EMBL Events

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 staffProgrammePractical 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... OverviewSpeakers, trainers, and staffProgrammePractical 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 protein...

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. Please see EMBL’s COVID-19 safety recommendations if attending the on-site event. 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 VIZBI can be found at https://vizbi.org.

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...

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 - 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.  

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...

18 April 2023

From transcriptomics to mechanistic models of signalling

Daniel V. Thomas Lopez

Cellular signalling networks are the communication pathways that govern the behaviour of cells They allow cells to receive and process external signals such as growth factors and hormones and respond appropriately by activating specific gene expression programs or inducing cellular behaviours like proliferation migration and differentiation Disruptions in these signalling networks can lead to various diseases including cancer metabolic disorders and immune disorders Understanding the regulatory mechanisms of signalling networks is critical to developing effective therapies for these diseases One approach to discover signalling network alterations from omics data is through the use of upstream regulatory pathway analysis which aims to identify the transcription factors and upstream signalling regulators that control the expression of downstream genes This can be achieved through the joint analysis of omics data and the signalling network structure using methods such as CARNIVAL By using powerful algorithms and general purpose integer optimization solvers CARNIVAL explores the vast space of potential signalling alterations to identify a parsimonious signalling network that explains the measurements In this course participants will learn how to process differential gene expression data to estimate transcription factor activities with DecoupleR obtain and process prior knowledge networks with OmniPath and pypath and use CARNIVAL to infer signalling networks... Cellular signalling networks are the communication pathways that govern the behaviour of cells. They allow cells to receive and process external signals, such as growth factors and hormones, and respond appropriately by activating specific gene expression programs or inducing cellular behaviours like proliferation, migration, and differentiation. Disruptions in these signalling networks can lead to various diseases, including cancer, metabolic disorders, and immune disorders. Understanding the regulatory mechanisms of signalling networks is critical to developing effective therapies for these diseases. One approach to discover signalling network alterations from omics data is through the use of upstream regulatory pathway analysis, which aims to identify the transcription factors and upstream signalling regulators that control the expression of downstream genes. This can be achieved...

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... OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety recommendations 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 limited to histone marks...

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 recommendations if attending the on site event Symposium overview We are at the dawn of a new era of biology where we will start to understand how organisms function together and... 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 recommendations if attending the on-site event. 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 stressors 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 in the context of dynamic environments. These can be environments which are changed by disease, commensal cohabitation or competition, as well...

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... 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 recommendations 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...

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 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 the docker images used for the analysis. Computers for hands-on exercises will be provided along with demo...

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...

22 May - 26 May 2023

Expansion microscopy

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

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 Expansion microscopy ExM physically magnifies specimens allowing to obtain super resolution images using a conventional diffraction limited microscope such as confocal... 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 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 respective institutes....

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 recommendations 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 long-term protection and...

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 recommendations 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... 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 recommendations 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 epigenetic code and...

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 recommendations 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... 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 recommendations 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 fields. This...

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

This practical course teaches the basics of multicellular modelling to any researcher wishing to enter the field particularly experimentalists with no prior experience of computational modelling... OverviewSpeakersPreliminary ProgrammePractical InformationSponsorsMedia kit Overview Overview It is a “hands-on” course with 60% of the time devoted to students working on laptops performing exercises designed to give a practical familiarity with different types of computational modelling. The course focuses on the dynamics of multicellular systems- from embryos to organoids, covering both the molecular side (how gene regulatory networks perform pattern formation) and also the mechanical side in 2D and 3D (how the movements and activities of many cells together leads to tissue-level morphogenesis and organisation). Attendees will also work through the week in small groups on group projects, which will be presented on the last day to the whole class. Each day will end with a keynote lecture by a prominent researcher in the field, putting the topic of the day into context through an...

19 June - 20 June 2023

Terra incognita: navigating ethical boundaries in the life sciences

Lucia von Bredow

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview EMBL is committed to sharing research advances and sustaining scientific interaction through onsite and virtual courses and conferences We are delighted to announce that this conference will be held as a virtual event and invite you to join us online The virtual conference includes talks from invited speakers... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview EMBL is committed to sharing research advances and sustaining scientific interaction through onsite and virtual courses and conferences. We are delighted to announce that this conference will be held as a virtual event and invite you to join us online. The virtual conference includes talks from invited speakers, short talk presenters and networking opportunities. Conference overview The 23rd Science and Society Conference will examine the breadth of ethical issues present in the life sciences through the lens of molecular biology research. It will explore both the historical context of the intersection between research and ethics, and the fast pace of emerging ethical challenges in the life sciences through two case studies: technology ethics and organoid research. It will present...

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

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...

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.

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 recommendations 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 scientists...

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...

3 July - 4 July 2023

Development and morphogenesis: Symposium in honour of Maria Leptin

Fiona Watt

You are cordially invited to this symposium in honour of Professor Maria Leptin current President of the European Research Council and past Director of EMBO 2010 2021... If you are not redirected, please visit the event website.

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.

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,...

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... 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 recommendations 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...

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. 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 impossible to study before. The course has three main objectives: – First, to educate and inspire the next generation of scientists, by...

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 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... OverviewSpeakersPreliminary programmePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Symposium overview Recent progress in biology has led to an explosion of factual knowledge about the living world over a huge range of scales in space and time. Yet, many questions about how to make sense of this data remain across the entire diversity of the living world from the smallest bacterium to the ecosystems of the Serengeti. This meeting 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 to provide a platform to discuss perspectives on the role of theory in biology, and importantly also vice...

24 July - 4 August 2023

Plasticity in developing systems: time, space, and environment

Alexander Aulehla, Aissam Ikmi, Nicoletta Petridou, Alessandra Reversi

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 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... 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 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 to fundamental questions and challenges related to the study of how the...

1 September 2023

EMBL webinar

mattermost test... mattermost test

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 recommendations 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... 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 recommendations 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 linked to...

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 This course will take place at EMBL Heidelberg Please see EMBL s COVID 19 safety recommendations for testing and other requirements to attend this on site course Course overview Bioimage analysis has become a keystone of biological research the deluge of data produced by increasingly advanced... OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview This course will take place at EMBL Heidelberg. Please see EMBL’s COVID-19 safety recommendations for testing and other requirements to attend this on-site course. Course overview Bioimage analysis has become a keystone of biological research: the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data. Due to the complexity of the data, without such expert guidance, it is very likely that image analysis algorithms may be applied incorrectly, possibly even producing erroneous results. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly that even experts are overwhelmed.  This advanced course...

12 September - 15 September 2023

Developmental metabolism: flows of energy, matter, and information

Alexander Aulehla, Heidi Lempradl, Jonathan Rodenfels

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 recommendations if attending the on site event Overview The fundamental question of the role of metabolism in development has seen a revival in interest This is fueled by recent work shedding... 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 recommendations if attending the on-site event. 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? How does metabolic activity impact and constrain the emergence of form and function? What are the...

17 September - 22 September 2023

Genome engineering: CRISPR/Cas from cells to mice

Neil Humphreys, Kristof Kersse, Birgit Koch, Elisabeth Zielonka

OverviewProgrammePractical InformationSponsors Overview Course overview This course will provide training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR Cas9 system Participants will learn design of CRISPR targets using bioinformatics tools generation of gene knock outs knock ins and target validation using the most... OverviewProgrammePractical InformationSponsors Overview Course overview This course will provide training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR/Cas9 system. Participants will learn design of CRISPR targets using bioinformatics tools, generation of gene knock-outs/knock-ins, and target validation using the most current technologies. The course will be split into two groups (mammalian cells OR mice) based on participants’ expertise. Please note that all participants are expected to engage in all sessions. Participants should plan for approximately 1 hour extra per day for self paced learning modules. Audience This course is aimed at researchers who are familiar with basic molecular and cell biology techniques and who want to learn how to create an engineered mammalian cell line or mouse model using the...

18 September - 22 September 2023

Single cell RNA-seq analysis using Python

Juanita Riveros

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

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 recommendations 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 microbiota for...

2 October - 6 October 2023

Structural bioinformatics

Sophie Spencer

This course provides a guide to the commonly used methods and tools in structural bioinformatics to analyse and interpret experimentally determined and AI predicted macromolecular structure data Structural biology determining the three dimensional shapes of biomacromolecules and their complexes can tell us a lot about how these molecules function and the roles they play within a cell Data derived from structure determination experiments and Artificial Intelligence AI assisted structure prediction enables life science researchers to address a wide variety of questions This course explores bioinformatics data resources and tools for the investigation analysis and interpretation of both experimentally determined and predicted biomacromolecular structures It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts The course content will also cover predicting function and exploring interactions with other macromolecules Successful 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 course provides a guide to the commonly used methods and tools in structural bioinformatics to analyse and interpret experimentally determined and AI-predicted macromolecular structure data. Structural biology, determining the three-dimensional shapes of biomacromolecules and their complexes, can tell us a lot about how these molecules function and the roles they play within a cell. Data derived from structure determination experiments and Artificial Intelligence (AI)-assisted structure prediction enables life-science researchers to address a wide variety of questions.   This course explores bioinformatics data resources and tools for the investigation, analysis, and interpretation of both experimentally determined and predicted biomacromolecular structures. It will focus on how best to analyse and interpret available structural data to gain useful information given...

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 recommendations 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 illustrate how imaging...

9 October - 14 October 2023

Liquid biopsies

Anders Ståhlberg, Karin Sundfeldt

OverviewSpeakersPreliminary programmeSponsorsMedia 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 There is an increasing interest and need to analyze biomarkers in... OverviewSpeakersPreliminary programmeSponsorsMedia 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 There is an increasing interest and need to analyze biomarkers in liquid biopsies, including basic research and clinical applications. Liquid biopsies have several advantages including being minimally invasive, allow repeated sampling and sampling is often a clinical routine. This course will provide an overview of several techniques to detect and analyze liquid biopsy-based analytes such as circulating tumor cells, cell free tumor-DNA (ctDNA), miRNA, extracellular vesicles, mRNA, carbohydrates and proteins. Participants will be introduced to all aspects of liquid biopsies...

9 October - 13 October 2023

Metagenomics bioinformatics at MGnify

Shereen Pethania

Overview Learn about the tools processes and analysis approaches used by MGnify in the field of genome resolved metagenomics This course will cover the use of publicly available resources to manage share analyse and interpret metagenomics data focussing primarily on the assembly based approaches used in MGnify analysis The delivered content will involve participants learning via live lectures and presentations followed by live Q As with the trainers Practical experience will be developed in group activities and in computational exercises run using containerised tools on our training infrastructure 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 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 We reserve the right to change the format of this course or cancel it due to the ongoing coronavirus pandemic 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 four weeks For more information please visit the UK Government website... Overview Learn about the tools, processes, and analysis approaches used by MGnify in the field of genome-resolved metagenomics. This course will cover the use of publicly available resources to manage, share, analyse, and interpret metagenomics data, focussing primarily on the assembly-based approaches used in MGnify analysis. The delivered content will involve participants learning via live lectures and presentations, followed by live Q&As with the trainers. Practical experience will be developed in group activities and in computational exercises run using containerised tools on our training infrastructure. 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. We plan to deliver this course in an in-person manner onsite...

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... OverviewSpeakersPreliminary programmePractical informationSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Plese see EMBL’s COVID-19 safety recommendations if attending the on-site event. 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 every known biological process, there are still many key open questions. Often these important problems are tackled and...

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 informatonSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety recommendations 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... OverviewSpeakersPreliminary programmePractical informatonSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety recommendations 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

... 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 recommendations if attending the on-site event. 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, in association with EMBL, in Heidelberg Germany. This year’s programme will focus on the latest technological...

6 November - 9 November 2023

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

Vladimir Benes, Bjorn Textor

OverviewSponsors Overview Please see EMBL s COVID 19 safety recommendations 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... OverviewSponsors Overview Please see EMBL’s COVID-19 safety recommendations 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...

6 November - 10 November 2023

Solution scattering from biological macromolecules

OverviewSpeakers trainers and staffPreliminary virtual programmePreliminary on site programmePractical informationSponsors Overview 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 a virtual module and an on site module The series of online lectures will take place from 6... OverviewSpeakers, trainers and staffPreliminary virtual programmePreliminary on-site programmePractical informationSponsors Overview 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: a virtual module and an on-site module. The series of online lectures will take place from 6 – 10 November 2023. In addition to this, a small number of selected students that have completed the virtual module will be offered to take part in the practical component of this course that will take place in Hamburg from 27 November – 1 December 2023. When applying for this course you will have the possibility to apply for only a virtual module or for both virtual and on-site modules. Please note that only students that have completed the virtual module will be taken into consideration in the selection...

7 November - 9 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 and from each other These facilities play an essential role in enabling research in the molecular life sciences The landscape is constantly evolving as new research tools emerge as experiments become increasingly data intensive and as their clients experimental researchers become more exposed to the power of data driven biology This course will allow participants to share experiences discuss challenges and solutions that they face and plan ways to cope with the ever changing demands raised by the molecular life science field It will include sessions to learn from bioinformatics service providers hear how others have tackled common problems and work together to design core services resource them and measure their impact 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, and from each other. These facilities play an essential role in enabling research in the molecular life sciences. The landscape is constantly evolving as new research tools emerge, as experiments become increasingly data intensive, and as their clients – experimental researchers – become more exposed to the power of data-driven biology. This course will allow participants to share experiences, discuss challenges and solutions that they face, and plan ways to cope with the ever changing demands raised by the molecular life science field. It will include sessions to learn from bioinformatics service providers, hear how others have tackled common problems, and work together to design core services, resource them, and measure their impact. Additional...

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 recommendations 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 genomes, ranging...

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

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... OverviewSpeakersProgrammePractical informationSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety recommendations if attending the on-site event. 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 Mutation and clonal selection Cancer evolution Cancer genome medicine Emerging technologies in cancer genomics Genomic instability and mutational processes Cancer ecosystems and micro-environment What past participants say about the conference We have had excellent feedback on our past...

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 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... OverviewSpeakersPreliminary programmePractical informationSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. 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 leading researchers in the field to discuss different subcortical circuits involving various sensory modalities and revisit their increasingly complex and interconnected contributions to perception, behavior, and cognition. Furthermore,...

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 Amaro, Christine Orengo, Sameer Velankar

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 recommendations 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... 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 recommendations 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...

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 recommendations 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... OverviewSponsors Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety recommendations 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 cardiovascular disease (CVD). New basic research...

12 March - 15 March 2024

AI and biology

Mohammed AlQuraishi, Wolfgang Huber, Anna Kreshuk, Emma Lundberg, Oliver Stegle

The aim of this symposium is to catalyse synergistic interactions between AI researchers in different subfields of biology by exploring shared theoretical approaches cross domain experiments and data integration as well as shared topics in dissemination of tools and collaboration with colleagues in experimental labs... OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Artificial intelligence (AI) is transforming virtually all areas of science, and the life sciences are no exception. AI-based methods are pushing the limits of what is possible in experiment design, data analysis, and modelling. The aim of this symposium is to catalyse synergistic interactions between AI researchers in different subfields of biology by exploring shared theoretical approaches, cross-domain experiments and data integration, as well as shared topics in dissemination of tools and collaboration with colleagues in experimental labs. Furthermore, we will look into the future and discuss how the concerted actions of...

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 recommendations 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... OverviewSpeakersSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Please see EMBL’s COVID-19 safety recommendations 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 diversity at the genomic, genetic...

15 April - 18 April 2024

The mechanics of life: from development to disease

Prisca Liberali, Nicoletta Petridou, Amy Shyer, Andela Saric, Xavier Trepat

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

14 May - 17 May 2024

Cellular mechanism using phase separation

This conference will bring together scientists from soft matter polymer physics molecular biology structural biology and cell and developmental biology to study condensates in biology and disease... OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Phase separation is emerging as a common biophysical basis underlying many important cellular functions. This conference will bring together scientists from soft matter, polymer physics, molecular biology, structural biology, and cell and developmental biology to study condensates in biology and disease. Goals are to increase the awareness how important phase separation is for our understanding of many biological processes to explore the large repertoire of new tools generated by other disciplines that are ripe to be applied to complex problems related to phase separation to close the gap in transdisciplinary training to...

5 June - 8 June 2024

Microtubules: from atoms to complex systems

In recent years interdisciplinary approaches embracing cell biology genetics molecular biology biochemistry biophysics structural biology and mathematical modelling have made a tremendous impact on the microtubule field... OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview The microtubule cytoskeleton is essential for a wide variety of cellular functions, such as chromosome segregation, directed vesicle and organelle transport, cell motility and cell polarity. Impaired microtubule function can lead to human diseases including cancer and neurodegenerative disorders, where microtubules serve as important therapeutic targets. In recent years, interdisciplinary approaches embracing cell biology, genetics, molecular biology, biochemistry, biophysics, structural biology and mathematical modelling have made a tremendous impact on microtubule research. The progressive diversification of the microtubule...

18 June - 21 June 2024

Innate immunity in host-pathogen interactions

Gordon Brown, Michaela Gack, Felix Randow, Dominique Soldati-Favre, Cyril Zipfel

OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Registration is not yet open for this event If you are interested in receiving more information please register your interest Symposium overview This symposium provides a discussion platform for all scientists interested in the biology of infection Cell biologists... OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview This symposium provides a discussion platform for all scientists interested in the biology of infection. Cell biologists, microbiologists and immunologists will discuss in joint sessions recent progress in our understanding of host-pathogen interactions. Talks will focus on common processes, rather than particular infectious agents or host cell types, and the strategies of all major types of pathogens in their interaction with plants and animals will be covered. A better understanding of infectious diseases will come from the simultaneous analysis of microbial and host variables, which may open new avenues for treatment and...

30 September - 3 October 2024

Defining and defeating metastasis

Eduard Batlle, Johanna Joyce, Daniel Klimmeck, Joan Massagué, Samra Turajlic

This symposium will bring together researchers from diverse fields to enhance our understanding of the dissemination and metastatic colonisation of tumour cells It will provide a unique opportunity for interdisciplinary exchange on current approaches and future collaborations on metastasis and its therapeutic challenges... OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview This symposium will bring together researchers from diverse fields to enhance our understanding of the dissemination and metastatic colonisation of tumour cells. It will provide a unique opportunity for interdisciplinary exchange on current approaches and future collaborations on metastasis and its therapeutic challenges. What past participants say about the Symposium “The ‘Defining and Defeating Metastasis’ Symposium was probably the best conference I have attended during my PhD. Engaging speakers, new science, and plenty of opportunity to network and socialise – all a stone’s throw from the...

15 October - 18 October 2024

The complex life of RNA

This symposium brings together leaders in the RNA field post docs and students with the aim of disseminating and discussing the most recent findings of information added to mRNAs The programme will include among others sessions on transcription RNA processing and modification mRNA export and localisation mRNA surveillance and decay translation and the control of mRNA expression by microRNAs... OverviewSponsorsAbout Overview This conference will take place at EMBL Heidelberg, with the option to attend virtually. Registration is not yet open for this event. If you are interested in receiving more information please register your interest. Symposium overview Before the genetic information stored in DNA can be used to direct cell growth and metabolism, it has to be transferred into RNA. Messenger RNAs (mRNAs) that code for proteins and noncoding RNAs are key components in the transmission of genetic information in all life forms – from viruses to complex mammalian organisms. Exciting recent findings now reveal a new layer of information added to RNAs in the form of chemical marks (the epitranscriptome) that play a critical role in gene expression control. Following the great success of the 2022 edition of this long-standing symposium, we are looking forward to returning in 2024,...