23 September 2021

The future of preprint peer review

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

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

27 September - 4 October 2021

Genome Engineering: CRISPR/Cas from Cells to Mice

Neil Humphreys, Birgit Koch, Premnath Rajakannu, Elisabeth 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 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 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 technologies. Please...

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

Jan Ellenberg, Jennifer Lippincott-Schwartz, Atsushi 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. OverviewSpeakersProgrammeSponsorsPractical InformationAboutPre-Symposium Webinars Overview EMBO and EMBL are 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. For late registrations please contact Iva Gavran (iva.gavran@embl.de). Symposium Overview Got something to say? Tweet it! #EESImaging 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...

6 October 2021

Open access: Data sharing and submission

Tony Burdett, Birgit Meldal

This webinar will be the first of our series of webinars on the topic of open access. In this webinar, we will discuss the importance of sharing research data and illustrate how EMBL-EBI provides some of the infrastructure to allow data sharing.  Our first speaker, Tony Burdett, will talk about the importance of FAIR data. He’ll discuss the common misconceptions around FAIR data and open data and talk about some of the impact GDPR can have on data sharing. In this section, he will explain the role that metadata and standards play in data sharing and submissions to large public repositories like those at EMBL-EBI. The second speaker, Birgit Meldal, works as a biocurator for IntAct and Complex Portal, resources for molecular interaction and protein complexes. In her part, she will illustrate how to submit data to these resources and will discuss the advantages and challenges of providing open access data. This webinar will be the first of our series of webinars on the topic of open access. In this webinar, we will discuss the importance of sharing research data and illustrate how EMBL-EBI provides some of the infrastructure to allow data sharing. Our first speaker, Tony Burdett, will talk about the importance of FAIR data. He’ll discuss the common misconceptions around FAIR data and open data and talk about some of the impact GDPR can have on data sharing. In this section, he will explain the role that metadata and standards play in data sharing and submissions to large public repositories like those at EMBL-EBI. The second speaker, Birgit Meldal, works as a biocurator for IntAct and Complex Portal, resources for molecular interaction and protein complexes. In her part, she will illustrate how to submit data to these resources and will discuss the advantages and challenges of providing...

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 early-career scientists entering the field of...

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

Irene Bozzoni, V. Narry Kim, Gisela Storz, Igor 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 InformationSponsorsAbout Overview EMBO and EMBL are 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...

13 October 2021

Open access: Why build open source software and how to do it successfully

Renato Alves, Brice Letcher

Continuing our series of webinars on the topic of open access, during this webinar we will define what open software is, discuss motivations and challenges of producing open code and software, as well as basic concepts that help to do so.  We will explain the many forms and dimensions of open software and its development, highlighting the importance of documentation, testing, packaging, communication and community in order to create successful and sustainable software. Speakers Renato Alves, Bio-IT EMBL Following a PhD in human bacterial metagenomics and metatranscriptomics I took the role of Bio-IT project coordinator at EMBL Heidelberg, providing computational support to the research community at EMBL. For over 15 years I have contributed to several open and closed-source software projects using a multitude of programming languages and technologies from web to big data and cloud. Brice Letcher, EMBL-EBI I am a 4th year PhD student at the Iqbal lab working in computational microbial genomics. In my PhD I develop an open-source tool to build and genotype graphs of genomes. I am passionate about good software engineering and a keen contributor to the bioinformatics community, notably through building a formatting tool for snakemake (workflow manager) files. Continuing our series of webinars on the topic of open access, during this webinar we will define what open software is, discuss motivations and challenges of producing open code and software, as well as basic concepts that help to do so. We will explain the many forms and dimensions of open software and its development, highlighting the importance of documentation, testing, packaging, communication and community in order to create successful and sustainable software. Speakers Renato Alves, Bio-IT EMBL Following a PhD in human bacterial metagenomics and metatranscriptomics I took the role of Bio-IT project coordinator at EMBL Heidelberg, providing computational support to the research community at EMBL. For over 15 years I have contributed to several open and closed-source software projects using a multitude of programming languages and technologies from web to big data and cloud. Brice...

20 October - 22 October 2021

Bringing Molecular Structure to Life: 50 Years of the PDB

Stephen Cusack, Gerard Kleywegt, Christoph Mueller, Christine Orengo, Janet Thornton, Sameer Valenkar, Matthias 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. Join this conference and celebrate the 50th anniversary of The Protein Data Bank (PDB) with us. With over 1 million unique users worldwide and more than 400 biomedical data resources, the PDB represents the achievements and milestones of the structural biology community.The PDB is one of the oldest surviving archives in any biomedical field. The structural biology community established the single worldwide archive for macromolecular structure data in 1971. The PDB has embraced a culture of open access leading to its widespread use by the research community (with nowadays more than 1...

20 October 2021

Open access: publications and preprints

Mariia Levchenko

Continuing our series on open access, in this webinar we will discuss the role of EMBL in making science open. We will introduce Europe PMC - an open, free database of life science publications and preprints and explain how Europe PMC supports open access policies of many organisations, including EMBL. We will highlight how open access underpins innovation and the importance of licensing for reuse. Then, we will illustrate how open access to publications supports scientific reproducibility and the role that proper data citation plays in this process. Finally, we will look at preprints, as a tool for researchers to rapidly and openly share their work decoupled from the formal peer review process. Continuing our series on open access, in this webinar we will discuss the role of EMBL in making science open. We will introduce Europe PMC - an open, free database of life science publications and preprints and explain how Europe PMC supports open access policies of many organisations, including EMBL. We will highlight how open access underpins innovation and the importance of licensing for reuse. Then, we will illustrate how open access to publications supports scientific reproducibility and the role that proper data citation plays in this process. Finally, we will look at preprints, as a tool for researchers to rapidly and openly share their work decoupled from the formal peer review process.

20 October 2021

Open access: Finding and accessing open data

Ugis Sarkans, Anna Swan

Our open access webinar series continues with an introduction to finding and accessing open data. The webinar will begin with an overview of the kind of open access data available from EMBL-EBI and a demonstration of finding data on the EMBL-EBI website using EBI Search. The concept of programmatic access will also be introduced, with information about how and why APIs can be used to access open data and guidance on where to find more detail about access to different EMBL-EBI resources.  The webinar will then focus on BioStudies, a database that holds descriptions of biological studies and links to data, both in EMBL-EBI resources and beyond. This section will provide an introduction to BioStudies, examples of how it can be used in your research and a demonstration of the resource itself. Our open access webinar series continues with an introduction to finding and accessing open data. The webinar will begin with an overview of the kind of open access data available from EMBL-EBI and a demonstration of finding data on the EMBL-EBI website using EBI Search. The concept of programmatic access will also be introduced, with information about how and why APIs can be used to access open data and guidance on where to find more detail about access to different EMBL-EBI resources. The webinar will then focus on BioStudies, a database that holds descriptions of biological studies and links to data, both in EMBL-EBI resources and beyond. This section will provide an introduction to BioStudies, examples of how it can be used in your research and a demonstration of the resource itself.

21 October 2021

Analysis of huge metabolic models with COBREXA.jl

Miroslav Kratochvil

COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models. by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base building block. We will talk about the problems that motivated the development of COBREXA.jl and show several of its main applications.  We will show the COBREXA.jl interface that allows biologists and bioinformaticians to easily specify large amounts of analyses and execute it on supercomputers.  Later, we will use COBREXA.jl for creating a model of a small microorganism community, and demonstrate how the software helps to answer questions about the viability and chemical activity of microbe ecosystems.  About the speaker Miroslav Kratochvíl has recently finished his PhD in computer science at Charles University in Prague; currently he is a researcher focusing on bioinformatics-oriented topics at Luxembourg Centre for Systems Biomedicine. His research concerns mainly the high-performance algorithms for processing large datasets from life sciences. COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models. by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base building block. We will talk about the problems that motivated the development of COBREXA.jl and show several of its main applications. We will show the COBREXA.jl interface that allows biologists and bioinformaticians to easily specify large amounts of analyses and execute it on supercomputers. Later, we will use COBREXA.jl for creating a model of a small microorganism community, and demonstrate how the software helps to answer questions about the viability and chemical activity of microbe ecosystems. About the speaker Miroslav Kratochvíl has recently finished his PhD in computer science at Charles...

25 October - 3 November 2021

Solution scattering from biological macromolecules

M. Gräwert, A. Kikhney, D. Svergun

28 October - 29 October 2021

Microglia 2021

Sonia Garel, Florent Ginhoux, Dorothy Schafer, Amada 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. Conference Overview 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...

29 October 2021

Open access: Let's talk about open access, open data and open software

Renato Alves, Anthony Burdett, Mariia Levchenko, Sandra Orchard

Join us for the final webinar of the series focusing on open access and open science. At this webinar, on the last day of Open Access Week 2021, we will be joined by four speakers from across EMBL who have knowledge and experience of being ‘open’, from software to data resources and open access publications. During this panel webinar, we will discuss: What does ‘open’ mean? Why should I share my data? Are there disadvantages of sharing data? What problems may I have with sharing data? Questions from the audience   We invite you to join us to listen to the panel’s discussion and submit your own questions on open access and open science. You may submit your questions prior to the webinar using the registration form or during the Zoom webinar.  Speakers Renato Alves, Bio-IT EMBL Following a PhD in human bacterial metagenomics and metatranscriptomics Renato took the role of Bio-IT project coordinator at EMBL Heidelberg, providing computational support to the research community at EMBL. For over 15 years Renato has contributed to several open and closed-source software projects using a multitude of programming languages and technologies from web to big data and cloud. Tony Burdett, EMBI-EBI Tony Burdett leads the Archival Infrastructure and Technology team, which develops services and provides technology to support the activities of EMBL-EBI’s molecular archives, including data submission, storage, validation, coordination and presentation.  Tony joined EMBL-EBI in 2005 and has personally built and led development teams for many resources such as the GWAS Catalog, ArrayExpress, the Expression Atlas and BioSamples. His team now develops the ingestion service for the Human Cell Atlas Data Coordination Platform, the infrastructure behind the European Nucleotide Archive, and the BioSamples database. Tony has a biological and medical background, having spent some time at medical school before graduating with a BSc in Biomedical Sciences and a MRes in Bioinformatics from the University of Newcastle-upon-Tyne. He has a special interest in developing federated, cloud-based data platforms and has many years of experience in developing semantically-rich RESTful APIs for the submission and distribution of life sciences data. He takes pride in his ability to marry profoundly complex biological problems with the very latest development techniques to create highly accomplished, open source, reusable software and services. Maria Levchenko, EMBL-EBI Maria Levchenko is a Community Manager for Europe PMC, an open literature database for life sciences developed by the European Bioinformatics Institute (EMBL-EBI). Europe PMC indexes over 300,000 preprints abstracts and full text COVID-19 preprints from 20 life sciences preprint servers alongside published journal articles. Before joining Europe PMC, Maria obtained a PhD in Biochemistry from Georg-August University in Goettingen, Germany, and has worked with the European Research Council (ERC) Executive Agency. Maria is passionate about innovative solutions in scholarly communications that help the research community to advance scientific knowledge. Sandra Orchard, EMBL-EBI Sandra Orchard is Team Leader for Protein Function Content, with a strong background in protein annotation. Her team is primarily responsible for the curation of UniProt at EMBL-EBI, and annotation of the Gene Ontology. Sandra and her team support professional training in data resources for exploring protein function, sequence analysis, interactions and pathways. She is a member and Treasurer of the Executive Committee of the International Society for Biocuration. Sandra's team applies advanced methods for ensuring the accuracy and quality of the universal protein resource, UniProt, carrying out manual annotation and producing the rules for automated annotation. They also create and maintain value-added interfaces for exploring protein data, for example the Enzyme Portal and Complex Portal. Join us for the final webinar of the series focusing on open access and open science. At this webinar, on the last day of Open Access Week 2021, we will be joined by four speakers from across EMBL who have knowledge and experience of being ‘open’, from software to data resources and open access publications. During this panel webinar, we will discuss: What does ‘open’ mean? Why should I share my data? Are there disadvantages of sharing data? What problems may I have with sharing data? Questions from the audience We invite you to join us to listen to the panel’s discussion and submit your own questions on open access and open science. You may submit your questions prior to the webinar using the registration form or during the Zoom webinar. Speakers Renato Alves, Bio-IT EMBL Following a PhD in human bacterial metagenomics and metatranscriptomics Renato took the role of Bio-IT project...

8 November - 12 November 2021

Metagenomics bioinformatics

Juanita Riveros

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.

17 November - 20 November 2021

Metabolism Meets Epigenetics

Theodore Alexandrov, Andreas Ladurner, Jane Mellor, Erika 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. OverviewSpeakersPreliminary ProgrammePractical InformationSponsors Overview The abstract submission will be closed on 24 September at 23:59 pm CEST, Berlin. 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...

18 November 2021

Introduction to qualitative modelling with MaBoSS

Vincent Noël

Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the representation of physical time, and of processes with different time scales. MaBoSS simulate multiple stochastic trajectories, and produces trajectories of the probabilities of the system state. This webinar will introduce the concepts of boolean modelling, and MaBoSS’ continuous time boolean modelling, and will then demonstrate the use of WebMaBoSS, a web interface designed for easily simulating MaBoSS models.   About the speaker Dr Vincent Noël (M) is a postdoctoral student at the Computational Systems Biology of Cancer team of the U900 in Institut Curie. His research interests concern modelling of biological systems, where he has experience in both construction and analysis of these models. He did his PhD in applied mathematics studying simplifications of ODE models, and then did his first postdoc within a molecular biology unit building a model of Ras-Mapk signaling in Y1 tumor cells. He also developed tools to simplify the construction and analysis of models, and the reproducibility of this work. He has a good experience in the optimisation of numerical simulation workflows, and has been working on MaBoSS for more than three years. Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the representation of physical time, and of processes with different time scales. MaBoSS simulate multiple stochastic trajectories, and produces trajectories of the probabilities of the system state. This webinar will introduce the concepts of boolean modelling, and MaBoSS’ continuous time boolean modelling, and will then demonstrate the use of WebMaBoSS, a web interface designed for easily simulating MaBoSS models. About the speaker Dr Vincent Noël (M) is a postdoctoral student at the Computational Systems Biology of Cancer team of the U900 in Institut Curie. His research interests concern modelling of...

22 November - 24 November 2021

Cancer Genomics

Jan Korbel, Núria López-Bigas, Seishi Ogawa, Elli 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. Session Topics Mutation and clonal selection in...

29 November - 1 December 2021

Recent Advances in Structural Biology of Membrane Proteins

Panagiotis Kastritis, Sandro Keller, Christian Löw, Cristina Paulino

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 structural and functional...

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? OverviewSpeakersPreliminary programmePractical informationMedia 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. 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 and land use, and the movement of animals and people, have a huge impact on the collective health of our...

6 December - 9 December 2021

IITM-EMBL-EBI Winter School 2021

IBSE Workshop Team

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

10 December 2021

SARS-CoV-2 – Two Years On: Science Meets the Challenge

Stephen Cusack, Jürgen Deka, Anna Pyle, David Stuart

OverviewSpeakersProgrammePractical Information 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. Conference Overview When the conference takes place it will be two years since the first identification of COVID-19 cases in China in late 2019 and since then the pandemic has become the most devastating challenge to global health for a century. In an unprecedented mobilisation, thousands of scientists world-wide have focused their attention, in a highly collaborative way, on understanding the SARS-CoV-2 virus, the disease it causes and its evolution, and, in developing counter measures. Most remarkably, highly efficient vaccines are now being deployed massively, starting less than...

13 December - 17 December 2021

CABANA Workshop: Plant bioinformatics - analysis of crop genomics data

Juanita Riveros

This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping. During the course participants will learn about genotyping experimental design, variant calling, comparative genomics using Ensembl, analyse variation data with Ensembl Variant Effect Predictor and explore concepts of genome wide association studies (GWAS).  The content will explain how to make use of existing public data, retrieve, submit and share your data with the community. Trainers will cover the basics of diversity analysis using R, before analyzing various genomes to assess diversity, investigating gene-phenotype relationships and microsatellites. The course will be delivered through a combination of hands-on training sessions and lectures. This course will be a virtual event. The content will be delivered over Zoom.  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.   This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping. During the course participants will learn about genotyping experimental design, variant calling, comparative genomics using Ensembl, analyse variation data with Ensembl Variant Effect Predictor and explore concepts of genome wide association studies (GWAS). The content will explain how to make use of existing public data, retrieve, submit and share your data with the community. Trainers will cover the basics of diversity analysis using R, before analyzing various genomes to assess diversity, investigating gene-phenotype relationships and microsatellites. The course will be delivered through a combination of hands-on training sessions and lectures. This course will be a virtual event. The content will be delivered over Zoom. In order to make the most out of the course, you...

16 December - 17 December 2021

PhD Symposium: The Big Picture – Zooming Into Life

2021 EMBL PhD Symposium Organising Committee

Join us for the 23nd Anniversary of the annual EMBL PhD Symposium. Since its conception in 1999, the EMBL PhD Symposium has evolved into a highly respected scientific meeting, connecting young researchers and high-profile scientists alike. This year, our Symposium centers on the theme “The Big Picture: Zooming into Life”

16 January - 20 January 2022

Deep Learning for Image Analysis

Anna Kreshuk, Constanin Pape, Pejman Rasti, David Rousseau, Martin Weigert

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

25 January - 26 January 2022

The Next Generation in Infection Biology

Pedro Beltrao, Maria Bernabeu, Jan Kosinski, Eva Kowalinski, Nassos Typas

OverviewOrganisersParticipating OrganisationsPract OverviewOrganisersParticipating OrganisationsPractical InformationSponsors Overview Conference Overview Infectious diseases are among the most prevalent causes of human illness and death in the world. Pathogens infect humans and all life forms on Earth, being able to cross species barriers, thereby adversely impacting human and planetary health. Fundamental research in Infection Biology is urgently needed to find therapies for longstanding and emerging infectious diseases.  The EMBL Conference: The Next Generation in Infection Biology is a platform for late-stage postdoctoral scientists in the field of infection biology to present their work and connect with the leading European institutions in infection biology. The speakers are chosen for their track record of research accomplishments and their high-reaching future plans. The audience will have the unique opportunity to experience...

30 January - 3 February 2022

Exploratory Analysis of Biological Data: Data Carpentry

Renato Alves, Fotis E. Psomopoulos, Christian Schudoma

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

9 February - 11 February 2022

The Epitranscriptome

Michaela Frye, V. Narry Kim, Dónal O'Carroll

OverviewSpeakersSponsors OverviewSpeakersSponsors 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...

21 February - 2 March 2022

Bioinformatics resources for protein biology

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. This course will take place over three separate days which might not be consecutive.  Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. This course will take place over three separate days which might not be consecutive.

21 February - 25 February 2022

Introduction to RNA-seq and functional interpretation

Meredith Willmott

Gain an introduction to the technology, data analysis, tools, and resources used in RNA sequencing and transcriptomics. The content will provide a broad overview of the subject area, and introduce participants to basic analysis of transcriptomics data using the command line. It will also highlight key public data repositories and methodologies that can be used to start the biological interpretation of expression data. Topics will be delivered using a mixture of lectures, practical exercises, and open discussions. Computational work during the course will use small, example data-sets; and there will be no opportunity to analyse personal data. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course, there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 09:30-16:00 GMT each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis during these times. Gain an introduction to the technology, data analysis, tools, and resources used in RNA sequencing and transcriptomics. The content will provide a broad overview of the subject area, and introduce participants to basic analysis of transcriptomics data using the command line. It will also highlight key public data repositories and methodologies that can be used to start the biological interpretation of expression data. Topics will be delivered using a mixture of lectures, practical exercises, and open discussions. Computational work during the course will use small, example data-sets; and there will be no opportunity to analyse personal data. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will...

21 February - 24 February 2022

Integrative Analysis of Multi-Omics Data

Wolfgang Huber, Oliver Stegle, Britta Velten

Experimental designs in basic biology research and biomedicine increasingly involve the use of multiple omics technologies to characterise a set of samples e.g. genomic variants, epigenetic marks, transcriptome, proteome, metabolome, functional assays, imaging. This is true for both bulk and single cell analyses. Therefore, data analysis techniques are required that are able to cope with such data in an efficient and generalisable manner. Thus, the proposed advanced course addresses one of the major data challenges scientists face today. Its core objective is to convey the conceptual and mathematical foundations that underpin integrative multimodal data analysis strategies and the practical trade-offs of different methods. OverviewSpeakers and TrainersPreliminary ProgrammePractical InformationSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Multi-omics studies that combine genomics, transcriptome, proteome and other modalities are increasingly common in fundamental biology research and biomedicine. Using multi-omics experimental designs at bulk or single-cell resolution can help identifying novel biomarkers or reveal insights into biological mechanisms. This course addresses the conceptual and mathematical foundations of state-of-the-art methods for analyzing the data that results from multi-omics studies. The course will provide an overview of advanced applications of multi-omics methods, provide insights into how to select the most appropriate methods and convey practical experiences by...

5 March - 10 March 2022

Analysis and Integration of Transcriptome and Proteome Data

Vladimir Benes, Raffaele Calogero, Jeroen Krijgsveld, Lennart Martens

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 - 9 March 2022

Biological Oscillators: Design, Mechanism, Function

Alexander Aulehla, Hanspeter Herzel, Eve Marder, Ueli Schibler

OverviewSpeakersSponsorsAbout OverviewSpeakersSponsorsAbout 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) – oscillations are...

7 March - 11 March 2022

Single-cell RNA-seq analysis using Galaxy

EMBL-EBI Training team

This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to trajectories.  Please note that although participants will not be able to use their own data during the course practicals, there will be ample time to discuss their research and ideas with both course participants and trainers.  As part of this, participants will present lightning talks on their research topics. Near the end of the course, participants will engage in small group discussion about their research challenges and problems with each other and the trainers at the ‘Talk with Trainers’. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.  Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI’s virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines. Participants will need to be available between the hours of 09:00-17:00 GMT each day of the course. Trainers will be available to assist, answer questions and further explain the analysis during these times. This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to trajectories. Please note that although participants will not be able to use their own data during the course practicals, there will be ample time to discuss their research and ideas with both course participants and trainers. As part of this, participants will present lightning talks on their research topics. Near the end of the course, participants will engage in small group discussion about their research challenges and problems with each other and the trainers at the ‘Talk with Trainers’. Virtual course Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical...

12 March - 17 March 2022

Extracellular Vesicles: From Biology to Biomedical Applications

An Hendrix, Cecilia Lässer, Esther Nolte-’t Hoen, Guillaume 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. OverviewSpeakers and TrainersSponsors 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,...

13 March - 16 March 2022

From 3D Light to 3D Electron Microscopy

Raffaella Carzaniga, Lucy Collinson, Alexandra Elli, Chris Guérin, Anneke Kremer, Saskia Lippens, Paolo Ronchi, Yannick Schwab

Overview Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Overview Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview The event is jointly organised by EMBL, ZEISS, The Francis Crick Institute and The VIB Ghent. Life happens in 3D – and understanding biological context in the three dimensions has been a major driver in the past decades in both light and electron microscopy. Today the trend towards 3D continues with large volume imaging and highest resolution with modern light and electron microscopy-based techniques now enabling previously impossible insights into functional and structural biology. Correlative microscopy can combine a large variety of different imaging techniques such as confocal microscopy, X-ray microscopy and different volume EM methods e.g. Array Tomography or Serial block face imaging. Comprehensive workflow solutions...

21 March - 25 March 2022

Introduction to multiomics data integration and visualisation

Juanita Riveros

Identify the challenges, strategies and resources for multiomics data integration using biological examples.  The virtual course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation. Working with public domain data can provide added value to data derived through a researcher’s own work and additionally  inform experimental design. This course is highly relevant in the current research scenario, where an increased volume of data across the whole spectrum of biology has created both more opportunities and challenges to identifying novel perspectives and answering questions in the life sciences. This course will focus on issues around data integration, but will not include systems biology modelling or machine learning approaches. A major element of this course is a group project, where participants will be organised in small groups to work together on a challenge set by the project mentors. These will allow participants to explore the bioinformatics tools and resources introduced in the course and to apply these to a set problem, providing hands-on experience of relevance to their own research. The group work will culminate in a presentation session involving all participants on the final day of the course, giving an opportunity for wider discussion on the benefits and challenges of integrating data. You may refer to the previous group projects that were organised for this course in February 2021. Virtual course The course will involve participants learning via pre-recorded lectures, live presentations, and trainer Q&A sessions. The content will be delivered over Zoom, with additional text communication over Slack. Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Trainers will be available to provide support, answer questions, and further explain the analysis during these practicals. Participants will need to be available between the hours of 09:30-18:00 GMT each day of the course Identify the challenges, strategies and resources for multiomics data integration using biological examples. The virtual course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation. Working with public domain data can provide added value to data derived through a researcher’s own work and additionally inform experimental design. This course is highly relevant in the current research scenario, where an increased volume of data across the whole spectrum of biology has created both more opportunities and challenges to identifying novel perspectives and answering questions in the life sciences. This course will focus on issues around data integration, but will not include systems biology modelling or machine learning approaches. A major element of this course is a group project, where participants will be...

21 March - 23 March 2022

Inter-Organ Communication in Physiology and Disease

Gerard Karsenty, Irene Miguel-Aliaga, Miguel Soares

OverviewSpeakersSponsorsAbout OverviewSpeakersSponsorsAbout 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...

4 April - 8 April 2022

Gene Expression at Single-Cell Resolution

Overview Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Overview Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

4 April - 8 April 2022

Data visualisation for biology

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

6 April - 9 April 2022

Microbial Infections and Human Cancer

Achim Breiling, Christian Jobin, Xin Lu, Thomas Meyer, Jacques Neefjes

OverviewSpeakersSponsorsAbout OverviewSpeakersSponsorsAbout 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. Speakers Keynote Speakers Hans Clevers Hubrecht Institute The...

23 April - 29 April 2022

Methods for Analysis of circRNAs: From Discovery to Function

Marie-Laure Baudet, Vladimir Benes, Irene Bozzoni, Christoph Dieterich

Circular RNAs (CircRNAs) are a rediscovered class of RNA species that originate from back-splicing events, which have been reported across all domains of life. Many circular RNAs are stable, abundant and conserved between species. They exhibit context-dependent expression patterns, which are often linked to disease states. Validated circular RNA functions are numerous and range from regulation of transcription and splicing to RNA/protein sponging and scaffolding. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Circular RNAs (CircRNAs) are a rediscovered class of RNA species that originate from back-splicing events, which have been reported across all domains of life. Many circular RNAs are stable, abundant and conserved between species. They exhibit context-dependent expression patterns, which are often linked to disease states. Validated circular RNA functions are numerous and range from regulation of transcription and splicing to RNA/protein sponging and scaffolding. However, CircRNAs are by and large the most underexplored class of all non-coding RNAs. This course will meet the specific need to explore complexity, distribution, function and mechanisms of circRNA action experimentally and computationally.The presented...

27 April - 28 April 2022

Grand Challenges in AI and Data Science

OverviewSponsors Overview OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. 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 sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information on sponsoring possibilities. If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

2 May - 6 May 2022

Hands-on Flow Cytometry: Learning by Doing!

Andrew Filby, Diana Ordonez, Malte Paulsen, Steffen Schmitt

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...

9 May - 13 May 2022

Attacking Open Chromatin with ATAC Sequencing

The goal of this introductory course is to teach the entire workflow of an ATAC-Seq experiment including library preparation, sequencing, data processing, and downstream analysis by addressing a real biological question that will be answered at the end of the course. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview ATAC-Seq stands for Assay of Transposase Accessible Chromatin and is, despite its recent invention, already a widespread method to profile open chromatin on a genome-scale. The goal of this introductory course is to teach the entire workflow of an ATAC-Seq experiment including library preparation, sequencing, data processing, and downstream analysis by addressing a real biological question that will be answered at the end of the course. We will start with the experimental ATAC-Seq protocol, highlighting the critical steps, potential pitfalls, and the most up-to-date tweaks to improve the quality of the results. After sequencing the samples we will go through the basic quality control and preprocessing steps using...

9 May - 11 May 2022

Building Networks: Engineering in Vascular Biology

OverviewSpeakersSponsors OverviewSpeakersSponsors 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...

9 May - 12 May 2022

Cellular Mechanisms Driven by Liquid Phase Separation

Simon Alberti, Dorothee Dormann, Edward Lemke, Tanja 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. OverviewSpeakersSponsorsAbout 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...

9 May - 13 May 2022

Microscopy data analysis: Machine learning and the BioImage Archive

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page.  We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest.

15 May - 18 May 2022

Mechanobiology in Development and Disease

Alba Diz-Muñoz, Carl-Philipp Heisenberg, Prisca Liberali, Anđela Šarić, Xavier Trepat

OverviewSpeakersSponsorsAbout OverviewSpeakersSponsorsAbout Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium Overview Environmental mechanics impact the behaviour of cells, which in turn modify their surroundings. These bi-directional cell-tissue interactions have important consequences for gene expression, cell fate and function and give rise to transient and permanent tissue modifications. These processes are key for immunity and homeostasis, but also play a role in pathological processes as they are critical for fibrosis, inflammation and cancer metastasis. This symposium will focus on the interplay of cells with their environment and will bring together clinicians, cell biologists and material scientists interested in mechanobiology at the molecular, cellular and tissue level to approach its role in human physiology...

17 May - 24 May 2022

Exploring genetic variation

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. This course will take place over three separate days which might not be consecutive.  Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. This course will take place over three separate days which might not be consecutive.

23 May - 25 May 2022

BioMalPar XVIII: Biology and Pathology of the Malaria Parasite

J. Rayner, A. Stone

Malaria remains one of the most significant global public health challenges, with more than 200 million clinical cases worldwide each year. The lack of an effective licensed vaccine and the continual emergence of drug-resistant malaria parasites emphasizes the need for new control and prevention strategies. This need for innovation has become even more apparent with the disruption of global malaria control programs due to the COVID-19 pandemic and potential reversal of gains made over the last few decades. Generation of fundamental knowledge lies at the heart of developing new tools and innovations for malaria intervention. The malaria research community has a long history of being a highly collaborative field, reliant on diverse technologies, sharing of resources and dissemination of biological advances made. Accessibility and timely sharing of these advances through the establishment of new collaborations is therefore vital for the translation of new ideas into public health impact. OverviewSponsors Overview Malaria remains one of the most significant global public health challenges, with more than 200 million clinical cases worldwide each year. The lack of an effective licensed vaccine and the continual emergence of drug-resistant malaria parasites emphasizes the need for new control and prevention strategies. This need for innovation has become even more apparent with the disruption of global malaria control programs due to the COVID-19 pandemic and potential reversal of gains made over the last few decades. Generation of fundamental knowledge lies at the heart of developing new tools and innovations for malaria intervention. The malaria research community has a long history of being a highly collaborative field, reliant on diverse technologies, sharing of resources and dissemination of biological advances made. Accessibility and timely sharing...

28 May - 4 June 2022

Characterization of Macromolecular Complexes by Integrative Structural Biology

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30 May - 3 June 2022

Whole Transcriptome Data Analysis

Marco Beccuti, Vladimir Benes, Raffaele Calogero, Francesca Cordero

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....

8 June - 11 June 2022

Microtubules: From Atoms to Complex Systems

Anna Akhmanova, Carsten Janke, Kassandra Ori-McKenney, Manuel Théry

In recent years, interdisciplinary approaches embracing cell biology, genetics, molecular biology, biochemistry, biophysics, structural biology and mathematical modelling have made a tremendous impact on the microtubule field. OverviewSpeakersSponsorsAbout Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium Overview The microtubule cytoskeleton is essential for a wide variety of cellular functions, such as chromosome segregation, directed vesicle and organelle transport, cell motility and cell polarity. Impaired microtubule function can lead to human diseases including cancer and neurodegenerative disorders, where microtubules serve as important therapeutic targets. In recent years, interdisciplinary approaches embracing cell biology, genetics, molecular biology, biochemistry, biophysics, structural biology and mathematical modelling have made a tremendous impact on microtubule research. The progressive diversification of the microtubule field has created the need for a strong meeting that unifies the community and...

8 June - 10 June 2022

Bioinformatics for principal investigators

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.   Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

8 June - 10 June 2022

Managing a bioinformatics core facility

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

12 June - 17 June 2022

Humanized Mice, Personalized Therapies and Big Data

Karl-Dimiter Bissig, Christian Münz, Isabel Rollan, J.J. Schuringa, Leonard Shultz, Brian Soper, Renata Stripecke

This course will train early and experienced researchers and consolidate interactions of the international scientific community in the field of humanized mouse models. OverviewSpeakers and TrainersSponsors 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 engraftment models (human immune system and/or human tissue) are 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. “Big pharma” and biotech companies include humanized mice in their pre-clinical development portfolio to test efficacy and safety of anti-cancer drugs. These platforms provide researchers and drug developers with human specific targets, physiological pathways and mechanisms of disease...

13 June - 17 June 2022

Summer school in bioinformatics

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

19 June - 22 June 2022

Defining and Defeating Metastasis

Johanna Joyce, Daniel Klimmeck, Joan Massagué, Charles Swanton

OverviewSponsorsAbout OverviewSponsorsAbout 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...

20 June - 24 June 2022

Cancer genomics

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

29 June - 1 July 2022

Timing Mechanisms in Linking Development and Evolution

James Briscoe, Megan Davey, Miki Ebisuya, Pierre 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 in the 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...

4 July - 8 July 2022

Systems biology: From large datasets to biological insight

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

11 July - 13 July 2022

Microfluidics 2022

Amy Herr, Christoph Merten, Angela Wu

The EMBL Microfluidics Conference brings together top researchers and emerging research leaders to spark scientific exchange and create community. Topics spanning from fundamental physics & chemistry to device design and nascent biological applications will be presented, which should be of interest to everyone from experts in microfluidic design to users of the next-generation of microfluidic tools, and from academic scholars and trainees to industry colleagues. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview Microfluidic tools have made recent biological and biomedical research leaps possible. At the physics, engineering, chemistry and biology interface, innovation in microfluidic approaches has positively impacted areas as diverse as nucleotide sequencing, functional genomics, single-cell and single-molecule studies, and biomedical diagnostics. Many of these applications – including next-generation sequencing devices – have been revolutionised by miniaturisation, paving the way for global gene analysis and hence transforming biology. Working on the pico- to nanoliter scale not only allows a high degree of parallelisation, but importantly offers superb spatiotemporal control. Small objects such as cells, or...

11 July - 15 July 2022

Bioinformatics for T-Cell immunology

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

17 July - 20 July 2022

Innate Immunity in Host-Pathogen Interactions

Bernhard Hube, Julie Pfeiffer, Felix Randow, Feng Shao, Cyril Zipfel

OverviewSpeakersSponsorsAbout OverviewSpeakersSponsorsAbout Overview Symposium Overview This symposium provides a discussion platform for all scientists interested in the biology of infection. Cell biologists, microbiologists and immunologists will discuss in joint sessions recent progress in our understanding of host-pathogen interactions. Talks will focus on common processes, rather than particular infectious agents or host cell types, and the strategies of all major types of pathogens in their interaction with plants and animals will be covered. A better understanding of infectious diseases will come from the simultaneous analysis of microbial and host variables, which may open new avenues for treatment and prevention strategies. Session Topics Sensing pathogensThe cell biology of infectionFungus-host interactionsCell-autonomous immunityPathological consequences of infection and inflammationMicrobiota and pathogen...

18 July - 22 July 2022

Proteomics bioinformatics

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

27 August - 30 August 2022

Transcription and Chromatin

Karen Adelman, Eileen Furlong, Jürg Müller, Peter Verrijzer

OverviewSpeakersSponsors OverviewSpeakersSponsors 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...

4 September - 13 September 2022

Current Methods in Cell Biology

Sara Cuylen-Häring, Simone Köhler

The major aim of the course is to allow participants to experience modern cell biology at work: not only to see but also to try out in practice how cutting-edge technologies can be used to answer questions at the frontiers of cell biology. It is a tradition that the entire faculty of the Cell Biology and Biophysics Unit of EMBL teaches the course to cover a broad spectrum of techniques. OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Experience modern cell biology at work: not only see but also try out in practice how cutting-edge technologies can be used to answer questions at the frontiers of cell biology. It is a tradition that the entire faculty of the Cell Biology and Biophysics Unit of EMBL teaches the course to cover a broad spectrum of techniques. The course also provides an excellent opportunity for participants and course faculty to discuss current and future challenges in cell biology. Audience The course will be primarily aimed at postdocs and advanced graduate students who have developed an interest in cell biology. We wish to attract cell biologists who want to acquire quantitative, biophysical, and computational methods as well as...

5 September - 8 September 2022

Chemical Biology 2022

Yimon Aye, Claire Deo, Kai Johnsson, Edward 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...

11 September - 18 September 2022

Synthetic Biology in Action: Beyond Standard Metabolism

Sven Panke, Vitor Pinheiro, Karen Polizzi, Elisabeth Zielonka

OverviewSpeakers and TrainersSponsors OverviewSpeakers and TrainersSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Synthetic Biology (SynBio) has become a rapidly developing area for tackling a large number of challenges in life science research. This course will provide the best and most exciting novelties in the field and focus on exploiting tools and concepts of SynBio for multi-scale engineering of bacterial systems. Audience The course is directed to PhD students and early post-doctoral researchers active in the areas of molecular microbiology, bacterial biotechnology, systems biology and bioengineering. Modules/Resources The program consists of practicals with two daily lectures on some of the hottest topics in bacterial SynBio, including: Genome engineering (incl. CRISPR and MAGE)RNA tools for system-wide...

12 September - 16 September 2022

Mathematics of life: Modelling molecular mechanisms

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page.  We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest.

13 September - 16 September 2022

Reconstructing the Human Past - Using Ancient and Modern Genomics

Johannes Krause, Anna-Sapfo Malaspinas, Ida Moltke, David Reich

The study of population genetic variation and the sequencing of ancient DNA represent promising new avenues for investigating human history and our evolutionary past. Population-scale sequencing projects investigating human diversity have provided us with more than a million genome wide datasets that allowed new insights into patterns of human variation and mobility, while others have obtained genome wide data from thousands of ancient human skeletons, allowing the investigation of human evolution in action and providing direct insights into population genetic dynamics in situ. OverviewOrganisersSponsorsAbout Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium Overview The study of population genetic variation and the sequencing of ancient DNA represent promising new avenues for investigating human history and our evolutionary past. Population-scale sequencing projects investigating human diversity have provided us with more than a million genome wide datasets that allowed new insights into patterns of human variation and mobility, while others have obtained genome wide data from thousands of ancient human skeletons, allowing the investigation of human evolution in action and providing direct insights into population genetic dynamics in situ. Large-scale genetic variation data sets can now be integrated with genomics data from ancient remains and history records to...

26 September - 30 September 2022

Bioinformatics and functional genomics in zebrafish

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

3 October - 7 October 2022

Single-cell RNA-seq analysis using R

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. To keep informed of changes to the course and to find out when the course opens for applications, please register your interest.

5 October - 8 October 2022

Molecular Mechanisms in Evolution and Ecology

Gianni Liti, Sara Mitri, Kiran Patil, Kimberley Kline, Antonis Rokas

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 This conference series has become known for exploring yeasts as models to study questions of general relevance to evolution and ecology. Experts will speak on a range of topics, including evolution theory, ecology, genetics, cell biology, genomics, systems biology, metabolic modelling and engineering. The focus of this conference will be on comparative and experimental strategies to explore evolutionary questions, from field studies to computer simulations to comparative genomics. Central evolutionary questions will be discussed, using yeast and a range of other species whose biology is well understood and to determine the degree to which that biology is conserved in more distantly related species. The aim is to move...

12 October - 15 October 2022

The Complex Life of RNA

Anne Ephrussi, Wendy V. Gilbert, Torben Heick Jensen, Ramesh Pillai

OverviewSponsorsAbout OverviewSponsorsAbout Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference Overview Before the genetic information stored in DNA can be used to direct cell growth and metabolism, it has to be transferred into RNA. Messenger RNAs (mRNAs) that code for proteins and noncoding RNAs are key components in the transmission of genetic information in all life forms – from viruses to complex mammalian organisms. Exciting recent findings now reveal a new layer of information added to RNAs in the form of chemical marks (the epitranscriptome) that play a critical role in gene expression control. Following the great success of the virtual 2020 edition of this long-standing symposium, we are looking forward to returning to an in-person meeting for 2022, bringing together leaders in the RNA field,...

16 October - 21 October 2022

Metabolite and Species Dynamics in Microbial Communities

Sandeep Krishna, Sunil Krishna, Kiran Patil, Elisabeth Zielonka, Maria Zimmermann

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 Metagenomics studies are rapidly uncovering the compositional richness of microbial communities in diverse habitats ranging from the oceans to the human gut. While their fundamental role in our health and environment is undeniable, there is an urgent need for unravelling molecular mechanisms underlying the dynamics of these communities. This requires a combined experimental and computational approach. Recent studies (including those from the organisers’ and speakers’ labs) have underlined the success of such integrative approaches. For example, emergence of cell subpopulations (Varahan et al. eLife 2019, 2020), and long-term stability (Blasche, Kim et al. Nat Microbiol. 2021) through metabolic cross-feeding.As...

17 October - 21 October 2022

Structural bioinformatics

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page.  We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest.

26 October - 29 October 2022

Plasticity Across Scales: From Molecules to Phenotypes

Ehab Abouheif, Alexander Aulehla, Axel Meyer, Sonia Sultan

OverviewSpeakersSponsorsAbout OverviewSpeakersSponsorsAbout 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.  Speakers Ian Baldwin Max Planck Institute for Chemical Ecology Germany Shelley Berger University of Pennsylvania USA Sinead Collins University of Edinburgh UK Ian Ehrenreich University of Southern California USA Anne Ferguson-Smith University...

30 October - 3 November 2022

The Fundamentals of High-End Cell Sorting

Derek Davis, Andrew Filby, Diana Ordoñez-Rueda, Malte Paulsen, Steffen Schmitt

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 on the fundamentals of high-end cell sorting will enable scientists to properly use the global upstream technology of cell sorting with high confidence. Cell sorting is essential to many studies, but researchers outside of core facilities have very limited knowledge how exactly sorting works and unknowingly produce erroneous samples or even scientifically crippling data. Audience The course is intended for PhD students and postdocs who are starting to use, or already using flow cytometry based cell sorting in their research projects. Applicants with some previous active knowledge of basic principles of flow cytometry and a regular use of flow cytometers in daily research will profit most from the content of...

31 October - 4 November 2022

Metagenomics bioinformatics

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page.  We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest.

7 November - 10 November 2022

The Neurovascular Interface

Amparo Acker-Palmer, Ralf Adams, Chenghua 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. OverviewSpeakersSponsorsAbout 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...

14 November - 18 November 2022

Genome bioinformatics: resequencing and variant calling

EMBL-EBI Training team

Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page.  We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest. Please note that the dates set for this 2022 course are subject to change, but all changes will be reflected on this course page. We are at this stage unable to confirm whether this course will be running onsite at Hinxton or will be delivered virtually. To keep informed of all changes to the course and to find out when the course opens for applications, please register your interest.

15 November - 18 November 2022

From Functional Genomics to Systems Biology

Arnaud Krebs, Prisca Liberali, Mikhail Savitski, Georg Seelig

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 Recent advances in genomics and proteomics technologies have transformed our ability to study diverse molecular processes. We can now use these technologies to study and understand mechanisms regulating transcription, translation, protein abundance, protein-protein, protein-metabolites and protein-drug interactions at a genome- and proteome-wide scale. The current challenge is to convert this data into predictive quantitative models of cellular processes. This massive task requires intensive integration of basic biology, genomics, proteomics, imaging, computational biology, mathematics, engineering and physics. This conference brings together scientists from diverse fields to promote cross-disciplinary collaborations...

23 November - 24 November 2022

Terra Incognita: Navigating Ethical Boundaries in the Life Sciences

Lucia von Bredow

Overview Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Overview Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest.