15 June - 17 June 2021

Open Virtual Ensembl API Workshop

Michal Szpak

Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 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 June - 17 June 2021

Bioinformatics for principal investigators

Jane Reynolds

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. 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.

16 June 2021

A guide to the maintenance of life science data by biocurators

Ajay Mishra

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. 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.

21 June - 25 June 2021

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

Rodrigo Ochoa

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. 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.

21 June - 25 June 2021

Systems biology: From large datasets to biological insight

Advanced Courses

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. 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...

21 June 2021

Preprints 101 for authors

Maria Levchenko

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.   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...

23 June 2021

A guide to proteomics data analysis using UniProt and InterPro

Ajay Mishra

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.   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...

28 June - 2 July 2021

Advanced Methods in Bioimage Analysis

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

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. OverviewSpeakers and TrainersProgrammePractical InformationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online. Course Overview Bioimage analysis has become a keystone of biological research: the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data. Due to the complexity of the data, without such expert guidance, it is very likely that image analysis algorithms may be applied incorrectly, possibly even producing erroneous results. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly that even experts are...

28 June - 2 July 2021

Summer school in bioinformatics

Scientific conferences

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. 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...

30 June 2021

A guide to analysing binding sites in protein structures

David Armstrong

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. 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.

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. OverviewSpeakers & Discussion PanelistsProgrammePractical InformationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. Symposium Overview 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. This meeting is the fifth of its kind, part of a successful series which started in 2013 and held biannually since, becoming a must-attend event for scientists...

7 July 2021

A guide to EBI Search

Matt Pearce

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 the 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. 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 the 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.

12 July - 16 July 2021

Super-Resolution Microscopy: Time-Resolved STED Nanoscopy

M. Lampe, R. Pepperkok, U. Schwarz

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. OverviewSpeakers and TrainersProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online. Course Overview This five-day comprehensive online microscopy course focuses on stimulated emission depletion microscopy (STED) and its application to biological questions. Through lectures, tutorials, demonstrations and practical workshops, the course provides in-depth knowledge on all aspects of STED Nanoscopy. It covers the fundamentals of STED microscopy, different technical implementations and has a strong emphasis on sample preparation – including choice of fluorophores and refractive index matching, as well as image acquisition strategies for fixed samples and living cells. Students will...

12 July - 16 July 2021

Proteomics bioinformatics

Advanced courses

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. 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...

12 July - 16 July 2021

Microscopy data analysis: Machine learning and the BioImage Archive

Marina Pujol

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. 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...

19 July - 30 July 2021

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

NextGenHelper

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.   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.

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. OverviewSpeakers and TrainersProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online. Course Overview Over the past decades it became evident that a RNA transcripts specific amount and localisation are important in order to understand the biological function of its (non-) coding gene. Whereby state-of-the-art in situ hybridisation (ISH) technologies are key to visualise these RNAs in a given tissue or cell. 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...

23 August - 27 August 2021

Advanced Fluorescence Imaging Techniques

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

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. OverviewSpeakers and TrainersProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online. Course Overview 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. Invited guest researchers together with experts from the EMBL and microscopy professionals will foster an intense information flow with a balance of lectures and practical workshops. The focus of the course will be on the use of fluorescence microscopy to obtain quantitative information about protein dynamics in living samples. Audience This course is directed towards...

29 August - 1 September 2021

The Mobile Genome: Genetic and Physiological Impacts of Transposable Elements

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

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. OverviewSpeakersProgrammeSponsorsPractical information Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. Conference Overview This conference is assembling 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. This conference provides a venue for cross-disciplinary discussions, with the goal of catalysing inter-disciplinary collaborations to address emerging questions in these scientific fields. Although often disparaged as “junk” DNA, it is now undeniable that transposable element (TE) activity has significantly shaped the structure and...

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. OverviewSpeakers and TrainersProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online. The application deadline for this course will be extended to 22 June Course Overview This interactive virtual 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 theoretical and interactive sessions as...

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. OverviewSpeakers and TrainersPreliminary ProgrammeSponsorsPractical Information Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online. Course Overview 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. Audience This course is intended for scientists with experience...

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. OverviewSpeakers and OrganisersPreliminary ProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. Conference Overview 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...

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. OverviewSpeakersProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the conference is going virtual and invite you to join us online. The virtual conference includes talks from invited speakers, short talk presenters, online group discussions and networking opportunities. Symposium Overview 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...

27 September - 4 October 2021

Genome Engineering: CRISPR/Cas from Cells to Mice

N. Humphreys, B. Koch, P. Rajakannu, E. Zielonka

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. OverviewSpeakers and TrainersPreliminary ProgrammePractical InformationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online. Course Overview This interactive virtual course will provide training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR/Cas9 system. The course will be split into two groups (mammalian cells OR mice) based on participants’ expertise. Through theoretical and interactive sessions as well as remote demonstrations of some of the practical work in the lab, the participants will learn to design CRISPR targets using bioinformatics tools, generating gene knock-outs/knock-ins and target validation using the most current...

27 September - 1 October 2021

Bioinformatics for Immunologists (Virtual)

Advanced courses

  Run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences, 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. Run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences, 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...

27 September - 1 October 2021

Mathematics of life: Modelling molecular mechanisms

Jane Reynolds

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. 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...

27 September - 1 October 2021

Bioinformatics for immunologists

Wellcome Connecting Science

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. 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...

5 October - 8 October 2021

Seeing is Believing: Imaging the Molecular Processes of Life

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

The symposium will bring together the leading developers of imaging methods with cutting-edge applications that illustrate how imaging can answer biological questions. We will place emphasis on methods that are able to capture the dynamics of life, spanning the whole range from molecular resolution to imaging of whole organisms. OverviewSpeakersSponsorsPractical information Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. The virtual conference includes talks from invited speakers, short talk presenters, digital poster sessions, online group discussions and networking opportunities. Symposium Overview The molecular processes of life are naturally dynamic in space and time from the atomic to the organismal level. The rapid development of imaging methods across the full scale of biological organisation is revolutionising our ability to visualise the inner workings of macromolecular complexes, organelles, cells, tissues, organs and whole organisms. Being able to see biological processes unfold in real time allows us to understand the...

8 October - 15 October 2021

Liquid Biopsies

Vladimir Benes, Anders Ståhlberg

Liquid biopsies have the advantage of being largely non-invasive and providing a vast amount of information for the detection and monitoring of diseases such as cancer. This course will provide hands-on experience in the several techniques to detect and analyse circulating tumor cells (CTCs), cell free tumor DNA (ctDNA), cell free tumor RNA (ctRNA) and proteins. Participants will have the opportunity to learn all aspects ranging from proper sampling through error free sequencing to data analysis. Lectures will also cover extracellular vesicles and clinical aspects using liquid biopsies, especially in the field of cancer diagnostics. OverviewSpeakers and TrainersProgrammePractical informationSponsors Overview Course Overview Liquid biopsies have the advantage of being largely non-invasive and providing a vast amount of information for the detection and monitoring of diseases such as cancer. This course will provide an overview in the several techniques to detect and analyse circulating tumour cells (CTCs), cell free tumor DNA (ctDNA), miRNA in liquid biopsies, cell free tumour RNA (ctRNA) and proteins. Participants will be introduced to all aspects ranging from proper sampling through error free sequencing to data analysis. Additional lectures will cover extracellular vesicles and clinical aspects using liquid biopsies, especially in the field of cancer diagnostics. Please note that all participants are expected to engage in all sessions. Audience This course targets young scientists entering the field of liquid...

11 October - 16 October 2021

From specimens to genomes

Lucie Smith

This course will cover the entire arc of a reference genome project; from sample acquisition and shipping, through nucleic acid extraction, sequencing, assembly, curation and annotation in public databases. It will promote the use and reuse of aquatic genomic data, build a community of researchers able to exploit these new data types, and introduce them to the theory and practice of reference quality genome sequencing and assembly. The course content will connect participants to researchers at the forefront of the biodiversity genomics revolution and meet with others worldwide who also aim to apply these new approaches to their study systems. Participants will develop bioinformatics skills to quality assess raw genomic sequence data, identify co-bionts, assemble data into a genome build, assess and then annotate the model with biological significance. Symbiosis lies at the heart of the origins of the eukaryotic cell, and new symbiosis events today shape much of the natural world, playing key roles in ecosystem engineering and in colonisation of extreme habitats such as hydrothermal vents. Biological understanding of symbiosis will be hugely enhanced through the deep analysis of the genomes of the interacting partners, and the Aquatic Symbiosis Genomics project is working globally to generate reference genomes for many symbints from marine and freshwater habitats. Virtual course Participants will learn via a mix of lectures, technical presentations, group work, and discussion 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. 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 09:45-17:30 GMT each day of the course. Trainers will be available to assist, answer questions and further explain the analysis during these times. This course will cover the entire arc of a reference genome project; from sample acquisition and shipping, through nucleic acid extraction, sequencing, assembly, curation and annotation in public databases. It will promote the use and reuse of aquatic genomic data, build a community of researchers able to exploit these new data types, and introduce them to the theory and practice of reference quality genome sequencing and assembly. The course content will connect participants to researchers at the forefront of the biodiversity genomics revolution and meet with others worldwide who also aim to apply these new approaches to their study systems. Participants will develop bioinformatics skills to quality assess raw genomic sequence data, identify co-bionts, assemble data into a genome build, assess and then annotate the model with biological significance. Symbiosis lies at the heart of the...

11 October - 15 October 2021

Structural bioinformatics

Meredith Willmott

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. 2021 marks 50 years of the Protein Data Bank (PDB), the single worldwide archive of experimental biomacromolecular structures, highlighting the depth of knowledge available for understanding molecular structure and function. 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 automated English closed captioning and transcription) with support and networking opportunities 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 and efforts will be made to make these accessible at different time zones across the week. 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. 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. 2021 marks 50 years of the Protein Data Bank (PDB), the single worldwide archive of experimental biomacromolecular structures, highlighting the depth of knowledge available for understanding molecular structure and function. 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...

13 October - 15 October 2021

The Non-Coding Genome

I. Bozzoni, N. Kim, G. Storz, I. Ulitsky

This symposium will explore the diverse, dynamic and multifaceted roles of RNA across a spectrum of cellular processes. It will provide an interdisciplinary discussion of the roles of non-coding RNAs in both prokaryotes and eukaryotes, with the aim of enhancing our understanding of gene regulation and function. OverviewSpeakersProgrammePractical InformationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. Symposium Overview This symposium will explore the diverse, dynamic and multifaceted roles of RNA across a spectrum of cellular processes. It will provide an interdisciplinary discussion of the roles of non-coding RNAs in both prokaryotes and eukaryotes, with the aim of enhancing our understanding of gene regulation and function. In the 50 years since RNA was identified as a central component in the flow of genetic information, it has become increasingly clear that RNA performs many additional diverse and interesting functions. Regulatory RNAs are known to play central roles across numerous biological...

20 October - 22 October 2021

Bringing Molecular Structure to Life: 50 Years of the PDB

S. Cusack, G. Kleywegt, C. Müller, C. Orengo, J. Thornton, S. Velankar, M. Wilmanns

In 1971, the structural biology community established the single worldwide archive for macromolecular structure data - the Protein Data Bank (PDB). It is one of the oldest surviving archives in any biomedical field. From its inception, the PDB has embraced a culture of open access leading to its widespread use by the research community (with nowadays more than 1 million unique users worldwide) and by more than 400 biomedical data resources. OverviewSpeakersPreliminary ProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. In 1971, the structural biology community established the single worldwide archive for macromolecular structure data – the Protein Data Bank (PDB). It is one of the oldest surviving archives in any biomedical field. From its inception, the PDB has embraced a culture of open access leading to its widespread use by the research community (with nowadays more than 1 million unique users worldwide) and by more than 400 biomedical data resources. Structural biology and...

25 October - 3 November 2021

Solution scattering from biological macromolecules

M. Gräwert, A. Kikhney, D. Svergun

28 October - 29 October 2021

Microglia 2021

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

Microglia are a resident macrophage of the central nervous system at the intersection of immunology and neuroscience. They have gained increasingly more attention over the past decade as more research shows that they are key contributors to neural circuit development and function. There is also increasing evidence that microglia are also important in the etiology of many nervous system diseases. This workshop will highlight the many important functions of microglia to nervous system physiology and function, the newest and most exciting literature and will bring together researchers using state-of the art imaging, genomics and molecular biology to study these enigmatic cells. OverviewSpeakersPreliminary ProgrammePractical InformationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. This workshop will highlight the many important functions of microglia to nervous system physiology and function, the newest and most exciting literature and will bring together researchers using state-of the art imaging, genomics and molecular biology to study these enigmatic cells. Microglia are a resident macrophage of the central nervous system at the intersection of immunology and neuroscience. They have gained increasingly more attention over the past decade as more research shows that they are key contributors to neural circuit development and function. There is also increasing evidence...

8 November - 12 November 2021

Metagenomics bioinformatics

Marina Pujol

Learn about the tools, processes and analysis approaches used in the field of metagenomics. This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data; including marker gene, whole gene shotgun (WGS) and assembly-based approaches. The virtually-delivered content will involve participants learning via pre-recorded lectures and live presentations, followed by live Q&As with the trainers. Practical experience will be developed in group activities and in computational exercises run in Docker containers on our virtual training infrastructure. Participants will need to be available between the hours of 09:00-17:00 GMT each day of the course. Learn about the tools, processes and analysis approaches used in the field of metagenomics. This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data; including marker gene, whole gene shotgun (WGS) and assembly-based approaches. The virtually-delivered content will involve participants learning via pre-recorded lectures and live presentations, followed by live Q&As with the trainers. Practical experience will be developed in group activities and in computational exercises run in Docker containers on our virtual training infrastructure. Participants will need to be available between the hours of 09:00-17:00 GMT each day of the course.

16 November - 19 November 2021

Metabolism Meets Epigenetics

T. Alexandrov, A. Ladurner, J. Mellor, E. Pearce

Metabolism and epigenetics are intricately linked, playing a key role in development, cancer, immune signalling and ageing. This symposium brings together world-leading researchers and young scientists to explore this nexus with a particular focus on how metabolites and metabolic networks impact gene regulation, on recently discovered roles of metabolites in disease and how this opens novel therapeutic avenues. OverviewSpeakers and OrganisersPractical InformationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. Symposium Overview Metabolism and epigenetics are intricately linked, playing a key role in development, cancer, immune signalling and ageing. This symposium brings together world-leading researchers and young scientists to explore this nexus with a particular focus on how metabolites and metabolic networks impact gene regulation, on recently discovered roles of metabolites in disease and how this opens novel therapeutic avenues. We will highlight enabling molecular and computational tools enabling detection of metabolites in time and space, shedding light on metabolism, and linking metabolism with...

22 November - 24 November 2021

Cancer Genomics

J. Korbel, N. López-Bigas, S. Ogawa, E. Papaemmanuil

This conference will provide an opportunity to learn about and keep up to date with the rapidly progressing area of cancer genomics. It will cover presentations from cancer genome projects, the areas of cancer functional genomics, systems biology, cancer immunogenomics and epigenomics, cancer mouse models and the translation and clinical impact of scientific results obtained. The meeting will bring together leading scientists from across these areas for a unique opportunity to interact and stimulate further integration of these efforts. OverviewSpeakersProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online. Conference Overview This conference will provide an opportunity to learn about and keep up to date with the rapidly progressing area of cancer genomics. It will cover presentations from cancer genome projects, the areas of cancer functional genomics, systems biology, cancer immunogenomics and epigenomics, cancer mouse models and the translation and clinical impact of obtained scientific results. The meeting will bring together leading scientists from across these areas for a unique opportunity to interact and stimulate further integration of these efforts.European cancer genomics research is particularly...

29 November - 1 December 2021

Recent Advances in Structural Biology of Membrane Proteins

Integral membrane proteins (IMPs) are encoded by 20-30 % of genes in a genome and provide key functions in the cell. Due to their hydrophobic nature, they are structurally and biochemically difficult to study. Traditionally, IMPs have been extracted using detergents which are a poor mimic of the lipid membrane and have been shown to denature membrane proteins. However, newly developed lipid-nanodisc approaches enable structural and functional studies of IMPs in a detergent-free, near-native membrane environment. Therefore, a central theme of this workshop is highlighting the importance of lipids in MP research and how they can be preserved. OverviewSpeakersProgrammePractical informationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the conference is going virtual and invite you to join us online. The virtual conference includes live talks from invited speakers, short talk presenters, digital poster sessions and networking opportunities. Conference Overview Integral membrane proteins (IMPs) are encoded by 20-30 % of genes in a genome and provide key functions in the cell. Due to their hydrophobic nature, they are structurally and biochemically difficult to study. Traditionally, IMPs have been extracted using detergents which are a poor mimic of the lipid membrane and have been shown to denature membrane proteins. However, newly developed lipid-nanodisc approaches enable...

3 December 2021

One Health: Integrating Human, Animal and Environmental Health

Lucia von Bredow

The 2021 Science & Society Conference will examine the potential societal benefits of the multifaceted One Health methodology, analyse how successful it has been to-date, determine whether One Health could be the key to future pandemic prevention, and ascertain what steps are needed to accelerate implementation. It will explore whether the interpretation of One Health has been biased towards an anthropocentric view of “health”, and it will also seek to answer the question: will something as far-reaching as the COVID-19 pandemic be the catalyst needed to finally make the aspirational goals of One Health a reality? OverviewPractical informationSpeakersMedia Partners Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the conference is going virtual and invite you to join us online.  This conference will be virtual and free to all attendees. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview The One Health movement, which has come to prominence in the last decade, advocates greater cross-sectoral collaboration and communication across the human-animal-environment interface. There has been a long-standing recognition that population health is intrinsically linked to both animal and environmental health, and that issues such as population growth, changes in climate...

8 February - 10 February 2022

The Epitranscriptome

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

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview The regulation of the transcriptome is key to cellular processes that underpin cell biology, development and tissue function. All classes of cellular RNA are subject to post-transcriptional modification, be it by direct chemical modification, editing or non-templated nucleotide additions. It is now emerging that the modification status of the transcriptome is dynamic and responsive to environmental/developmental cues. Together, this has elicited the realisation of an ‘epitranscriptome’ where post-transcriptional RNA modification coupled with recruitment of effector RNA binding proteins dynamically regulates genomic output. Importantly, mutations in setting or reading RNA modifications are causative of many human...

5 March - 10 March 2022

Analysis and Integration of Transcriptome and Proteome Data

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Systems biology is a still expanding field of research aiming to understand at the molecular level how cells, tissues and organism operate in their biological context. Among the key technologies driving this forward are next-generation sequencing and proteomics, as they provide powerful means to determine global expression levels of genes and proteins. Both fields have matured to a degree that they have now become accessible to researchers in many areas of biology. During this course participants will gain theoretical insight in the structure of sequencing and proteomic data, and will receive training in data analysis using various computational tools. Audience This course is targeted at biologists and biochemists who...

6 March - 8 March 2022

Biological Oscillators

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

OverviewOrganisers Practical informationSponsors OverviewOrganisers Practical informationSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview Are you interested in oscillatory phenomena and biological dynamics? At this symposium, multiple disciplines will come together in order to discuss common mechanisms underlying the generation of oscillations. This meeting provides a unique platform for the emerging new community working at the interface between quantitative biology, complex oscillatory systems, and physics. Oscillations are abundant – from hormonal oscillations with periods of days and months, to genetic fluctuations in the range of hours (circadian clock, embryonic oscillators), and metabolic and biochemical oscillations in the order of minutes (glycolytic oscillations) and seconds (Calcium-dynamics)...

12 March - 17 March 2022

Extracellular Vesicles: From Biology to Biomedical Applications

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

This course is intended for PhD students and Postdoctoral researchers who are interested in learning how to work with extracellular vesicles and know more about their biomedical applications. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview A rapidly increasing number of researchers aim to purify and identify extracellular vesicles and many methodologies to isolate and analyse these vesicles are available and have been implemented. This course will cover the basics, possibilities and limitations of different purification and characterisation techniques and will address strategies to understand their role in biomedical applications. Audience This course is intended for PhD students and Postdoctoral researchers who are interested in learning how to work with extracellular vesicles and know more about their biomedical applications. Modules/Resources Extracellular vesicles (continuous and discontinuous density gradient ultracentrifugation, ultrafiltration...

19 March - 22 March 2022

Inter-Organ Communication in Physiology and Disease

OverviewSponsors Overview Registration is not yet open for this event. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview One of the major outcomes of research using model organisms is that we are far from knowing all the functions fulfilled by various organs in vertebrates or invertebrates. Deleting one gene at a time in a single cell type is at the origin of unprecedented progress in our understanding of how homeostasis is maintained at the level of an entire organism. As a result, modern physiology has slowly moved from a purely molecular discipline back to being a truly holistic one. This molecular, genetic and yet holistic approach to physiology has had an effect on energy metabolism, the control of blood pressure, the plasticity of cognitive and immune functions, as well as the multiple ways in which organs such as fat, bone or...

6 April - 9 April 2022

Microbial Infections and Human Cancer

A. Breiling, C. Jobin, X. Lu, T. Meyer, j. Neefjes

OverviewSponsors Overview OverviewSponsors Overview Symposium Overview This symposium will build on the success of the first, focused conference on microbial carcinogenesis, an EMBO Workshop held in October 2019, which successfully began to connect the various research views regarding bacterial infections and human cancer. It will bring together key players and leading researchers from complementary fields, thereby comprehensively highlighting and discussing the various aspects of pathogen-induced carcinogenesis (ecology, immunology, metabolism, genomics and epigenetics, barrier function and defence etc.) from an interdisciplinary perspective. This conference will also provide a larger audience of young researchers and students with a stimulating platform to present their research, to network and to develop this emerging field further. Sponsors Sponsorship Opportunities We offer a variety of event sponsoring...

2 May - 8 May 2022

EMBL Course: Hands-on Flow Cytometry: Learning by Doing!

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Flow Cytometry is one of the most powerful single cell analysis methods used throughout the life sciences and medicine. Utilising Flow Cytometry we can identify and quantify many different parameters from heterogeneous samples, analyse the corresponding state of proliferation or simply detect the expression of fluorescent reporters. In line with the suggestions from our course in 2017, we will significantly enhance the number of analysis sessions together with our partners from FlowJo. We will cover the theory of Flow Cytometry and corroborate this information intensively with the practical issues of the most frequent assays as part of our practical course curriculum. Audience The course is designed for researchers at...

8 May - 12 May 2022

Cellular Mechanisms Driven by Liquid Phase Separation

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

Liquid phase separation is emerging as a common biophysical basis underlying many important cellular functions. This conference will bring together scientists from soft matter polymer physics, molecular “un”-structural biologists, and biologists working in cell, developmental and neurobiology to increase the awareness for how important phase separation is for our understanding of many biological processes. OverviewSponsors Overview Symposium Overview Liquid phase separation is emerging as a common biophysical basis underlying many important cellular functions. This conference will bring together scientists from soft matter polymer physics, molecular “un”-structural biologists, and biologists working in cell, developmental and neurobiology to increase the awareness for how important phase separation is for our understanding of many biological processesto explore the large repertoire of new tools generated by other disciplines that are ripe to be applied to complex problems related to phase separationto close the gap in human potential and transdisciplinary training to tackle the role of phase separation in biology Session Topics Liquid compartments in the cellMolecular mechanisms of phase separationPhase separation, a polymer physics perspectivePhase separation in developmental biology and...

9 May - 11 May 2022

Building Networks: Engineering in Vascular Biology

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview Blood vessels arise during early development and are essential for the formation and maintenance of larger tissues and organs. The vascular system regulates exchange of oxygen, nutrients, toxins and immune cells — the dysfunction of which can cause pathologies, as well as be consequent to the later stages of disease. Classical mouse models, genetics and histology, have provided significant knowledge to the field of vascular biology, in addition to recent advancements in diverse imaging modalities, single-cell approaches and computational modelling. Yet, there remain many open questions surrounding human vascular development and disease. Blood vessels present numerous research challenges due to their complex 3D...

30 May - 3 June 2022

Whole Transcriptome Data Analysis

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview This course will teach the biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq package, which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq package uses docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages: the user does not need to install all the software on its local server, the results generated by different containers can be organised in pipelines and reproducible research is guarantee by the possibility of sharing the docker images used for the analysis....

12 June - 17 June 2022

Humanized Mice, Personalized Therapies and Big Data

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

This course will train early and experienced researchers and consolidate interactions of the international scientific community in the field of humanized mouse models. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Humanized mouse models became an integral part of basic and translational research for the understanding of human diseases and for development of new therapies. The Ebola Virus outbreak has demonstrated the relevance of humanized mouse models for the understanding of emerging diseases and testing new medicines. The same can apply for the Coronavirus (COVID-19) pandemic. Several groups have recently shown that fully human antibodies targeted against pathogens can be generated in humanized mice for future clinical translation. “Big pharma” and biotech companies include humanized mice in the non-clinical development portfolio to test efficacy and safety of anti-cancer drugs to be used in “personalized medicine”. During the...

19 June - 22 June 2022

Defining and Defeating Metastasis

OverviewSponsors Overview Registration is not yet open for this ev OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium Overview This symposium will bring together researchers from diverse fields to enhance our understanding of the dissemination and metastatic colonisation of tumour cells. It will provide a unique opportunity for interdisciplinary exchange on current approaches and future collaborations on metastasis and its therapeutic challenges. Session Topics Metastasis initiating cells, circulating tumour cellsMotility and invasionTranscriptional and epigenetic control of metastasisMetastasis heterogeneity, EMT and plasticityMetastasis signalling and latencyMetastasis imaging, tumour microenvironment and immune evasion Sponsors Sponsorship Opportunities We offer a variety of event sponsoring possibilities, with the flexibility to select a...

29 June - 1 July 2022

Timing Mechanisms in Linking Development and Evolution

J. Briscoe, M. Davey, M. Ebisuya, P. Vanderhaeghen

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview Time is inherent to biological processes. It determines the order of events and the speed at which they take place. This is particularly obvious during embryonic development where the sequence and rate of events ensures that structures develop inthe right place, at the right time. Modifying the developmental tempo can affect the final size and composition of tissues, as well as their plasticity and function. Strikingly, comparisons between species reveals that, although the order and underlying molecular mechanisms are often indistinguishable, the pace at which they advance can differ substantially. Hence comparison of biological processes between species is likely to provide insight into time-keeping mechanisms and...

27 August - 30 August 2022

Transcription and Chromatin

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview The EMBL Transcription and Chromatin meeting has a long-standing tradition in shaping the field of transcriptional regulation. The meeting brings together leading experts covering all aspects of transcription including cis-regulatory function, long range regulation, 3-dimensional looping, the basal transcriptional machinery, RNA polymerase regulation and function, nucleosome positioning, chromatin modifications, chromatin remodelling and epigenetic inheritance of transcriptional silencing. The meeting contains many talks selected from the abstracts that are interspersed with invited speakers, discussing the latest breakthroughs in transcriptional regulation. The conference is designed to promote interactive...

5 September - 8 September 2022

Chemical Biology 2022

Y. Aye, C. Deo, K. Johnsson, E. Lemke

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview The conference sets the stage for the dissemination and exchange of new developments in diverse, hot fields within chemical biology. It is the largest and longest standing conference in the field, being a platform for inspiration, collaboration and networking for researchers in academia and industry. We aim to provide the possibility for every chemical biologist to meet and discuss with peers topics ranging from tool development to biological applications, from computational drug design to synthetic chemistry. Session Topics Drug and target discoveryCarbohydrates and (engineered) natural productsChemical optogeneticsOrigin of lifeSensing and probesProtein modificationsCellular reprogramming and synthetic biology...

26 October - 29 October 2022

Plasticity Across Scales: From Molecules to Phenotypes

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium Overview This symposium aims to bring together a diverse group of scientists to discuss phenotypic, developmental and transgenerational plasticity from a wide range of disciplines and perspectives, focusing on its underlying molecular mechanisms and its role in driving evolutionary novelty. The meeting is designed to provide an interactive platform for scientists who share a common interest in plasticity but usually do not meet, within an intensive conference setting.  Sponsors Sponsorship Opportunities We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies...

6 November - 9 November 2022

The Neurovascular Interface

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

In this symposium, we bring together researchers from vascular biology and neurobiology to foster interdisciplinary exchange and new emerging concepts on how vascular and nervous systems crosstalk to maintain organ homeostasis and function. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium Overview Neurovascular biology is a young, emerging field that aims to unravel the molecular communication between the nervous system and the vasculature. Both the nervous system and the vascular system share striking conceptual similarities in the assembly of cellular networks through guided growth and branching processes. Vascular and neural cells work together to form a number of functional tissue compartments. Endothelial cells, certain mural support cells (i.e., pericytes), astrocytes and neurons assemble the neurovascular unit, which establishes the blood-brain and blood-retina barriers. In fact, many of the most debilitating neurodegenerative diseases and cognitive decline involve disruption of the neurovascular unit or...