert, M. Hentze, C. Spahn

2 September - 4 September 2019

CABANA Symposium: Bioinformatics and Biodiversity - Unlocking new tools for biodiversity research

This symposium will cover a broad range of topics in DNA barcoding and metabarcoding bioinformatics for biodiversity studies. Biodiversity experts from across Latin America and beyond will provide an introduction to the field, including general approaches and technologies for studying biodiversity in different contexts. Sample collection and processing, selecting appropriate markers and various analysis methods will be covered, as will regulatory issues in Latin America. 2 day symposium in Bragança, Pará State There will be a second symposium titled, “IV North Northeast Symposium on Bioinformatics” in Bragança - PA between 4-5th September. The topic will also be biodiversity. It will be a good opportunity to connect with a wider bioinformatics community and to also see a beautiful spot near the coast. For further information please follow this link.

Derrin Crawte

1 September - 5 September 2019

Chromatin Signatures During Differentiation: Integrated Omics

P. Grandi, K. -M. Noh

29 August - 30 August 2019

CABANA Train the Trainer in Belém, Brazil

This course is currently under development and full details about the course are not yet available.  Once the programme is confirmed we will post it here along with details on how to apply and registration costs.  If you would like to be informed when applications open for this course then please click on the “Register your interest” button above.  If you would like to see details of similar course from previous years, please take a look at our course listings, using the filter boxes to refine your search by year and subject.

Piraveen Gopalasingam

27 August - 28 August 2019

A Life for Science - Symposium in Memory of Fotis Kafatos

G. K. Christophides, S. M. Cohen, A. Ephrussi, I. Mattaj

26 August - 30 August 2019

Attacking Open Chromatin with ATAC Sequencing

V. Benes, U. Litzenburger, J. Zaugg

8 August - 8 August 2019

CABANA Webinar: Passport to a world of biodata

This webinar will provide an introduction to public data resources, with an emphasis on those provided by EMBL-EBI.

6 August - 9 August 2019

CABANA Workshop: Genotyping by Sequencing Applied to Plant Breeding

This workshop will provide training around the experimental design and multiple applications of Genotyping by Sequencing (GBS) in plants. In addition, detailed computational analysis of GBS data and resources will be explored. Genomic analysis tools for GBS, such as Tassel, iPyrad, STACKS, as well as publicly available resources for plant data process and application will we implemented during the workshop. The analysis of genomic variation is an essential part of plant genetics and crop improvement programs. DNA polymorphisms can be directly related to phenotype differences, be genetically linked to its causative factor, or indicate relationships between individuals in populations. Over the last years, the use of genotyping has enabled the characterization and mapping of genes and metabolic pathways in plants as well as the study of species diversity and evolution, marker-assisted selection (MAS), germplasm characterization and seed purity. Genotyping by sequencing (GBS) is a high throughput method to identify and genotype, at the same time, molecular markers as part of breeding activities, genetic mapping, and population genomics. Another advantage is that this method can be applied to organisms without reference genome and imputation of SNPs can be done as part of haplotype blocks. It was first published in 2011 and since then multiple crops have been improved including maize, potato, and rice. 

Laura Brenes Guillén, Andrés Gatica-Arias

29 July - 2 August 2019

Hands-on Flow Cytometry - Learning by Doing!

A. Filby, D. Ordonez, M. Paulssen, S. Schmitt

21 July - 26 July 2019

Proteomics bioinformatics

This course, run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences, provides hands-on training in the basics of mass spectrometry and proteomics bioinformatics, search engines and post-processing software, quantitative approaches, MS data repositories, the use of public databases for protein analysis, annotation of subsequent protein lists and incorporation of information from molecular interaction and pathway databases.

Advanced courses

17 July 2019

BioStudies database: aggregating all outputs of a life sciences study

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.

Ugis Sarkans

15 July - 19 July 2019

Bioinformatics for immunologists

The course will provide participants with an overview of best-practice methods in applying bioinformatics approaches and enable them to become confident users of their own and public domain data. The resources introduced during the course will cover a variety of data types, from genomic and proteomic data; to computational models, biological pathways and reaction information. Participants will gain experience of the analysis pipelines for NGS experiments relevant to immunology, and will be led through an exploration of this data to identify information of interest. Additionally participants will be introduced to how data from a number of sources can be integrated to provide a wider view of their research.

Scientific conferences