EMBL Events

17 February - 21 February 2025

Single-cell RNA-seq analysis with Python

Juanita Riveros

This course covers the analysis of single cell RNA sequencing scRNA seq data using Python and command line tools Participants will be guided through droplet based scRNA seq analysis pipelines from raw reads to cell clusters You will explore and interpret single cell RNA seq data using Python as well as the Single Cell Expression Atlas Finally you will put their knowledge into practice through a group challenge on the last day Please note that you will not analyse your own data as part of the course There will however be ample opportunity to discuss your research and ideas with other course participants and trainers Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning you will not require access to a powerful computer or install complex software on your own machines Participants will need to be available between the hours of 09 00 17 30 BST each day of the course Trainers will be available to assist answer questions and provide further explanations during these times Please note that we will operate this course virtually Hybrid options are not currently available We reserve the right to change the format of this course or cancel it... This course covers the analysis of single cell RNA sequencing (scRNA-seq) data using Python and command line tools. Participants will be guided through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. You will explore and interpret single-cell RNA seq data using Python as well as the Single Cell Expression Atlas. Finally, you will put their knowledge into practice through a group challenge on the last day.Please note that you will not analyse your own data as part of the course. There will, however, be ample opportunity to discuss your research and ideas with other course participants and trainers.Virtual courseParticipants 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...

17 February - 21 February 2025

Advanced deep learning for image analysis

Anna Kreshuk, Florian Jug, Constantin Pape, Martin Weigert

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview 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... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview 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, and for high-throughput imaging and large-scale processing in 3D. Despite these advances, training and deployment of such neural networks remains difficult for practitioners of image analysis. The aim of our course is to close this gap and teach the participants, in the most hands-on way possible, to apply deep learning-based methods to their own data and image analysis problems. This time, we aim not to start from scratch but to address participants who already...

23 February - 28 February 2025

Extracellular vesicles: from biology to biomedical applications

An Hendrix, Cecilia Lässer, Esther Nolte-T Hoen, Guillaume Van Niel

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... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview The extracellular vesicle (EV) research field is still growing with many researchers entering the field with a continued strength of demand for such specialized training. As research progresses, it becomes clear that EV’s regulate an increasing number of (Patho)physiological processes and are harnessed in a variety of biomedical applications. Appropriate methodologies to prepare and characterize EV from biofluids are key to understanding the mechanisms that regulate their formation, composition and function. Given the large number of methods used, it is particularly important to provide practical hands-on training to new researchers covering the possibilities and limitations of the most widely used methods. This course will deliver such state-of-the-art training to participants, particularly...

24 February - 28 February 2025

Introduction to RNA-seq and functional interpretation

Barbara Etzi

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 Please note that this course covers different topics related to bulk RNA Seq data analysis Other related techniques such as single cell and spatial transcriptomics will not be covered Nonetheless the overview lecture will describe the potentials and limitations of the most commonly used RNA Sequencing analysis techniques and the context in which they are used If you are seeking training on single cell please consider applying to the 2025 Single cell RNA seq analysis with Python virtual course which will run about the same dates Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 08 00 18 00 GMT each day of the course Trainers will be available to assist answer questions and provide further explanations 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.Please note that this course covers different topics related to bulk RNA-Seq data analysis. Other related techniques such as single-cell and spatial transcriptomics will not be covered. Nonetheless, the overview lecture will describe the potentials...

26 February 2025

Basics of Large Language Models - transformers to LLMs

This webinar is now at full capacity A recording will be available on this page after the session ends and no registration is required to watch it We will introduce Large Language Models LLMs focusing on their core architecture training methodologies practical applications and some important considerations We begin with a brief exploration of the transformer architecture examining how architectural choices and scaling laws have shaped modern language models We then investigate key training paradigms with particular emphasis on Reinforcement Learning from Human Feedback RLHF and instruction tuning while briefly touching on emerging approaches like Direct Preference Optimisation DPO The discussion progresses through the evolution of knowledge integration techniques from basic context stuffing to Retrieval Augmented Generation RAG highlighting their practical implications We will discuss the critical issue of hallucinations in LLM outputs providing concrete examples and verification strategies To conclude a quick overview of the current software landscape and immediate future developments in the field and a look ahead to the rest of the webinar series... This webinar is now at full capacity. A recording will be available on this page after the session ends, and no registration is required to watch it.  We will introduce Large Language Models (LLMs), focusing on their core architecture, training methodologies, practical applications, and some important considerations. We begin with a brief exploration of the transformer architecture, examining how architectural choices and scaling laws have shaped modern language models. We then investigate key training paradigms, with particular emphasis on Reinforcement Learning from Human Feedback (RLHF) and instruction tuning, while briefly touching on emerging approaches like Direct Preference Optimisation (DPO). The discussion progresses through the evolution of knowledge integration techniques, from basic context stuffing to Retrieval-Augmented Generation (RAG), highlighting their...

27 February 2025

Workshop on Artificial Intelligence Competencies: training challenges and needs of research infrastructures and core facilities

Juanita Riveros

Update the application period is closed but additional spaces may be available please contact the organisers if interested The Biodata Developers BioDev Network Wellcome Sanger Institute and ELIXIR EMBL EBI as part of RItrainPlus project are organising a knowledge exchange workshop on Artificial Intelligence Competencies training challenges and needs of research infrastructures and core facilities The overall purpose of the workshop is to create a space to discuss the professional roles and competencies needed to support the implementation of Artificial Intelligence AI for research in research infrastructures RIs Core Facilities CFs and similar organisations as well as the training gaps and current actions they are already carrying out to address the training needs This will be an interactive workshop where attendees will actively participate through discussions group work or short presentations The workshop has been shaped with the input gathered through dedicated scoping discussions with different experts In particular we would like to thank the following experts and their organisations for their input Nina Norgren SciLifeLabFotis Psomopoulos Center for Research and Technology HellasDan MacLean The Sainsbury Lab TSL Edward Lukyamuzi Pan African Mosquito Control Association PAMCA Dr Michelle Skelton Data Science for Health Discovery and Innovation in Africa DS I Africa Helder Nakaya Albert Einstein Hospitals BrazilMoises Sotelo University of GuadalajaraRolanda Julius Data Science for Health Discovery and Innovation in Africa DS I Africa... Update: the application period is closed, but additional spaces may be available, please contact the organisers if interested.The Biodata Developers’ (BioDev) Network, Wellcome Sanger Institute and ELIXIR / EMBL-EBI, as part of RItrainPlus project, are organising a knowledge-exchange workshop on ‘Artificial Intelligence Competencies: training challenges and needs of research infrastructures and core facilities’. The overall purpose of the workshop is to create a space to discuss the professional roles and competencies needed to support the implementation of Artificial Intelligence (AI) for research in research infrastructures (RIs), Core Facilities (CFs) and similar organisations, as well as the training gaps and current actions they are already carrying out to address the training needs.This will be an interactive workshop where attendees will actively participate through...

3 March - 7 March 2025

Introduction to multi-omics data integration and visualisation

Meredith Willmott

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

5 March 2025

Developing a dataset for LLM projects

As large language models LLMs continue to revolutionise artificial intelligence applications the importance of high quality data preparation has never been more critical This webinar dives into the art and science of preparing datasets for effective LLM training offering actionable insights for AI practitioners data scientists and engineers We will explore the end to end process of data preparation beginning with data collection strategies and progressing through cleaning preprocessing tokenisation and annotation Emphasis will be placed on identifying and mitigating biases managing multilingual datasets and ensuring data quality and diversity to enhance model performance Real world case studies will illustrate common pitfalls and solutions while hands on demonstrations will provide practical techniques for optimising datasets Participants will gain a deeper understanding of how well structured and curated data can significantly impact an LLM s capabilities reduce training costs and improve ethical AI outcomes Whether you are building LLMs from scratch or fine tuning existing models this session will equip you with the knowledge to leverage your data assets effectively Join us to unlock the potential of data preparation and enable your LLMs to achieve unparalleled performance and generalisation... As large language models (LLMs) continue to revolutionise artificial intelligence applications, the importance of high-quality data preparation has never been more critical. This webinar dives into the art and science of preparing datasets for effective LLM training, offering actionable insights for AI practitioners, data scientists, and engineers.We will explore the end-to-end process of data preparation, beginning with data collection strategies and progressing through cleaning, preprocessing, tokenisation, and annotation. Emphasis will be placed on identifying and mitigating biases, managing multilingual datasets, and ensuring data quality and diversity to enhance model performance. Real-world case studies will illustrate common pitfalls and solutions, while hands-on demonstrations will provide practical techniques for optimising datasets.Participants will gain a deeper understanding...

6 March 2025

UniProt for proteomics scientists

UniProt is a comprehensive expert led publicly available database of protein sequence function and variation information It also encompasses a wealth of large scale proteomics data resources and tools that users from the proteomics community can benefit from This webinar will introduce proteomics data in UniProt and highlight resources that users with large protein datasets may find useful in analysing their data This will encompass our proteomes service how to carry out a peptide search and where to find large scale proteomics derived data in UniProt The webinar will then go on to briefly introduce programmatic access to the UniProt Proteins API and will give examples on how to download reference proteomes and download large scale proteomics datasets programmatically Finally the speakers will take live questions from the audience Attendees will have access to a Google Colab workbook following the webinar which will provide coding examples that they can use in their own analysis pipelines The UniProt APIs are available at https www uniprot org help programmatic access... UniProt is a comprehensive, expert-led, publicly available database of protein sequence, function and variation information. It also encompasses a wealth of large-scale proteomics data, resources and tools that users from the proteomics community can benefit from.This webinar will introduce proteomics data in UniProt and highlight resources that users with large protein datasets may find useful in analysing their data. This will encompass our proteomes service, how to carry out a peptide search and where to find large scale proteomics-derived data in UniProt.The webinar will then go on to briefly introduce programmatic access to the UniProt Proteins API and will give examples on how to download reference proteomes, and download large-scale proteomics datasets programmatically.Finally the speakers will take live questions from the audience.Attendees will have access to a Google Colab...

9 March - 14 March 2025

Quantitative proteomics: strategies and tools to probe biology

Jeroen Krijgsveld, Christina Ludwig, Mikhail Savitski

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Proteomic technologies continue to develop at a rapid pace offering the potential to address imminent questions in a range of biological research areas Mass spectrometry has become widely accessible to many biologists either through core facilities or scientific collaborations Because... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Proteomic technologies continue to develop at a rapid pace, offering the potential to address imminent questions in a range of biological research areas. Mass spectrometry has become widely accessible to many biologists, either through core facilities or scientific collaborations. Because quantitative proteomics includes a variety of specialised technologies and workflows, each with specific advantages and limitations, this hands-on practical course aims to train biologists on how to best integrate these evolving proteomics technologies into their own research. To achieve this, expert tutors will offer hands-on training in the analysis, interpretation, and statistical evaluation of various types of proteomic data through teaching methodological concepts integrated with software-driven data analysis...

11 March - 14 March 2025

The expanding world of RBPs: from posttranscriptional control to riboregulation

Francesca Cuttruzola, Imed Gallouzi, Matthias Hentze, V. Narry Kim

OverviewSpeakersProgrammePractical InformationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview Based on recent methodological breakthroughs the number of identified mammalian RNA binding proteins RBPs has skyrocketed from around 700 to over 2000 More importantly completely new classes of proteins... OverviewSpeakersProgrammePractical InformationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview Based on recent methodological breakthroughs, the number of identified mammalian RNA-binding proteins (RBPs) has skyrocketed from around 700 to over 2000. More importantly, completely new classes of proteins (including enzymes, signaling molecules, transporters and channels etc.) were recognized as RBPs, posing questions regarding the biological functions of RNA binding. This meeting will bring together leaders in the field of RBPs – classical and newly discovered – and discuss exciting progress on all fronts, from posttranscriptional regulation of RNA expression to the riboregulation of protein functions, facilitated by rapidly emerging experimental technologies and data analysis tools. Discussion topics...

17 March - 21 March 2025

Gene-environment interactions in human health and disease

Juanita Riveros

This introductory course explores the complex interplay between genes and the environment in shaping human phenotypes Participants will gain knowledge of cohort datasets environmental readouts and computational resources to investigate gene environment interactions Ethical and legal frameworks related to data privacy and consent will be discussed The course also covers computational modelling techniques for integrating genotype and environmental effects By the end attendees will be equipped to analyse cohort datasets make use of computational resources and interpret the results Please note that you will not analyse your own data as part of the course There will however be ample opportunity to discuss your research and ideas with other course participants and trainers... This introductory course explores the complex interplay between genes and the environment in shaping human phenotypes. Participants will gain knowledge of cohort datasets, environmental readouts, and computational resources to investigate gene-environment interactions. Ethical and legal frameworks related to data privacy and consent will be discussed. The course also covers computational modelling techniques for integrating genotype and environmental effects. By the end, attendees will be equipped to analyse cohort datasets, make use of computational resources, and interpret the results. Please note that you will not analyse your own data as part of the course. There will, however, be ample opportunity to discuss your research and ideas with other course participants and trainers

18 March - 21 March 2025

Mechanisms of drug resistance and tolerance in bacteria, fungi, and cancer

Judith Berman, Markus Ralser, Luiz Carvalho, Marina Rodnina

OverviewSpeakersAboutProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview Resilience to antimicrobial drugs is a rapidly increasing problem of global health Similarly cancer cells that become drug resistant or tolerant affect therapy outcomes for instance during cancer... OverviewSpeakersAboutProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview Resilience to antimicrobial drugs is a rapidly increasing problem of global health. Similarly, cancer cells that become drug-resistant or tolerant affect therapy outcomes, for instance during cancer chemotherapy. The underlying biological mechanisms of tolerance, resistance, and persistence are increasingly being studied and reveal a complex interplay between (cellular) evolution, biochemistry, and metabolism. Understanding these mechanisms holds the long-term promise of developing new therapeutic strategies less prone to drug resistance and, in the short term, enhances our understanding of clonal evolution and single-cell biology. With this new symposium, we aim to gather a highly international group of...

19 March 2025

LLM generated summaries for protein classification at InterPro

This webinar will explore how Large Language Models can accelerate protein classification by automatically generating descriptive annotations for previously unannotated protein families Traditionally the process of curating protein family descriptions relies on manual literature review and expert knowledge a time consuming approach that often delays integration into biological databases In this session we will discuss our innovative workflow that leverages LLMs to synthesise functional summaries from existing curated data thereby streamlining the annotation process We will also highlight a comparative evaluation of using both a state of the art GTP model and a fine tuned local model demonstrating that smaller cost effective LLMs can produce high quality descriptions that support rapid protein classification... This webinar will explore how Large Language Models can accelerate protein classification by automatically generating descriptive annotations for previously unannotated protein families. Traditionally, the process of curating protein family descriptions relies on manual literature review and expert knowledge, a time-consuming approach that often delays integration into biological databases. In this session, we will discuss our innovative workflow that leverages LLMs to synthesise functional summaries from existing curated data, thereby streamlining the annotation process. We will also highlight a comparative evaluation of using both a state-of-the-art GTP model and a fine-tuned local model, demonstrating that smaller, cost-effective LLMs can produce high-quality descriptions that support rapid protein classification.

23 March - 28 March 2025

Measuring translational dynamics by ribosome profiling

Pasha Baranov, Jan Medenbach, Sebastian Leidel, Elisabeth Zielonka

Quantitative assessment of mRNA translation is critical to understanding gene expression in many biological settings In this practical course we will summarise the state of the art in the theoretical sessions combined with hands on experiments and computational analyses Participants will learn a robust protocol and how to adapt it to different experimental systems and also learn the key steps of computational quality control... OverviewSpeakers, trainers and staffPreliminary ProgrammePractical informationMedia kitSponsors Overview Course overview Regulation of translation is key in the control of gene expression, playing a critical role in many biological and pathophysiological settings. In the last decade, methodological advances have provided comprehensive insights into cellular transcriptomes and proteomes, however, the systems-wide analysis of translation remained an unsolved experimental challenge. The advent of ‘ribosome-profiling’ provided the methodological basis for comprehensive transcriptome-wide analyses of translation at sub-codon resolution by the precise and high-throughput determination of ribosomal positions on mRNA. Its application in a variety of organisms yielded novel insights into protein synthesis and its dynamic regulation, significantly advancing our understanding of the...

26 March 2025

BioChatter and the future of LLM driven bioscience

LLMs are the biggest new industry on our planet Considering the amount of research and investments in the field large and rapid progress is expected for the coming decade However to make use of the technology we need to have a solid grasp on its technical as well as infrastructural aspects LLM deployment entails a layered tech stack the LLM itself deployment use of services or self hosting technical guardrails instruction fine tuning auxiliary technologies retrieval augmented generation knowledge integration and end user accessibility programming APIs user interfaces Applying the latest knowledge about LLMs in a robust and trustworthy way is an operative challenge despite the large improvements we already see in the wider field In this webinar we will talk about the LLM stack with a focus on open source frameworks that facilitate deployment at various levels The base layer are the deployment frameworks themselves e g Ollama as well as harmonising APIs for open source LLMs by commercial providers The second layer are frameworks for LLM integration into user systems as championed by LangChain The third layer are domain specific frameworks such as our own development BioChatter which also reaches over into the fourth layer dedicated user interfaces To future proof our approach to this powerful technology it is imperative to avoid redundancies in order to not reinvent the wheel we need to be aware of which problems are solved and which are worth tackling We will discuss a flexible framework for using open source technologies at various stages of project maturity from proof of concept to service provision Finally we will discuss the scope of LLM application what can they safely be used for and which applications are still out of reach... LLMs are the biggest new industry on our planet. Considering the amount of research and investments in the field, large and rapid progress is expected for the coming decade. However, to make use of the technology, we need to have a solid grasp on its technical as well as infrastructural aspects. LLM deployment entails a layered tech stack: the LLM itself, deployment (use of services or self-hosting), technical guardrails (instruction, fine-tuning), auxiliary technologies (retrieval-augmented generation, knowledge integration), and end-user accessibility (programming APIs, user interfaces). Applying the latest knowledge about LLMs in a robust and trustworthy way is an operative challenge despite the large improvements we already see in the wider field.In this webinar, we will talk about the LLM stack with a focus on open-source frameworks that facilitate deployment at various levels. The...

31 March - 2 April 2025

AI in one health

Oliver Billker, Lionel Christiaen, Anna Kreshuk, Giancarlo Russo, Sameer Velankar, Qi Zhang

OverviewScientific OrganisersSpeakersYoung Investigators MeetingProgrammePractical InformationSponsorsMedia kit Overview Overview The 5th EMBL Partnership Conference will be held in Heidelberg from 31 March 02 April 2025 The conference brings together EMBL and its partner institutes to enable the exchange of expertise and build new collaborations and research networks The programme will... OverviewScientific OrganisersSpeakersYoung Investigators MeetingProgrammePractical InformationSponsorsMedia kit Overview Overview The 5th EMBL Partnership Conference will be held in Heidelberg from 31 March – 02 April 2025. The conference brings together EMBL and its partner institutes to enable the exchange of expertise and build new collaborations and research networks.  The programme will focus on the impact of the recent advances in artificial intelligence (AI) on topics related to Health and related life science areas across 3 different sessions. Session topics Molecular medicine and precision health Genetics and genomics Technology and imaging “The Partnership Conference takes place at EMBL every 3 years and allows us to incite interactions with and across the EMBL Partnership network. It is organized by EMBL’s International Relations in close collaboration with scientific...

31 March - 4 April 2025

Microscopy data analysis: machine learning and the BioImage Archive

Anca Belu

This virtual course will show how public bioimaging data resources centred around the BioImage Archive enable and enhance machine learning based image analysis The content will explore a variety of data types including electron and light microscopy and miscellaneous or multi modal imaging data at the cell and tissue scale Participants will cover contemporary biological image analysis with an emphasis on machine learning methods as well as how to access and use images from databases Virtual courseThis 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 sessions all fully password protected with automated English closed captioning and transcription with support and both scientific and social networking opportunities provided by Slack and other methods taking different time zones into account In order to make the most out of the course you should make sure to have a stable internet connection throughout the week and are available between 08 00 18 00 BST each day 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 Selected participants may 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 engage with the course... This virtual course will show how public bioimaging data resources, centred around the BioImage Archive, enable and enhance machine learning based image analysis. The content will explore a variety of data types including electron and light microscopy and miscellaneous or multi-modal imaging data at the cell and tissue scale. Participants will cover contemporary biological image analysis with an emphasis on machine learning methods, as well as how to access and use images from databases. Virtual courseThis 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 sessions (all fully password protected with automated English closed captioning and transcription) with support and both scientific and social networking opportunities provided by Slack and other methods,...

2 April 2025

Domain-specific knowledge extraction from scientific texts using LLMs

This webinar will explore how Large Language Models LLMs can streamline the extraction of critical information from scientific texts focusing on patient derived cancer models PDCMs PDCMs are vital tools for cancer research and preclinical studies with a growing body of literature in this field However manually extracting and curating information from scientific texts is labor intensive and prone to delays In this session we will introduce two innovative approaches direct prompting and soft prompting Direct prompting uses manually created instructions to extract PDCM related entities while soft prompting leverages machine learning to train continuous vector prompts We will discuss our comparative evaluation using state of the art proprietary and open source LLMs demonstrating how tailored prompt engineering can elevate the performance of smaller open models to match proprietary counterparts This session will highlight the potential of LLMs to enhance domain specific knowledge extraction and accelerate research workflows... This webinar will explore how Large Language Models (LLMs) can streamline the extraction of critical information from scientific texts, focusing on patient-derived cancer models (PDCMs). PDCMs are vital tools for cancer research and preclinical studies, with a growing body of literature in this field. However, manually extracting and curating information from scientific texts is labor-intensive and prone to delays. In this session, we will introduce two innovative approaches: direct prompting and soft prompting. Direct prompting uses manually created instructions to extract PDCM-related entities, while soft prompting leverages machine learning to train continuous vector prompts. We will discuss our comparative evaluation using state-of-the-art proprietary and open-source LLMs, demonstrating how tailored prompt engineering can elevate the performance of smaller, open models to match...

7 April - 14 April 2025

Microbial metagenomics: a 360º approach

Vladimir Benes, Giuseppe D´Auria, José Eduardo González-Pastor, Elisabeth Zielonka

OverviewSpeakers trainers and staffPreliminary programmePractical informationSponsorsMedia kit Overview Course overview This course will provide a global overview of the different metagenomic approaches to study microbial communities covering methods for the functional search of genes sequencing of metagenomes using the most recent technologies and in silico methods for sequence analysis... OverviewSpeakers, trainers, and staffPreliminary programmePractical informationSponsorsMedia kit Overview Course overview This course will provide a global overview of the different metagenomic approaches to study microbial communities, covering methods for the functional search of genes, sequencing of metagenomes using the most recent technologies and in silico methods for sequence analysis. During the course, participants will receive an overview of state-of-the-art genomic technologies and bioinformatic tools. A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines. The course will begin with experimental training in functional metagenomics by preparing metagenomic libraries for gene searching. Metagenomic DNA will be isolated from soil samples to analyze...

8 April - 11 April 2025

Wild frontiers of model organisms

Susana Coelho, Gautam Dey, Michael Dorrity, Nicole Dubilier, Flora Vincent

OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview The scientific community relies on a small number of model organisms to study larger themes in biology with the assumption that gained insights can be extrapolated to most other organisms... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview The scientific community relies on a small number of model organisms to study larger themes in biology, with the assumption that gained insights can be extrapolated to most other organisms. However, recent advances in our ability to study organisms in the context of their natural environments have revealed that Jacques Monod’s famous quote, ‘What is true for E. coli is true for the elephant’ does not do justice to the vast diversity of life on our planet. We will highlight research that challenges classical model organisms by looking at fluctuating, natural environments as a rich, relevant inspiration for new experiments in the lab and explore the challenges associated with the establishment...

29 April 2025

Sustainable research: fit for the future

Brendan Rouse, Marta Rodríguez-Martínez, Philipp Weber, Martin Farley, Valeria Scagliotti

Overview Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview The symposium will delve into the critical role of sustainable practices within the scientific community As researchers grapple with global challenges it becomes imperative to adopt environmentally responsible and socially equitable research methodologies This... Overview Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview The symposium will delve into the critical role of sustainable practices within the scientific community. As researchers grapple with global challenges, it becomes imperative to adopt environmentally responsible and socially equitable research methodologies. This symposium will explore topics such as green laboratory practices, the inspiring role of grassroots movements, organisation’s sustainability strategies, and the vital role of funders, always with an eye on the future. By fostering a culture of sustainability within science, we can reduce our ecological footprint, enhance research integrity, and ensure the long-term viability of scientific research. Through a series of keynote presentations, panel discussions, and interactive workshops, participants will...

4 May - 9 May 2025

Analysis and integration of transcriptome and proteome data

Vladimir Benes, Raffaele Calogero, Daria Fijalkowska, Jeroen Krijgsveld, Lennard Martens

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Course overview Systems biology is a still expanding field of research aiming to understand at the molecular level how cells tissues and organisms operate in their biological context Among the key technologies driving this forward are next generation sequencing and proteomics as they provide powerful means... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Course overview Systems biology is a still expanding field of research aiming to understand at the molecular level how cells, tissues and organisms 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 they will receive training in data analysis for the annotation, quantification, and statistical analysis of gene and protein expression using various computational tools. In addition, training will be provided...

6 May - 9 May 2025

Theory and concepts in biology

Alexander Aulehla, Christina Hueschen, Jordi Garcia-Ojalvo, Sriram Ramaswamy, Kirsty Wan

The goal of this symposium is to assemble an interdisciplinary community and to provide a platform to discuss perspectives on the role of theory in biology and importantly also vice versa the impact that biology can have on theory... OverviewSpeakersPreliminary ProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview Recent progress in biology has led to an explosion of factual knowledge about the living world over a huge range of scales in space and time. Yet, many questions about how to make sense of this data remain across the entire diversity of the living world from the smallest bacterium to the ecosystems of the Serengeti. This meeting is the 2nd edition in a series of symposia aiming to bring together a diverse community of researchers interested in finding ways to transform into conceptual knowledge the ever-increasing amount of factual knowledge produced by biological research. The goal is to provide a platform to discuss perspectives on the role of theory in biology, and importantly also vice...

12 May - 16 May 2025

Cancer genomics and transcriptomics

Meredith Willmott

This course will focus on the analysis of data from genomic studies of cancer It will also highlight the application of transcriptomic analysis and single cell technologies in cancer Talks and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the trainers Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 08 45 17 30 BST each day of the course Trainers will be available to assist answer questions and provide further explanations during these times... This course will focus on the analysis of data from genomic studies of cancer. It will also highlight the application of transcriptomic analysis and single-cell technologies in cancer. Talks and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data, whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the trainers.Virtual courseParticipants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.Pre-recorded material may be provided before the course starts that participants will need to watch,...

13 May - 16 May 2025

Chromatin and epigenetics

Asifa Akhtar, Amanda Fisher, Dirk Schubeler, Bing Ren

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

18 May - 23 May 2025

Advanced fluorescence imaging techniques

Manuel Gunkel, Aliaksandr Halavatyi, Joana Delgado Martins, Stefan Marawske

This practical course will cover advanced light microscopy techniques and participants will learn how to derive qualitative and quantitative insights on molecular mechanisms in cells and developing organisms Invited guest researchers together with experts from the EMBL and microscopy professionals will foster an intense information flow with a balance of lectures and practical workshops The focus of the course will be on the use of fluorescence microscopy to obtain information about protein localisation dynamics and functions at different spatial scales... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Course overview This practical course will cover advanced light microscopy techniques and participants will learn how to derive qualitative and quantitative insights on molecular mechanisms in mechanisms in cells, tissues and developing organisms. Invited guest researchers together with microscopy experts from EMBL will foster an intense information flow with a balance of lectures and practical workshops. The focus of the course will be on the use of fluorescence microscopy to obtain information about localisation and functions of proteins and other bio-molecules at different spatial scales. Audience This course is directed towards researchers in the life sciences with access to light microscopy equipment, who have an immediate need to apply the techniques they will learn to solve biological problems at...

20 May - 23 May 2025

Introduction to metabolomics analysis

Juanita Riveros

This course will provide an introduction to metabolomics through lectures and hands on sessions using publicly available data software and tools Participants will become familiar with standardised workflows as well as with the current state of experimental design data acquisition LC MS MS imaging processing and modelling In addition they will learn about community standards and sharing in metabolomics particularly through the use of EMBL EBI s MetaboLights repository and Galaxy infrastructure Participants will learn through hands on tutorials to use tools available for data analysis and data submission Additionally case studies will be discussed to show how to employ the week s learning... This course will provide an introduction to metabolomics through lectures and hands-on sessions, using publicly available data, software, and tools. Participants will become familiar with standardised workflows as well as with the current state of experimental design, data acquisition (LC-MS, MS imaging), processing, and modelling. In addition, they will learn about community standards and sharing in metabolomics, particularly through the use of EMBL-EBI’s MetaboLights repository and Galaxy infrastructure. Participants will learn through hands-on tutorials to use tools available for data analysis and data submission. Additionally, case studies will be discussed to show how to employ the week’s learning.

20 May - 22 May 2025

BioMalPar XXI: biology and pathology of the malaria parasite

Yaw Aniweh, Liliana Mancio-Silva, Wiebke Nahrendorf, Stuart Ralph

OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview Malaria remains a significant global public health challenge with increasing drug resistance COVID interruptions to interventions and rising malaria deaths confounding our efforts against this... OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview Malaria remains a significant global public health challenge, with increasing drug resistance, COVID interruptions to interventions, and rising malaria deaths confounding our efforts against this persistent disease. BioMalPar reaffirms our commitment to understanding the Plasmodium parasite and its interactions with hosts and vectors. Despite the challenges, there are promising developments: new drug combinations are showing efficacy, and we now have two approved vaccines that offer hope for the future. Meeting for the 21st time, BioMalPar 2025 focusses on strengthening our global research community by fostering new partnerships and collaborations. We acknowledge that defeating malaria requires a...

26 May - 28 May 2025

Infection: pathogens, hosts, and microbiomes

Maria Bernabeu, Pascale Cossart, Hiten Madhani, Kim Orth, Michael Way

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview Infectious diseases are among the most prevalent causes of human illness and death in the world Epidemics pandemics have shaped human evolution and history and although for a while they were... OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview Infectious diseases are among the most prevalent causes of human illness and death in the world. Epidemics & pandemics have shaped human evolution and history, and although for a while they were considered a solved problem for the developed world, the recent past has showed us all why this is not the case. Antimicrobial resistance, global warming, human population size increase, modern lifestyles (urbanization, traveling), decrease of wild-life habitats for pathogen reservoirs all contribute to creating an ideal setting for infectious diseases becoming an even greater challenge in the future. This symposium will bring together experts working on different pathogens (viruses, bacteria, fungi, and...

1 June - 6 June 2025

Whole transcriptome data analysis

Marco Beccuti, Vladimir Benes, Raffaele Calogero, Francesca Cordero

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 and rCASC packages which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis... OverviewSpeakers, trainers and staffPreliminary programmePractical informationSponsorsMedia kit Overview Course overview This course will teach biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq and rCASC packages, which were developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq and rCASC packages use 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. Computers for hands-on exercises...

2 June - 6 June 2025

Interdisciplinary challenges in the physics of complexity and life 2025 (IntCha25)

This conference aims at connecting young researchers from diverse backgrounds at the interface between the physics of complex systems and biology to build networks and new collaborations both across fields and between theoreticians and experimentalists... OverviewSpeakersProgrammePractical information Overview Conference overview This conference aims at connecting young researchers from diverse backgrounds at the interface between the physics of complex systems and biology, to build networks and new collaborations both across fields and between theoreticians and experimentalists. The talks will span a variety of topics from soft matter to biology and statistical physics. As the conference is aimed at early-career researchers, we strongly support applications from PhD students, postdocs and early-career permanent researchers.Since we are aware of the financial difficulties faced by young researchers, participants that are accepted for poster presentations will have the opportunity to apply to a travel grant. We will notably support environmentally friendly travelling options within our financial capabilities. Keynote Speakers Pierre...

3 June - 6 June 2025

25th international meeting of the European Light Microscopy Initiative

Elisa D’Este, Ulrike Engel, Elisa May, Rainer Pepperkok, Stefan Terjung, Timo Job Kristian Zimmermann

The primary goals of this conference are to advocate for light microscopy as an essential research tool in the life sciences and to enhance communication among researchers core facilities and the industry... OverviewSpeakersPreliminary programmeIndustry workshopsExhibitionSponsorshipPractical informationMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview Founded in 2001, the European Light Microscopy Initiative (ELMI) was established to create a pivotal communication network among European scientists involved in light microscopy and equipment manufacturers. Its primary goals are to advocate for light microscopy as an essential research tool in the life sciences and to enhance communication among researchers, core facilities, and the industry. The 2025 edition of the European Light Microscopy Initiative conference sees a return to the European Molecular Biology Laboratory (EMBL) in Heidelberg, for the first time since 2010. With EMBL’s tradition of excellence in light microscopy, this event promises to be a...

10 June - 13 June 2025

The ageing genome: from mechanisms to disease

George Garinis, Jaqueline Jacobs, Björn Schumacher, Agnel Sfeir

OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview Ageing is often considered a complex phenotype that affects multiple organs and tissues in a time dependent manner This may result in the aged population consuming a myriad of medications... OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview Ageing is often considered a complex phenotype that affects multiple organs and tissues in a time-dependent manner. This may result in the aged population consuming a myriad of medications, each aimed to treat, but not cure, the affected tissue. Recent studies have demonstrated that the “Primary Hallmarks of Ageing” are a set of five molecular mechanisms that malfunction, independent of tissue type, and drive ageing. Hence, focusing on these five hallmarks simplifies the efforts to understand ageing-associated disease. This, the second edition of this symposium will bring together an all-new, international line-up of speakers to continue the exchange on the basic/mechanistic aspects of...

14 June - 20 June 2025

Computational modelling of multicellular systems

Katie Bentley, James Sharpe, Alejandro Torres-Sanchez

This practical course teaches the basics of multicellular modelling to any researcher wishing to enter the field particularly experimentalists with no prior experience of computational modelling... OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsMedia kit Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course overview This practical course teaches the basics of multicellular modelling to any researcher wishing to enter the field, particularly experimentalists with no prior experience of computational modelling. It is a “hands-on” course with 60% of the time devoted to students working on laptops performing exercises designed to give a practical familiarity with different types of computational modelling. The course focuses on the dynamics of multicellular systems- from embryos to organoids, covering both the molecular side (how gene regulatory networks perform pattern formation) and also the mechanical side in 2D and 3D (how the movements and activities of many cells together...

15 June - 20 June 2025

Imaging-based spatial-omics

Alvaro Crevenna, Andrea Radtke, Emerald Perlas, Sinem Saka,

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview The aim of the course is to provide participants a comprehensive introduction to the various methods of spatial omics and in particular those of multiplex immunofluorescence and spatial transcriptomics We want to provide a general overview of the methods and assist researchers choose the right method for... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview The aim of the course is to provide participants a comprehensive introduction to the various methods of spatial-omics and in particular those of multiplex immunofluorescence and spatial transcriptomics. We want to provide a general overview of the methods and assist researchers choose the right method for their needs. With hands-on practicals, the course will teach participants how to carry out open-source imaging-based methods for cost-effective spatial transcriptomics and multiplex immunofluorescence. The course will cover all experimental stages, including custom reagent preparation, sample preparation and data acquisition (with various microscopy modalities) as well as image processing and basic data analysis. Audience This course is open to PhD students, postdocs and staff. We seek participants...

16 June - 17 June 2025

In science we trust?

Flavien Affaki, Sandra Bendiscioli, Thomas Keane, Bernd Pulverer, Giorgia Renne, Lucia von Bredow

This conference will analyse the importance of public trust in science in a post truth society from public involvement in science to implications on funding and resource allocation and the political consequences of losing societal trust and buy in Above all it will ask what we role we can all play in shaping the future path of increased societal trust in science... OverviewSpeakersPreliminary programmePractical informationCall for postersSponsorsMedia kit Overview This conference will take place as an in-person meeting on-site at EMBL Heidelberg. Conference overview We live in an era characterised by dazzling scientific and technological progress on an unprecedented scale. From the application of new gene editing techniques, pioneering stem cell research, or rapid vaccine development to emerging technologies such as AI or organoid research, advances in life sciences offer a myriad of potential benefits to society. However, these scientific endeavours exist against a backdrop of misinformation and disinformation in the scientific arena, which have the potential to cast a shadow on the public perception of science. From attitudes surrounding scientific issues in the pandemic, highly publicised cases of scientific fraud and misconduct, or ethical...

16 June - 20 June 2025

Data science for life scientists

Meredith Willmott

This course will introduce life scientists to practical data science topics used in life sciences such as data visualisation image analysis application of AI and use of publicly available databases You will initially be introduced to data science theory and practice including best practices for undertaking analyses data management and reproducibility The course will provide hands on training in tools and resources appropriate to your research including introducing the use of Python for handling and visualising data statistical analysis and the application of machine learning Group projectsThis course includes group projects where you will be placed in small groups to work together on a challenge set by trainers from EMBL EBI This allows you to explore the data sciences methods and resources you will learn about during the course and apply them to a set problem providing you with hands on experience The group work will culminate in a flash talk session involving everyone on the final day of the course Groups are mentored and supported by the trainers who set the initial challenge but the groups will be responsible for driving their projects forward with all members expected to take an active role There are two different group project topics gene expression and protein structure Both these projects will provide an opportunity for participants to apply the knowledge and skills learnt during the other sessions of the course including data handling in Python data visualisation statistics and machine learning The projects will also allow participants to gain experience of using EMBL EBI data resources including Expression Atlas and the Single Cell Expression Atlas for the gene expression project and the resources PDBe and AlphaFold for the protein structures project You will be asked during your application to select the group project topic you would most benefit from The projects cover mammalian data sets however in many cases the methods and approaches taught are transferable to data from various species... This course will introduce life scientists to practical data science topics used in life sciences, such as data visualisation, image analysis, application of AI, and use of publicly available databases. You will initially be introduced to data science theory and practice, including best practices for undertaking analyses, data management, and reproducibility. The course will provide hands-on training in tools and resources appropriate to your research, including introducing the use of Python for handling and visualising data, statistical analysis, and the application of machine learning.Group projectsThis course includes group projects where you will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI. This allows you to explore the data sciences methods and resources you will learn about during the course and apply them to a set problem,...

24 June - 27 June 2025

New approaches and concepts in microbiology

Pascale Cossart, Sophie Helaine, KC Huang, Michael Laub, Nassos Typas

This symposium will cover a broad range of topics in microbiology including antibiotic related research bacterial communities and microbiome cell biology regulation signalling pathogenesis and evolution Emphasis will be placed on novel approaches and technologies from systems based to single cell that drive each field or have the potential to revolutionise future research in microbiology... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kitAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview This symposium is the seventh edition of a successful series started in 2013 and held biannually since. It has established itself as a must-attend fixture in the calendar for scientists working with bacteria and new technologies. The meeting covers a broad range of cutting-edge topics in microbiology, featuring diverse research. Emphasis is placed on novel approaches and technologies (from systems-based to single-cell) that drive each field or have the potential to revolutionise future microbiology research. The meeting is always oversubscribed and manages to bring together scientists from different areas, who usually don’t meet, creating a highly interactive and dynamic atmosphere. Session...

24 June - 26 June 2025

Data visualisation for biology

Anca Belu

This course will give insights into and practical experience in data visualisation for exploring complex and multi dimensional biological data Biological and life sciences data often consists of multiple dimensions a combination of numerical values ordered data categories and time series To make sense of this data simple plots like scatterplots barcharts and boxplots are often not enough Still visualisation is critical in gaining deep insight into the data This is why many custom visualisations originated in the biological field In this course we will dive into the topic of visualisation of complex biological data and how it can be used to gain insight into and get a feel for a dataset so that targeted analyses can be defined It will be delivered through a mixture of lectures and workshop sessions and will provide hands on experience in developing visualisations The course will focus on working with omics e g genomics transcriptomics data rather than e g imaging data... This course will give insights into, and practical experience in, data visualisation for exploring complex and multi-dimensional biological data.Biological and life sciences data often consists of multiple dimensions: a combination of numerical values, ordered data, categories, and time-series. To make sense of this data, simple plots like scatterplots, barcharts, and boxplots are often not enough. Still, visualisation is critical in gaining deep insight into the data. This is why many custom visualisations originated in the biological field.In this course, we will dive into the topic of visualisation of complex biological data and how it can be used to gain insight into and get a "feel" for a dataset, so that targeted analyses can be defined. It will be delivered through a mixture of lectures and workshop sessions, and will provide hands-on experience in developing visualisations. The...

2 July - 9 July 2025

Transitions in developing systems: from theory to experiments

Karen Alim, James Briscoe, Jordi van Gestel, Nicoletta Petridou, Hanh Vu

This hands on training course will deliver the state of the art in knowledge concepts and methods utilised to study developmental transitions across biological scales through lectures discussions and application through practical sessions on model and non model systems... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Course overview Developing systems at all biological scales are subject to transitions between states of collective organisation that are critical for their function and evolution. The study of transitions requires bridging biological scales and integrating diverse disciplines, including statistical physics, nonlinear dynamics, and developmental biology. Recent technological advances in quantitative biology, the acquisition of big data and machine-learning based analysis now make it possible to study this topic. This course will give applicants the unique opportunity to closely interact with a diverse group of renowned scientists (speakers/trainers) who work on biological transitions in fundamental developmental processes including morphogenesis, signal transduction, gene expression, collective cell and...

7 July - 11 July 2025

Systems biology: from large datasets to biological insight

Juanita Riveros

This course covers the use of computational tools to extract biological insight from omics datasets The content will explore a range of approaches from network inference and data integration to machine learning and logic modelling that can be used to extract biological insights from varied data types Together these techniques will provide participants with a useful toolkit for designing new strategies to extract relevant information and understanding from large scale biological data The motivation for running this course is a result of advances in computer science and high performance computing that have led to groundbreaking developments in systems biology model inference With the comparable increase of publicly available large scale biological data the challenge now lies in interpreting them in a biologically valuable manner Likewise machine learning approaches are making a significant impact in our analysis of large omics datasets and the extraction of useful biological knowledge... This course covers the use of computational tools to extract biological insight from omics datasets. The content will explore a range of approaches – from network inference and data integration to machine learning and logic modelling – that can be used to extract biological insights from varied data types. Together these techniques will provide participants with a useful toolkit for designing new strategies to extract relevant information and understanding from large-scale biological data.The motivation for running this course is a result of advances in computer science and high-performance computing that have led to groundbreaking developments in systems biology model inference. With the comparable increase of publicly-available, large-scale biological data, the challenge now lies in interpreting them in a biologically valuable manner. Likewise, machine learning approaches are making a...

14 July - 18 July 2025

Proteomics bioinformatics

Barbara Etzi

This course provides hands on training in the basics of mass spectrometry MS and proteomics bioinformatics You will receive training on how to use search engines and post processing software quantitative approaches MS data repositories the use of public databases for protein analysis annotation of subsequent protein lists and incorporation of information from molecular interaction and pathway databases The practical elements of the course will take raw data from a proteomics experiment and analyse it You will be able to go from MS spectra to identifying and quantifying peptides and finally to obtaining lists of protein identifiers that can be analysed further using a wide range of resources The final aim is to provide you with the practical bioinformatics knowledge you need to go back to the lab and process your own data when collected This course is organised in association with the Vlaams Instituut voor Biotechnologie VIB the Flemish Institute for Biotechnology Pre recorded material may be provided before the course starts that you will need to watch read or work through to gain the most out of the actual training event... This course provides hands-on training in the basics of mass spectrometry (MS) and proteomics bioinformatics. You will receive training on how to use search engines and post-processing software, quantitative approaches, MS data repositories, the use of public databases for protein analysis, annotation of subsequent protein lists, and incorporation of information from molecular interaction and pathway databases.The practical elements of the course will take raw data from a proteomics experiment and analyse it. You will be able to go from MS spectra to identifying and quantifying peptides, and finally to obtaining lists of protein identifiers that can be analysed further using a wide range of resources. The final aim is to provide you with the practical bioinformatics knowledge you need to go back to the lab and process your own data when collected.This course is organised in association...

14 July - 18 July 2025

Fluorescence imaging beyond intensity

Luis Alvarez, Manuel Gunkel, Andrea Mülter

As fluorescence lifetime based readouts become more accessible this course aims to provide a broad understanding of how the lifetime based information can be leveraged to solve biological questions... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This course is organised in cooperation with Leica Microsystems. Course overview As fluorescence lifetime-based readouts become more accessible, this course aims to provide a broad understanding of how the lifetime-based information can be leveraged to solve biological questions. This application-centred course will provide insights into how this additional dimension of fluorescence information can help unveil functional and mechanistic information. Audience This course is aimed at PhD students and Post Docs with experience in fluorescence microscopy. It will enable them to better apply confocal fluorescence microscopy and in particular lifetime-based readouts to their cutting-edge research, disseminate their gained expertise to colleagues at their home institution and, eventually, to develop imaging...

15 July - 18 July 2025

Gene regulation: one molecule at a time

Stirling Churchman, Arnaud Krebs, Mounia Lagha, Daniel Larson

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview Gene expression is controlled by the dynamic action of dozens of macromolecular complexes that assemble on DNA to transcribe genes and translate mRNAs to proteins Understanding of these mechanisms has... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview Gene expression is controlled by the dynamic action of dozens of macromolecular complexes that assemble on DNA to transcribe genes and translate mRNAs to proteins. Understanding of these mechanisms has historically been driven by biochemical and structural characterisation of the players, as well as probing their function through genetic deletions. The genomics revolution has provided us with a near- comprehensive picture of where these factors bind to regulate the genome and which transcripts are processed in various biological contexts. A key limitation of the resulting models is that they are derived using data that are static by nature, unfaithfully representing the dynamics of these regulatory processes...

3 August - 8 August 2025

Drosophila genetics and genomics

Justin Crocker, Kate O’Connor-Giles, Ella Preger-Ben Noon, Andreas Prokop

The EMBO Practical Course on Drosophila genetics and genomics offers advanced conceptual overviews used to train Drosophila leaders for nearly 30 years paired with hands on introductions to cutting edge experimental techniques taught by experts in the field... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Course overview Drosophila as a model system has remained a powerful driver of biological research for over a century. Emergence of techniques like CRISPR-Cas9, next-generation sequencing, single-molecule(sm) FISH, and single-cell genomics have dramatically expanded the toolkit available for research in Drosophila. These techniques are now routinely applied to answer important knowledge gaps in developmental biology, cell biology, physiology, neurobiology, genome regulation, evolution, behavior and population genetics. This course will cover the latest advances in this direction through a combination of lectures delivered by world-renowned experts and hands-on practical sessions on the above topics delivered by excellent trainers – to help the participants rapidly absorb knowledge towards...

31 August - 5 September 2025

FISHing for RNAs: classical to single molecule approaches

Florence Besse, Imre Gaspar, Emerald Perlas, Elisabeth Zielonka

OverviewSpeakerPreliminary 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 Over the past decades it became evident that the specific amount and localisation of an RNA transcript are important to understand the biological function of its non... OverviewSpeakerPreliminary 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 Over the past decades, it became evident that the specific amount and localisation of an RNA transcript are important to understand the biological function of its (non-) coding gene. Whereby state-of-the-art in situ hybridisation (ISH) technologies are key to visualise these RNAs in a given tissue or cell. This course will teach participants to apply three powerful RNA visualisation techniques, all in histological tissue samples: conventional in situ hybridisation (ISH), hybridisation chain reaction ISH (HCR-ISH), and the cutting edge single molecule fluorescent ISH (smFISH). In addition, essential tissues embedding protocols adapted to facilitate...

3 September - 7 September 2025

Protein synthesis and translational control

Alfredo Castello, Christopher Fraser, Fatima Gebauer, Christian Spahn

This conference focuses on the process of protein synthesis from the molecular and structural understanding of the translational machinery to its regulation its implications in cell and organismal biology and its alteration in disease... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview Mechanisms that shape cellular proteomes are critical for life. This conference focuses on the process of protein synthesis, from the molecular and structural understanding of the translational machinery to its regulation, its implications in cell and organismal biology, and its alteration in disease. The regulation of mRNA translation is critical to maintaining cell homeostasis and mediates cellular responses to environmental, physiological, and pathological cues. Given the central importance of protein synthesis, it is unsurprising that dysregulation or defects in mRNA translation are widely linked to disease, including cancer, neurological or metabolic disorders, and viral infection. In recent...

9 September - 12 September 2025

Developmental metabolism: flows of energy, matter, and information

Alexander Aulehla, Heather Christofk, Heidi Lempradl, Jonathan Rodenfels

This meeting will create an intellectual space to exchange ideas across disciplines and help form a vibrant diverse community at the interphase between developmental biology molecular metabolism mathematics and physics... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview The fundamental question of the role of metabolism in development has seen a revival in interest over recent years, creating the need for the first edition of this workshop in 2023. This second edition is set to reunite the community two years on, and to ensure the ongoing interactions that can propel progress in developmental metabolism. In this rapidly advancing field, metabolomic methods play a crucial role in unraveling complex processes. The workshop will again aim to bring together researchers from diverse backgrounds: developmental biology, genetics, epigenetics, ecology, physics and math, to provide the developmental metabolism community with cutting-edge research and methodologies applied...

14 September - 19 September 2025

Methods for infectious disease modelling using genomics

Barbara Etzi

This EMBO Practical course will introduce concepts methods and tools for carrying out infectious disease modelling as well as for developing models further by leveraging the power of genomics Modelling infectious diseases can help to understand the mechanisms of pathogen evolution and predict the development of epidemics This had an immense impact on the COVID 19 pandemic and is crucial for the general surveillance of pathogens In this course participants will learn about compartmental models such as Susceptible Infectious Recovered SIR models how to adapt them to a pathogen of their interest and the differences between stochastic and deterministic models Taking this further participants will apply these models to epidemic settings in order to predict changes in case numbers and disease severity Additionally the participants will learn how to implement and adapt genomics informed models for pathogen evolution and they will learn how to make use of genomics to create timed phylogenies and reconstruct ancestral states Finally bringing together transmission modelling and genomic data participants will learn about phylodynamic models and how this can help to detect changes in case numbers and pathogenicity earlier and more reliably than with transmission models alone... This EMBO Practical course will introduce concepts, methods, and tools for carrying out infectious disease modelling, as well as for developing models further by leveraging the power of genomics. Modelling infectious diseases can help to understand the mechanisms of pathogen evolution and predict the development of epidemics. This had an immense impact on the COVID-19 pandemic and is crucial for the general surveillance of pathogens. In this course, participants will learn about compartmental models, such as Susceptible-Infectious-Recovered (SIR) models, how to adapt them to a pathogen of their interest, and the differences between stochastic and deterministic models. Taking this further, participants will apply these models to epidemic settings in order to predict changes in case numbers and disease severity. Additionally, the participants will learn how to implement and...

14 September - 19 September 2025

Advanced methods in bioimage analysis

Ignacio Arganda-Carreras, Anna Klemm, Perrine Paul-Gilloteaux, Christian Tischer

OverviewTrainers speakers staffPractical informationSponsorsMedia kit Overview This course will take place at EMBL Heidelberg with the option to attend virtually Course overview Bioimage analysis has become a keystone of biological research the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software... OverviewTrainers, speakers, staffPractical informationSponsorsMedia kit Overview This course will take place at EMBL Heidelberg, with the option to attend virtually. Course overview Bioimage analysis has become a keystone of biological research: the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data. Due to the complexity of the data, without such expert guidance, it is very likely that image analysis algorithms may be applied incorrectly, possibly even producing erroneous results. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly that even experts are overwhelmed. This advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis and will...

16 September - 19 September 2025

The human microbiome

Mani Arumugam, Ami Bhatt, Peer Bork, Nicola Segata

OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview Human microbiota the collection of microbes living in and on our body have a significant impact on human health and well being They have been associated with numerous diseases yet we... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview Human microbiota – the collection of microbes living in and on our body – have a significant impact on human health and well-being. They have been associated with numerous diseases, yet we are still far from understanding their role in the context of life-style and genetics. Various initiatives are underway around the world to survey the human microbiota at several body sites, characterize them, understand their interactions with the human hosts, elucidate their role in diseases, and design possible therapeutic or dietary interventions. Recent efforts have started mining the human microbiome data to discover bioactive compounds; detect interactions between microbes and molecules; and design...

29 September - 2 October 2025

NicE-RNA sequencing for multiomics on open chromatin and transcription

Vladimir Benes, Björn Textor

OverviewSponsorsMedia kit Overview Course overview This course will focus on the latest state of the art novel library preparation protocols We will start with experimental design focusing on hands on library preparation including best practices standards and potential pitfalls concluding with sequencing of libraries bioinformatic evaluation best practices Multiomic data in... OverviewSponsorsMedia kit Overview Course overview This course will focus on the latest state-of-the-art novel library preparation protocols. We will start with experimental design, focusing on hands-on library preparation (including best practices, standards, and potential pitfalls), concluding with sequencing of libraries, bioinformatic evaluation & best practices. Multiomic data in scientific projects have become more and more important. NicE-Seq is a novel method enabling detection of open chromatin in fixed low numbers of cells without any additional instrumentation. Combining open chromatin with transcriptome information is crucial for interpretation of cellular states. Therefore, the course participants will also prepare mRNA libraries from the same cell populations.  Participants will carry out a complete workflow, from isolation of DNA & RNA from fixed cells,...

6 October - 10 October 2025

Metagenomics bioinformatics at MGnify

EMBL-EBI Training

Learn about the tools processes and analysis approaches used by MGnify in the field of genome resolved metagenomics This course will cover the use of publicly available resources to manage share analyse and interpret metagenomics data focussing primarily on the assembly based approaches used in MGnify analysis The delivered content will involve participants learning via live lectures and presentations followed by live Q As with the trainers Practical experience will be developed in group activities and in computational exercises run using containerised tools on our training infrastructure This course is currently under development please check back again soon for further details... Learn about the tools, processes, and analysis approaches used by MGnify in the field of genome-resolved metagenomics. This course will cover the use of publicly available resources to manage, share, analyse, and interpret metagenomics data, focussing primarily on the assembly-based approaches used in MGnify analysis. The delivered content will involve participants learning via live lectures and presentations, followed by live Q&As with the trainers. Practical experience will be developed in group activities and in computational exercises run using containerised tools on our training infrastructure. This course is currently under development, please check back again soon for further details.

8 October - 11 October 2025

Seeing is believing: imaging the molecular processes of life

Jan Ellenberg, Jennifer Lippincott-Schwartz, Satyajit Mayor, Atsushi Miyawaki

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview The molecular processes of life are naturally dynamic in space and time from the atomic to the organismal level The rapid development of imaging methods across the full scale of biological... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview The molecular processes of life are naturally dynamic in space and time from the atomic to the organismal level. The rapid development of imaging methods across the full scale of biological organisation is revolutionising our ability to visualise the inner workings of macromolecular complexes, organelles, cells, tissues, organs and whole organisms. Being able to see biological processes unfold in real time allows us to understand the mechanisms of life as well as disease.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 emphasize methods that can capture the dynamics of...

13 October - 17 October 2025

Liquid biopsies

Anders Ståhlberg, Martin Dalin

OverviewSponsorsMedia kit Overview Registration is not yet open for this event If you are interested in receiving more information please register your interest Course Overview There is an increasing interest and need to analyse biomarkers in liquid biopsies including basic research and clinical applications Liquid biopsies have several advantages including being minimally invasive... OverviewSponsorsMedia kit Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview There is an increasing interest and need to analyse biomarkers in liquid biopsies, including basic research and clinical applications. Liquid biopsies have several advantages including being minimally invasive, allowing repeated sampling and sampling is often clinical routine. This course will provide an overview of the several techniques to detect and analyse liquid biopsy-based analytes such as circulating tumour cells, cell-free tumor-DNA (ctDNA), miRNA, extracellular vesicles, mRNA, carbohydrates and proteins. Participants will be introduced to all aspects ranging from proper sampling through analyte analysis and final data analysis. Experimentally, we will demonstrate ultrasensitive ctDNA analysis using...

14 October - 17 October 2025

Spatial biology: the melting pot

Sean Bendall, Leeat Keren, Arutha Kulasinghe, Sinem Saka, Denis Schapiro

This EMBL Conference offers the next generation of spatial biologists an opportunity to exchange with the scientists who develop and implement spatial technologies Renowned speakers will cover the latest advances in the field... OverviewSpeakersSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information, please register your interest. Overview This EMBL Conference, co-organised with the European Society for Spatial Biology (ESSB), builds on the momentum of the Society’s inaugural meeting in Berlin in December 2024. Spatial biology extends beyond analyzing the molecular composition of individual cells—it considers their spatial arrangement and interactions within complex tissues and organisms. This dynamic, interdisciplinary field integrates insights from medicine, biology, physics, computer science, and other disciplines to deepen our understanding of biological systems in health and disease. ​The meeting aims to bring together the rapidly growing academic community, fostering discussions on cutting-edge spatial technologies, innovative data analysis...

22 October - 25 October 2025

Organoids: modelling organ development and disease in 3D

Meritxell Huch, Karl R. Koehler, Madeline Lancaster, Esther Schnapp

The aim of this meeting is to bring together researchers from different fields to enhance our understanding of how organoids can be formed and maintained how they can be used to study disease and how we might eventually use them to regenerate and replace human organ tissue... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview The ability to grow tissues from stem cells in 3D culture to generate so-called organoids has revolutionised the study of tissue biology, especially human biology. This exciting technology has great potential for drug discovery and regenerative medicine. Because organoids model a variety of tissues with remarkably high fidelity, they allow for new discoveries in human development, homeostasis, regeneration, and disease. This symposium will bring together the leading researchers in this field, representing the premier conference for this research community, and providing a much-anticipated program that demonstrates how this field is truly pushing the boundaries for our understanding of tissue...

27 October - 31 October 2025

Structural bioinformatics

Juanita Riveros

This course provides a guide to the commonly used methods and tools in structural bioinformatics to analyse and interpret experimentally determined and AI predicted macromolecular structure data 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 and Artificial Intelligence AI assisted structure prediction enables life science researchers to address a wide variety of questions This course explores bioinformatics data resources and tools for the investigation analysis and interpretation of both experimentally determined and predicted 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 function and exploring interactions with other macromolecules This course is currently under development please check back again soon for further details... This course provides a guide to the commonly used methods and tools in structural bioinformatics to analyse and interpret experimentally determined and AI-predicted macromolecular structure data. 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 and Artificial Intelligence (AI)-assisted structure prediction enables life-science researchers to address a wide variety of questions.   This course explores bioinformatics data resources and tools for the investigation, analysis, and interpretation of both experimentally determined and predicted biomacromolecular structures. It will focus on how best to analyse and interpret available structural data to gain useful information given...

28 October - 30 October 2025

The epitranscriptome

Michaela Frye, Tsutomiu Suzuki, Chengqi Yi

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually 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... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. 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. Now, in its fourth edition, ‘The epitranscriptome’ meeting first held at EMBL in 2016 (and repeated in 2018, then in 2022 as a virtual conference) was the first RNA modification-dedicated meeting with a focus on mammalian systems. It is now established that biochemical...

4 November - 7 November 2025

The mobile genome: genetic and physiological impacts of transposable elements

Deborah Bourc'his, Josefa Gonzalez Perez, Joseph Peters, Julius Brennecke

OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview Disparaged as selfish DNA for decades it s now clear that transposable elements TEs underlie the remarkably dynamic nature of bacterial plant and animal genomes This conference builds on... OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview Disparaged as “selfish DNA” for decades, it’s now clear that transposable elements (TEs) underlie the remarkably dynamic nature of bacterial, plant, and animal genomes. This conference builds on the highly successful 2021 and 2023 Mobile Genome EMBO workshops and has emerged as the major European venue in this ever-growing cross-disciplinary research field. The 2025 Mobile Genome conference will assemble recognized experts from diverse disciplines (e.g., genomics, epigenetics, structural biology, evolutionary biology, and developmental biology), as well as the next generation of scientists who will become leaders in the field, to discuss the broad impact of TEs on organismal...

10 November - 14 November 2025

Hands-on flow cytometry: learning by doing!

Daniel Gimenes, Diana Ordonez, Steffen Schmitt

This course aims to provide a comprehensive understanding of the underlying principles of flow cytometry while also emphasising practical considerations related to the most frequently used assays... 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 a highly effective method for analysing individual cells that has become widely used in the fields of life sciences and medicine. By utilising flow cytometry, researchers can accurately identify and measure specific cell populations within complex mixtures, as well as assess cell cycle progression, proliferation status, and expression of fluorescent markers. Our course aims to provide a comprehensive understanding of the underlying principles of flow cytometry, while also emphasising practical considerations related to the most frequently used assays. Through a combination of theoretical instruction and hands-on training, students will gain the knowledge and skills necessary to effectively design,...

11 November - 14 November 2025

Cancer genomics

Kathleen Burns, Isidro Cortés-Ciriano, Mariam Jamal-Hanjani, Young Seok Ju

OverviewSpeakersPreliminary programmePractical informationSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Registration is not yet open for this event If you are interested in receiving more information please register your interest Conference overview This conference will provide an opportunity to learn about and keep up to... OverviewSpeakersPreliminary programmePractical informationSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference overview This conference will provide an opportunity to learn about and keep up to date with the 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, and the translation and clinical impact of scientific results. The meeting will bring together leading scientists and academic clinicians from across these areas for a unique opportunity to interact and stimulate further integration of these efforts. What past participants say about the conference...

17 November - 21 November 2025

Solution scattering from biological macromolecules

Clement Blanchet, Melissa Gräwert, Tobias Gräwert, Annette Langkilde

The course is aimed at young biochemists biophysicists and researchers active in related structural methods with little or no experience in solution scattering... OverviewSponsorsMedia kit 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 consists of two parts: a virtual module and an on-site module. The series of online lectures will take place from 6 – 10 October 2025. In addition to this, a small number of selected students that have completed the virtual module will be offered to take part in the practical component of this course that will take place in Hamburg from 17 – 21 November 2025. Small-angle scattering (SAS) is an analytical technique that provides insights into the conformation of biological macromolecules over various length scales: from small polymers to large assemblies. The macromolecules (including proteins, lipids, and nucleic acids) are measured in solution, so in their quasi-native...

17 November - 21 November 2025

Genome bioinformatics: from short- to long-read sequencing

EMBL-EBI Training

A guide to the technology analysis workflows tools and resources for next generation sequencing data analysis This course will provide insights and training into how biological knowledge can be derived from genomics experiments and explain different approaches in analysing such data The main focus will be on introducing sequence informatics re sequencing differences between short and long read sequencing and variant calling during the analysis of higher eukaryotes with an emphasis on human genetic research Throughout the week more advanced topics will introduce the creation of pipelines automation and the scaling up of analysis experiments Practical sessions will be run on datasets prepared by the trainers not on personal research data Participants will learn how to process these training datasets and to apply appropriate statistical methods in their analyses This course is currently under development please check back again soon for further details... A guide to the technology, analysis workflows, tools, and resources for next-generation sequencing data analysis. This course will provide insights and training into how biological knowledge can be derived from genomics experiments and explain different approaches in analysing such data. The main focus will be on introducing sequence informatics, re-sequencing, differences between short- and long-read sequencing, and variant calling during the analysis of higher-eukaryotes, with an emphasis on human genetic research. Throughout the week, more advanced topics will introduce the creation of pipelines, automation, and the scaling-up of analysis experiments. Practical sessions will be run on datasets prepared by the trainers, not on personal research data. Participants will learn how to process these training datasets and to apply appropriate statistical methods in their analyses....

18 November - 21 November 2025

Cell biology of the nucleus

Simone Koehler, Patrick Lusk, Thomas Quail, Sara Wickström

OverviewSpeakersPractical informationSponsorsMedia Kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview The nucleus houses the genome and plays a central role in all cellular processes Over the last decade advances in modern genomics have provided important insight into 3D genome organisation but the underlying cell... OverviewSpeakersPractical informationSponsorsMedia Kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview The nucleus houses the genome and plays a central role in all cellular processes. Over the last decade, advances in modern genomics have provided important insight into 3D genome organisation but the underlying cell biology of the nucleus is often not considered. The nucleus is not just a passive scaffold for the genome: it is a highly dynamic organelle with a suite of unique mechanisms that help control its biochemical compartmentalization, its integration into both intra and extracellular mechanical networks, and its response to pathological and environmental insults. The goal of this conference is to showcase the cell biological mechanisms that define the nucleus as an organelle. To meet this goal, we intend to...

23 November - 28 November 2025

Volume electron microscopy by automated serial SEM

Christel Genoud, Amanda Lewis, Paolo Ronchi, Yannick Schwab

This course will further contribute to disseminating knowledge on fast evolving techniques to a growing community of vEM users and service providers... OverviewSponsors Overview Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course overview Recent developments in scanning electron microscopes (SEM) have led to ground-breaking opportunities in volume imaging of cells and tissues. This course aims to provide extensive theoretical and practical knowledge on the three main techniques for volume EM based on SEM: microtome-based serial block-face SEM, focused ion beam SEM, and array tomography. The participants will be able to assess the potential of each technique to understand which fits best with their own projects, and acquire the theoretical background to understand the different techniques as well as how to optimize the imaging conditions, the data processing, analysis and management.  This course will further contribute to disseminating knowledge on...

2 December - 5 December 2025

Computational structural biology

Rommie Amaro, Charlotte Deane, Jan Kosinski, Christine Orengo, Sameer Velankar

This conference will update on the impact of AI based structure prediction provide a forum to present new methods and applications build a wider community by integrating the new scientists now massively joining the field and open a platform to discuss future directions and opportunities... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Conference overview This second edition of the EMBO “Computational Structural Biology” workshop builds on the success of the 2023 meeting. It aims to present and discuss advancements in computational studies of biomolecular structures, functions, and interactions, encompassing AI-driven innovations and classical methods while exploring future directions in the field. The program offers a diverse range of sessions covering key topics, from molecular modeling to systems-level analyses and evolution. New sessions for 2025 include drug design, focusing on computational approaches in therapeutic innovation, and infrastructures and software platforms, highlighting the technological frameworks essential for computational...

7 December - 12 December 2025

Genome engineering: CRISPR/Cas in cells and mice

Silke Deckert, Neil Humphreys, Kristof Kersse, Birgit Koch, Elisabeth Zielonka

OverviewSponsorsMedia kit 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 provide 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... OverviewSponsorsMedia kit 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 provide 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. Please note that all participants are expected to engage in all sessions. Participants should plan for approximately 1 hour extra per day for self paced learning modules. Audience This course is aimed at researchers who are familiar with basic molecular and cell biology...

8 December - 10 December 2025

Managing a bioinformatics core facility

EMBL-EBI Training

This knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL EBI s service teams and from each other These facilities play an essential role in enabling research in the molecular life sciences The landscape is constantly evolving as new research tools emerge as experiments become increasingly data intensive and as their clients experimental researchers become more exposed to the power of data driven biology This course will allow participants to share experiences discuss challenges and solutions that they face and plan ways to cope with the ever changing demands raised by the molecular life science field It will include sessions to learn from bioinformatics service providers hear how others have tackled common problems and work together to design core services resource them and measure their impact This course is currently under development please check back again soon for further details... This knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL-EBI’s service teams, and from each other. These facilities play an essential role in enabling research in the molecular life sciences. The landscape is constantly evolving as new research tools emerge, as experiments become increasingly data-intensive, and as their clients – experimental researchers – become more exposed to the power of data-driven biology. This course will allow participants to share experiences, discuss challenges and solutions that they face, and plan ways to cope with the ever-changing demands raised by the molecular life science field. It will include sessions to learn from bioinformatics service providers, hear how others have tackled common problems, and work together to design core services, resource them, and measure their impact. This course is...

2 February - 6 February 2026

Single-cell RNA-seq analysis with Python

EMBL-EBI Training

This course covers the analysis of single cell RNA sequencing scRNA seq data using Python and command line tools Participants will be guided through droplet based scRNA seq analysis pipelines from raw reads to cell clusters You will explore and interpret single cell RNA seq data using Python as well as the Single Cell Expression Atlas Finally you will put their knowledge into practice through a group challenge on the last day This course is currently under development please check back again soon for further details You can find more information about the previous iteration of this course here Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack... This course covers the analysis of single cell RNA sequencing (scRNA-seq) data using Python and command line tools. Participants will be guided through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. You will explore and interpret single-cell RNA seq data using Python as well as the Single Cell Expression Atlas. Finally, you will put their knowledge into practice through a group challenge on the last day.This course is currently under development, please check back again soon for further details. You can find more information about the previous iteration of this course here. Virtual courseParticipants 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...

9 February - 13 February 2026

Introduction to RNA-seq and functional interpretation

EMBL-EBI Training

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 This course is currently under development please check back again soon for further details You can find more information about the previous iteration of this course here Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack... 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.This course is currently under development, please check back again soon for further details. You can find more information about the previous iteration of this course here. Virtual courseParticipants will learn via a mix of pre-recorded...

16 February - 19 February 2026

The new cardiobiology: engineering, vascular, and molecular insights

Johannes Backs, Roger Foo, Kristina Haase, Sara S. Nunes de Vasconcelos

This next edition will focus on cardiovascular regeneration modeling the cardiovascular system in synthetic 3D multicellular systems cardiometabolic mechanisms leading to both vascular and cardiac complications the contribution of cardiovascular communication to multi organ disease and on new translational breakthroughs... OverviewSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference overview The dysfunction of the cardiovascular system is the leading cause of human mortality. New molecular and engineering approaches are revolutionising cardiovascular discovery research. For instance in vivo and human cell-based 2D and 3D disease modeling is today more closely mimicking the human situation and is leaving its infancy.These developments led to the concept of “The new cardiobiology” (NCB) conference that took place the first time in 2024. Due to the success of the first meeting and due to further advances in studying the multicellularity and the development of cardiovascular engineering approaches, we will...

24 February - 27 February 2026

Collectivity in living systems: emergence, function, and evolution

Tomás Alarcón, Bernat Corominas-Murtra, Jordi van Gestel, Nicoletta Petridou, Allyson Sgro

OverviewSpeakersSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Registration is not yet open for this event If you are interested in receiving more information please register your interest Symposium overview Many of life s most fascinating phenomena emerge from interactions among its building blocks The... OverviewSpeakersSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Many of life’s most fascinating phenomena emerge from interactions among its building blocks. The initiation of a heartbeat, the formation of bird flocks or the appearance of several pathologies can be explained with surprising accuracy through simple and universal principles arising from the interactions of the microscopic constituents of the system. Understanding how collective behaviour propagates across levels in biological systems – from cells, tissues, organs, organisms to animal groups – becomes, in consequence, a key and pressing issue lying at the core of the understanding of living systems. This...

2 March - 6 March 2026

Introduction to multi-omics data integration and visualisation

EMBL-EBI Training

With the increase in the volume of data across the whole spectrum of biology more opportunities as well as challenges have been created to identify novel perspectives and answer questions in life sciences This may also include public domain data which can provide added value to data derived through the researcher s own work and inform experimental design This course is currently under development please check back again soon for further details You can find more information about the previous iteration of this course here... With the increase in the volume of data across the whole spectrum of biology, more opportunities, as well as challenges, have been created to identify novel perspectives and answer questions in life sciences. This may also include public domain data, which can provide added value to data derived through the researcher’s own work and inform experimental design. This course is currently under development, please check back again soon for further details. You can find more information about the previous iteration of this course here.  

16 March - 20 March 2026

Microscopy data analysis: machine learning and the BioImage Archive

EMBL-EBI Training

This virtual course will show how public bioimaging data resources centred around the BioImage Archive enable and enhance machine learning based image analysis The content will explore a variety of data types including electron and light microscopy and miscellaneous or multi modal imaging data at the cell and tissue scale Participants will cover contemporary biological image analysis with an emphasis on machine learning methods as well as how to access and use images from databases This course is currently under development please check back again soon for further details You can find more information about the previous iteration of this course here Virtual courseThis 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 sessions all fully password protected with automated English closed captioning and transcription with support and both scientific and social networking opportunities provided by Slack and other methods taking different time zones into account... This virtual course will show how public bioimaging data resources, centred around the BioImage Archive, enable and enhance machine learning based image analysis. The content will explore a variety of data types including electron and light microscopy and miscellaneous or multi-modal imaging data at the cell and tissue scale. Participants will cover contemporary biological image analysis with an emphasis on machine learning methods, as well as how to access and use images from databases. This course is currently under development, please check back again soon for further details. You can find more information about the previous iteration of this course here. Virtual courseThis 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 sessions (all fully password...

17 March - 20 March 2026

The cellular mechanics of symbiosis: sensing friend from foe

Aileen Berasategui, Thomas Richards, Hassan Salem, Flora Vincent

OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Registration is not yet open for this event If you are interested in receiving more information please register your interest Symposium overview Host microbe interactions can be positive or negative for both a host organism and its symbiotic microbes Interacting... OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Host-microbe interactions can be positive or negative for both a host organism and its symbiotic microbes. Interacting with microbes can allow eukaryotes to acquire crucial functions such as metabolite synthesis or production of defensive chemicals. However, such interactions are often pathogenic in nature. This cross-disciplinary meeting will bring together scientists using cellular, molecular, ecological, physiological, and theory-based approaches to explore the evolution of intimate species-species interactions. The aim is to understand the cellular systems, metabolic pathways and ecological circumstances that drive...

13 April - 17 April 2026

Data-driven approaches to understanding dementia

EMBL-EBI Training

This course provides individuals working in dementia research with the skills to access and analyse dementia data Participants will learn to apply bioinformatics methodologies combine different data types and utilise relevant dementia data resources enhancing their research capabilities in the field This course is currently under development please check back again soon for further details You can find more information about the previous iteration of this course here... This course provides individuals working in dementia research with the skills to access and analyse dementia data. Participants will learn to apply bioinformatics methodologies, combine different data types, and utilise relevant dementia data resources, enhancing their research capabilities in the field.This course is currently under development, please check back again soon for further details. You can find more information about the previous iteration of this course here. 

27 April - 30 April 2026

Sex differences in health and disease

Brian Aguado, Kristina Haase, Edith Heard, Irene Miguel-Aliaga

OverviewSpeakersSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Registration is not yet open for this event If you are interested in receiving more information please register your interest Symposium overview Sex differences range from distinct dimorphisms in appearance and physiology to behaviour variations... OverviewSpeakersSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Sex differences range from distinct dimorphisms in appearance and physiology to behaviour variations across males and females of the same species. These differences are numerous and varied and are often driven by combinations of genetic, hormonal and environmental factors. These differences also appear in manifestations of infectious disease, ageing and age-related diseases (cancer, cardiovascular and neurodegenerative diseases). Response to treatments can also vary drastically between females and males. Despite these wide-spread differences between sexes observed across species, the underlying mechanisms are...

27 April - 1 May 2026

Introduction to metabolomics analysis

EMBL-EBI Training

This course will provide an introduction to metabolomics through lectures and hands on sessions using publicly available data software and tools Participants will become familiar with standardised workflows as well as with the current state of experimental design data acquisition LC MS MS imaging processing and modelling In addition they will learn about community standards and sharing in metabolomics particularly through the use of EMBL EBI s MetaboLights repository and Galaxy infrastructure Participants will learn through hands on tutorials to use tools available for data analysis and data submission Additionally case studies will be discussed to show how to employ the week s learning This course is currently under development please check back again soon for further details You can find more information about the previous iteration of this course here... This course will provide an introduction to metabolomics through lectures and hands-on sessions, using publicly available data, software, and tools. Participants will become familiar with standardised workflows as well as with the current state of experimental design, data acquisition (LC-MS, MS imaging), processing, and modelling. In addition, they will learn about community standards and sharing in metabolomics, particularly through the use of EMBL-EBI’s MetaboLights repository and Galaxy infrastructure. Participants will learn through hands-on tutorials to use tools available for data analysis and data submission. Additionally, case studies will be discussed to show how to employ the week’s learning.This course is currently under development, please check back again soon for further details. You can find more information about the previous iteration of this course here. 

9 June - 12 June 2026

Mechanobiology across the tree of life

Alba Diz-Munoz, Nicoletta Petridou, Enrique Rojas, Xavier Trepat, Kirsty Wan

OverviewAboutSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Registration is not yet open for this event If you are interested in receiving more information please register your interest Symposium overview How do cells and tissues build themselves and respond to their environment Over the past decade it has become... OverviewAboutSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview How do cells and tissues build themselves and respond to their environment? Over the past decade it has become clear that physico-chemical properties are rapidly modulated to accommodate or drive changes in shape or behavior and to exchange matter and information with the environment. Solving the grand challenges of this field requires integrating expertise from biology, physics, and engineering. Furthermore, understanding which processes are system-specific and which represent generalizable principles requires us to use the lens of evolution to compare across the tree of life. Responding to this important challenge,...

21 July - 24 July 2026

Metabolic interactions shape ecosystems

Kathrin Fenner, Diane Newman, Mohammad R. Seyedsayamdost, Michael Zimmermann

OverviewSponsorsAboutMedia Kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Registration is not yet open for this event If you are interested in receiving more information please register your interest Symposium overview Metabolic interactions shape all kind biological ecosystems from holobionts to planetary scale environmental... OverviewSponsorsAboutMedia Kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Metabolic interactions shape all kind biological ecosystems, from holobionts to planetary-scale environmental systems, and to anthropogenic, engineered environments. Their paramount importance is evident by a pervasive influence on the development, resilience, and sustainability of ecosystems. In environmental systems, whether marine or land ones, understanding metabolic interactions is key to deciphering nutrient cycling, carbon sequestration, and overall ecosystem functioning. Recognizing the interconnectedness of these metabolic networks is crucial for advancing our comprehension of ecosystem dynamics and for...