EMBL Events

31 January - 1 February 2023

EuroFAANG GENE-SWitCH workshop: utilisation of GENE-SWitCH data in Ensembl and beyond

Peter Harrison

This one and a half day workshop will provide detailed training on the utilisation of the wealth of data generated by the EuroFAANG GENE SWitCH project that is delivering new underpinning knowledge for pig and chicken agriculture The workshop will primarily focus on the comprehensive and integrated annotation of the chicken and pig genomes by the Ensembl Genome Browser The course will also include a deeper dive from the Ensembl analysis teams into gene annotation and regulation and demonstrations of the specific analyses and genomic prediction models generated by GENE SWitCH researchers... This one and a half day workshop will provide detailed training on the utilisation of the wealth of data generated by the EuroFAANG GENE-SWitCH project that is delivering new underpinning knowledge for pig and chicken agriculture. The workshop will primarily focus on the comprehensive and integrated annotation of the chicken and pig genomes by the Ensembl Genome Browser. The course will also include a deeper dive from the Ensembl analysis teams into gene annotation and regulation, and demonstrations of the specific analyses and genomic prediction models generated by GENE-SWitCH researchers.  

31 January 2023

Federated analysis for polygenic risk score calculations

Will Rayner, Anshika Chowdhary

Polygenic risk scores PRS provide an estimate of an individual s disposition to a trait or complex disease which are calculated as the sum of the risk alleles weighted by the effect size estimate of the genome wide association study data on the phenotype PRS scores help in understanding the shared aetiology of certain traits and also in risk prediction and prevention of certain diseases As a part of the CINECA project we have been working on the development of a demonstrator of federated genetic analyses utilising a computational pipeline for PRS analysis We have implemented this workflow using Nextflow a modular and reproducible workflow manager that can be deployed and autoscaled to many different working environments including Slurm based clusters and Kubernetes deployed using AWS amongst other computing environments In this webinar we will provide an overview of this PRS pipeline utilising the CINECA UK1 synthetic dataset derived from the 1000 genomes project as a demonstrator As part of the work we will further extend the demonstrator to other datasets and GWAS workflows and integrate it to be run in a federated setting utilising the GA4GH guidelines on using Beacons for data discovery along with AAI passports for data access authorisation and deployments The CINECA Common Infrastructure for National Cohorts in Europe Canada and Africa project aims to develop a federated cloud enabled infrastructure to make population scale genomic and biomolecular data accessible across international borders to accelerate research and improve the health of individuals across continents About the speakers Will Rayner is the head of the Data and Analytics group at the Institute of Translational Genomics in the Computational Health Department at Helmholtz Munich He is interested in all aspects of data management and data privacy and has been leading the CINECA WP4 PRS use case Anshika Chowdhary is a Data informatician at the Institute of translational genomics in Helmholtz Zentrum Munich She has been working on the development of the workflows in WP4 of the PRS use case and analysis of the eQTL catalog on the datasets at HMGU... Polygenic risk scores (PRS) provide an estimate of an individual’s disposition to a trait or complex disease which are calculated as the sum of the risk alleles weighted by the effect size estimate of the genome-wide association study data on the phenotype. PRS scores help in understanding the shared aetiology of certain traits and also in risk prediction and prevention of certain diseases.   As a part of the CINECA project we have been working on the development of a demonstrator of federated genetic analyses utilising a computational pipeline for PRS analysis. We have implemented this workflow using Nextflow, a modular and reproducible workflow manager that can be deployed and autoscaled to many different working environments including Slurm-based clusters and Kubernetes deployed using AWS amongst other computing environments. In this webinar, we will provide an overview of this...

1 February 2023

Exploring reproducible and reusable systems biology models with BioModels

Rahuman Sheriff Malik Sheriff

This webinar will give an overview of BioModels a popular repository of curated systems biology models This will include a recent update on model content and features It will also briefly introduce BioModels Parameters a sub resource within BioModels that provides model parts It will show how modellers can easily find access and reuse interoperable systems biology models We will also discuss how curation efforts in BioModels tackle the reproducibility crisis... This webinar will give an overview of BioModels, a popular repository of curated systems biology models. This will include a recent update on model content and features. It will also briefly introduce BioModels Parameters, a sub-resource within BioModels that provides model parts. It will show how modellers can easily find, access and reuse, interoperable systems biology models.  We will also discuss how curation efforts in BioModels tackle the reproducibility crisis.

6 February - 10 February 2023

Single-cell RNA-seq analysis using Galaxy

Jane Reynolds

This course utilises Galaxy pipelines an online open access resource that allows even the most computer phobic bench scientists to analyse their biological data Participants will be guided through the droplet based scRNA seq analysis pipelines from raw reads to trajectories Please note that although participants will not be able to use their own data during the course practicals there will be ample time to discuss their research and ideas with both course participants and trainers As part of this participants will present posters on their research topics Virtual course This course will now be held virtually it was previously advertised as an on site course Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic Participants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Trainers will be available to assist answer questions and provide further explanations during the course... This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to trajectories. Please note that although participants will not be able to use their own data during the course practicals, there will be ample time to discuss their research and ideas with both course participants and trainers.  As part of this, participants will present posters on their research topics. Virtual course This course will now be held virtually, it was previously advertised as an on-site course. Hybrid options are not currently available. We reserve the right to change the format of this course or cancel it, due to the ongoing coronavirus pandemic. Participants will learn via a mix of pre-recorded lectures,...

8 February - 11 February 2023

In situ structural biology: from cryo-EM to multi-scale modelling

Martin Beck, Jan Kosinski, Julia Mahamid, Suliana Manley

There is an increasing awareness that mechanistic structural information on molecular machines is ideally generated within the context of intact cells in order to fully grasp how they function in a complex native environment Recent technological advances have nurtured the development of such in situ structural biology approaches in several disciplines including cryo EM mass spectrometry super resolution microscopy NMR computational modelling and others This conference will bring together experts and early stage researchers from these separate fields... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Workshop overview There is an increasing awareness that mechanistic structural information on molecular machines is ideally generated within the context of intact cells in order to fully grasp how they function in a complex native environment. Recent technological advances have nurtured the development of such in situ structural biology approaches in several disciplines, including cryo-EM, mass spectrometry, super-resolution microscopy, NMR, computational modelling and others. This conference will bring together experts and early stage researchers from the separate fields to provide a platform for structural...

8 February 2023

Data submission for genome-wide association studies at the GWAS Catalog

Elliot Sollis

The GWAS Catalog is a major repository for full summary statistics from genome wide association studies We encourage authors to submit their data to us to make them accessible and reusable by the wider GWAS community In 2023 we are introducing some improvements to the submission process to enhance the precision and reusability of the data we collect This webinar provides a step by step guide to the submission process including recent changes to the standard summary statistics format... The GWAS Catalog is a major repository for full summary statistics from genome-wide association studies. We encourage authors to submit their data to us, to make them accessible and reusable by the wider GWAS community. In 2023, we are introducing some improvements to the submission process to enhance the precision and reusability of the data we collect. This webinar provides a step-by-step guide to the submission process, including recent changes to the standard summary statistics format.

9 February 2023

The case of data reuse: ethical, legal, and societal issues in international genomic data access and sharing

Melanie Goisauf, Emmanuelle Rial-Sebbag

Health data collected in cohort studies are valuable sources for knowledge generation and the advance of biomedical research However the use of these data for research projects beyond the initial purpose raises several ethical legal and societal questions regarding the sensitivity of genomic data sourced from vulnerable and ethnic groups such as African genetic data and material The webinar addresses these challenges regarding reuse of health genomic data in CINECA from the ELSI perspective and FAIR principles and highlights GDPR provisions and their institutional sources of interpretation national laws the corresponding legal ethical and social science literature as well as outcomes from stakeholder engagement workshops with patient representatives African researchers and CINECA technical experts The webinar provides ethical and legal recommendations that take societal implications into account for data access to European Canadian and African cohorts and responsible sharing mainly on four key areas 1 Engagement and benefit sharing as prerequisites for data sharing 2 Informed consent and reuse of data 3 Safeguards and respect for privacy and 4 Further uses and data access The webinar concludes with an outlook on upcoming ELSI developments regarding data reuse synthetic data and artificial intelligence AI... Health data collected in cohort studies are valuable sources for knowledge generation and the advance of biomedical research. However, the use of these data for research projects beyond the initial purpose raises several ethical, legal, and societal questions regarding the sensitivity of genomic data sourced from vulnerable and ethnic groups, such as African genetic data and material. The webinar addresses these challenges regarding reuse of health/genomic data in CINECA from the ELSI perspective and FAIR principles, and highlights GDPR provisions and their institutional sources of interpretation, national laws, the corresponding legal, ethical, and social science literature, as well as outcomes from stakeholder engagement workshops with patient representatives, African researchers, and CINECA technical experts. The webinar provides ethical and legal recommendations that take societal...

10 February 2023

Accessing human disease and protein variant information in UniProtKB

Yvonne Lussi

UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive high quality and freely accessible resource of protein sequence and functional information This webinar will provide an overview on how to access human disease and protein variant information available in UniProtKB The annotation of protein molecular function involvement in human disease as well as disease associated variant positions variant characterisation and their impact on protein structure and function will be outlined Protein variant information will be presented in tabular view or in the feature viewer and shown how the feature viewer facilitates visualising the impact of variants on protein features and 3D structure Cross links to human specific databases and other relevant resources will be briefly discussed In addition it will be demonstrated how to access and download human variation datasets available in UniProtKB We hope that this introduction will give you an understanding of how to access disease related protein data in UniProtKB and how to make use of the different protein molecular data to analyse protein variant impact on protein function and structure... UniProt knowledgebase (UniProtKB) supports biomedical research by providing a comprehensive, high-quality, and freely accessible resource of protein sequence and functional information. This webinar will provide an overview on how to access human disease and protein variant information available in UniProtKB. The annotation of protein molecular function, involvement in human disease, as well as disease-associated variant positions, variant characterisation and their impact on protein structure and function will be outlined. Protein variant information will be presented in tabular view or in the feature viewer and shown how the feature viewer facilitates visualising the impact of variants on protein features and 3D structure. Cross-links to human-specific databases and other relevant resources will be briefly discussed. In addition, it will be demonstrated how to access and download human...

12 February - 17 February 2023

In situ CLEM at room temperature and in cryo

Ori Avinoam, Rachel Mellwig, Martin Schorb

Correlative Light and Electron Microscopy CLEM allows precise localisation of an event of interest within cells and tissues During this course we will focus on a specific method that has been developed at EMBL that enables the location of fluorescent proteins with high accuracy at the ultrastructural level The course will cover both the theory and practicals of high precision CLEM as well as opportunities to discuss their research with CLEM experts and receive practical and troubleshooting advice... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview Correlative Light and Electron Microscopy (CLEM) allows precise localisation of an event of interest within cells and tissues. During this course, we will focus on a specific method that has been developed at EMBL that enables the localisation of fluorescent proteins with high accuracy at the ultrastructural level. The course will cover both the theory and practicals of high precision CLEM, as well as opportunities to discuss their research with CLEM experts and receive practical and troubleshooting advice. Audience This course is intended for scientists with experience in EM who want to further develop their skills in high-accuracy correlated microscopy. Modules/resources The course will...

20 February - 24 February 2023

Introduction to RNA-seq and functional interpretation

Sophie Spencer

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 In person course We plan to deliver this course in person in our training suite at EMBL EBI Hinxton Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing... 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. In-person course We plan to deliver this course in-person in our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at...

22 February 2023

Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models

St. Elmo Wilken

Metabolic models are typically characterised by a large number of parameters Traditionally metabolic control analysis has been applied to differential equation based models to investigate the sensitivity of predictions to parameters A corresponding theory for constraint based metabolic models is lacking due to their formulation as optimization problems In this webinar we will show several applications of differentiating optimal solutions of constraint based models and show how it connects to classic metabolic control analysis Efficient differentiation of constraint based models can be used to calculate the sensitivities of predicted reaction fluxes and enzyme concentrations to turnover number parameters in an enzyme constrained metabolic model of Escherichia coli Further it unlocks the ability to use gradient information for parameter estimation We demonstrate this by improving genome wide the state of the art turnover number estimates for E coli Finally this technique can be used to differentiate the optimal solution of a model incorporating both thermodynamic and kinetic rate equations The predicted growth rate sensitivity to metabolite concentrations was shown to align well against experimentally measured metabolome changes subject to gene knockouts About the speaker St Elmo Wilken completed his undergraduate degree in Chemical Engineering at the University of Pretoria His Ph D at the University of California Santa Barbara leveraged both computational and wet lab aspects to investigate and understand the metabolism of anaerobic gut fungi His current postdoc at the Institute of Quantitative and Theoretical Biology at the Heinrich Heine University in D sseldorf is focused on using quantitative models to elucidate the contribution of metabolism to the stability and composition of microbial consortia He partnered with PerMedCoE researchers including Dr Miroslav Kratochvil to develop a way to differentiate constraint based models to conduct sensitivity analyses efficiently... Metabolic models are typically characterised by a large number of parameters. Traditionally, metabolic control analysis has been applied to differential equation-based models to investigate the sensitivity of predictions to parameters. A corresponding theory for constraint-based metabolic models is lacking due to their formulation as optimization problems. In this webinar we will show several applications of differentiating optimal solutions of constraint-based models, and show how it connects to classic metabolic control analysis. Efficient differentiation of constraint-based models can be used to calculate the sensitivities of predicted reaction fluxes and enzyme concentrations to turnover number parameters in an enzyme-constrained metabolic model of Escherichia coli. Further, it unlocks the ability to use gradient information for parameter estimation. We demonstrate this by...

22 February 2023

Accessing variant data at the European Variation Archive

Baron Koylass

The European Variation Archive EVA is a primary open repository for archiving accessioning and distributing genome variation including single nucleotide variants short insertions and deletions indels and larger structural variants SVs in any species This webinar will demonstrate how to access the latest EVA release consisting of submitted variants clustered into RS IDs It will also provide an overview of the recent updates to this data including what species have had their variant data remapped and how we annotate remapped variant data... The European Variation Archive (EVA) is a primary open repository for archiving, accessioning, and distributing genome variation including single nucleotide variants, short insertions and deletions (indels), and larger structural variants (SVs) in any species. This webinar will demonstrate how to access the latest EVA release, consisting of submitted variants clustered into RS IDs. It will also provide an overview of the recent updates to this data including what species have had their variant data remapped and how we annotate remapped variant data.

26 February - 3 March 2023

Analysis and integration of transcriptome and proteome data

Vladimir Benes, Raffaele Calogero, Jeroen Krijgsveld, Lennart Martens

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course 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... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. 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...

1 March 2023

Exploring plant genes and genomes with Ensembl

Guy Naamati

The Ensembl Plants genome browser provides visualisation and analysis of integrated genomic data including genes variants comparative genomics and gene regulation for over 100 plant species and cultivars This webinar will provide an overview of the range of available data and through Ensembl Plants and use examples to explore the various interfaces for visualising and exporting data... The Ensembl Plants genome browser provides visualisation and analysis of integrated genomic data, including genes, variants, comparative genomics and gene regulation, for over 100 plant species and cultivars. This webinar will provide an overview of the range of available data and through Ensembl Plants and use examples to explore the various interfaces for visualising and exporting data.  

5 March - 10 March 2023

Techniques for mammary gland research

Martin Jechlinger, Renée van Amerongen, María dM Vivanco

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview The mammary epithelium is a unique organ in that the majority of its development occurs postnatally This combined with ease of experimental access and a stereotypical growth pattern make it... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview The mammary epithelium is a unique organ in that the majority of its development occurs postnatally. This, combined with ease of experimental access and a stereotypical growth pattern, make it an ideal tissue for studying cellular homeostasis, branching morphogenesis, hormonal effects, stem cell biology and breast cancer. This theoretical and practical course will present techniques for the dissection and dissociation of different subpopulations of both mouse and human mammary cells, including stem/progenitor cells. It will also include flow cytometry to separate single cell populations for the consequent in vitro (mammosphere and 3D cultures) and in vivo...

6 March - 10 March 2023

Introduction to multiomics data integration and visualisation

Shereen Pethania

With the increase in the volume of data across the whole spectrum of biology more opportunities as well as challenges have been created to identify novel perspectives and answer questions in life sciences This may also include public domain data which can provide added value to data derived through researcher s own work and inform experimental design This introductory course will highlight the challenges that researchers face in integrating multiomics data sets using biological examples The course will focus on the use of public data resources and open access tools for enabling integrated working with an emphasis on data visualisation This course will not include systems biology modelling or machine learning A major element of this course is a group project where participants will be placed in small groups to work together on a challenge set by trainers from EMBL EBI data resource and research teams This allows people to explore the bioinformatics tools and resources introduced in the course and to apply these to a set problem providing hands on experience of relevance to their own research The group work will culminate in a presentation session involving all participants on the final day of the course giving an opportunity for wider discussion on the benefits and challenges of integrating data You may refer to the previous group projects that were organised for this course in March 2022 Additional information The course fee is inclusive of four nights accommodation and catering including dinner We plan to deliver this course in an in person manner onsite at our training suite at EMBL EBI Hinxton Hybrid options are not currently available Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing Please also note that there are delays in the issuing of visas from the UK Government We encourage you to check if you need a visa and apply in plenty of time before travelling Current waiting times are more than six weeks For more information please visit the UK Government website... With the increase in the volume of data across the whole spectrum of biology, more opportunities as well as challenges have been created to identify novel perspectives and answer questions in life sciences. This may also include public domain data, which can provide added value to data derived through researcher’s own work and inform experimental design. This introductory course will highlight the challenges that researchers face in integrating multiomics data sets using biological examples. The course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation. This course will not include systems biology modelling or machine learning. A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI data...

7 March - 8 March 2023

Introduction to HPC for Life Scientists

Marta Lloret Llinares

High performance computing HPC is a fundamental technology used to solve a wide range of scientific research problems Many important challenges in science such as protein folding drug discovery and tumour evolution all depend on simulations models and analyses run on HPC facilities to make progress This course introduces HPC to life science researchers focusing on the aspects that are most important for those new to this technology to understand It will help you judge how HPC can best benefit your research and equip you to go on to successfully and efficiently make use of HPC facilities in future The course will cover basic concepts in HPC hardware software user environments filesystems and programming models It also provides an opportunity to gain hands on practical experience and assistance using an HPC system MARENOSTRUM through examples drawn from the life sciences such as biomolecular simulation GROMACS and multicellular simulations PhysiCell The course is organised and funded by PerMedCoE the HPC Exascale Centre of Excellence in Personalised Medicine https permedcoe eu and BioExcel the Centre of Excellence for Computational Biomolecular Research http bioexcel eu using the HPC infrastructure at the Barcelona Supercomputing Centre... High-performance computing (HPC) is a fundamental technology used to solve a wide range of scientific research problems. Many important challenges in science such as protein folding, drug discovery, and tumour evolution, all depend on simulations, models and analyses run on HPC facilities to make progress. This course introduces HPC to life science researchers, focusing on the aspects that are most important for those new to this technology to understand. It will help you judge how HPC can best benefit your research, and equip you to go on to successfully and efficiently make use of HPC facilities in future. The course will cover basic concepts in HPC hardware, software, user environments, filesystems, and programming models. It also provides an opportunity to gain hands-on practical experience and assistance using an HPC system (MARENOSTRUM) through examples drawn from the life...

8 March - 11 March 2023

The cellular mechanics of symbiosis

Toby Kiers, John McCutcheon, Thomas Richards

OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview For late onsite registrations please contact Lina Nikolajeva lina nikolajeva embl de This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Symposium overview... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview For late onsite registrations please contact Lina Nikolajeva: lina.nikolajeva@embl.de This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. 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, like nutrient production, but interactions can also be 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. Our aim is to understand the...

9 March 2023

Supercomputer-based modelling and simulation for advanced biomedical applications

Mariano Vázquez

In this talk we will show advancements on the usage of supercomputer based modelling and simulation in advanced biomedical applications including tools for creating virtual populations of Virtual Human Twins and Twinoids In particular we will showcase computational achievements on coupled multi scale and multi physics problems to create in silico clinical trials to understand physiology and to improve old and create new and better therapies Regarding the application problems we will present contributions on blood circulatory system cardiac hemodynamics bioprosthetic heart valves implants and valve reparation surgical procedures respiratory fluid mechanics from upper airways down to alveoli inhalers and nebulizers lung models spinal intrathecal fluid mechanics etc About the speaker Mariano V zquez is CTO CSO of the company ELEM Biotech which develops and commercialises supercomputer based applications for the biomedical sector and researcher of the Barcelona Supercomputing Center from which ELEM spun off in 2018 He has a PhD from the Technical University of Catalunya UPC with postdocs in Dassault Aviation and in INRIA Sophia Antipolis in France... In this talk we will show advancements on the usage of supercomputer-based modelling and simulation in advanced biomedical applications, including tools for creating virtual populations of Virtual Human Twins and “Twinoids”. In particular, we will showcase computational achievements on coupled multi-scale and multi-physics problems to create in-silico clinical trials to understand physiology and to improve old and create new and better therapies. Regarding the application problems, we will present contributions on blood circulatory system, cardiac hemodynamics, bioprosthetic heart valves implants and valve reparation surgical procedures, respiratory fluid mechanics from upper airways down to alveoli, inhalers and nebulizers, lung models, spinal intrathecal fluid mechanics, etc. About the speaker Mariano Vázquez is CTO/CSO of the company ELEM Biotech, which develops and commercialises...

12 March - 17 March 2023

Extracellular vesicles: from biology to biomedical applications

An Hendrix, Cecilia Lässer, Esther Noltet 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... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview A rapidly increasing number of researchers aim to purify and identify extracellular vesicles and many methodologies to isolate and analyse these vesicles are available and have been implemented. This course will cover the basics, possibilities, and limitations of different purification and characterisation techniques and will address strategies to understand their role in biomedical applications. Audience This course is intended for PhD students and Postdoctoral researchers who are interested in learning how to work with extracellular vesicles and know more about their biomedical applications. Modules/resources Extracellular vesicles (continuous and discontinuous density gradient...

15 March 2023

Applying mathematical modelling to biological problems in plant science

Rea Laila Antoniou-Kourounioti

This webinar will give an overview of the ways in which mathematical models closely integrated with experimental data can be used to give new insights into biological problems We will discuss models for various biological processes and problems at different spatial resolutions and timescales from subcellular to whole plants We will also describe the challenges in integrating models and experimental data and suggest strategies for successful interdisciplinary collaborations... This webinar will give an overview of the ways in which mathematical models, closely integrated with experimental data, can be used to give new insights into biological problems. We will discuss models for various biological processes and problems, at different spatial resolutions and timescales, from subcellular to whole plants. We will also describe the challenges in integrating models and experimental data, and suggest strategies for successful interdisciplinary collaborations.

21 March - 30 March 2023

Exploring human genetic variation

Juanita Riveros

Do you want to learn more about genetic variation Are you aware of the resources available for finding viewing and exploring variant data Are you trying to link variant data to phenotypes This four day workshop will demonstrate resources and bioinformatics tools available at EMBL EBI and the Wellcome Sanger Institute that will aid understanding of human genetic variation During the first three days you will learn how to browse retrieve and use human genetic variation data via talks demos and tutorials You will then be provided with exercises to work through the resources on your own with remote trainer support available if needed and provided space to meet other participants if you wish to do so We will meet again on 30 March for a Q A session and discussion about any questions or issues that occurred while working on the materials provided Virtual course Participants will learn via a mix of live talks demos hands on exercises and trainer Q A sessions Practical experience will be developed through homework activities with remote trainer support Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Participants will need to be available between the hours of 09 30 15 30 GMT each day of the course from 21 23 March 2023 and from 09 30 12 00 BST on 30 March 2023 Trainers will be available to assist answer questions and provide further explanations during these times... Do you want to learn more about genetic variation? Are you aware of the resources available for finding, viewing, and exploring variant data? Are you trying to link variant data to phenotypes? This four-day workshop will demonstrate resources and bioinformatics tools available at EMBL-EBI and the Wellcome Sanger Institute that will aid understanding of human genetic variation.  During the first three days, you will learn how to browse, retrieve, and use human genetic variation data via talks, demos, and tutorials. You will then be provided with exercises to work through the resources on your own with remote trainer support available if needed and provided space to meet other participants if you wish to do so. We will meet again on 30 March for a Q&A session and discussion about any questions or issues that occurred while working on the materials provided. Virtual course...

26 March - 1 April 2023

Measuring translational dynamics by ribosome profiling

Pavel Baranov, Sebastian Leidel, Jan Medenbach, Elisabeth Zielonka

OverviewSpeakers trainers and staffPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course 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... OverviewSpeakers, trainers, and staffPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. 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...

28 March - 31 March 2023

Introduction to metabolomics analysis

Jane Reynolds

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 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 using the 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 used to discuss and show how to employ the week s learning In person course We plan to deliver this course in an in person manner onsite at our training suite at EMBL EBI Hinxton Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing Additional information The course fee is inclusive of three nights accommodation and catering including dinner Please note that we will operate this course face to face at EMBL EBI Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic Please also note that there are delays in the issuing of visas from the UK Government We encourage you to check if you need a visa and apply in plenty of time before travelling Current waiting times are more than six weeks For more information please visit the UK Government website... 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 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 using the 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 used to discuss and show how to employ the week’s learning. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as...

28 March - 31 March 2023

Visualizing biological data (VIZBI 2023)

Barbora Kozlikova, Marc A. Marti-Renom, Andrea Schafferhans, Nico Scherf, Michelle Scott, Srigokul Upadhyayula

The conference will feature talks from 21 world leading researchers showcasing visualizations transforming how life scientists view data and driving key advances in molecular biology systems biology biomedical science and ecology... This conference will take place at EMBL Heidelberg, with the option to attend virtually. Proof of COVID-19 vaccination or recovery is required for on-site attendance. Please see EMBL’s COVID-19 safety policy for on-site events.  Registration is not yet open for this event. If you are interested in receiving more information please register your interest.  Conference overview Visualisation is increasingly important in life science as data grows rapidly in volume and complexity. The VIZBI initiative is an international conference series bringing together researchers developing and using computational visualisation to address a broad range of biological research areas; the conference also attracts participation from medical illustrators, graphic designers, and graphic artists. VIZBI is held annually, usually alternating between Europe and the USA. More information on...

12 April 2023

Pangenomics and machine learning for crop improvement

Dave Edwards

The changing climate and increasing human population mean that we need to accelerate the production of improved crop varieties Advances in genomics and phenomics are helping to accelerate crop improvement but the quantity and diversity of data being generated is vast and needs new methods for integrated analysis Artificial intelligence AI approaches provide one solution to this analysis challenge This webinar will provide an overview on recent advances in pangenomics and application of machine learning and deep learning for crop genomic and phenomic data analysis... The changing climate and increasing human population mean that we need to accelerate the production of improved crop varieties. Advances in genomics and phenomics are helping to accelerate crop improvement, but the quantity and diversity of data being generated is vast and needs new methods for integrated analysis. Artificial intelligence (AI) approaches provide one solution to this analysis challenge. This webinar will provide an overview on recent advances in pangenomics and application of machine learning and deep learning for crop genomic and phenomic data analysis

17 April - 24 April 2023

Microbial metagenomics: a 360º approach

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

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview The course focuses on the highly interdisciplinary topic of metagenomics During the course participants will receive an overview of state of the art genomic technologies and... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview The course focuses on the highly interdisciplinary topic of metagenomics. During the course, participants will receive an overview of state-of-the-art genomic technologies and bioinformatic tools. A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines. The course will start with training the participants about experimental design and the preparation of their own metagenomic libraries with soil or their (environmental) samples. The metagenomic DNA will be sequenced onsite using third generation sequencing technologies and subsequent data analysis. Thus, the...

17 April - 18 April 2023

EuroFAANG AQUA-FAANG workshop: methods to use and reuse the AQUA-FAANG data and Ensembl resources to advance science

Peter Harrison

This one and a half day workshop will provide detailed training on methods to use and reuse the wealth of data generated by the EuroFAANG AQUA FAANG project AQUA FAANG aims to improve understanding the genome function and usage of genotype to phenotype prediction in the six most important European farmed fish species EUROPEAN SEABASS GILTHEAD SEABREAM RAINBOW TROUT ATLANTIC SALMON COMMON CARP TURBOT The workshop will primarily focus on the comprehensive and integrated annotation of these six species by the Ensembl genome browser The course will also include a deeper dive from the Ensembl analysis teams into gene annotation and regulation and demonstrations of the specific analyses and research conducted by AQUA FAANG scientists... This one and a half day workshop will provide detailed training on methods to use and reuse the wealth of data generated by the EuroFAANG AQUA-FAANG project. AQUA-FAANG aims to improve understanding the genome function and usage of genotype-to-phenotype prediction in the six most important European farmed fish species (EUROPEAN SEABASS | GILTHEAD SEABREAM | RAINBOW TROUT | ATLANTIC SALMON | COMMON CARP | TURBOT). The workshop will primarily focus on the comprehensive and integrated annotation of these six species by the Ensembl genome browser. The course will also include a deeper dive from the Ensembl analysis teams into gene annotation and regulation, and demonstrations of the specific analyses and research conducted by AQUA-FAANG scientists.  

19 April 2023

Kew tree of life project: discovering the phylogeny of all flowering plants

Bill Baker, Paul Kersey

High throughput sequencing has transformed approaches to phylogenetic analysis allowing the construction of trees based on multiple loci and consideration of incongruence between nuclear and plastid data This webinar will highlight how the Hyb Seq method enriches whole genome sequence data for target genes and can be used on preserved specimens enabling a cost effective and practicable strategy for the rigorous investigation of plant evolutionary relationships over a broad taxonomic scope The Royal Botanic Gardens Kew has already generated a phylogeny covering over half of all flowering plant genera and aims to complete the tree at the generic level by 2025... High throughput sequencing has transformed approaches to phylogenetic analysis, allowing the construction of trees based on multiple loci and consideration of incongruence between nuclear and plastid data. This webinar will highlight how the Hyb-Seq method enriches whole-genome sequence data for target genes and can be used on preserved specimens, enabling a cost-effective and practicable strategy for the rigorous investigation of plant evolutionary relationships over a broad taxonomic scope.  The Royal Botanic Gardens, Kew, has already generated a phylogeny covering over half of all flowering plant genera and aims to complete the tree (at the generic level) by 2025.

25 April - 28 April 2023

Brain genome: regulation, evolution, and function

Roberto Bonasio, Matthieu Boulard, Magdalena Götz, Kyung-Min Noh

This symposium will explore how the brain genome is regulated in order to support neural function and neural plasticity... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Symposium overview This symposium explores the many ways by which the genome is regulated in the brain in order to support neural function and plasticity. The extraordinary complexity of the brain places unique demands on the genome: How are several hundreds of different neural types specified by the same genetic instructions? Does the genome provide information that guides their connectivity? How is neural activity regulated by and how does it affect genome output? We will explore these fundamental questions from the standpoint of transcriptional regulation and chromatin-based processes, including but not...

25 April - 27 April 2023

Bioinformatics resources for protein biology

Juanita Riveros

Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research Do you want to know more about the sequence of your protein and its functions Wondered whether a structure of your protein exists and how to explore it Want to know more about the potential complexes and reaction pathways your protein of interest is involved in giving you a better overview of its biological context This short virtual course will introduce you to data resources and tools developed by EMBL EBI that can help you in your protein studies During the first three days you will learn about how to browse retrieve and use EMBL EBI protein data in theory Those who are interested in learning more about programmatic access to EMBL EBI protein resources can attend an optional section on this topic on 25 April 2023 For an introduction to the concept of web services and how you can use them to access the tools and data available at EMBL EBI please watch our webinar You will then be provided exercises for each resource you will work through on your own in the following week with remote trainer support available if needed We will meet again on 4 May 2023 to discuss issues that occurred while working through the material in more detail Additional information 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 due to the ongoing coronavirus pandemic Virtual course Participants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there may be a brief induction session Participants will need to be available between the hours of 09 45 16 30 GMT each day of the course Trainers will be available to assist answer questions and provide further explanations during these times... Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research? Do you want to know more about the sequence of your protein and its functions? Wondered whether a structure of your protein exists and how to explore it? Want to know more about the potential complexes and reaction pathways your protein of interest is involved in, giving you a better overview of its biological context? This short virtual course will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies. During the first three days you will learn about how to browse, retrieve, and use EMBL-EBI protein data in theory. Those who are interested in learning more about programmatic access to EMBL-EBI protein resources can attend an optional section on this topic on 25 April 2023. For an introduction to the concept of...

26 April 2023

Applications and impacts of the BrAPI project on plant breeding

Peter Selby

Modern genomic breeding methods rely heavily on very large amounts of phenotypic and genotypic data presenting new challenges in effective data management and integration The datasets are often large and complex and the data is often stored on multiple systems sometimes separated by country and organisation As the common analyses methods increasingly require aggregation of datasets from diverse sources data exchange between disparate systems becomes a challenge This webinar will be an introduction to The Breeding API BrAPI Project The BrAPI Project began in 2014 when a small group of plant breeding and technology experts came together to try to standardise their data Since then BrAPI has become internationally accepted as one of the primary data exchange standards in the plant breeding domain This webinar will give an overview of what BrAPI is how it works what it is capable of and the impact the project has had so far on the community... Modern genomic breeding methods rely heavily on very large amounts of phenotypic and genotypic data, presenting new challenges in effective data management and integration. The datasets are often large and complex, and the data is often stored on multiple systems, sometimes separated by country and organisation. As the common analyses methods increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. This webinar will be an introduction to The Breeding API (BrAPI) Project. The BrAPI Project began in 2014 when a small group of plant breeding and technology experts came together to try to standardise their data. Since then, BrAPI has become internationally accepted as one of the primary data exchange standards in the plant breeding domain. This webinar will give an overview of what BrAPI is, how it works, what it is...

3 May 2023

Historical perspectives on plant science databases

Helen Anne Curry

This webinar will discuss the history of database development in the plant sciences with a focus on European efforts to build international cross institutional genebank databases Although accounts of these often focus on the need for well curated and cross linked databases to adequately serve research communities it is equally important to consider the political and economic motivations behind database development Exploring the history of data management in the plant sciences can potentially help researchers recognise and navigate contemporary challenges... This webinar will discuss the history of database development in the plant sciences, with a focus on European efforts to build international, cross-institutional genebank databases. Although accounts of these often focus on the need for well curated and cross-linked databases to adequately serve research communities, it is equally important to consider the political and economic motivations behind database development. Exploring the history of data management in the plant sciences can potentially help researchers recognise and navigate contemporary challenges.

7 May - 12 May 2023

Advanced fluorescence imaging techniques

Aliaksandr Halavatyi, Stefan Marawske, Rainer Pepperkok, Stefan Terjung

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 Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview This practical course will cover advanced light microscopy techniques and participants will learn how to derive qualitative and quantitative insights on molecular mechanisms in cells and developing organisms. Invited guest researchers together with 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...

8 May - 12 May 2023

Data visualisation for biology

Jane Reynolds

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 Additional information The course fee is inclusive of four nights accommodation and catering including dinner We plan to deliver this course in an in person manner onsite at our training suite at EMBL EBI Hinxton Hybrid options are not currently available Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing Monday 8 May will be a bank holiday in the UK to mark the Coronation of King Charles III The course will take place as outlined in the programme including sessions as planned on Monday 8 May Should you be selected as a participant please take extra care planning your travel to the course as public transport may be affected by the Coronation Saturday 6 May and bank holiday Please also note that there are delays in the issuing of visas from the UK Government We encourage you to check if you need a visa and apply in plenty of time before travelling Current waiting times are more than six weeks For more information please visit the UK Government website... 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...

9 May - 12 May 2023

The organism and its environment

Detlev Arendt, Edith Heard, Maria Leptin, Fiona Watt, Detlef Weigel

OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview We are at the dawn of a new era of biology where we will start to understand how organisms function together and react or adapt to changes at different molecular levels. This includes the multitude of stresses that organisms are exposed to, from malnutrition and adverse climate events to many other biological, chemical and physical insults. Progress in biological analyses at both a single scale and across scales, have allowed us to further understand organisms...

10 May 2023

Developing an improved understanding of the structure and function of the wheat root microbiome

Tim Mauchline

The root microbiome is selected by plants and can benefit crop plants in several ways including improved plant nutritional status as well as protection against biotic and abiotic stresses There are various factors which determine the wheat root microbiome community structure and developing a robust understanding of these is imperative for the development of sustainable agricultural systems This webinar explores the relative importance of factors such as fertilisation regime land management and plant genotype in shaping the structure and function of the wheat root microbiome and how this knowledge can be taken forward to develop microbiome facilitated agriculture... The root microbiome is selected by plants and can benefit crop plants in several ways including improved plant nutritional status as well as protection against biotic and abiotic stresses. There are various factors which determine the wheat root microbiome community structure and developing a robust understanding of these is imperative for the development of sustainable agricultural systems. This webinar explores the relative importance of factors such as fertilisation regime, land management and plant genotype in shaping the structure and function of the wheat root microbiome and how this knowledge can be taken forward to develop microbiome facilitated agriculture.   

15 May - 18 May 2023

Chromatin and epigenetics

Asifa Akhtar, Yehudit Bergman, Nicola Iovino, Gary Karpen, Sarah Teichmann

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... OverviewSpeakersPractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. 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...

16 May - 18 May 2023

Practical biocuration

Sophie Spencer

This three day course will introduce concepts vital to biocuration including metadata and ontologies the role of identifiers and extracting data from literature During the course there will be a focus on practical skills required by biocurators including programming for handling large biological datasets and querying databases Participants will have the opportunity to use these skills in a real life practical biocuration exercise during the group projects There will also be an opportunity to network with biocurators and learn more about their roles and data resources Group projects A major element of this course is a group project where participants will be placed in small groups to work together on a challenge set by trainers from EMBL EBI and external institutes This allows people to explore the role of biocurators and provide participants with hands on experience in biocuration The group work will culminate in a presentation session involving all participants on the final day of the course giving an opportunity for wider discussion in the whole course group Groups are mentored and supported by the trainers who set the initial challenge but the groups will be responsible for driving their projects forward with all members expected to take an active role Groups are pre organised before the course Basic outlines of the projects on offer this year are given below In your registration you must indicate your first and second choice of project Not all projects may be offered and final decisions on which projects will be run during the course will be made based on the number of applicants per project Project one Curating a protein complex In this project a new protein complex has been published and it is your role to find out as much information as possible about the complex Using literature and bioinformatics resources you will provide an overview of the protein complex including a full list of the complex members a description of the role of each protein and an overview of the role of the complex You will use resources such as UniProt PDB and EuropePMC Project mentor Michelle Magrane Project two Exploring data and metadata from a genome wide association study The GWAS Catalog is a richly annotated database of human genome wide association studies which analyse associations between genetic variants and a disease or other trait of interest in a sample of individuals from a particular population In this mini project you will examine a GWAS publication in detail to extract information about the traits and samples under investigation and decide how to represent these metadata using standardised vocabularies and ontologies You will also use simple command line tools to look at a GWAS dataset and explore the role of standard formats and quality control in biocuration Project mentor Elliot Sollis Project three Curating a mathematical model of biological pathway In this project you will find a short mathematical model of your area of interest and try to encode and reproduce the simulation results using COPASI Using EuropePMC you will find a small ordinary differential model ODE mathematical model of a pathway You will encode the pathway using the software COPASI and reproduce the result of the published pathway There may also be an opportunity to submit a model to BioModels Project mentor Krishna Tiwari Project four Using alignments to improve Rfam families a case of curating non coding RNA families Rfam is the database of non coding RNAs ncRNAs families These families are built out of a sequence alignment metadata describing the family and an infernal model Each family is built by curating alignments from publications or user submitted alignments In this project we will demonstrate the process of updating an existing family with an improved alignment We will examine the reports generated during curation In this process we will examine the phylogenetic distribution sequence alignment and model results to determine how the family should be updated to reflect the improved alignment Additionally we will show how to connect this information to resources like Wikipedia Project mentor Nancy Ontiveros Project five Annotating an electron microscopy image dataset EMPIAR Electron Microscopy Public Image Archive is a free public resource for raw images underpinning 3D cryo EM maps and tomograms EMPIAR also accommodates 3D datasets obtained with volume EM techniques and soft and hard X ray tomography In this project you will use EMPIAR to annotate a selected electron microscopy image dataset Project mentor Simone Weyand... This three-day course will introduce concepts vital to biocuration, including metadata and ontologies, the role of identifiers, and extracting data from literature.  During the course, there will be a focus on practical skills required by biocurators, including programming for handling large biological datasets, and querying databases. Participants will have the opportunity to use these skills in a real-life practical biocuration exercise during the group projects.  There will also be an opportunity to network with biocurators and learn more about their roles and data resources. Group projects A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI and external institutes. This allows people to explore the role of biocurators and provide participants with hands-on...

21 May - 26 May 2023

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 package which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis... OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview This course will teach the biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq and rCASC packages, which was 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...

22 May - 26 May 2023

Expansion microscopy

Niccolo Banterle, Gautam Dey, Paul Guichard, Virginie Hamel, Marine Laporte

OverviewSpeakers trainers and staffPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview Expansion microscopy ExM physically magnifies specimens allowing to obtain super resolution images using a conventional diffraction limited microscope such... OverviewSpeakers, trainers, and staffPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview Expansion microscopy (ExM) physically magnifies specimens, allowing to obtain super-resolution images using a conventional diffraction-limited microscope such as confocal microscopy. This powerful technique is easy to implement but it requires some hands-on training. This workshop aims at disseminating and discussing expansion microscopy protocols and is intended for cell biologists, parasitologists, etc, with applications ranging from tissue to cells. Audience This course is intended for researchers ranging from PhD students to post-docs and senior scientists as well as staff from bioimaging platforms who wish to establish expansion microscopy in their...

22 May - 26 May 2023

Microscopy data analysis: machine learning and the BioImage Archive

Shereen Pethania

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 Further instruction will be offered using applications such as ZeroCostDL4Mic ilastik ImJoy the BioImage Model Zoo and CellProfiler Virtual course This course will be a virtual event delivered via a mixture of live streamed sessions pre recorded lectures and tutorials with live support We will be using Zoom to run the live 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. Further instruction will be offered using applications such as ZeroCostDL4Mic, ilastik, ImJoy, the BioImage Model Zoo, and CellProfiler. Virtual course This course will be a virtual event delivered via a mixture of live-streamed sessions, pre-recorded lectures, and tutorials with live support. We will be using Zoom to run the live sessions (all fully password protected with automated English closed...

23 May - 25 May 2023

BioMalPar XIX: biology and pathology of the malaria parasite

BioMalPar XVIII will showcase the multidisciplinary nature of malaria research with a programme that welcomes clinical malaria epidemiological studies immunology and evolution and ecology alongside core BioMalPar topics... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Travel grants and fee waivers are available for BioMalPar XIX. Please note that the deadline to apply for this financial assistance to attend onsite is 7 December 2022 (earlier than the general abstract deadline). Participants are encouraged to submit their abstract for an oral presentation. In total, more than 15 short talk speakers will be selected from both onsite and virtual abstract submissions. Conference overview Malaria remains one of the most significant global public health challenges, with more than 200 million clinical cases worldwide each year. The lack of a vaccine that provides effective...

4 June - 7 June 2023

The ageing genome: from mechanisms to disease

Jacqueline Jacobs, Gaëlle Legube, Brian Luke, Björn Schumacher

OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Symposium overview Time stands still for no one or for no molecule for that matter Of the... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Symposium overview “Time stands still for no one” or for no molecule, for that matter. Of the molecules that undergo changes over time, it is chromosomal alterations that may have some of the most profound and long-lasting cellular and organismal effects. In contrast to any other macromolecule, the genome is irreplaceable and requires constant repair. Despite sophisticated genome maintenance mechanisms, DNA damage accumulates over time and hence with age. The ensuing chromosomal alterations may lead to genome instability, somatic mutations, impaired gene expression and DNA replication, alterations of the...

5 June - 9 June 2023

Deep learning for image analysis

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

... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview The advent of deep learning has brought a revolution in the field of computer vision, including most tasks and research questions concerned with microscopy image analysis. Neural networks have been successfully used for image restoration, classification and segmentation, for the detection of objects and characterisation of their morphology, for high-throughput imaging and large-scale processing in 3D. Despite these advances, training and deployment of such neural networks remains difficult for practitioners of image analysis. The aim of our course is to close this gap and teach the participants – in the most hands-on way possible – to apply deep learning-based methods to their own...

11 June - 16 June 2023

Quantitative proteomics: strategies and tools to probe biology

Jeroen Krijgsveld, Christina Ludwig, Mikhail Savitski

OverviewSpeakersPreliminary programmePractical InformationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview This course will provide both theoretical and practical training in the use of quantitative proteomics Participants will learn the principles of the most frequently used data... OverviewSpeakersPreliminary programmePractical InformationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Course overview This course will provide both theoretical and practical training in the use of quantitative proteomics. Participants will learn the principles of the most frequently used data acquisition methods (DDA, DIA, and targeted proteomics) and proteomic quantification approaches (label-free, SILAC, and TMT). The major aim of this course is to practically train the participants in the use of readily available bioinformatic tools as well as in the statistical interpretation of proteomic data, in order to empower them to make informed decisions in their own research. Audience This course is aimed at researchers who know the basics of proteomics and who want to get a deeper understanding of...

12 June - 15 June 2023

Life at the periphery: mechanobiology of the cell surface

Alba Diz Muñoz, Zemer Gitai, KC Huang, Ewa Paluch

OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Symposium overview After a very engaging virtual first edition in 2021 this hybrid symposium on cell... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Symposium overview After a very engaging virtual first edition in 2021, this hybrid symposium on cell surface mechanics will bring together researchers across kingdoms of life interested in dynamic processes occurring at the cell surface. The focus will be on new technologies that empower studies of cell wall, cytoskeleton, and membrane biology, such as advanced imaging in in vitro and in vivo systems, as well as approaches combining molecular biology with computational and biophysical approaches. The first edition started building a much-needed bridge between the wall and wall-less...

12 June - 16 June 2023

Summer school in bioinformatics

Sophie Spencer

This course provides an introduction to the use of bioinformatics in biological research giving participants guidance for using bioinformatics in their work whilst also providing hands on training in tools and resources appropriate to their research Participants will initially be introduced to bioinformatics theory and practice including best practices for undertaking bioinformatics analysis data management and reproducibility To enable specific exploration of resources in their particular field of interest participants will then be divided into focused groups to work on a project Participants will be required to review some pre recorded material prior to the start of the course Group projects A major element of this course is a group project where participants will be placed in small groups to work together on a challenge set by trainers from EMBL EBI and external institutes This allows people to explore the bioinformatics tools and resources available in their area of interest and apply them to a set problem providing participants with hands on experience relevant to their own research The group work will culminate in a presentation session involving all participants on the final day of the course giving an opportunity for wider discussion on the benefits and challenges of working with biological data Groups are mentored and supported by the trainers who set the initial challenge but the groups will be responsible for driving their projects forward with all members expected to take an active role Groups are pre organised before the course and all group members will be sent some short homework in preparation for their project work prior to the start of the course Basic outlines of the projects on offer this year are given below In your application you must indicate your first and second choice of project based on which you think would benefit your research most Not all projects may be offered and final decisions on which projects will be run during the course will be made based on the number of applicants per project Most of the projects cover mammalian data sets however in many cases the methods and approaches taught are transferable to data from various species Group project one Genome variation across human populations Natural variation between individuals or between different human populations is a result of genome mutations throughout evolutionary history Some mutations may become fixed because of their beneficial effect while most drift among individuals During this project you will investigate genomic variation between two separate human populations of European and Asian descent Using sequence data from a number of individuals from each population you will use a range of bioinformatics tools to discover variants that exist between them In the second section of the project you will attempt to analyse the functional consequences of the variants you have identified attempting to find clinical association and linking them to phenotypes Project mentor Baron Koylass EMBL EBI Group project two Interpreting functional information from large scale protein structure data This project will introduce you to the wealth of publicly available data in the Protein Data Bank PDB and give you the opportunity to investigate how large subsets of structure data can be used to analyse protein features and determine function In the project you will learn how to identify relevant protein structures collate and interpret functional information and implement this process programmatically Project mentor Preeti Choudhary EMBL EBI Marcus Bage EMBL EBI Group project three Modelling cell signalling pathways Curating models of biological processes is an effective training in computational systems biology where the curators gain an integrative knowledge of biological systems modelling and bioinformatics You will learn to encode and simulate ordinary differential equation models of signalling pathways from a recent publication using user friendly software such as COPASI even without extensive mathematical background You will learn to perform in silico experiments new predictions and develop hypotheses Furthermore you will learn how to annotate models and re use pre existing models from open repositories such as BioModels Project mentors Rahuman Sheriff EMBL EBI Krishna Tiwari EMBL EBI Group project four Networks and pathways This project will cover typical bioinformatics analysis steps needed to put differentially expressed genes into a wider biological context You will start with gene expression data RNA seq to build an initial interaction network Next you will learn to combine public network datasets identify key regulators of biological pathways and explore biological function through network analysis You will get first hand experience in integration and co visualising with additional data and functional enrichment analysis All this helps to put the initial results into a previously known context and provide hypotheses for potential follow up experiments We will use Cytoscape Expression Atlas g Profiler StringDb among other tools We also may give a few R packages a try Project mentor Priit Adler University of Tartu Group project five Reusing FAIR Bioimage data an AI application Biological imaging is a rapidly growing field with a vast potential of re use for further scientific research and development Re use of bioimage data requires FAIR Findable Accessible Interoperable Reusable data by public repositories that support FAIR sharing such as the BioImage Archive This project aims to showcase one of many ways of reusing bioimage data by applying artificial intelligence AI models on selected datasets in the BioImage Archive In this project you will learn to search and download the extensive variety of data that is held in this publicly available data resource You will also use Jupyter Python notebooks to visualise image data in the archive and deploy AI models on selected datasets Project mentors Aybuke Kupcu Yoldas EMBL EBI Teresa Zulueta Coarasa EMBL EBI Additional information Please note that we will operate this course face to face at EMBL EBI in Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic... This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research. Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management, and reproducibility. To enable specific exploration of resources in their particular field of interest, participants will then be divided into focused groups to work on a project. Participants will be required to review some pre-recorded material prior to the start of the course. Group projects A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI and external...

18 June - 23 June 2023

Computational modelling of multicellular systems

Katie Bentley, James Sharpe, Alejandro Torres-Sánchez

Proof of COVID 19 vaccination or recovery is required to attend this on site course Please see EMBL s COVID 19 safety policy for on site events Registration is not yet open for this event If you are interested in receiving more information please register your interest... Proof of COVID-19 vaccination or recovery is required to attend this on-site course. Please see EMBL’s COVID-19 safety policy for on-site events.  Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

19 June - 20 June 2023

Terra incognita: navigating ethical boundaries in the life sciences

Lucia von Bredow

Overview Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest What past participants say about the conference... Overview Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. What past participants say about the conference “The excellent EMBL Science & Society conferences are a terrific opportunity for scientists at all career stages, and from anywhere in the world, to join wide-ranging debates on the practical, ethical and social implications of today’s research.” – Chris Dye, University of Oxford, UK “The conference was awesome. I enjoyed the interesting topics covered by experts from reputable institutions from all top universities in the world. I felt like I physically attended the...

19 June - 21 June 2023

Bioinformatics for principal investigators

Jane Reynolds

This course has been designed to provide principal investigators PI s working in the life sciences with an introduction to the challenges of working with biological data as a research leader Starting with a look at where bioinformatics and data science fits into their research teams the course will enable PI s to take a strategic look at the requirements for undertaking such work and how bioinformatics capacity can be developed from personnel through to computational needs It will additionally provide guidance on strategies for managing data the importance of data sharing how to work with computational collaborators and what resources are available across the life sciences to support such work During this course we will not be teaching hands on bioinformatics analysis but we will be signposting appropriate training resources to upskill you and your team In person course We plan to deliver this course in an in person manner onsite at our training suite at EMBL EBI Hinxton Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing Additional information This course is currently under construction and so details are subject to change Please note that we will operate this course face to face at EMBL EBI in Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic... This course has been designed to provide principal investigators (PI's) working in the life sciences with an introduction to the challenges of working with biological data as a research leader. Starting with a look at where bioinformatics and data science fits into their research teams, the course will enable PI’s to take a strategic look at the requirements for undertaking such work and how bioinformatics capacity can be developed from personnel through to computational needs. It will additionally provide guidance on strategies for managing data, the importance of data sharing; how to work with computational collaborators and what resources are available across the life sciences to support such work. During this course, we will not be teaching hands-on bioinformatics analysis, but we will be signposting appropriate training resources to upskill you and your team. In-person course We...

25 June - 30 June 2023

PerMedCoE summer school: from pathway modelling tools to cell-level simulations

Juanita Riveros

The course will combine lectures and hands on exercises to Introduce attendees to key practicalities of working with high performance computing HPC clusters Build first hand experience in using PerMedCoE modelling tools CellNOpt CARNIVAL COBREXA MaBoSS PhysiCell and PhysiBoSS Develop a practical appreciation of using workflow managers and containerised PerMedCoE modelling tools to execute biomedical workflows It will also include poster sessions where participants can present their work and plenty of time for interaction between participants and between participants and trainers This course will take place at the Hotel Montany in Seva less than an hour away from Barcelona Visit the PerMedCoE summer school website for more information... The course will combine lectures and hands-on exercises to: Introduce attendees to key practicalities of working with high-performance computing (HPC) clusters Build first-hand experience in using PerMedCoE modelling tools (CellNOpt, CARNIVAL, COBREXA, MaBoSS, PhysiCell and PhysiBoSS) Develop a practical appreciation of using workflow managers and containerised PerMedCoE modelling tools to execute biomedical workflows It will also include poster sessions where participants can present their work and plenty of time for interaction between participants and between participants and trainers. This course will take place at the Hotel Montanyà in Seva, less than an hour away from Barcelona. Visit the PerMedCoE summer school website for more information.

25 June - 30 June 2023

Imaging-based spatial-omics

Alvaro Crevenna, Emerald Perlas, Sinem Saka

OverviewSpeakersPreliminary programmePractical 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... OverviewSpeakersPreliminary programmePractical 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 data analysis. Audience This course is open to PhD students, postdocs and staff. We seek...

27 June - 30 June 2023

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 kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Symposium overview This symposium will cover a broad range of topics in microbiology, featuring diverse research on bacterial physiology, bacterial communities and microbiomes, bacterial–host and –phage interactions, and bacteria in their natural ecological contexts. Emphasis will be placed on novel approaches and technologies (from systems-based to single-cell) that drive each field or have the potential to revolutionise future research in microbiology. This meeting is the sixth of its kind, part of a successful series which started in 2013 and held biannually since, becoming a must-attend event for...

3 July - 7 July 2023

Proteomics bioinformatics

Shereen Pethania

This course provides hands on training in the basics of mass spectrometry MS and proteomics bioinformatics Participants 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 This course is organised in association with the Vlaams Instituut voor Biotechnologie VIB In person course The course fee is inclusive of four nights of accommodation and catering including dinner We plan to deliver this course in person onsite at our training suite at EMBL EBI Hinxton Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing Please also note that there are delays in the issuing of visas from the UK Government We encourage you to check if you need a visa and apply in plenty of time before travelling Current waiting times are more than six weeks For more information please visit the UK Government website... This course provides hands-on training in the basics of mass spectrometry (MS) and proteomics bioinformatics. Participants 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. This course is organised in association with the Vlaams Instituut voor Biotechnologie (VIB). In-person course The course fee is inclusive of four nights of accommodation and catering, including dinner. We plan to deliver this course in-person onsite at our training suite at EMBL-EBI, Hinxton. Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to...

10 July - 14 July 2023

Fluorescence imaging beyond intensity

Luis Alvarez, Manuel Gunkel, Birgit Koch, Andrea Mülter

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course 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... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. 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,...

10 July - 14 July 2023

Cancer genomics and transcriptomics

Sophie Spencer

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 In person course We plan to deliver this course in an in person manner onsite at our training suite at EMBL EBI Hinxton Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing... 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. In-person course We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

11 July - 14 July 2023

Predicting evolution

Justin Crocker, Gautam Dey, Joshua Payne, Patricia Wittkopp

The conference will explore the evolution of biological systems at different levels from genes and molecules to organism development and ecology... OverviewSpeakersPractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Conference overview Advances in genome sequencing and gene editing tools are providing unprecedented insights into biological mechanisms and evolutionary processes. In parallel, computational and theoretical approaches are providing new insights into our understanding of these new data. A goal for this conference is to unite people across theoretical and experimental backgrounds into a coherent focus on “predicting evolution”. The conference will explore the evolution of biological systems at different levels: from genes and molecules to organism development and ecology. As such, we have invited leaders in their respective fields...

16 July - 21 July 2023

Drosophila genetics and genomics

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

The course combines interactive theoretical discussions that have been successfully used to train generations of Drosophila researchers for nearly 30 years combined with cutting edge experimental approaches taught by experts in the field... OverviewSpeakersPreliminary onsite programmePreliminary virtual programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course overview The fruit fly Drosophila has played a leading role in the discovery and dissection of basic biological processes, uncovering general principles of development, evolution and disease. Almost a century of research has generated a powerful genetic toolbox that provides a unique arsenal of methods that can tackle almost any biological question. This, combined with exciting new technologies developed in recent years have changed the way Drosophila research is conducted, enabling biologists to address questions that were...

18 July - 21 July 2023

Theory and concepts in biology

Alexander Aulehla, Jordi Garcia-Ojalvo, Robert Phillips. Kirsty Wan

OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Symposium overview Recent progress in biology has led to an explosion of factual knowledge about the... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. 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 aims to bring together a diverse collection of researchers interested in finding ways to parlay this ever-increasing factual knowledge into a corresponding array of conceptual knowledge. The goal of this symposium is to assemble an interdisciplinary community and...

24 July - 4 August 2023

Plasticity in developing systems: time, space, and environment

Alexander Aulehla, Aissam Ikmi, Nicoletta Petridou, Alessandra Reversi

OverviewSpeakersSponsors Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Registration is not yet open for this event If you are interested in receiving more information please register your interest Course Overview Studying organisms in their original context and environment is one of the current grand challenges... OverviewSpeakersSponsors Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Studying organisms in their original context and environment is one of the current grand challenges in the life sciences and a central goal of modern Developmental Biology. The interactions between organisms, and their chemical, physical and biotic environments have important consequences at the level of form, physiology and behaviour. To gain an understanding and uncover mechanistic links between these interconnected and dynamic processes, novel, interdisciplinary approaches and cutting-edge technologies are needed. The aim of this course is to expose and introduce graduate students and postdoctoral fellows...

6 September - 10 September 2023

Protein synthesis and translational control

Alfredo Castello, Fátima Gebauer, Matthias Hentze, Jerry Pelletier,Christian Spahn

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Conference overview Mechanisms that shape cellular proteomes are critical for life This conference focuses on... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. 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 maintain 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...

10 September - 15 September 2023

Advanced methods in bioimage analysis

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

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Registration is not yet open for this event If you are interested in receiving more information please register your interest Course overview Bioimage analysis has become a keystone of... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. 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...

12 September - 15 September 2023

Developmental metabolism: flows of energy, matter, and information

Alexander Aulehla, Heidi Lempradl, Jonathan Rodenfels

OverviewSpeakersSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest Overview The fundamental... OverviewSpeakersSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Overview The fundamental question of the role of metabolism in development has seen a revival in interest. This is fueled by recent work, shedding new light onto previously unrecognized roles of metabolism. This work revealed the intricate relationship between energy flux, spatial and temporal control of metabolites, the environment and embryogenesis. This emerging view is stimulating research designed to answer fundamental questions including: How does the cellular machinery process information linked to the flow of energy and matter?...

17 September - 22 September 2023

Genome engineering: CRISPR/Cas from cells to mice

Neil Humphreys, Birgit Koch, Elisabeth Zielonka

OverviewSponsors Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Registration is not yet open for this event If you are interested in receiving more information please register your interest Sponsors Sponsorship opportunities We offer a variety of event sponsoring possibilities with the flexibility to select a set... OverviewSponsors Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Sponsors Sponsorship opportunities We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information. If you are interested in becoming a media partner of this event, please visit our media partnerships webpage. Request a sponsorship brochure Warning EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes...

18 September - 22 September 2023

Single-cell RNA-seq analysis using Python

EMBL-EBI Training

This course covers the analysis of scRNA seq data Participants will be guided through droplet based scRNA seq analysis pipelines from raw reads to cell clusters They will explore and interpret data using Python and the Single Cell Expression Atlas Additional information To receive alerts and updates on this course please click the Register Interest button on the right hand side This course is currently under construction and so details are subject to change 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 due to the ongoing coronavirus pandemic... This course covers the analysis of scRNA-seq data. Participants will be guided through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. They will explore and interpret data using Python and the Single Cell Expression Atlas. Additional information To receive alerts and updates on this course, please click the 'Register Interest' button on the right-hand side. This course is currently under construction and so details are subject to change. 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, due to the ongoing coronavirus pandemic.

20 September - 23 September 2023

The human microbiome

Manimozhiyan Arumugam, Ami Bhatt, Peer Bork, Nicola Segata

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 have barely understood 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 characterise them understand their interactions with the human hosts elucidate their role in diseases and design possible therapeutic or dietary interventions There is a new wave of studies mining the human microbiota for bioactive compounds such as antibiotics and for characterising specific microbial strains This conference will provide plentiful opportunities for researchers to learn about and to connect to important developments in studying the human microbiota... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. 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 lifestyle and genetics. Various initiatives are underway around the world to survey the human microbiota at several body sites, characterise them, understand their interactions with the human hosts, elucidate their role in diseases, and design possible therapeutic or dietary interventions. There is a new wave of studies mining the human...

2 October - 6 October 2023

Structural bioinformatics

EMBL-EBI Training

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 Additional information To receive alerts and updates on this course please click the Register Interest button on the right hand side This course is currently under construction and so details are subject to change Please note that we will operate this course face to face at EMBL EBI in Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic... 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. Additional information To receive alerts and updates on this course, please click the 'Register Interest' button on the right-hand side. This course is currently under construction and so details are subject to change. Please note that we will operate this course face-to-face at EMBL-EBI in Hinxton. Hybrid options are not currently available. We reserve the right to change the format of this course or cancel it, due to the ongoing coronavirus pandemic.

4 October - 7 October 2023

Seeing is believing: imaging the molecular processes of life

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

The symposium will bring together the leading developers of imaging methods with cutting edge applications that illustrate how imaging can answer biological questions We will emphasize methods that can capture the dynamics of life spanning the whole range from molecular resolution to imaging of whole organisms From its beginning in 2011 Seeing is Believing has embraced novel imaging technologies that open new windows for biological discovery including single molecule and super resolution light sheet and correlative light electron microscopy... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Symposium overview The molecular processes of life are naturally dynamic in space and time from the atomic to the organismal level. The rapid development of imaging methods across the full scale of biological organisation is revolutionising our ability to visualise the inner workings of macromolecular complexes, organelles, cells, tissues, organs and whole organisms. Being able to see biological processes unfold in real time allows us to understand the mechanisms of life as well as disease.The symposium will bring together the leading developers of imaging methods with cutting-edge applications that...

9 October - 13 October 2023

Metagenomics bioinformatics

Shereen Pethania

Learn about the tools processes and analysis approaches used 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 assembly based approaches Additional information To receive alerts and updates on this course please click the Register Interest button on the right hand side This course is currently under construction and so details are subject to change Please note that we will operate this course face to face at EMBL EBI in Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic... Learn about the tools, processes and analysis approaches used 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 assembly-based approaches. Additional information To receive alerts and updates on this course, please click the 'Register Interest' button on the right-hand side. This course is currently under construction and so details are subject to change. Please note that we will operate this course face-to-face at EMBL-EBI in Hinxton. Hybrid options are not currently available. We reserve the right to change the format of this course or cancel it, due to the ongoing coronavirus pandemic.

9 October - 14 October 2023

Liquid biopsies

Anders Ståhlberg, Karin Sundfeldt

OverviewSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Registration is not yet open for this event If you are interested in receiving more information please register your interest Course Overview Liquid biopsies have the advantage of being largely non invasive and providing a vast amount of... OverviewSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course Overview Liquid biopsies have the advantage of being largely non-invasive and providing a vast amount of information for the detection and monitoring of diseases such as cancer. This course will provide an overview in the several techniques to detect and analyse circulating tumour cells (CTCs), cell free tumor DNA (ctDNA), miRNA in liquid biopsies, cell free tumour RNA (ctRNA) and proteins. Participants will be introduced to all aspects ranging from proper sampling through error free sequencing to data analysis. Additional lectures will cover extracellular vesicles and clinical aspects using liquid biopsies,...

11 October - 14 October 2023

The non-coding genome

Marc Bühler, Anna Eulálio, Joshua Mendell, Gisela Storz, Igor Ulitsky

This symposium will explore the diverse dynamic and multifaceted roles of RNA across a spectrum of cellular processes It will provide an interdisciplinary discussion of the roles of non coding RNAs in both prokaryotes and eukaryotes with the aim of enhancing our understanding of gene regulation and function... OverviewSpeakersPractical informationSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Over the past two decades, advances in transcriptomic methods have led to the discovery of a very rich and diverse set of RNA transcripts, short and long, that serve as regulators rather than templates for protein production. Many of these transcribed elements are encoded in noncoding regions of the genome with other regulatory and structural DNA elements of known and unknown functions. While the catalogs of such elements are very rich, and an ever-increasing number are implicated in almost...

18 October - 21 October 2023

Organoids: modelling organ development and disease in 3D culture

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

OverviewSpeakersPreliminary programmePractical informatonSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Symposium overview The ability to grow human tissues from stem cells in 3D culture has the potential to... OverviewSpeakersPreliminary programmePractical informatonSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Symposium overview The ability to grow human tissues from stem cells in 3D culture has the potential to revolutionise the drug discovery process and regenerative medicine. Building on a long tradition of cell and developmental biology knowledge, organoids resembling a variety of human tissues have been generated. This conference will bring together the leading researchers in this field to establish a new research community and reveal parallels between various tissue models. The aim of this meeting is to bring together researchers from different fields to enhance our understanding of how organoids can be formed and...

22 October - 27 October 2023

FISHing for RNAs: classical to single molecule approaches

Monica Ballarino, Imre Gaspar, Emerald Perlas, Elisabeth Zielonka

OverviewSpeakersSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course 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 a RNA transcripts specific amount and... OverviewSpeakersSponsorsMedia kit Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. 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 a RNA transcripts specific amount and localisation are important in order to understand the biological function of its (non-) coding gene. Whereby state-of-the-art in situ hybridisation (ISH) technologies are key to visualise these RNAs in a given tissue or cell. This course aims to highlight three powerful RNA visualisation techniques in histological tissue samples. During this course, the participants will learn to validate the cellular localisation of candidate genes from transcriptome studies through conventional ISH and, the more recent cutting-edge,...

23 October - 27 October 2023

Systems biology: from large datasets to biological insight

Jane Reynolds

This course covers the use of computational tools to extract biological insight from omics datasets The content will explore a range of approaches ranging 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 Additional information To receive alerts and updates on this course please click the Register Interest button on the right hand side This course is currently under construction and so details are subject to change Please note that we will operate this course face to face at EMBL EBI in Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic... This course covers the use of computational tools to extract biological insight from omics datasets. The content will explore a range of approaches - ranging 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...

25 October - 27 October 2023

Proteomics in cell biology and disease mechanisms

Yu-Ju Chen, Ileana Cristea, Albert Heck, Matthias Mann

... OverviewSpeakersPractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference overview Even after a few decades of great accomplishments, the field of proteomics remains to develop further, fueled by continued technological and computational advances in high-throughput methods and multi-omics big data integration. The Proteomics in Cell Biology and Disease Mechanisms conference will provide attendees with a program that provides the current “state-of-affairs” in proteomics including a future perspective. It will be held at a pioneering hot spot for proteomics in Europe,...

6 November - 10 November 2023

Solution scattering from biological macromolecules

OverviewSponsors Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Registration is not yet open for this event If you are interested in receiving more information please register your interest This course consists of two parts virtual and onsite The virtual course takes place 6 10 November 2023 and the onsite part takes... OverviewSponsors Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. This course consists of two parts: virtual and onsite. The virtual course takes place 6 – 10 November 2023 and the onsite part takes place 27 November – 1 December 2023. Course overview The virtual course will cover the basics of SAXS/SANS, instrumentation, data collection, modelling techniques and complementary use with other methods. The students are encouraged to sign-up for a self-paced practical tutorial that covers basic and advanced SAXS data processing steps (including quizzes to keep track of successful participation). In addition, students are encouraged to apply to the ‘add on module’ which includes an on-site...

6 November - 10 November 2023

Preparation of genomic libraries for an emerging next-gen sequencing platform

Vladimir Benes, Bjorn Textor

OverviewSponsors Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Registration is not yet open for this event If you are interested in receiving more information please register your interest What past participants say about this course I truly recommend this course to anyone interested in RNASeq We were pushed... OverviewSponsors Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. What past participants say about this course “I truly recommend this course to anyone interested in RNASeq. We were pushed to go below the limits of RNA input to construct libraries and it was an exciting challenge. The spirit of science “go beyond our limits” was present through all of the course. The knowledge sharing environment with all the participants, trainers, and speakers, made this one of the best courses I have ever attended.” – Anna Sofia Varanda, University of Aveiro, Portugal Sponsors Sponsorship opportunities We offer a variety of event sponsoring possibilities, with the flexibility to select a...

8 November - 10 November 2023

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 from each other and from potential users of their services These facilities play an essential role in enabling research in the molecular life sciences The landscape is constantly evolving as new research tools emerge experiments become increasingly data intensive and their clients experimental researchers become more exposed to the power of data driven biology Additional information To receive alerts and updates on this course please click the Register Interest button on the right hand side This course is currently under construction and so details are subject to change Please note that we will operate this course face to face at EMBL EBI in Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic... This knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL-EBI’s service teams, from each other, and from potential users of their services. These facilities play an essential role in enabling research in the molecular life sciences. The landscape is constantly evolving as new research tools emerge, experiments become increasingly data-intensive, and their clients – experimental researchers – become more exposed to the power of data-driven biology. Additional information To receive alerts and updates on this course, please click the 'Register Interest' button on the right-hand side. This course is currently under construction and so details are subject to change. Please note that we will operate this course face-to-face at EMBL-EBI in Hinxton. Hybrid options are not currently available. We reserve the right to change the format of...

8 November - 11 November 2023

The mobile genome: genetic and physiological impacts of transposable elements

Déborah Bourc’his, Julius Brennecke, Jose L. Garcia-Perez, Susan Wessler

This conference is assembling world leading experts from diverse fields including genomics epigenetics structural biology developmental biology immunology cancer biology and neurobiology to discuss the broad impacts of TEs on organismal biology... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Conference overview This conference assembles world-leading experts from diverse fields including genomics, epigenetics, structural biology, developmental biology, immunology, cancer biology, and neurobiology to discuss the broad impacts of transposable elements (TEs) on organismal biology. The meeting provides a venue for cross-disciplinary discussions, with the goal of catalysing inter-disciplinary collaborations to address emerging questions in these scientific fields. Although often disparaged as “junk” DNA, it is now undeniable that TE activity has significantly shaped the structure and function of all...

13 November - 17 November 2023

Hands-on flow cytometry: learning by doing!

Andrew Filby, Diana Ordonez, Malte Paulsen, Steffen Schmitt

Flow Cytometry is one of the most powerful single cell analysis methods used throughout the life sciences and medicine By utilising Flow Cytometry we can identify and quantify specific cell populations from heterogeneous samples analyse the cell cycle or proliferation state or simply detect the expression of fluorescent reporters In line with the suggestions from our course in 2019 we will significantly enhance the number of analysis sessions together with our partners from FlowJo We will cover the theory of Flow Cytometry and corroborate this information intensively with the practical issues of the most frequent assays as part of our practical course curriculum... OverviewSponsors Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course overview Flow Cytometry is one of the most powerful single cell analysis methods used throughout the life sciences and medicine. By utilising Flow Cytometry we can identify and quantify specific cell populations from heterogeneous samples, analyse the cell cycle or proliferation state or simply detect the expression of fluorescent reporters. In line with the suggestions from our course in 2019, we will significantly enhance the number of analysis sessions together with our partners from FlowJo. We will cover the theory of Flow Cytometry and corroborate this information intensively with the practical issues of the most...

15 November - 17 November 2023

Cancer genomics

Isidro Cortes Ciriano, Christina Curtis, Nuria Lopez-Bigas, Young Seok Ju

OverviewSpeakersPractical InformationSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest Conference... OverviewSpeakersPractical InformationSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference overview This meeting will provide an opportunity to learn about and keep up to date with the rapidly progressing area of cancer genomics. We aim to bring together scientists from across several disciplines connected with cancer research, for a unique opportunity to interact and stimulate further integration of these efforts. Session topics Cancer evolution Mutation & clonal selection Emerging technologies in cancer genomics Genomic instability & mutational processes Cancer ecosystems &...

20 November - 22 November 2023

25th EMBL PhD Symposium

2023 EMBL PhD Symposium Organising Committee

Join us for the 25th Anniversary of the annual EMBL PhD Symposium Since its conception in 1999 the EMBL PhD Symposium has evolved into a highly respected scientific meeting connecting young researchers and high profile scientists alike...

20 November - 24 November 2023

Genome bioinformatics: resequencing and variant calling

EMBL-EBI Training

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 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 Additional information To receive alerts and updates on this course please click the Register Interest button on the right hand side This course is currently under construction and so details are subject to change Please note that we will operate this course face to face at EMBL EBI in Hinxton Hybrid options are not currently available We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic... 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, 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. Additional information To receive alerts and updates on this course, please click the 'Register Interest' button on the right-hand side. This course is currently under construction and so details are subject to change. Please note that we will operate this course face-to-face at EMBL-EBI in Hinxton. Hybrid options are not currently available. We reserve the right to change the format of this course or...

28 November - 1 December 2023

Subcortical sensory circuits: visual, auditory, somatosensory, and beyond

Hiroki Asari, Martha Bickford, Carl Petersen, Santiago Rompani

OverviewSpeakersPreliminary programmePractical informationSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your... OverviewSpeakersPreliminary programmePractical informationSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference overview Subcortical sensory circuits play a fundamental role in the perception of the outside world. However, they are often thought of as relay stations that passively transmit sensory information to the cortex or simple effectors of behavioral reflexes. Recent studies, however, suggest that subcortical pathways also perform sophisticated computations, such as integrating peripheral information among many sensory pathways and the animal’s internal states. This meeting will gather...

4 December - 8 December 2023

Fundamentals of widefield and confocal microscopy and imaging

Heiko Gaethje, Aliaksandr Halavatyi, Stefan Marawske, Jens Marquardt

OverviewSponsors Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Registration is not yet open for this event If you are interested in receiving more information please register your interest Course overview Light microscopy is the most widely used form of microscopy for life science research The correct handling... OverviewSponsors Overview Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Course overview Light microscopy is the most widely used form of microscopy for life science research. The correct handling of the microscope and optimising image quality (e.g. contrast, resolution) as well as experimental design according to different applications are crucial to obtain the best results. This course will provide the participants with an overview about the basics of microscopy (light and optics, contrast techniques and imaging). The confocal part will include multicolor, 3D and time lapse imaging as well as spectral imaging, photobleaching (FRAP, FLIP, FLAP) and photoactivation techniques. Basic image analysis tools...

6 December - 9 December 2023

Computational structural biology

Jan Kosinski, Rommie Omaro, Christine Orengo, Samir Velankar

OverviewSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest Conference overview The field of... OverviewSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference overview The field of computational structural biology is undergoing a revolution. AlphaFold, a program based on Artificial Intelligence (AI), has transformed the structural modeling of proteins and protein complexes by reaching accuracy similar to experimental structures. Over 200 million structural models have already been released in AlphaFold Database. Following AlphaFold, other protein modeling programs proliferated from researchers worldwide. AI has started advancing RNA modeling too. The wealth of protein models has sparked...

20 February - 23 February 2024

The new cardiobiology

Pilar Alcaide, Johannes Backs, Tina Haase, Enzo Porrello

OverviewSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest Conference overview The cardiovascular... OverviewSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Conference overview The cardiovascular system is a multicellular and disseminated organ consisting of the heart, a network of vessels and circulating blood, thereby forming an intricately interdependent system, whose dysfunction is the leading cause of human mortality. Despite translational progress with impactful new interventional and pharmacological therapies, cardiovascular dysfunction continues to plague mankind. The current therapeutic approaches are either organ-centric or tackle the consequences of end-stage...

9 April - 12 April 2024

Diversity of plants: from genomes to metabolism

Barbara Ann Halkier, Sarah E. O’Connor, Detlef Weigel

OverviewSpeakersSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Registration is not yet open for this event If you are interested in receiving more information please register your interest Symposium overview This... OverviewSpeakersSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety policy for testing and other requirements if attending the on-site event. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview This inaugural EMBO | EMBL Symposium aims to showcase the future of plant biology. Going beyond the limited number of model plants that plant biologists have historically focused on (e.g. Arabidopsis, corn, rice), it is nowadays possible to use comparative approaches to uncover the mechanistic basis and the evolutionary drive for the enormous phenotypic variation among the 400,000 species of plants on Earth. Europe has a large and thriving community of plant biologists, with particular expertise in plant...