Events archive

10 October 2024

A guide to UniProt for students

UniProt provides the scientific community with a comprehensive high quality and freely accessible resource of protein sequence and functional information This webinar will guide you through ways in which students and researchers at all career stages may take a structured approach to access the data in the UniProtKB and Proteomes sections of the UniProt protein function database The webinar will discuss the types of data that can be accessed and using sequence analysis tools how this data can be analysed to answer biological questions We will demonstrate how to find the function of a protein how the protein components of a pathway may be identified features of proteins of interest can be compared similar sections of sequence can be sought in other species and how whole data sets containing all the proteins expressed in an organism can be obtained By accessing sequence structural and functional data through UniProt we want researchers to be part of data s biological journey and support further work and adventures along the way...

9 October 2024

Visualising integrated single cell and spatial transcriptomics datasets

Spatial transcriptomics is a cutting edge field that has revolutionised our understanding of biological systems by integrating spatial information with transcriptomics technologies WebAtlas is a data pipeline and visualisation platform for integrated single cell and spatial transcriptomic data This webinar will introduce the WebAtlas platform and its collaboration with the BioImage Archive which is a free public archive for the biological imaging data particularly showcasing the importance of open FAIR data and cloud compatible scalable open data formats...

8 October - 11 October 2024

Molecular mechanisms in evolution and ecology

This conference series has become known for exploring yeasts as models to study questions of general relevance to evolution and ecology Experts will speak on a range of topics including evolution theory ecology genetics cell biology genomics systems biology metabolic modelling and engineering...

Gilles Fischer, Jordi van Gestel, Kimberley Kline, Sara Mitri, Antonis Rokas

2 October 2024

Building a spatial transcriptomics platform

The Light Imaging Facility LIF at EMBL Rome offers training and support to users for experimental design tissue sample processing imaging data acquisition and image analysis Importantly the LIF is also involved in technology development ensuring access to innovative sample and imaging techniques such as spatial transcriptomics and expansion microscopy This webinar will demonstrate how we built a service platform for spatial transcriptomics using our in house developed methods...

1 October - 5 October 2024

Computational Biology Training in Hematology 2024, Module 2

Computational Biology Training in Hematology CBTH provides early career researchers aiming to specialize in computational and quantitative biology aspects of hematology with a unique year long training and mentoring experience by top tier faculty CBTH is a joint effort of the European Hematology Association EHA and the European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI that aims to support the development of quantitative skills for hematology researchers through training and mentoring in computational biology...

Barbara Etzi

30 September - 3 October 2024

Defining and defeating metastasis

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...

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

25 September 2024

Developing data infrastructures and analytical systems for spatial omics

Spatially resolved omics technologies are revolutionising our understanding of biological tissues by introducing new ways to characterise tissue architectures and identify cell cell interactions However handling spatial omics datasets remains challenging due to the large heterogeneity of profiling technologies resulting in fragmented file formats and the plethora of arbitrary ways to store analysis results further exacerbates this fragmentation Additionally the data volume often exceeds the memory capacity of standard computing environments These challenges make it difficult to construct scalable interoperable workflows and to share them reproducibly with the scientific community In this webinar we will present a software solution the SpatialData framework that we developed in Python to address these data representation challenges Specifically we will demonstrate how our software infrastructure can be used to Represent data from the most commonly available assays in a unified wayManipulate query and compute statistics on the dataVisualise and annotate the data interactivelyPrepare the data for sharing to maximise interoperability...

23 September - 27 September 2024

Metagenomics bioinformatics at MGnify

Learn about the tools processes and analysis approaches used in the field of genome resolved metagenomics This course will cover the use of publicly available resources to manage share analyse and interpret metagenomics data focussing primarily on assembly based approaches 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...

Meredith Willmott

23 September - 27 September 2024

Single-cell RNA-seq analysis with Python

This course covers the analysis of single cell RNA seq data using Python and command line tools Participants will be guided through droplet based single cell RNA seq analysis pipelines from raw reads to cell clusters Furthermore you ll learn how to generate common plots for visualisation and analysis of gene expression data including TSNE UMAP and violin plots Please note that participants will not analyse their own data as part of the course There will however be ample opportunity to discuss their research and ideas with other course participants and trainers Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through trainer led computational exercises and group activities Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 00 17 30 BST each day of the course Trainers will be available to assist answer questions and provide further explanations during these times...

Juanita Riveros

18 September 2024

Inferring cell-cell communication through spatial transcriptomics data

By leveraging spatial coordinate information with expression levels of ligands and target receptors computational methods developed for analysing spatial transcriptomics data can predict biologically relevant signalling activity This activity is important for healthy tissue function and disease pathogenesis This webinar will present an overview of published computational approaches and databases used to infer spatially confined secreted and or cell contact mediated signalling with a particular focus on data generated from the 10X Genomics Visium assay Furthermore methods to link inferred cell signalling with specific cell types and downstream pathway activation will be briefly explored...

17 September - 20 September 2024

Reconstructing the human past: using ancient and modern genomics

Combining genome wide data from ancient and modern populations opens new windows into the past Population scale sequencing projects investigating past and present human diversity have already provided us with extraordinary insights into patterns of human variation and mobility through time and space This meeting will involve scientists from population genetics bioinformatics microbiology anthropology archaeology and history and will strengthen future interactions in this young research field that is already changing the way we think about our past and will shape how we study genetic variation in the future...

Johannes Krause, Ida Moltke, Maanasa Raghavan, Pontus Skoglund

15 September - 22 September 2024

Synthetic biology in action: engineering synthetic systems

OverviewSpeakersProgrammePractical InformationSponsorsMedia kit Overview Course overview Synthetic Biology SynBio has become a rapidly developing area for tackling a large number of challenges in life science research This is due to a combination of foundational advances in technologies such as large scale DNA synthesis and new methods that allow integrating such raw synthesis power...

Sven Panke, Vitor Pinheiro, Karen Polizzi, Nico Claassens, Velia Siciliano

11 September 2024

Technological advances and computational approaches for spatially-resolved transcriptomics

Spatially resolved transcriptomics enables high throughput gene expression profiling within the spatial context of tissues offering valuable insights into cellular function and tissue organisation By integrating spatial coordinates with gene expression data researchers can identify spatially co localised cell populations and uncover the spatial dynamics of gene expression This webinar will explore the latest technological advances and computational approaches for analysing spatially resolved transcriptomics data equipping participants to critically plan their experimental design and analyses...

9 September - 12 September 2024

Chemical biology 2024

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview The conference sets the stage for the dissemination and exchange of new developments in diverse emerging fields within chemical biology It is the largest and longest standing conference in the field being a...

Yimon Aye, Bryan Dickinson, Maja Köhn

9 September - 16 September 2024

Membrane protein expression, purification, and characterisation 3 (mPEPC3)

OverviewSpeakers and TrainersPreliminary pogrammePractical informationSponsorsMedia kit Overview Course overview This hands on course focuses on training participants on how to work with membrane proteins troubleshooting in the wet lab during solubilisation and reconstitution and conducting experiments at the beamlines and during early stages of cryoEM screening To perform integrated...

Maria Garcia Alai, Simon Mortensen, Kim Remans, Henning Tidow

2 September - 5 September 2024

Imaging mouse development

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview This workshop aims to bring together and help establish an emerging community with the common goal of four dimensional reconstruction of mammalian development A number of long standing questions surrounding...

Jan Ellenberg, Kate McDole, Isabel Espinosa Medina, Robert Prevedel, Shankar Srinivas

1 September - 6 September 2024

Genome engineering: CRISPR/Cas in cells and mice

OverviewSpeakersProgrammePractical informationSponsorsMedia kit 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...

Neil Humphreys, Kristof Kersse, Birgit Koch, Elisabeth Zielonka

1 September - 10 September 2024

Current methods in cell biology

The course aims to expose researchers with different backgrounds to the diverse cutting edge methods developed for cell biology to showcase how integrated approaches can address the current big questions in cell biology...

Niccolò Banterle, Beth Cimini, Simone Koehler

24 August - 27 August 2024

Transcription and chromatin

The meeting brings together leading experts covering all aspects of transcription including cis regulatory function long range regulation 3 dimensional looping the basal transcriptional machinery RNA polymerase regulation and function nucleosome positioning chromatin modifications chromatin remodelling and epigenetic inheritance of transcriptional silencing...

Shelley Berger, Eileen Furlong, Luca Giorgetti, Jürg Müller

18 August - 26 August 2024

Advances in cryo-electron microscopy and 3D image processing

This course provides the theoretical and practical foundations of advanced cryoEM techniques from sample preparation to data collection to image processing...

Julia Mahamid, Sebastian Eustermann, Simone Mattei, Lori Passmore, Henning Stahlberg

15 July - 19 July 2024

Proteomics bioinformatics

Thank you to those of you who have applied we have now selected our participants and wait list There are no more spaces available You can however register your interest for the 2025 course here This course provides hands on training in the basics of mass spectrometry MS and proteomics bioinformatics You will receive training on how to use search engines and post processing software quantitative approaches MS data repositories the use of public databases for protein analysis annotation of subsequent protein lists and incorporation of information from molecular interaction and pathway databases The practical elements of the course will take raw data from a proteomics experiment and analyse it You will be able to go from MS spectra to identifying and quantifying peptides and finally to obtaining lists of protein identifiers that can be analysed further using a wide range of resources The final aim is to provide you with the practical bioinformatics knowledge you need to go back to the lab and process your own data when collected This course is organised in association with the Vlaams Instituut voor Biotechnologie VIB the Flemish Institute for Biotechnology Pre recorded material may be provided before the course starts that you will need to watch read or work through to gain the most out of the actual training event In person courseThe 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...

Barbara Etzi

8 July - 9 July 2024

Hands-on Arthropod Bioinformatics Workshop

Join us for a 2 day workshop focused on hands on training on utilising web based data mining resources for arthropods Ensembl Metazoa and VectorBase to analyse both public and private datasets Omics data technologies allow scientists to analyse the genomes transcriptomes proteomes and genetic variability of arthropods These analyses enable the exploration of diverse research inquiries such as host pathogen interactions insecticide resistance diversity and many other aspects of behaviour biology and ecology In this workshop participants will learn to formulate testable hypotheses leveraging the power of these omics technologies To promote the accessibility and reuse of different data types numerous web based bioinformatics resources have been created Notably Ensembl and VectorBase stand out among a select group of essential resources for global research known as the Global Core Biodata Resources GCBRs and the Elixir Core Data Resources CDRs comprising only 31 and 37 members respectively As VectorBase is part of VEuPathDB insights gained can be extended to its other component sites encompassing parasites fungi and vertebrates Similarly within the Ensembl Genome project Ensembl Metazoa has the same type of tools and resources as Ensembl s sister sites...

Gloria I. Giraldo-Calderón

8 July - 12 July 2024

Time-resolved macromolecular serial crystallography

OverviewSpeakers and trainersProgrammePractical informationSponsorsMedia kit Overview Course overview The advent of serial crystallography at free electron laser sources and the following adaptation of these methods at 3rd and 4th generation synchrotrons have opened new possibilities to perform room temperature time resolved studies in macromolecular crystallography This course aims to...

Oskar Aurelius, Shibom Basu, Gisela Brändé, Arwen Pearson, Daniele de Sanctis

8 July - 13 July 2024

Time-resolved STED nanoscopy in life sciences

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview This six day comprehensive advanced microscopy course focuses on stimulated emission depletion microscopy STED and its application to biological questions Through lectures tutorials and practical workshops the course provides in depth knowledge on all aspects of STED Nanoscopy It covers the...

Marko Lampe, Andrea Mülter, Manuel Gunkel, Julia Roberti

4 July - 5 July 2024

From atoms to ecosystems – a new era in life sciences

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview The symposium will take place at EMBL Heidelberg Registration for the onsite event is now closed EMBL staff and alumni can join a waiting list via the link being circulated internally and in EMBL s alumni network Late virtual registration are still open to all by 3 July 2024 To take part in the symposium virtually ple...

Rolf Apweiler, Elena Conti, Anne Ephrussi, Eileen Furlong, Cornelius Gross, Rainer Pepperkok, Pavel Tomancak, Nassos Typas

4 July 2024

Ensembl Browser Workshop, Cenicafe

The one day browser workshop offers participants the possibility of gaining lots of hands on experience in the use of the Ensembl genome browser but also provides them with the necessary background information The workshop is primarily targeted at wetlab researchers The workshop will consist of a series of modules listed in the content Most modules consist of a presentation and a demonstration of the tools followed by the opportunity to do exercises Participants are encouraged to bring problems questions about their research and we will try to tackle these during the workshop using Ensembl...

Marco Aurelio Cristancho Ardila 

1 July - 5 July 2024

Bioinformatics for immunologists

This course will provide participants with an introduction to a range of bioinformatics resources and approaches applicable to immunological research Participants will gain experience in analysis pipelines for NGS experiments relevant to immunology including immune receptor sequencing RNA sequencing single cell RNA sequencing and flow cytometry data analysis Additionally participants will be introduced to how data from several sources can be integrated to provide a wider view of their research thereby enabling them to be more confident users of their own data and that from public sources...

Juanita Riveros

26 June 2024

Data visualisation principles for enhancing effective scientific communication

This webinar will provide an introduction to data visualisation principles It includes a review of basic concepts and showcases tools to improve your understanding and use of data visualisation for improved accessibility to your research As we know collecting data is just the first step to advancing scientific knowledge Data presentation techniques are the key to communicating your findings in a concise manner to improve understanding across audiences and ultimately strengthening your contributions to your field The webinar speaker Isabel Romero Calvo PhD MS Scientific Illustrator will present information that will help you gain insights into Gestalt principlesConcept of salience and graphic perceptionUse of colour in data visualisationAccessibility in data visualisationWe will conclude with a Q A session for the webinar attendees...

24 June - 28 June 2024

Cancer genomics and transcriptomics

This course will focus on the analysis of data from genomic studies of cancer It will also highlight the application of transcriptomic analysis and single cell technologies in cancer Talks and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the trainers Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 08 45 17 00 BST each day of the course Trainers will be available to assist answer questions and provide further explanations during these times...

Meredith Willmott

18 June - 21 June 2024

Innate immunity in host-pathogen interactions

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview This follow up meeting to the successful EMBO EMBL Symposia Innate immunity in Host Pathogen Interactions in 2016 2018 and 2022 will provide a discussion and networking platform for all scientists...

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

17 June - 21 June 2024

Summer school in bioinformatics

This course provides an introduction to the use of bioinformatics in biological research giving you guidance for using bioinformatics in your work whilst also providing hands on training in tools and resources appropriate to your research You will initially be introduced to bioinformatics theory and practice including best practices for undertaking bioinformatics analysis data management and reproducibility You will be required to review some pre recorded material for their group project prior to the start of the course Group projectsA major element of this course is a group project where you ll be placed in small groups to work together on a challenge set by trainers from EMBL EBI and external institutes This allows you to explore the bioinformatics tools and resources available in your area of interest and apply them to a set problem providing you with hands on experience relevant to your own research The group work will culminate in a presentation session involving everyone 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 your 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 Anu Shivalikanjli EMBL EBI Group project two Interpreting functional information from large scale protein structure dataThis 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 Marcus Bage EMBL EBI and Joseph Ellaway EMBL EBIGroup project three Modelling cell signalling pathwaysCurating 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 and Krishna Tiwari EMBL EBI Group project four Improving AI based bioimage analysis Artificial Intelligence AI algorithms outperform classical image analysis methods however the performance of these models is highly dependent on the quality of the annotated image datasets used to train them In this project you will explore the application of AI for biological imaging and the relationship between model training data and model performance You will use models stored in the BioImage Model Zoo and data in the BioImage Archive to fine tune and aggregate AI outputs The aim of this project will be to test evaluate and improve model performance on a diverse set of microscopy images and annotations within the BioImage Archive You will learn how to apply train tune and employ the most performant state of the art computer vision models This project serves as a valuable demonstration of how FAIR Findable Accessible Interoperable Reusable data plays an essential role in the training and enhancement of AI models Project mentors Aybuke Kupcu Yoldas EMBL EBI and Craig Russel EMBL EBI Group project five Single cell RNA sequencing analysis with PythonIn this project you will learn how to perform single cell RNA sequencing data analysis to investigate cell type heterogeneity and expression differences across conditions The analysis will be based on the SCANPY framework in Python You will start by collecting the raw count matrix and relevant metadata from the Single cell Expression Atlas After constructing the AnnData objects you will perform quality control preprocessing dimensionality reduction cell type annotation and differential expression analysis We will also explore the batch effect and its correction Project mentors Yuyao Song EMBL EBI and Anna Vathrakokoili Pournara EMBL EBI Group project six Networks and pathwaysThis 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 may also give a few R packages a try Project mentor Priit Adler University of Tartu...

Barbara Etzi

10 June - 14 June 2024

Systems biology: from large datasets to biological insight

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...

Juanita Riveros

9 June - 15 June 2024

C. elegans: from genome editing to imaging

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview C elegans is a popular experimental model that combines transparency reproducible anatomy traceable cell lineage sequenced genome and facile genetics allowing to dissect animal development physiology and behaviour across scales of genes cells and tissues This 7 day course will present...

Henrik Bringmann, Simone Koehler, Georgia Rapti, Pavak Shah

7 June 2024

AlphaMissense predictions for human genetic variation research

This webinar will explore AlphaMissense a model based on AlphaFold AlphaMissense is designed to analyse missense variants which are individual amino acid changes in proteins Classifying these variants is crucial for understanding which ones might contribute to disease development Our guest speaker from Google DeepMind will introduce AlphaMissense You will gain insights into its underlying technology how it analyses variants and what the generated scores represent Importantly all predictions from AlphaMissense are freely available to the scientific community The webinar will then showcase how EMBL EBI resources integrate AlphaMissense data This includes details on how the data is stored displayed and accessed by researchers studying human genetic variations We will conclude by a question and answer session with all the presenters...

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...

Carsten Janke, Thomas Müller-Reichert, Shinsuke Niwa, Kassandra Ori-Mckenney

1 June - 8 June 2024

Structural characterisation of macromolecular complexes

OverviewSpeakers and trainersFinal programmePractical informationSponsorsMedia kit Overview Course overview Recent developments in cryo EM ET super resolution microscopy and protein structure prediction coupled with increasingly sophisticated methods of sample preparation have revolutionised structural biology Educating the next generation of researchers on how to strategically...

Ana Casanal, Wojciech Galej, Eva Kowalinski, Carlo Petosa, Montserrat Soler López

26 May - 31 May 2024

Whole transcriptome data analysis

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...

Marco Beccuti, Vladimir Benes, Raffaele Calogero, Francesca Cordero

24 May 2024

Interpreting the effects of genetic variants on protein structure and function

Genetic variation between individuals results in a range of human phenotypes Variants that fall within coding regions of genes generally have direct effects on the proteins encoded by the genes with which they overlap This six hour virtual workshop will provide participants with an opportunity to gain hands on experience of using EMBL EBI tools and resources to assess the effects of genetic variants on the structure and function of proteins in a common workflow During the course a single example will be used throughout using different EMBL EBI tools and resources at each stage of the analysis pipeline The example will involve running a VCF file through the Ensembl Variant Effect Predictor VEP then following links to UniProt PDBe and AlphaFoldDB for further variant information and interpretation Virtual courseThis course will take place on Zoom Trainers will be available to assist during practical sessions answer questions and provide further explanations during the Zoom To join the course you will need to create an EMBL EBI Training website account...

Meredith Willmott

21 May - 23 May 2024

BioMalPar XX: biology and pathology of the malaria parasite

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview Malaria remains a major global public health challenge The emergence and spread of resistance to existing antimalarial drugs further complicates the fight against this ancient foe As the BioMalPar...

Sabrina Absalon, Jess Bryant, Fredros Okumu, Taco Kooij

15 May 2024

Accessing sequence analysis tools via the new Job Dispatcher website

The Job Dispatcher team at EMBL EBI provides access to various bioinformatics sequence analysis tools EMBOSS Clustal omega NCBI BLAST etc and biological datasets This webinar will introduce the new Job Dispatcher website showcasing how to navigate through various categories of tools and access them for sequence analysis We will also demonstrate the latest features and user documentation of the Job Dispatcher...

14 May - 16 May 2024

Open Virtual Ensembl REST API Workshop

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

Louisse Paola Mirabueno

14 May - 17 May 2024

Cellular mechanisms driven by 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...

Simon Alberti, Sara Cuylen-Häring, Dorothee Dormann, Alex Holehouse

14 May - 17 May 2024

Introduction to metabolomics analysis

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

Meredith Willmott

12 May - 17 May 2024

Advanced fluorescence imaging techniques

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...

Manuel Gunkel, Aliaksandr Halavatyi, Debora Keller-Olivier Joana Delgado Martins, Irina Rakotoson

9 May 2024

Exploring human disease and protein variant data in UniProtKB

UniProt KnowledgeBase UniProtKB supports biomedical research by providing a comprehensive high quality and freely accessible resource of protein sequence and functional information This webinar will provide an overview on how to access human disease and protein variant information available in UniProtKB It will outline the annotation of protein molecular function involvement in human disease as well as disease associated variants including variant position variant characterisation and their impact on protein structure and function It will present the protein variant viewer and feature viewer and demonstrate how the feature viewer facilitates visualisation of variant impact on protein features and 3D structure We will discuss the cross links to human specific databases and tools such as BLAST and Align In addition we will also demonstrate how to access and download human variation datasets available in UniProtKB By the end of this webinar attendees will have a solid foundation in navigating UniProtKB to access disease related protein data and utilising the various protein molecular data to analyse the impact of protein variants on protein function and structure...

8 May 2024

Wine yeasts as a model system in community ecology

Wine fermentation constitutes a transient microbial ecosystem wherein numerous yeast species originating from the grape surface engage in interactions This leads to an ecological succession anticipated to culminate in the ultimate dominance of Saccharomyces cerevisiae The diversity of yeast species found in grape musts has a direct impact on the final chemical and aroma complexity of the resulting wines Understanding the molecular and ecological interaction patterns between wine yeast communities is essential to harness diverse yeast functionalities with the final aim of producing tailored high quality wines In this webinar we will introduce the expectable phylogenetic and functional diversity in wine yeast communities we will discuss how to engineer wine yeast communities top down and bottom up and we will finally conclude about the necessity of adopting the adequate theoretical framework to address challenging questions in applied ecology and to finally improve microbiome based industrial processes You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionFirst global map of vineyard microbiomeBuilding a wine yeast collectionProspecting non conventional yeastQ A...

7 May - 9 May 2024

Open Virtual Ensembl Browser Workshop

Work with the Ensembl Outreach team to get to grips with the Ensembl browser accessing gene variation comparative genomics and regulation data and mine these data with BioMart...

Aleena Mushtaq

6 May - 8 May 2024

Building networks 2024: engineering in vascular biology

In this meeting we intend to bring together vascular biologists and bioengineers from across the world to build research synergies to tackle long standing questions in the field of vascular biology...

Maria Bernabeu, Claudio Franco, Stephan Huveneers, Milica Radisic

1 May 2024

Harmony in diversity: exploring the rich microbiomes of South American wildlife

Colombia and northern South America is known as a biodiversity hotspot but at the basis of that diversity is the microbial communities With recent advances in metagenomics the microbial communities and genomic composition has started to be characterised by unveiling a whole new world that is highly interconnected with macro organisms and the environment This webinar will illustrate the intricate world of microbial communities associated with diverse South American fauna From the high altitude realms of neotropical bumblebees to the depths of coral reefs we ll journey through the microbiome landscapes of beings like spectacled bears woolly monkeys lichens shrimps among others Discover the unseen connections shaping the health and resilience of these unique ecosystems You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionExploring microbial diversity in pacific coralsHow do probiotic species protect shrimp from disease The gut microbiota in Andean bearsMicrobiota diversity is related to dietary diversityMicrobial diversity during the fermentation of cacaoQ A...

24 April 2024

Introduction to the Ensembl Bacteria genome browser

Ensembl Bacteria is a browser for bacterial and archaeal genomes In this webinar we will explore Ensembl Bacteria to learn more about the latest data and where it came from view annotation of molecular interactions involving bacterial genes and comparative genomics data involving key bacterial species You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionWhy do we need genome browsers Ensembl Bacteria featuresTools in Ensembl BacteriaFinding a bacterial speciesHelp and documentation...

23 April - 26 April 2024

Organismal physiology

This symposium aims to provide a high visibility platform to scientists from multiple disciplines who use molecular genetic tools to probe inter organ communication signals that maintain homeostasis It will also directly address a fundamental and long term goal of the study of physiology how can recent developments in whole organism physiology pave the way to novel adapted and efficient therapies for multiple degenerative diseases...

Gerard Karsenty, Irene Miguel-Aliaga, Asya Rolls, Miguel Soares

22 April - 26 April 2024

Fundamentals of widefield and confocal microscopy and imaging

This course will provide the participants with an overview of the basics of microscopy light and optics contrast techniques and imaging...

Heiko Gaethje, Jens Marquard

22 April - 26 April 2024

Microscopy data analysis: machine learning and the BioImage Archive

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 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...

Meredith Willmott

17 April 2024

Statistical thinking for microbial ecology

Most microbial ecologists understand the importance of rigorous statistical analysis for conducting a replicable study However formal courses in the statistical analysis of high dimensional ecological data are rare and traditional courses in applied statistics may not teach skills applicable to modern microbiome analysis This webinar will introduce foundational concepts in statistics with a focus on applying these concepts to the analysis of modern microbiome datasets To illustrate these concepts we will use the field of differential abundance as a case study We will contrast popular differential abundance parameters and estimators specifically focusing on estimating meaningful contrasts using high throughput sequencing data You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionThree approaches to analysing dataCase study Microbial abundance parametersRadEmu and its applicationExamples of statistical tools suitable for different parametersQ A...

16 April - 20 April 2024

Computational Biology Training in Hematology 2024, Module 1

Computational Biology Training in Hematology CBTH provides early career researchers aiming to specialize in computational and quantitative biology aspects of hematology with a unique year long training and mentoring experience by top tier faculty CBTH is a joint effort of the European Hematology Association EHA and the European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI that aims to support the development of quantitative skills for hematology researchers through training and mentoring in computational biology The CBTH program will be organized with two multi day workshops in a city in Europe and a follow up session at the EHA Congress...

Sophie Spencer

15 April - 18 April 2024

The mechanics of life: from development to disease

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview The building blocks of life macromolecules cells tissues and organs act on each other via physical forces This interplay of physical forces between the units of life gives rise to complex behaviour...

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

15 April - 19 April 2024

Ultrastructure expansion microscopy

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...

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

11 April 2024

Curating proteins involved in Antimicrobial Resistance (AMR) in UniProt

UniProt is a comprehensive expert led publicly available database of protein sequence function and variation information This webinar will give a brief introduction to the UniProt website and then highlight resources which should be of interest to people beginning work on antimicrobial resistance AMR including students early stage researchers and clinicians AMR constitutes one of the world s most urgent public health problems We have been improving the annotation of various protein classes with a known role in AMR including beta lactamases efflux pumps ABC transporters and a group of proteins essential for the survival of resistant bacteria under therapeutic concentrations of antimicrobials collectively known as the secondary resistome Using these as examples we will introduce some of the UniProt resources UniProt annotations are widely disseminated to other databases including Rhea EnsemblBacteria PATRIC Bacterial Viral Bioinformatics Resource Center BioCyc EcoCyc and KEGG Please also take this opportunity to suggest additional curation targets to us to enable us to better support ongoing AMR research...

9 April - 12 April 2024

Diversity of plants: from genomes to metabolism

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview This inaugural EMBO EMBL Symposium will showcase the future of plant biology Going beyond the limited number of wild and crop plants that have historically been focused on modern comparative approaches...

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

8 April - 12 April 2024

scATAC-seq: attacking open chromatin in single cells

ATAC Seq stands for Assay of Transposase Accessible Chromatin and is a widespread method to profile open chromatin on a genome scale The goal of this introductory course is to teach the entire workflow of a single cell and bulk ATAC Seq experiment including library preparation sequencing data processing and downstream analysis by addressing a real biological question that will be answered at the end of the course...

Vladimir Benes, Ulrike Litzenburger, Judith Zaugg

8 April - 12 April 2024

Data-driven approaches to understanding dementia

This course provides individuals working in dementia research with the skills to access and analyse dementia data Participants will learn to apply bioinformatics methodologies combine different data types and utilise relevant dementia data resources enhancing their research capabilities in the field...

Juanita Riveros

28 March 2024

Explore Human Pangenome Reference Consortium (HPRC) data in Ensembl

The Human Pangenome Reference Consortium HPRC aims to construct a comprehensive and representative human pangenome reference to better illustrate the genomic landscape of diverse human populations In this webinar we will guide you on how to access HPRC data via the Ensembl genome browser We will explore the available gene annotation and genetic variation data of the sequence assemblies produced by the project...

27 March 2024

The Pathogens Portal: A gateway to vast biomolecular data for pathogen research

The COVID 19 pandemic starkly illuminated the crucial role of open biodata in combating infectious diseases EMBL EBI recognising this significance swiftly launched the COVID 19 Data Portal a centralised repository for SARS CoV 2 related biomolecular data Building upon this success the Pathogens Portal emerges as the spiritual successor expanding its scope to encompass a broader spectrum of pathogens The Pathogens Portal serves as a comprehensive resource for researchers clinicians and policymakers seeking access to a wealth of biomolecular data related to a diverse range of pathogens It aims to facilitate rapid knowledge discovery accelerate disease prevention and treatment strategies and foster collaboration across the scientific community This webinar introduces the Pathogens Portal to users demonstrating the why and how it exists how we decide what pathogens are included as well as a tour of the features in the portal It will deepen participants understanding of how to use the portal and introduce features that are part of the broader platform such as the datahubs a system for sharing data in a controlled access environment You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below Introduction to the pathogens portalWhat data types are included in the portalPathogens portal tourSearching and browsing dataQ A...

20 March 2024

Microbial biodiversity at schools and its link with children’s health

There is a wealth of microbial diversity in the environment in soil on plants and in the atmosphere Urbanisation usually involves disturbance and sealing of soil along with a decrease and alteration of vegetation This process drastically reduces natural microbial sources such as soil and phyllosphere leaf surfaces which also contribute to enriching the atmosphere Nevertheless in an urban environment other microbial sources are more common such as wastewater treatment trash and human associated microbes Significant differences have been observed in the environmental microbial communities between urban and non urban environments Several hypotheses highlight the importance of contact with diverse natural microbial communities for human health especially for children In this webinar using a case study of the Belgian B SEBALL project we will illustrate how to investigate microbial biodiversity at school playgrounds and its potential contribution to different aspects of children s health This case study showcases the possibilities and limits of 16S rRNA amplicon sequencing in the context of the biodiversity hypothesis Does microbial diversity benefit human health The answer seems to be more nuanced than expected We will also demonstrate the power of adjusting and generating hypotheses based on field microbiome data You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionCharacteristics of urban environments associated with urban diseasesThe human microbiome and its importanceMicrobiomes connecting One healthThe biodiversity hypothesisInvestigating the biodiversity hypothesis in Belgian schoolsQ A...

19 March - 21 March 2024

Metabarcoding and data sharing for environmental DNA

This course will demonstrate applying metabarcoding analysis to eDNA for assessing biodiversity Sequencing DNA barcodes from mixed sources of DNA is being increasingly used to survey biodiversity whether analysing dietary content from faecal derived DNA or monitoring aquatic species from water derived DNA This course will give an overview of metabarcoding with different barcoding genes to target particular taxa Using an example data set we will go from raw sequence data through to assigning taxonomy to the sequence variants and some examples of downstream community analysis Sessions will comprise presentations and self paced computer practicals guided by an online interactive book containing theory and practice code This virtual course will be delivered via live streamed talks on Zoom with support from instructors via Zoom and Slack during the timetabled sessions Computer practicals will run on a virtual training platform so attendees will not need access to a powerful computer or to install any software We are willing to make reasonable adjustments to facilitate learning where possible and will provide clear routes to enable anyone that requires this to discuss this with us ahead of the training...

Ajay Mishra

19 March - 22 March 2024

Biological oscillators: rhythms and synchronisation across scales

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia Kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview Are you interested to discuss oscillatory phenomena and biological dynamical systems accross temporal and spatial scales At this symposium multiple disciplines will come together in order to discuss...

Alexander Aulehla, Alan Hastings, Hanspeter Herzel, Carrie Partch

19 March - 22 March 2024

Protein quality control for downstream processes

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Purified proteins are used in various types of scientific experiments and fields For example in structural biology insights into the functional mechanisms can be obtained by elucidating the 3D molecular structure of proteins and protein complexes using technologies such as X ray crystallography cryo...

Karine Lapouge, Kim Remans, Bertrand Raynal

18 March - 22 March 2024

Livestock genomics

This hands on virtual course will introduce participants to methods and approaches for analysing genomic data from common livestock species including cattle pig chicken and sheep During the course participants will learn about the use of sequencing methods in the field of livestock genomics resequencing genomes locating variant data annotating genomes and carrying out GWAS approaches The course will also cover the use of public EMBL EBI resources such as Ensembl EVA and ENA to progress in your research as well as to submit and share your discoveries with the community and will present relevant use cases in the field The course will enable you to harness the wealth of publicly available farmed animal datasets held in EMBL EBI public archives and utilise our free services and tools to for example identify genetic variants associated with disease identify genetic markers associated with desirable breeding traits or use Ensembl Variant Effect Predictor VEP tool to predict the functional impact of genetic variants EMBL EBI is committed to support the livestock research community and industry to improve animal health and welfare increase productivity and reduce environmental impact Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available during the course hours maximum 09 00 18 30 GMT each day of the course Trainers will be available to assist answer questions and provide further explanations during these times...

Sophie Spencer

13 March 2024

Strain-resolved approaches for human microbiome studies

In the last few years the human microbiome has received great attention by the community due to its fundamental role in health and disease Advancements in the field have also been possible due to technological improvements in shotgun metagenomics including the development and application of computational approaches This webinar will introduce metagenomics for characterisation of the human microbiome with focus on computational tools to achieve strain level resolution This will comprise pipelines for generation of profiles as well as extraction of draft genomes It will also present some recent analyses aiming at conducting large scale scenario investigations including the use of machine learning approaches and the integration of human microbiomes with other sources You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionHow can we study the microbiome The shotgun metagenomics workflowMicrobiome and colorectal cancer CRC Strain resolved metagenomicsToward full mappability of the human microbiomeThe curated Food Metagenomic Data resourceQ A...

12 March - 15 March 2024

AI and biology

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...

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

11 March - 15 March 2024

Mathematics of life: modelling molecular mechanisms

This course will provide participants with an introduction and hands on training on modelling approaches tools and resources used in systems biology as well as touch on network analysis Computer models are increasingly used to understand the essential processes of biology Researchers in academic institutions as well as the pharmaceutical industry use mathematical models to generate hypotheses on how complex biomolecular systems work Modelling of biochemical pathways deregulated in disease conditions can offer mechanistic insights into the pathology help to elucidate mechanisms behind drug action and predict the dose required for treatment thus facilitating fundamental research and drug discovery This course will provide a helpful brief introduction to key modelling concepts and hands on training to use popular tools and resources used in this scientific field Virtual courseParticipants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 00 17 30 GMT each day of the course Trainers will be available to assist answer questions and provide further explanations during these times...

Juanita Riveros

6 March 2024

Bioinformatic approaches to understand the role of the human microbiome in health and disease

The human microbiome represents a diverse community of microbes with important roles for the maintenance of human health The wealth of metagenomics data currently available has brought about a new era of research for the human microbiome field The ability to reconstruct high quality microbial genomes purely from metagenomic sequencing data has unlocked our ability to study the hidden microbial universe living alongside us Given there are thousands of human associated bacterial species that cannot yet be experimentally characterised there is a need to develop and apply bioinformatics methods to better understand their role in health and disease This webinar will provide an overview of current metagenomic approaches to study the human microbiome and introduce several statistical methods that can be used to link its composition and function to different human phenotypes and populations You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionThe microbiome in human biologyWhat can metagenomics tell us What is genome assembly Evaluating genome MAG qualityLinking microbiome composition to phenotypeAdditional resourcesQ A...

4 March - 8 March 2024

Introduction to multi-omics data integration and visualisation

With the increase in the volume of data across the whole spectrum of biology more opportunities as well as challenges have been created to identify novel perspectives and answer questions in life sciences This may also include public domain data which can provide added value to data derived through researcher s own work and inform experimental design This introductory course will highlight the challenges that researchers face in integrating multi omics data sets using biological examples The course will focus on the use of public data resources and open access tools for enabling integrated working with an emphasis on data visualisation This course will not include systems biology modelling or machine learning A major element of this course is a group project where participants will be placed in small groups to work together on a challenge set by trainers from EMBL EBI data resource and research teams This allows people to explore the bioinformatics tools and resources introduced in the course and to apply these to a set problem providing hands on experience of relevance to their own research The group work will culminate in a presentation session involving all participants on the final day of the course giving an opportunity for wider discussion on the benefits and challenges of integrating data You may refer to the previous group projects that were organised for this course in March 2023...

Meredith Willmott

4 March - 8 March 2024

Gene expression at spatial resolution

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview This interactive course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics Objectives The Visium Cytassist Spatial Gene Expression Solution uses probes targeting the whole transcriptome for intact tissue sections in morphological...

Vladimir Benes, Dirk Jürgensen, Elisabeth Zielonka

29 February 2024

UniProt for proteomics scientists

UniProt is a comprehensive expert led publicly available database of protein sequence function and variation information This webinar will give a brief introduction to the UniProt website and then highlight resources available that proteomics scientists or users with large protein datasets may find useful in analysing their data This will encompass our proteomes service how to convert and retrieve ID mappings how to carry out a peptide search and how to visualise new large scale proteomics derived PTM data The webinar will then go on to introduce the UniProt Proteins API which allows researchers to access and download UniProt data alongside large scale genomic proteomics and variation data without needing prior in depth knowledge of programmatic languages Data is available for download and querying in a range of formats including XML FASTA and PEFF The API multi query search functions will be demonstrated and useful features such as searching the database by peptide finding proteomic evidence of post translational modifications and accessing a protein entry to find its peptides will be explained The UniProt Proteins API is available at www ebi ac uk proteins api doc...

28 February 2024

Exploring metagenomes to assess microbiomes across the globe

A metagenome is a sequencing sample of a bulk microbial community providing a genetic snapshot of the entire microbiome sampled Metagenomics offers a comprehensive genetic overview of microbial communities without the limitations of culture based methods The introduction of the shotgun method of metagenomics has added the ability to quantify the phylogenetic and functional roles of microbes without primer bias As sequencing becomes more affordable shotgun metagenomics is becoming an increasingly popular method for assessing microbiomes This webinar will offer a brief introduction to metagenomics and discuss various concepts and methods used in modern metagenomics Specifically we will explore topics such as using microbial composition as an indicator of ecosystem state using functional genes as biosensors and the insights that can be gleaned from genomic structure You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionTowards a planetary microbiomeWhat is a metagenome Scientific concepts and toolsMetagenome assembled genome MAG Metagenomics datasetsUseful toolsQ A...

27 February - 1 March 2024

Integrative analysis of multi-omics data

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Biological and biomedical research is increasingly driven by assays that measure multiple omics data types multi omics at single cell resolution and or with spatial resolution transcriptome proteome genomic variants epigenetic marks metabolome functional assays imaging Joint...

Wolfgang Huber, Oliver Stegle, Britta Velten

20 February - 23 February 2024

The new cardiobiology

OverviewSpeakersProgrammePractical informationSponsorsMedia kitPre conference workshop Overview This conference will take place at EMBL Heidelberg with the option to attend virtually 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...

Pilar Alcaide, Johannes Backs, Tina Haase, Enzo Porrello

19 February - 23 February 2024

Exploring gene and environmental exposure interactions to understand human health and disease

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

Sophie Spencer

14 February 2024

Investigating microbial ecology in extreme habitats

Understanding the mechanisms by which microorganisms have adapted over geological time is crucial in anticipating how they will evolve in the future in the light of climate change and global warming Changes in climatic conditions may drive ecosystems which are currently characterised by average levels of main environmental parameters into the extreme which may in turn lead to higher abundances of extremophilic microbes The advent of high throughput sequencing has allowed researchers to further explore microbiomes in extreme habitats and investigate the mechanisms that they employ to overcome such hostile conditions This webinar will discuss publicly available shotgun metagenomics data from various extreme habitats It will also showcase how data processing with state of the art tools can provide valuable insights regarding the genomic potential of the microorganisms who inhabit such habitats You may either watch the entire presentation from the introduction or navigate directly to a specific section by clicking the links provided below IntroductionWhat is EMBRCExtreme habitats and extremophilesMethods and challenges to study extremophilesmetaGOflowClimate change and thermophilesQ A...

12 February - 16 February 2024

Introduction to RNA-seq and functional interpretation

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

Juanita Riveros

8 February 2024

Sequence analysis tools in UniProt: BLAST and Align

UniProt provides the scientific community with a freely accessible collection of protein sequences and functional information and is one of the most widely used protein resources in the world BLAST and the multiple sequence alignment are essential methods commonly used to find and compare protein or nucleotide sequences In this webinar we will demonstrate how you can access and run these sequence analysis tools in UniProt We will show you how to navigate the results and how you can exploit UniProt protein annotation to expand further the analysis of your results...

4 February - 9 February 2024

Analysis and integration of transcriptome and proteome data

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Systems biology is a still expanding field of research aiming to understand at the molecular level how cells tissues and organisms operate in their biological context Among the key technologies driving this forward are next generation sequencing and proteomics as they provide powerful means to...

Vladimir Benes, Raffaele Calogero, Jeroen Krijgsveld, Lennard Martens

31 January 2024

Exploring target-disease associations with the Open Targets Platform’s new interface

The Open Targets Platform https platform opentargets org is a comprehensive research tool that supports systematic identification and prioritisation of potential therapeutic drug targets By integrating publicly available datasets along with data generated by the Open Targets consortium the Platform builds and scores target disease associations Users can also explore relevant annotation information about targets diseases phenotypes and drugs as well as their most relevant relationships This webinar will provide an introduction to the capabilities and use cases for the Open Targets Platform and demonstrate two newly introduced features The new associations view enables users to dynamically modify the relative importance of the different data sources on the fly and the Target Prioritisation view provides an assessment of target specific properties of interest when evaluating the suitability of a target for a drug discovery programme There are major steps in our ongoing effort both to refresh the look and feel of the Platform and to enhance the Platform s capabilities to help build therapeutic hypotheses...

29 January - 31 January 2024

Cryo-EM in academia and industry

OverviewSpeakersProgrammePractical informationSponsors PartnersIndustry workshopsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually For late registrations please contact Lea Hohmann Due to the announced railway strike in Germany there will be additional buses on Sunday evening 28 January and Monday morning 29 January from...

Edward Avenell, Chun-wa Chung, Simone Mattei, Christoph Mueller, Chiara Rapisarda

22 January - 26 January 2024

Exploratory analysis of biological data: data carpentry

This hands on workshop teaches researchers the fundamental data skills they need to conduct their work and provides high quality domain specific training covering the full lifecycle of data driven research...

Renato Alves, Lisanna Paladin, Fotis E. Psomopoulos, Christian Schudoma

18 January 2024

Automated annotation in UniProt

UniProt is a high quality comprehensive protein resource in which the core activity is the expert review and annotation of proteins where the function has been experimentally investigated At the same time the UniProt database contains large numbers of proteins which are predicted to exist from gene models but which do not have associated experimental evidence indicating their function UniProt commits significant resources to developing computational methods for functional annotation of these predicted proteins based on the data in entries that have gone through the expert review process We will describe the two main automated annotation systems currently in use First UniRule which is an established UniProt system in which curators manually develop rules for annotation Second ARBA Association Rule Based Annotator which is a multi class learning system which uses rule mining techniques to generate concise annotation models ARBA employs a data exclusion algorithm that censors data not suitable for computational annotation and generates human readable rules for each UniProt release As part of our interest in engaging with the machine learning community we will also introduce the contribution of ProtNLM Protein Natural Language Model from Google Research which annotates proteins which have uncharacterised names We will also introduce UniFIRE an open source software that enables researchers to annotate their own protein dataset by using the above mentioned annotation systems In order to provide an easy and straightforward way to download and set up this tool we have containerised UniFIRE together with all its dependencies and the latest set of UniRule and ARBA rules In this webinar we will show how to create functional predictions for protein sequences by using this container image...

17 January 2024

An introduction to EMBL-EBI resources

EMBL EBI is the home of the world s most comprehensive range of freely available molecular databases and resources Our resources help researchers share and analyse data and perform complex queries in many different ways Join us for a tour of the core data resources at EMBL EBI During this webinar we will introduce the types of data available how you can search for data and the various ways of getting assistance We will also discuss the role of EMBL EBI in making data open and accessible and how you can include EMBL EBI data in your workflows We will also provide information on further online training to help you learn more about specific topics in bioinformatics and EMBL EBI resources including an introduction to the training collections The collections bring together videos and online tutorials on a specific topic to help get started...

14 December 2023

Uncovering protein function with UniProt

UniProt provides the scientific community with a freely accessible collection of protein sequence and functional information and is one of the most widely used protein resources in the world This webinar will cover what functional information is available in UniProt and where that information comes from It will also describe how the information is added to the resource and how to find it on the UniProt website...

12 December 2023

From transcriptomics to mechanistic models of signalling

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...

Daniel V. Thomas Lopez

6 December - 9 December 2023

Computational structural biology

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually 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...

Jan Kosinski, Rommie Amaro, Christine Orengo, Sameer Velankar

4 December - 8 December 2023

Fundamentals of widefield and confocal microscopy and imaging

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview 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...

Heiko Gaethje, Stefan Marawske, Jens Marquardt, Stefan Terjung

30 November 2023

Interpreting the effects of genetic variants on protein structure and function

Genetic variation between individuals results in a range of human phenotypes Variants that fall within coding regions of genes generally have direct and effects on the proteins encoded by the genes with which they overlap This four hour virtual workshop will provide participants with an opportunity to gain hands on experience of using EMBL EBI tools and resources to assess the effects of genetic variants on the structure and function of proteins in a common workflow During the course a single example will be used throughout using different EMBL EBI tools resources at each stage of the analysis pipeline The example will involve running a VCF file through the Ensembl Variant Effect Predictor VEP then following links to UniProt PDBe and AlphaFoldDB for further variant information and interpreation Virtual courseThis course will take place on Zoom Trainers will be available to assist answer questions and provide further explanations during the Zoom...

Meredith Willmott

29 November 2023

Studying metabolites and small molecules with MetaboLights and ChEBI

Metabolites are small molecules that play important roles in biological and cellular processes They act as signalling molecules serve as cofactors involved in energy production and storage and thus responsible for the maintenance growth and development of living organisms In this webinar we will first introduce metabolomics which focuses on the comprehensive analysis of metabolites within biological systems such as cells biofluids tissues or organisms from different ecosystems and health and environmental backgrounds In the second part of the webinar we will show how metabolite data is represented in MetaboLights an open access cross species and cross technique database for metabolomic experiments and derived information Studies in MetaboLights contain information across study design sample origin collection processing spectral data measurement data processing and metabolite identification The re use of data from MetaboLights can take various forms from identified metabolites towards interpretation with pathways reactions literature to a matrix for statistical modelling or even re processing of raw data In the final part of the webinar we will introduce MetaboLights partner database ChEBI that focuses on the nomenclature structure and biological properties of small molecules...

28 November - 1 December 2023

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

OverviewSpeakersProgrammePractical informationSponsorsMedia kit 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...

Hiroki Asari, Martha Bickford, Carl Petersen, Santiago Rompani

23 November - 24 November 2023

Exploring EMBL-EBI sequence analysis tools and managing bioinformatics workflows

The European Bioinformatics Institute EMBL EBI offers a wide range of bioinformatics sequence analysis applications for free through web and programmatic access This two day course is designed to provide a comprehensive overview of sequence analysis tools and how to use the workflows effectively covering hands on exercises and demonstrations throughout The first day focuses on learning about the types of sequence analysis tools and how to use different tools in your analysis There will be a focus on sequence alignment e g Clustal Omega EMBOSS sequence similarity search tools mainly on how to perform Blast against the UniProt databases and using InterProScan for protein functional analysis The second day focuses on alternative methods of accessing the tools and how they help enhance flexibility in sequence analysis using web service clients and managing workflows...

Ajay Mishra

22 November 2023

Accessing single cell transcriptome data with the Human Cell Atlas Data Portal

The Human Cell Atlas is an ambitious project that aims to map the transcriptome of all the cell types in the human body This effort relies on single cell data generated from hundreds of labs across the globe which will be combined together into one comprehensive reference atlas The Data Portal helps to coordinate the data produced and standardise the format of data and metadata to reduce the burden of the integration efforts In this webinar we will provide an overview of data generation for HCA and how the data is curated for the Data Portal We will demonstrate how to navigate the Data Portal to find data that can be used for integration or as controls for your studies how to access the data and how to find the latest data from the integration efforts...

20 November - 22 November 2023

25th EMBL PhD Symposium

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...

2023 EMBL PhD Symposium Organising Committee

20 November - 24 November 2023

Genome bioinformatics: from short- to long-read sequencing

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

Sophie Spencer

16 November 2023

Programmatic access to UniProt using Python

UniProt is a comprehensive expert led publicly available database of protein sequence function and variation information This webinar will give an overview of programmatic access to the UniProt database using Python and cover key aspects of protein entry searches data filtering batch downloads and give examples of further processing of downloaded target data Following a brief introduction to UniProt services where to find relevant documentation and help features the webinar will focus on worked examples These will include how to programmatically search and retrieve protein entries and sequences within the results we will then show how to align orthologous sequences and filter for features of interest The webinar will also cover programmatic examples of the UniProt ID mapping service batch downloads filtering and processing data...

15 November 2023

Complex Portal: from proteins to complexes

Complex Portal is a curated resource designed to offer insights into proteins and their higher level complexes These complexes play a crucial role in governing protein functionality and stability In this webinar we will introduce the portal and address how we define protein complexes how they are different from molecular interactions including the data curation priorities and coverage We will also demonstrate how to search complexes using a variety of accession numbers keywords and how to use the organism specific search Further we will also demonstrate examples of complex details pages that include visualisation tools and link outs to related databases...

15 November - 17 November 2023

Cancer genomics

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...

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

13 November - 17 November 2023

Hands-on flow cytometry: learning by doing!

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...

Daniel Gimenes, Diana Ordonez, Steffen Schmitt

12 November - 14 November 2023

Protein Structure Determination in Industry 2023

EMBL EBI and GSK are co organising the 31st Protein Structure Determination in Industry Meeting hosted at the Hinxton Hall Conference Centre...

8 November 2023

Exploring protein families and domains using InterPro

InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites using predictive models provided by 13 different databases This webinar will take you through the different ways to search the InterPro website and its API to identify protein families and domains We will explore different use cases including how to use the InterPro sequence search functionality to identify the protein family membership the different domains and potentially the protein function of unknown proteins We will also explain how InterPro can be used to identify new protein domains using AlphaFold structure predictions...

8 November - 11 November 2023

The mobile genome: genetic and physiological impacts of transposable elements

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...

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

7 November 2023

Multiscale model of the different modes of invasion: a PhysiBoSS application

The tumour microenvironment encompasses many different cell types including cancer cells stromal cells immune cells and the extracellular matrix ECM that interact and collectively influence cancer progression and treatment outcomes Recently computational mathematical models have been proved efficient in testing hypotheses and giving insights about tumour microenvironment functionalities Among those hybrid multiscale models combine different techniques that simulate both inter and intra cellular interactions In this context we present a 3D model of cancer cell invasion aiming to study the different modes of cell migration through the extracellular matrix and to predict means to block it by considering spatial information molecules diffusion and intracellular regulation The model was constructed using PhysiBoSS a multiscale framework which combines agent based modelling and continuous time Markov processes applied on Boolean network models Our multiscale model successfully reproduces single and collective migration processes reported in published experiments on cell invasion These experiments include various aspects such as the role of p63 expression in regulating MT1 MMP the spatio temporal activation of SRC triggering collective migration and the influence of different collagen densities on invasion modes In silico experiments can be performed to suggest potential targets capable of inhibiting highly invasive tumour phenotypes About the speakerMarco Ruscone is a PhD student in the Computation Systems Biology of Cancer group at Institut Curie Paris He started his academic career in Turin Italy where he pursued his bachelor degree in Physics and master degree in Physics of Complex Systems for the Biology at Universit degli Studi di Torino Currently his work focuses on developing multiscale models of cancer using a mixed approach of agent based modelling and simulation on Boolean networks...

Marco Ruscone

7 November 2023

How to make your research open with Europe PMC

Europe PMC is an open global database of life science publications and preprints hosted by European Bioinformatics Institute EMBL EBI Europe PMC is endorsed and supported by a group of international science funders including Wellcome World Health Organisation European Research Council and many others as their repository of choice The Europe PMC funders expect research outputs arising from research they support to be made freely and readily available In this webinar we will explain how researchers can make their research open using Europe PMC and cover the benefits of including publications and preprints in Europe PMC for authors and readers We will provide guidance on open access policies of Europe PMC funders and demonstrate how to include research publications in Europe PMC and PubMed Central USA...

7 November - 9 November 2023

Managing a bioinformatics core facility

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 A limited number or travel bursaries are available Please see the Additional information tab for conditions...

Juanita Riveros

6 November - 9 November 2023

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

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview This course will focus on the latest state of the art sequencing platform technology and novel library preparation protocols We will start with experimental design focusing on the hands on library preparation including best practices standards and potential pitfalls concluding with sequencing of...

John Baeten, Vladimir Benes, Björn Textor, Pingfang Liu, Laura Villacorta

6 November - 10 November 2023

Solution scattering from biological macromolecules

OverviewSpeakersVirtual programme 6 10 November 2023 On site programme 27 Nov 1 December 2023 Practical informationSponsorsMedia kit Overview Course overview This course consists of two parts a virtual module and an on site module The series of online lectures will take place from 6 10 November 2023 In addition to this a small number of selected students that have completed the...

Melissa Gräwert, Clement Blanchet

1 November 2023

Exploring protein sequences and functional annotations with UniProt

UniProt provides the scientific community with a comprehensive high quality and freely accessible resource of protein sequence and functional information This webinar will guide you through ways in which students and researchers at all career stages may take a structured approach to access the data in the UniProt KnowledgeBase UniProtKB section of the UniProt protein function database We will discuss the types of protein data that can be accessed and using sequence analysis tools how this data can be analysed to answer biological questions We will demonstrate how to find the function of a protein how the protein components of a pathway may be identified features of proteins of interest can be compared similar sections of sequence can be sought in other species and how whole data sets containing all the proteins expressed in an organism can be obtained By accessing sequence structural and functional data through UniProt we want researchers to be part of a journey through biology and support further work and adventures along the way...

25 October - 27 October 2023

Proteomics in cell biology and disease mechanisms

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

23 October - 27 October 2023

Systems biology: from large datasets to biological insight

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 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...

Jane Reynolds

22 October - 27 October 2023

FISHing for RNAs: classical to single molecule approaches

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Over the past decades it became evident that the specific amount and localisation of an RNA transcript are important to understand the biological function of its non coding gene Whereby state of the art in situ hybridisation ISH technologies are key to visualise these RNAs in a given tissue or...

Monica Ballarino, Imre Gaspar, Emerald Perlas, Elisabeth Zielonka

18 October 2023

Finding and interpreting protein structure and function data using PDBe-KB

Proteins are the workhorses of the cell responsible for most biological functions Though we can group related proteins through sequence similarity it is the 3 dimensional structure of these proteins that determines the functions of these molecules of life Therefore knowledge of protein structure and its relation to additional biological context can help us create a more complete understanding of how a protein works PDBe KB https pdbe kb org is an open collaborative data resource which aims to support the access and integration of structural biology data helping users to easily generate biological insights The Aggregated Views of Proteins provided through PDBe KB provide a unique way to display all the relevant structure and function data for a specific protein in one place This allows us to determine trends across these structures including common binding and interaction sites and identification of different conformations of the protein This webinar will give an introduction to the PDBe KB Aggregated Views of Proteins and how they can be used to access and interpret structure and function data...

18 October - 21 October 2023

Organoids: modelling organ development and disease in 3D culture

The aim of this meeting is to bring together researchers from different fields to enhance our understanding of how organoids can be formed and maintained how they can be used to study disease and how we might eventually use them to regenerate and replace human organ tissue...

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

17 October - 19 October 2023

Open Virtual Ensembl REST API Workshop

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

Louisse Paola Mirabueno

11 October 2023

Accessing and interpreting predicted protein structures from AlphaFold database

AlphaFold database AlphaFold DB provides open access to over 200 million protein structure predictions to accelerate scientific research This webinar aims to provide a comprehensive introduction to AlphaFold DB Participants will gain a clear understanding of the fundamental concepts principles and functionalities of the database They will learn how to access and evaluate predicted protein structures explore the underlying technologies and algorithms used in AlphaFold and identify the potential applications of AlphaFold DB in their research...

11 October - 14 October 2023

The non-coding genome

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...

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

10 October - 12 October 2023

Open Virtual Ensembl Browser Workshop

Work with the Ensembl Outreach team to get to grips with the Ensembl browser accessing gene variation comparative genomics and regulation data and mine these data with BioMart...

Benjamin Moore

9 October - 13 October 2023

Liquid biopsies

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course Overview There is an increasing interest and need to analyse biomarkers in liquid biopsies including basic research and clinical applications Liquid biopsies have several advantages including being...

Anders Ståhlberg, Karin Sundfeldt

9 October - 13 October 2023

Metagenomics bioinformatics at MGnify

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...

Meredith Willmott

5 October 2023

Poster winners, PerMedCoE Summer School 2023

This special edition of the PerMedCoE webinar series features speakers who were awarded poster prizes at the PerMedCoE Summer School 2023 Find out more about our speakers and their research Towards Tailored Cancer Therapies Robust platform for drug testing in patient specific Boolean models Viviam Berm dezComputational modelling of High Grade Serous Ovarian Cancer HGSOC Marco Fari asDissecting cellular communication in the tumour microenvironment through multiscale dynamical modelling Malvina MarkuAbout the speakerViviam Berm dez is a PhD candidate at the Norwegian University of Science and Technology specialising in Boolean models Her academic journey began in general biology back in her home country Venezuela at Sim n Bol var University Then she hopped over to Norway for a one year student exchange where she unexpectedly found herself staying longer to complete a master s degree in molecular cell biology diving deep into systems biology and cell modelling Now in her Computational Cancer Biology PhD she combines machine learning and modelling to address complex challenges of precision medicine Beyond her coding skills she also has green fingers so she finds peace caring for her plants during her free time Looking ahead she aspires to contribute to the field of precision medicine through her PhD project and continue exploring the fascinating world of digital twins without forgetting the ethical side of things Marco Fari as originally from Ponferrada in north western Spain is an enthusiastic nature lover who enjoys spending free time outdoors His academic journey began with a Bachelor s degree in Biology at the Complutense University of Madrid Following his interest for cellular and molecular biology he moved to Trondheim Norway where he pursued a Master s degree at the Norwegian University of Science and Technology NTNU During this period Marco did his thesis focusing on Boolean modelling of macrophage polarisation and its relevance to acute COVID 19 This research was conducted under the guidance of Martin Kuiper within the DrugLogics group Following the completion of the Master s program Marco moved to Barcelona and joined Marta Cascante s research group at Barcelona University There he delved into the intricate metabolic alterations triggered by SARS CoV 2 infection In his latest pursuit Marco returned to Trondheim to start his PhD journey at NTNU under the supervision of Kaisa Lehti His research leverages Boolean modelling to explore the dynamics of the tumour microenvironment and its influence on the aggressiveness of high grade serous ovarian cancer Malvina Marku studied her undergraduate degree in Physics at the University of Tirana Albania where she pursued her MSci project in the field of Nonlinear Dynamics studying the qualitatively universal behaviour of recursive systems As a PhD student on Computational Physics at the University of Tirana her PhD thesis focused on mathematical modelling of regulatory networks and inference methods of network reaction rates She joined Pancaldi s lab at the Cancer Research Center of Toulouse as a postdoc where she is currently working on multi scale dynamical modelling of the tumour microenvironment The research is focused on Chronic Lymphocytic Leukaemia CLL microenvironment and the crucial role of the cancer cell immune cell interaction in defining the cancer cell survival Her main interest is in applying dynamical modelling and networks theory to study the dynamics and emerging behaviour of complex biological systems and to gain a deeper understanding of systems evolution from the molecular network perspective She is interested in using computational models that are able to capture emerging biological behaviour and evolving patterns in spatially structured tumours for enabling more accurate and clinically relevant predictions regarding disease course and treatment outcome...

Viviam Bermúdez, Marco Fariñas, Malvina Marku

4 October 2023

Studying genes and genomes with Ensembl genome browser

The Ensembl genome browser provides data on genes variants comparative genomics and gene regulation for over 300 species Its sister project Ensembl Genomes www ensemblgenomes org consists of five sub portals bacteria fungi protists plants and invertebrate metazoa which contain data for over 2 000 eukaryotic including wheat barley tomato and brassicas and over 30 000 prokaryotic genomes This webinar will provide the participants with an introduction on how to use the Ensembl genome browser navigate the website and export data...

4 October - 7 October 2023

Seeing is believing: imaging the molecular processes of life

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...

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

2 October - 6 October 2023

Structural bioinformatics

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...

Sophie Spencer

2 October - 4 October 2023

Signaling through Chromatin: from molecules to ecosystems

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27 September 2023

Nucleotide sequencing data submission and retrieval at the ENA

The European Nucleotide Archive ENA is an open access supported platform for the management sharing integration archiving and dissemination of sequence data The archive provides a comprehensive record of the world s nucleotide sequencing information covering raw sequencing data sequence assembly information and functional annotation This webinar will introduce you to the data and metadata structures for nucleotides at the ENA It will support you in learning about how you can submit data to this archive and retrieve submitted data relevant to your field of work...

21 September 2023

A guided tour of improvements to the UniProt website

This webinar will provide an interactive introduction to the UniProt website Developed with our user community in mind the website aims to allow users to access all data provided by the UniProt consortium while being adaptable enough to meet the evolving needs of our users Join us to find out how our website is structured to enable users to better navigate and find content in our various databases Also discover how to use our tools BLAST Align Peptide search and ID mapping and how to organise them in the Tools results dashboard where the user can view and revisit their previous BLAST Align Peptide search or ID mapping jobs save them as favourites or resubmit them We hope that this interactive webinar will introduce you to all the features and show you some of the latest improvements we implemented into the new website...

20 September 2023

Using RNAcentral to explore and investigate non-coding RNA sequences

Non coding RNAs ncRNAs are a key molecule for life They are involved in many complex biological processes from gene regulation to translation This complexity has led to an explosion of many different databases with specialised focuses and data RNAcentral provides users a single entry point into the complexity of ncRNA data This webinar will show users how to effectively navigate and search RNAcentral Additionally we will show users how to download data for their own analysis and tooling We will highlight commonly used data formats such as BED GFF3 and FASTA files Finally we will demonstrate how to use the RNAcentral sequence search to quickly explore sequences...

20 September - 23 September 2023

The human microbiome

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...

Manimozhiyan Arumugam, Ami Bhatt, Peer Bork, Nicola Segata

19 September - 22 September 2023

CCPBioSim workshop: structural bioinformatics resources and tools for molecular dynamics simulations

This introductory workshop will provide hands on training on protein and structural bioinformatics resources in the context of molecular dynamics biomolecular modelling and simulations The workshop is sponsored by the Collaborative Computational Project for Biomolecular Simulation CCPBioSim Participants will gain knowledge and skills for searching selecting and assessing publicly available protein biodata for use in downstream methods relating to biomolecular modelling and molecular dynamics simulations The workshop will begin with an introduction to basic concepts in genomics and associated resources then to protein resources their uses and limitations and validation of both experimentally and predicted protein structures Finally the workshop will cover variant effect prediction and offer participants hands on group projects to bring together the previous days training with highly experienced mentors During this time participants will work with simulated datasets to answer small research questions then present findings thereafter Participants will also get the chance to network with one another trainers and workshop organisers...

Jane Reynolds

18 September - 22 September 2023

Single cell RNA-seq analysis using Python

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...

Juanita Riveros

17 September - 22 September 2023

Genome engineering: CRISPR/Cas from cells to mice

OverviewSpeakersProgrammePractical InformationSponsorsMedia kit 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...

Neil Humphreys, Kristof Kersse, Birgit Koch, Elisabeth Zielonka

13 September 2023

Digital twins for drug repurposing by integrating mathematical modelling and machine learning: bridging the gap between in silico and real-world data

The rapid development of computational approaches has revolutionised the field of drug discovery and repurposing Here I will show a practical application of digital twins built by the synergistic combination of mathematical modelling of the cell and machine learning techniques to identify potential drug candidates for repurposing and subsequently validate their efficacy using real world data After discussing the inherent challenges associated with traditional drug discovery methods and the need for alternative approaches I will introduce the concept of digital twins virtual replicas of real biological systems which leverage mathematical models to capture the intricacies of cellular behaviour and response to drugs By integrating machine learning algorithms these digital twins can be trained on vast datasets to predict drug effectiveness and identify promising candidates for repurposing Moreover I will emphasise the importance of validating these predictions with real world data obtained from biomedical databases to ensure reliability and efficacy The presentation aims to showcase the power of integrating mathematical modelling digital twins and machine learning for drug repurposing paving the way for accelerated and cost effective drug discovery processes About the speaker Dr Joaqu n Dopazo is the director of the Computational Medicine Platform of Fundaci n Progreso y Salud He holds a degree in Chemistry and a PhD in Biological Sciences He has previously worked in public centres like the CIPF Valencia CNIO Madrid and companies like GlaxoWellcome SA Tres Cantos His field of work is personalised medicine with an approach that includes systems biology mathematical modelling and artificial intelligence areas in which he has published more than 350 articles...

Joaquín Dopazo

12 September - 15 September 2023

Developmental metabolism: flows of energy, matter, and information

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety 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...

Alexander Aulehla, Heidi Lempradl, Jonathan Rodenfels

10 September - 15 September 2023

Advanced methods in bioimage analysis

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This course will take place at EMBL Heidelberg 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...

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

6 September - 10 September 2023

Protein synthesis and translational control

OverviewSpeakersProgrammePractical informationSponsorsMedia kitPre conference workshop Overview For late registrations please contact Diah Yulianti at diah yulianti embl de This conference will take place at EMBL Heidelberg with the option to attend virtually Conference overview Mechanisms that shape cellular proteomes are critical for life This conference focuses on the process...

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

24 July - 4 August 2023

Plasticity in developing systems: time, space, and environment

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview 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...

Alexander Aulehla, Aissam Ikmi, Nicoletta Petridou, Alessandra Reversi

18 July - 21 July 2023

Theory and concepts in biology

OverviewSpeakersProgrammePractical 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...

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

18 July - 20 July 2023

Open Virtual Ensembl REST API Workshop

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

Louisse Paola Mirabueno

16 July - 21 July 2023

Drosophila genetics and genomics

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...

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

11 July - 14 July 2023

Predicting evolution

The conference will explore the evolution of biological systems at different levels from genes and molecules to organism development and ecology...

Justin Crocker, Gautam Dey, Joshua Payne, Patricia Wittkopp

11 July - 13 July 2023

Open Virtual Ensembl Browser Workshop

Work with the Ensembl Outreach team to get to grips with the Ensembl browser accessing gene variation comparative genomics and regulation data and mine these data with BioMart...

Louisse Paola Mirabueno

10 July - 14 July 2023

Fluorescence imaging beyond intensity

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This course is organised in cooperation with Leica Microsystems Course overview As fluorescence lifetime based readouts become more accessible this course aims to provide a broad understanding of how the lifetime based information can be leveraged to solve biological questions This application centred course will...

Luis Alvarez, Manuel Gunkel, Birgit Koch, Andrea Mülter

10 July - 14 July 2023

Cancer genomics and transcriptomics

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...

Sophie Spencer

5 July 2023

A guide to sequence analysis resources in Job Dispatcher

The Job Dispatcher team at EMBL EBI provides access to various bioinformatics sequence analysis tools and biological datasets This webinar will introduce different tool categories and explain how to find access and use these tools for your sequence analysis It will cover the latest features and user documentation of the sequence analysis tools and also demonstrate how to access these tools programmatically...

3 July - 7 July 2023

Proteomics bioinformatics

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...

Shereen Pethania

3 July - 4 July 2023

Development and morphogenesis: Symposium in honour of Maria Leptin

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...

Fiona Watt

28 June 2023

Developing community resources for bioimage analysis training

Bioimage analysis is becoming an established field in bioinformatics however consolidated curricula and reusable training material are still hard to come by This webinar will showcase the development of an open website for hosting bioimage analysis training materials where everyone can use and contribute to the material...

27 June - 30 June 2023

New approaches and concepts in microbiology

This symposium will cover a broad range of topics in microbiology including antibiotic related research bacterial communities and microbiome cell biology regulation signalling pathogenesis and evolution Emphasis will be placed on novel approaches and technologies from systems based to single cell that drive each field or have the potential to revolutionise future research in microbiology...

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

25 June - 30 June 2023

Imaging-based spatial-omics

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview The aim of the course is to provide participants a comprehensive introduction to the various methods of spatial omics and in particular those of multiplex immunofluorescence and spatial transcriptomics We want to provide a general overview of the methods and assist researchers choose the right method...

Alvaro Crevenna, Emerald Perlas, Sinem Saka

25 June - 30 June 2023

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

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...

Juanita Riveros

21 June 2023

A guide to identifying suitable patient-derived cancer models in CancerModels.Org

Patient derived cancer models PDCMs have become an essential tool in both cancer research and preclinical studies Each model type offers unique advantages and is better suited for specific research areas cell lines are low cost and allow high throughput assays organoids model the impact of intratumour heterogeneity tumour evolution and drug response and patient derived xenografts PDXs retain the tumour architecture to better predict patient response to treatment Seamless access to PDCMs is however hindered by the lack of shared data standards As such PDCMs stakeholders i e researchers clinicians bioinformaticians and analytical tool developers are faced with the challenge to navigate a complex and siloed landscape across multiple commercial and academic resources CancerModels Org is a new cancer research platform that aggregates clinical genomic and functional data from PDXs organoids and cell lines The platform addresses the needs of the stakeholders by standardising harmonising and integrating the complex and diverse data associated with patient derived cancer models Its foundation is underpinned by our efforts to develop and promote the use of descriptive standards e g PDX MI PMID 29092942 to facilitate data interoperability and global sharing of models Further value is provided by enriching the models and data with concepts from well established terminologies e g NCI Thesaurus and links to external resources such as publication platforms raw data archives and cancer specific annotation tools enabling exploration and prioritisation of cancer model variation data CancerModels Org is freely available under an Apache 2 0 license https github com PDCMFinder...

19 June - 20 June 2023

Terra incognita: navigating ethical boundaries in the life sciences

OverviewSpeakersProgrammePractical 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...

Lucia von Bredow

19 June - 21 June 2023

Bioinformatics for principal investigators

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...

Jane Reynolds

18 June - 23 June 2023

Computational modelling of multicellular systems

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...

Katie Bentley, James Sharpe, Alejandro Torres-Sánchez

15 June 2023

Utilising GPUs in scientific algorithms

Nowadays GPU programming plays an important role in software development The massive parallel hardware enables us to analyze bigger datasets process data in finer details or visualize simulations in real time Still due to the programming complexity and the lack of knowledge GPUs are not regularly used in many scientific fields Thankfully GPU programming matures and provides simpler tools to utilize GPU hardware In this presentation we describe multiple GPU programming frameworks ranging from high level to low level and showcase them on selected bioinformatics algorithms About the speaker Adam melko is a third year doctoral student in the Department of Distributed and Dependable Systems at Charles University in Prague with the dissertation topic of Employing parallel computing in data intensive tasks He specializes in GPU programming and in the analysis of memory accesses in programs His current research topic involves development of tools for effective memory layouts and traversals of data structures...

Adam Smelko

12 June - 16 June 2023

Summer school in bioinformatics

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...

Sophie Spencer

12 June - 15 June 2023

Life at the periphery: mechanobiology of the cell surface

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually 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...

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

11 June - 16 June 2023

Quantitative proteomics: strategies and tools to probe biology

OverviewSpeakersProgrammePractical InformationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview This course will provide both theoretical and practical training in the use of quantitative proteomics Participants will learn the principles of the most frequently used data acquisition...

Jeroen Krijgsveld, Christina Ludwig, Mikhail Savitski

8 June 2023

Improving the accessibility of the EMBL-EBI website: background, process, and lessons

In the last couple of years there has been an increased interest in digital accessibility at EMBL EBI and our parent organisation EMBL In this webinar we will share how we have been making the case for accessibility and how we have made the EMBL EBI home page move to the top 1 for accessibility among the 1 000 000 most visited home pages in 2023 We will include practical tips on how to incorporate accessibility in the design and development process and share the lessons that we learned For more information please read this article written by Nikiforos Karamanis About the speakers Dr Nikiforos Karamanis is a Senior User Experience UX Designer at EMBL EBI who enjoys spending time with users developers and other stakeholders and helping them work together to achieve their goals using Lean UX methods He is the Product Owner of EMBL s Design System which provides components to build life science websites that follow best UX practices and meet accessibility standards Carla Oliveira is a UX Designer currently working at EMBL EBI in the Web development team In her role she applies her expertise to help design intuitive and user friendly interfaces for scientific and bioinformatics applications Carla s work involves collaborating with scientists researchers and developers to ensure that the complex data and tools provided by the institute are easily accessible and understandable to users...

5 June - 9 June 2023

Deep learning for image analysis

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

4 June - 7 June 2023

The ageing genome: from mechanisms to disease

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually 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...

Jacqueline Jacobs, Gaëlle Legube, Brian Luke, Björn Schumacher

24 May 2023

Contextualising human missense variation with ProtVar

Genomic variation can impact normal biological function in complex ways and so understanding variant effects requires a broad range of data to be coherently assimilated Understanding variation in proteins offers unique opportunities over and above diagnostics such as identifying drug targets and synthetic biology applications however it also poses unique challenges which is why most missense variation remain of unknown effect ProtVar is a new updated and maintained human variant annotation and assessment web tool which offers users unparalleled flexibility and ease of accessibility and integration It combines data and analyses from a plethora of resources to bring together genomic protein sequence functional as well as structural insights and predictions to better understand the potential effects of missense variation on humans This webinar will cover the variety of data types which can be used to access ProtVar and the ways in which such data can be submitted It will also cover the annotation and prediction types available as well as the visualisations available and the methods by which data can be retrieved...

23 May 2023

A beginner’s guide to interpreting results from biostatistics

This webinar will cover the general concepts behind hypothesis testing workflow including summary statistics null and alternative hypotheses and p values We will focus specifically on what you should pay attention to when you interpret results from a biostatistical analysis During the webinar we will be using gene expression as an example and work with visuals rather than equations to make the topic accessible to a broad audience...

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...

22 May - 26 May 2023

Microscopy data analysis: machine learning and the BioImage Archive

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...

Shereen Pethania

22 May - 26 May 2023

Expansion microscopy

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview 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...

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

21 May - 26 May 2023

Whole transcriptome data analysis

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...

Marco Beccuti, Vladimir Benes, Raffaele Calogero, Francesca Cordero

18 May - 19 May 2023

EMBL in Italy 2023: Chance and necessity-the indispensable role of curiosity-driven life sciences

This two day event includes speakers representing a diverse group of EMBL faculty and basic life science researchers and foundations from around Italy Its focus will be the indispensable role of curiosity driven fundamental research and its funding It is an excellent opportunity to reflect on basic research today and to connect with an impressive community of life scientists and funders...

17 May 2023

Annotating genomes with non-coding RNAs using Rfam and Infernal

Rfam is a database of RNA families that currently contains over 4 000 families Together with the Infernal software Rfam is commonly used to annotate non coding RNAs in newly sequenced genomes In this webinar we will give an overview of the data available in Rfam and give a live demo of annotating a genome with non coding RNAs using Rfam and the Infernal software We will also discuss recent efforts to synchronise Rfam and miRBase...

16 May - 18 May 2023

Practical biocuration

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 Group project 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 Michele Magrane Group project 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 Group project 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...

Sophie Spencer

15 May - 18 May 2023

Chromatin and epigenetics

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...

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

10 May 2023

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

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...

Tim Mauchline

10 May 2023

Data protection and privacy preservation in software development

When writing software to process health genetic or other sensitive data in High Performance Computing HPC clusters software developers and researchers must consider the requirements of the General Data Protection Regulation including the principle of privacy by design and the duties of data protection In this webinar we will highlight the risks of working with sensitive data on an HPC cluster and what are common software vulnerabilities We will discuss general best practices in software development and provide guidelines on how to handle data in applications We will also raise awareness of outside factors that affect data security and briefly mention important generic organisational measures that should be in place About the speaker Sarah Peter studied Bioinformatics and worked for a few years as a researcher and data manager at the Max Planck Institute Now she works at the Luxembourg Centre for Systems Biomedicine UNILU as an Infrastructure Engineer in the R3 and IT Infrastructure team She is also the liaison for the HPC team Since GDPR has come into effect she spends some of her time doing risk analysis for the institute s IT infrastructure and the HPC cluster...

9 May - 12 May 2023

The organism and its environment

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually 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...

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

8 May - 12 May 2023

Data visualisation for biology

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...

Jane Reynolds

7 May - 12 May 2023

Advanced fluorescence imaging techniques

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...

Aliaksandr Halavatyi, Stefan Marawske, Rainer Pepperkok, Stefan Terjung

3 May 2023

Historical perspectives on plant science databases

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...

Helen Anne Curry

26 April 2023

Applications and impacts of the BrAPI project on plant breeding

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...

Peter Selby

25 April - 27 April 2023

Bioinformatics resources for protein biology

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 3 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...

Juanita Riveros

25 April - 28 April 2023

Brain genome: regulation, evolution, and function

This symposium will explore how the brain genome is regulated in order to support neural function and neural plasticity...

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

19 April 2023

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

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...

Bill Baker

18 April 2023

From transcriptomics to mechanistic models of signalling

Event registration is now full 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...

Daniel V. Thomas Lopez

17 April - 18 April 2023

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

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...

Peter Harrison

17 April - 24 April 2023

Microbial metagenomics: a 360º approach

OverviewSpeakersPreliminary programmePractical informationSponsorsMedia kit Overview 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...

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

12 April 2023

Pangenomics and machine learning for crop improvement

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...

Dave Edwards

28 March - 31 March 2023

Introduction to metabolomics analysis

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...

Jane Reynolds

28 March - 31 March 2023

Visualizing biological data (VIZBI 2023)

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...

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

26 March - 1 April 2023

Measuring translational dynamics by ribosome profiling

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...

Pavel Baranov, Sebastian Leidel, Jan Medenbach, Elisabeth Zielonka

23 March 2023

Development of a virtual Rheumatoid Arthritis synovial fibroblast for large-scale dynamic analysis and efficient drug-target identification

Rheumatoid arthritis RA is a complex systemic autoimmune disease that primarily affects the lining of the synovial joints and involves an intricate interplay among genotype and environmental triggers Early RA starts with the infiltration of the synovial compartment by leukocytes Then the synovial fluid is inundated with pro inflammatory mediators inducing an inflammatory cascade characterised by fibroblast like synoviocytes FLS interactions with cells of the innate and adaptive immune system Cytokines are key mediators whereas drugs inhibiting these cytokines lead to RA therapies Unfortunately 40 of patients fail to respond to therapy Recently many studies have shown that RA FLS activation and the subsequent joint damage they perpetuate are associated with an altered metabolism that may be therapeutically targetable Thus RA FLS directed therapies could become a complementary approach to immune directed therapies I will present our efforts to construct a virtual RA FLS and develop a computational method to simulate large scale coupled logical and metabolic models using Boolean and constraint based modelling The digital RA FLS can be used to predict intervention points for minimising the sustained inflammation bone erosion and cartilage destruction and identify druggable metabolic switches that could help us reprogram these cells to acquire an anti inflammatory phenotype About the speaker Dr Anna Niarakis is an Associate Professor HDR at UEVE Paris Saclay affiliated with GenHotel European Research Laboratory for Rheumatoid Arthritis Genopole She holds a 3 year delegation for research at INRIA in the group Lifeware She has a broad scientific background in Biochemistry Biology and Pharmaceutical Technology and post doctoral studies in Computational Systems Biology Bioinformatics with expertise in complex human diseases She is a co leader of the Disease Maps consortium an active member of CoLoMoTo Consortium for Logical Modelling Tools and a former coordinator of SysMod Systems Modelling...

Anna Niarakis

22 March 2023

Single-cell and spatial omics technologies in plant science

Recent technological advances in single cell and spatial omics have revolutionised how we study biology by enabling researchers to see what used to be hidden behind the heterogeneity within the tissue Such technologies have been readily applied to study plants recently This webinar will showcase the application of single cell multiomics transcriptome and epigenome and spatial transcriptomics in plant research focusing on the development of a plant cell atlas and the understanding of plant microbe interactions...

Tatsuya Nobori

21 March 2023

Discover drug targets with Europe PMC Machine Learning Dataset and Open Targets

This webinar introduces the Europe PMC human annotated full text corpus for Gene Proteins Diseases and Organisms and highlights how it has been used to train machine learning models for systematic identification and prioritisation of potential therapeutic drugs by the Open Targets Platform This webinar will explain how to access and reuse the annotated corpus as an open community resource and provide an overview of the Open Targets Platform Europe PMC is an open access life science database of journal articles and preprints containing over 41 million abstracts and 8 7 million full text articles Open Targets Platform is an innovative public private partnership that uses human genetics and genomics data for systematic drug target identification and prioritisation Speakers Santosh Tirunagari is a Senior Machine Learning Developer at EMBL EBI with a PhD in Computer Science from the University of Surrey In 2018 Santosh was recognised with the prestigious Outstanding AI post doc research award from CogX The focus of his research is machine learning applied to problems of predictive analytics data driven modelling feature extraction and natural language processing Helena Cornu is the Communications Lead for Open Targets In this role she is responsible for both internal and external communications including running the Open Targets social media accounts writing and commissioning content for the blog and external outreach events She is always looking for opportunities to collaborate so please don t hesitate to get in touch Annalisa Buniello is the Product Manager for Open Targets In her role she oversees development and delivery of the Open Targets bioinformatics resources whilst liaising with users and stakeholders to ensure the products meet their needs...

21 March - 30 March 2023

Exploring human genetic variation

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...

Juanita Riveros

15 March 2023

Applying mathematical modelling to biological problems in plant science

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

Rea Laila Antoniou-Kourounioti, John Fozard

14 March - 16 March 2023

Open Virtual Ensembl REST API Workshop

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

Aleena Mushtaq

12 March - 17 March 2023

Extracellular vesicles: from biology to biomedical applications

A rapidly increasing number of researchers aim to purify and identify extracellular vesicles and many methodologies to isolate and analyse these vesicles are available and have been implemented This course will cover the basics possibilities and limitations of different purification and characterisation techniques and will address strategies to understand their role in biomedical applications...

An Hendrix, Cecilia Lässer, Esther Noltet Hoen, Guillaume Van Niel

9 March 2023

Supercomputer-based modelling and simulation for advanced biomedical applications

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

Mariano Vázquez

8 March 2023

Non-invasive phenotyping to quantify the dynamics of plant-environment interaction

Genes provide a toolbox by which plants can interact with their spatially and temporally highly dynamic environment The environment of shoots and roots are distinctly different in their spatial and temporal structures State of the art phenotyping allows deep analysis of these interactions using imaging and even tomographic devices above and below ground This webinar will introduce the concept of plant environment interaction in different spatial and temporal domains and will describe some case studies with modern technologies to study these interactions It will also define the ESFRI Plant Phenotyping Research Infrastructure EMPHASIS and the opportunities for accessing these globally unique facilities for deep phenotyping as well as high throughput and field phenotyping...

Ulrich Schurr, Roland Pieruschka, Sven Fahrner

8 March - 11 March 2023

The cellular mechanics of symbiosis

OverviewSpeakersProgrammePractical informationSponsorsAboutMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Symposium overview Host microbe interactions can be positive or negative for both a host organism and its symbiotic microbes Interacting with microbes can allow eukaryotes to acquire crucial functions like nutrient...

Toby Kiers, John McCutcheon, Thomas Richards

7 March 2023

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

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

Elliot Sollis

7 March - 8 March 2023

Introduction to HPC for Life Scientists

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

Marta Lloret Llinares

7 March - 9 March 2023

Open Virtual Ensembl Browser Workshop

Work with the Ensembl Outreach team to get to grips with the Ensembl browser accessing gene variation comparative genomics and regulation data and mine these data with BioMart...

Aleena Mushtaq

6 March - 10 March 2023

Introduction to multi-omics data integration and visualisation

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

Shereen Pethania

5 March - 10 March 2023

Techniques for mammary gland research

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview The mammary epithelium is a unique organ in that the majority of its development occurs postnatally This combined with ease of experimental access and a stereotypical growth pattern make it...

Martin Jechlinger, Renée van Amerongen, María dM Vivanco

2 March 2023

UniProt for proteomics scientists

UniProt is a comprehensive expert led publicly available database of protein sequence function and variation information This webinar will give a brief introduction to the UniProt website and then highlight resources available that proteomics scientists or users with large protein datasets may find useful in analysing their data This will encompass our proteomes service how to convert and retrieve ID mappings how to carry out a peptide search and how to visualise new large scale proteomics derived PTM data The webinar will then go on to introduce the UniProt Proteins API which allows researchers to access and download UniProt data alongside large scale genomic proteomics and variation data without needing prior in depth knowledge of programmatic languages Data is available for download and querying in a range of formats including XML FASTA and PEFF The API multi query search functions will be demonstrated and useful features such as searching entries by peptide and the new functionality of searching for proteomic peptides and modifications will be explained The UniProt Proteins API is available at www ebi ac uk proteins api doc...

Emily Bowler-Barnett

1 March 2023

Exploring plant genes and genomes with Ensembl

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

Guy Naamati

26 February - 3 March 2023

Analysis and integration of transcriptome and proteome data

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview Systems biology is a still expanding field of research aiming to understand at the molecular level how cells tissues and organisms operate in their biological context Among the key...

Vladimir Benes, Raffaele Calogero, Jeroen Krijgsveld, Lennart Martens

22 February 2023

Accessing variant data at the European Variation Archive

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

Baron Koylass

22 February 2023

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

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

St. Elmo Wilken

20 February - 24 February 2023

Introduction to RNA-seq and functional interpretation

Gain an introduction to the technology data analysis tools and resources used in RNA sequencing and transcriptomics The content will provide a broad overview of the subject area and introduce participants to basic analysis of transcriptomics data using the command line It will also highlight key public data repositories and methodologies that can be used to start the biological interpretation of expression data Topics will be delivered using a mixture of lectures practical exercises and open discussions Computational work during the course will use small example data sets and there will be no opportunity to analyse personal data In person course We plan to deliver this course in person in our training suite at EMBL EBI Hinxton Please be aware that we are continually evaluating the ongoing pandemic situation and as such may need to change the format of courses at short notice Your safety is paramount to us you can read our COVID guidance policy for more information All information is correct at time of publishing...

Sophie Spencer

12 February - 17 February 2023

In situ CLEM at room temperature and in cryo

Correlative Light and Electron Microscopy CLEM allows precise localisation of an event of interest within cells and tissues During this course we will focus on a specific method that has been developed at EMBL that enables the location of fluorescent proteins with high accuracy at the ultrastructural level The course will cover both the theory and practicals of high precision CLEM as well as opportunities to discuss their research with CLEM experts and receive practical and troubleshooting advice...

Ori Avinoam, Rachel Mellwig, Martin Schorb

10 February 2023

Accessing human disease and protein variant information in UniProtKB

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

Yvonne Lussi

9 February 2023

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

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

Melanie Goisauf, Emmanuelle Rial-Sebbag

8 February - 11 February 2023

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

There is an increasing awareness that mechanistic structural information on molecular machines is ideally generated within the context of intact cells in order to fully grasp how they function in a complex native environment Recent technological advances have nurtured the development of such in situ structural biology approaches in several disciplines including cryo EM mass spectrometry super resolution microscopy NMR computational modelling and others This conference will bring together experts and early stage researchers from these separate fields...

Martin Beck, Jan Kosinski, Julia Mahamid, Suliana Manley

6 February - 10 February 2023

Single-cell RNA-seq analysis using Galaxy

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

Jane Reynolds

1 February 2023

Exploring reproducible and reusable systems biology models with BioModels

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

Rahuman Sheriff Malik Sheriff

31 January 2023

Federated analysis for polygenic risk score calculations

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

Will Rayner, Anshika Chowdhary

31 January - 1 February 2023

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

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

Peter Harrison

26 January - 27 January 2023

Amity University EMBL-EBI workshop 2023

Amity University EMBL EBI workshop 2023...

Ben Moore

25 January 2023

Accessing fine-grained Molecular Interactions data with IntAct

This webinar will provide an introduction to molecular interactions and how to find these through the molecular interaction database IntAct We will demonstrate examples of how you can search for interaction data using advanced filter options how to create molecular interaction networks using our network viewer based on Cytoscape js and how to download the data for further analysis We will show how to access mutation data affecting the outcome of molecular interactions We will also provide a brief overview of two other resources PSICQUIC and IMEx that integrate molecular interactions from several sources...

Kalpana Panneerselvam

25 January 2023

Data-driven modelling of intercellular interactions in the tumour microenvironment

Monocyte derived macrophages help maintain tissue homeostasis and defend the organism against pathogens In tumours recent studies have uncovered complex macrophage populations including tumour associated macrophages which support tumorigenesis through cancer hallmarks such as immunosuppression angiogenesis or matrix remodelling In the case of chronic lymphocytic leukaemia these macrophages are known as nurse like cells and they protect leukemic cells from spontaneous apoptosis contributing to their chemoresistance We propose an agent based model of monocyte differentiation into nurse like cells upon contact with leukemic B cells in vitro We performed patient specific model calibrations using cultures of peripheral blood mononuclear cells from patients Using our model we were able to reproduce temporal survival dynamics of cancer cells in a patient specific manner and to identify patient groups related to distinct macrophage phenotypes Our results show a potentially important role of phagocytosis in the polarization process of nurse like cells and in promoting cancer cells enhanced survival About the speaker Dr Vera Pancaldi was trained as a physicist and soon found her way in systems and computational biology Since 2018 she leads a computational biology team at the Cancer Research Center of Toulouse CRCT working on modelling cancer and its interactions with the immune system Her main current focus is understanding the relationship between genome architecture and heterogeneity at various levels and relating heterogeneity in the phenotype of tumour infiltrating immune cells to patient s response to immunotherapy...

Vera Pancaldi

24 January - 27 January 2023

Computing skills for reproducible research: data carpentry

The course is aimed at graduate students and other researchers in the life sciences who would like to learn good practices in data management and analysis The course is ideally suited to students without prior experience in computational research but some familiarity with working with tabular data on a computer is welcome...

Renato Alves, Lisanna Paladin, Fotis Psomopoulos, Christian Schudoma

18 January 2023

Introduction to EMBL-EBI for teachers and trainers

EMBL EBI is the home of the world s most comprehensive range of freely available molecular databases and resources Our resources help researchers share and analyse data and perform complex queries in many different ways EMBL EBI also provides open access on demand training materials which are usable by teachers lecturers or trainers for teaching bioinformatics methods and tools During this webinar we will provide an overview of the range of EMBL EBI data resources and the role of EMBL EBI in making data open and accessible and an introduction to the training and materials EMBL EBI provides We will finish the webinar with a panel discussion to highlight the support for teachers that EMBL EBI Training provides which includes a large variety of free to access training material content This will help you identify specific topics in bioinformatics or EMBL EBI databases and tools the on demand training available and how you can access and adapt the training materials in your own teaching session Meet the panel Anna Swan Anna is a scientific training officer for e Learning at EMBL EBI She has a PhD in Bioinformatics from the University of Nottingham where she focused on the bioinformatic identification of biomarkers of osteoarthritis Following her PhD Anna worked as a medical writer spanning many therapeutic areas and working both on promotional and educational content for clinicians She has also worked as a data wrangler for the International Mouse Phenotyping Consortium at the project s data coordination centre based in the Medical Research Council s Harwell Institute Benjamin Moore Ben is Ensembl outreach manager and he organises workshops and other training events for Ensembl resources Ben has a PhD in Biological Sciences from the MRC Laboratory of Molecular Biology at the University of Cambridge Summer Rosonovski Summer is a Community Outreach Officer for Europe PMC an open literature database for life sciences developed by the European Bioinformatics Institute EMBL EBI Europe PMC indexes over 300 000 preprints abstracts and full text COVID 19 preprints from 20 life sciences preprint servers alongside published journal articles Before joining Europe PMC Summer obtained a PhD in Biophysics from The University of East Anglia investigating the alternative DNA structure the i motif Summer is passionate about accessibility in science believing that everyone should have access to research results and have the tools and training to understand scientific literature...

Anna Swan, Benjamin Moore, Summer Rosonovski

15 December 2022

Introducing PerMedCoE Building Blocks and Workflows to streamline biological analysis pipelines

Analysing biological datasets is nearly always a multi step process involving many interconnected stages Even so the lack of transparent approaches to managing complex data analysis pipelines remains a common challenge in the life sciences Another limiting factor is that completing such pipelines often requires in depth knowledge of many data analysis tools and programming languages There is therefore a continued need for methodologies that make complex biological data analysis pipelines easier to implement This webinar will present some of the main practical ways through which PerMedCoE seeks to make data analysis pipelines more manageable and accessible to researchers In particular the webinar will provide an overview of how the project addresses many biological use cases using a single shared approach in which semi automated workflows are constructed using purpose designed building blocks About the speaker Dr Jesse Harrison is a Senior Data Scientist and Project Manager at CSC IT Center for Science Ltd where he currently leads the Horizon EU BioDT project His other tasks have included R environment design maintenance and support on CSC computing platforms bioinformatics tool development and teaching Prior to joining CSC in 2019 Jesse held postdoctoral positions in microbial ecology astrobiology and environmental chemistry at the universities of Helsinki Turku Vienna and Edinburgh 2012 2019...

Jesse Harrison

14 December 2022

Exploring somatic mutations in cancer with the COSMIC database and analysis tools

COSMIC the Catalogue of Somatic Mutations in Cancer helps the global cancer research community conduct their science faster and better by presenting easy to understand streamlined and quality filtered data on cancer mutations We do this by providing high quality datasets curated by experts over the course of 18 years standardising our data into easily integrable formats and innovating with collaborators to provide analysis tools and actionable insights With 23 million genomic variants expertly curated from nearly 30 000 publications covering 6 800 precise forms of human cancer COSMIC is the world s largest manually curated database of somatic mutation information relating to human cancers This vast breadth and depth of high quality data is the gold standard relied upon by academic research and industry alike including pharmaceutical drug discovery and biotech companies This webinar will provide an introduction to COSMIC our process and demonstrate the vast range of data and analyses available via our multiple tools and projects We will focus particularly on two of our newer projects Cancer Mutation Census and Actionability which will be freely available for non commercial download as of 29 November 2022 We will also provide an opportunity for questions and hope that by the end of the webinar you will feel confident in exploring COSMIC s tools and understand how they can add value to your work...

Rebecca White, Steven Jupe, Jennifer Wilding, Michael Starkey, Helder Pedro

8 December 2022

Automated annotation in UniProt

UniProt is a high quality comprehensive protein resource in which the core activity is the expert review and annotation of proteins where the function has been experimentally investigated At the same time the UniProt database contains large numbers of proteins which are predicted to exist from gene models but which do not have associated experimental evidence indicating their function UniProt commits significant resources to developing computational methods for functional annotation of these predicted proteins based on the data in entries that have gone through the expert review process We will describe the two main automated annotation systems currently in use First UniRule which is an established UniProt system in which curators manually develop rules for annotation Second ARBA Association Rule Based Annotator which is a multi class learning system which uses rule mining techniques to generate concise annotation models ARBA employs a data exclusion algorithm that censors data not suitable for computational annotation and generates human readable rules for each UniProt release As part of our interest in engaging with the machine learning community we will also introduce the contribution of ProtNLM Protein Natural Language Model from Google Research which annotates proteins which have uncharacterised names We will also introduce UniFIRE an open source software that enables researchers to annotate their own protein dataset by using the above mentioned annotation systems In order to provide an easy and straightforward way to download and set up this tool we have containerised UniFIRE together with all its dependencies and the latest set of UniRule and ARBA rules In this webinar we will show how to create functional predictions for protein sequences by using this container image...

Pedro Raposo, Elena Speretta

7 December 2022

Chemical biology Q&A session

This Q A question and answer webinar will provide an opportunity for anyone who has completed Chemical biology A curated set of EMBL EBI online courses to join some of EMBL EBI s experts and ask their own questions This session will focus on exploring chemical compounds or drug molecules finding drug targets and target disease associations using resources such as ChEMBL and Open Targets The questions covered during the Q A webinar will depend on those asked by attendees however we will likely cover topics such as Curation and maintenance of chemical compounds database Chemogenomics Finding data about interactions between drugs or drug like molecules and their targets Drug discovery and target identification...

7 December - 9 December 2022

The spectra of life: dimensional breadth in biological research

Join us for the 24th 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...

2022 EMBL PhD Symposium Organising Committee

30 November 2022

Biocuration Q&A session

This Q A question and answer webinar will provide an opportunity for anyone who has completed Biocuration A curated set of EMBL EBI online courses to join some of EMBL EBI s experts and ask their own questions This session will focus on the role of biocuration in maintaining life science data and general data management It will also highlight the application of programming and text mining in biocuration The questions covered during the Q A webinar will depend on those asked by attendees however we will likely cover topics such as Biocuration principles Data management of biological data and open data Programming and text mining for biocurators Finding the right EMBL EBI resource for accessing or submitting data...

29 November - 2 December 2022

Protein quality control for downstream processes

The course will focus on the importance of protein quality control and introduce methodologies that can be used to assess and improve sample quality...

Karine Lapouge, Kim Remans

23 November 2022

The environmental impact of computational biology

The environmental impact of scientific computing computational biology in particular is a growing concern in light of the urgency of the climate crisis and there is widespread interest in the research community so what can we all do about it Tackling this issue and making it easier for scientists to engage with sustainable computing is what motivated the Green Algorithms project During this webinar we will discuss what we learned along the way how to estimate the impact of our work and dive into the carbon footprint of common bioinformatic analyses We will also highlight the levers scientists and institutions have to make their research more sustainable debate the ethical implications of these environmental costs and examine what is still needed moving forward About the speaker Dr Lo c Lannelongue is a Research Associate in Biomedical Data Science in the Cardiovascular Epidemiology Unit and the Inouye lab at the University of Cambridge He is also a College Post Doctoral Associate at Jesus College Cambridge and an Associate Fellow of Advance HE Lo c developed the Greener Algorithms project in collaboration with Jason Grealey and Michael Inouye to understand the carbon footprint of analyses and promote best practices in green computing...

Loïc Lannelongue

23 November - 25 November 2022

Managing a bioinformatics core facility

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 data providers at EMBL EBI hear how others have tackled common problems and work together to design core services...

Sophie Spencer

22 November - 24 November 2022

Open Virtual Ensembl API Workshop

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

Aleena Mushtaq

17 November 2022

Uncovering protein function with UniProt

The webinar will cover what functional information is available in UniProt and where that information comes from It will also describe how the information is added to the resource and how to find it on the UniProt website...

Michele Magrane

15 November 2022

Croupier, an user-centric meta-orchestrator for cross-platform workflow delivery and execution

The orchestration of complex application workflows executed in the context of High Performance Computing HPC infrastructures requires the joint collaboration of application designers developers HPC engineers and application consumers i e end users In the context of HPC complex workflows can be executed with either HPC schedulers e g Slurm workflow managers e g PyCOMPSs NextFlow with meta orchestrators e g Croupier or with a combination of them While schedulers and workflow managers are restricted to execute applications within a single HPC cluster Croupier supports cross platform application delivery execution monitoring and data management In this webinar we will introduce Croupier from the application designers and consumers perspective and the use of Croupier with a demo on how to deploy execute and monitor one of the PerMedCoE use case applications About the speaker Jes s has been working in diverse ICT companies as Software Analyst and Architect for 20 years In Atos Research Innovation ARI he is Chief Architect and Senior Researcher on the AI Data HLS Unit member of the Advanced Parallel Computing Group where he designs and develops cross platform meta orchestrators for HPC infrastructures in EC R D i projects such as EUXDAT Hidalgo Grapevine or PerMedCoE He is also Atos Technical Team Leader of AI centric project IoT NGIN...

15 November 2022

Systematising complex and combined metabolic analyses with COBREXA.jl

Constraint based reconstruction and analysis COBRA refers to a vast collection of methods that build and scrutinise large metabolic networks traditionally using the methodology of linear optimization Many current analysis methods work with models that are personalised or customised to reflect genomic proteomic and other measurements At the same time there is a natural need to simulate more complex phenomena that emerge from combinations of many individual models such as multi organ and multi organism networks The complexity of the computations that need to be organised to run such simulations naturally grows up to a point where the analysis may become infeasible In this course we will introduce COBREXA jl a toolkit for working with large constraint based metabolic models and running very large parallel analysis tasks on these models Its main purpose is to make the COBRA methods scale to problem sizes that require the use of large computer clusters and high performance computing HPC Visit COBREXA jl website to find more information and guides The course will combine lectures and hands on exercises using several new design patterns implemented in COBREXA jl to organise many different model combinations constraints modifications and personalizations in a systematic way allowing short and concise implementations of extremely complex huge scale analyses...

Daniel Thomas López

15 November - 17 November 2022

Open Virtual Ensembl Browser Workshop

Work with the Ensembl Outreach team to get to grips with the Ensembl browser accessing gene variation comparative genomics and regulation data and mine these data with BioMart...

Aleena Mushtaq

15 November - 18 November 2022

From functional genomics to systems biology

OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Conference overview Genomics proteomics and quantitative imaging are rapidly moving fields with technological...

Arnaud Krebs, Prisca Liberali, Mikhail Savitski, Georg Seelig

14 November - 18 November 2022

Genome bioinformatics: resequencing and variant calling

A guide to the technology analysis workflows tools and resources for next generation sequencing data analysis This virtual 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 Practical sessions will enable participants to process training datasets and apply appropriate statistical methods in their analyses There will be no opportunity to work with personal research data during the course Virtual course Participants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and communication via Slack Pre recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 30 18 00 GMT each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Juanita Riveros

13 November - 18 November 2022

Single-cell omics: deeper to genomics

OverviewSpeakersProgrammePractical informationSponsors Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview Single cell sequencing is a rapidly evolving technique and is increasingly implemented in various research fields The whole workflow contains several critical and challenging steps from cell...

Qiaolin Deng, Jan O. Korbel, Anders Ståhlberg, Elisabeth Zielonka

10 November 2022

Modular and reproducible workflows for federated molecular QTL analysis

Genetic analysis of molecular traits such as gene expression splicing and chromatin accessibility requires a number of complex analysis steps that can easily take weeks or months for an analyst to implement from scratch In the CINECA project we have developed a number of modular Nextflow workflows that standardise and automate these steps In this webinar we will give an overview of the CINECA workflows for genotype imputation gene expression and splicing quantification data normalisation and association testing and demonstrate how these workflows can be used in a federated setting without transferring identifiable personal data between partners The CINECA Common Infrastructure for National Cohorts in Europe Canada and Africa project aims to develop a federated cloud enabled infrastructure to make population scale genomic and biomolecular data accessible across international borders to accelerate research and improve the health of individuals across continents About the speaker Kaur Alasoo is a Lecturer of Bioinformatics at the University of Tartu His research is focussed on genetic analysis of diverse molecular traits and building data resources to facilitate secondary use of molecular QTL datasets Kaur is also a co lead of the eQTL Catalogue project...

9 November 2022

Improving data reproducibility for chemosensitivity assays using MICHA

Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimisation However poor inter and intra laboratory reproducibility has been reported largely attributed to uncharacterised variation in the assay protocols Central to improving the data reproducibility is the standardisation of assay ontologies using minimal information MI To facilitate the open data in chemosensitivity assays we have launched MICHA minimal information for chemosensitivity assays available at http micha protocol org MICHA is an integrative pipeline to annotate chemosensitivity assays based on four major components including 1 compounds 2 samples 3 reagents and 4 data processing references This webinar will demonstrate how MICHA can automatically extract publicly available information for compounds including primary and secondary targets disease indications and physio chemical properties Users may next fill in the annotations including cell line or patient clinical variables assay types detection technologies and other experimental parameters Finally a tabular report can be generated to include the annotation results for the users to download In addition users may also browse the catalogue of drug sensitivity assay protocols which were already FAIRified by MICHA Using the platform of MICHA we aim to increase acceptance and adoption of the principles of FAIR Findable Accessible Interoperable and Reusable by making the assay annotation as smoothly as possible This webinar will showcase the utility of MICHA including FAIRified protocols from several major cancer drug screening studies including CCLE CTRP GDSC as well as recently conducted COVID 19 drug screening studies...

Jing Tang

8 November - 9 November 2022

Bioinformatics tools and data retrieval

The Job Dispatcher service at the EMBL EBI provides access to various sequence analysis tools and a database retrieval system Dbfetch This virtual course is split into two sessions running over two days During the first session you will learn how to access and use our sequence analysis tools Eg NCBI BLAST Clustal Omega EMBOSS and retrieve various database entries at the EMBL EBI using Dbfetch This session will also explain how to use sequence alignment and search effectively to find relevant results The second session focuses on alternative ways to access these services beyond the website This session will introduce the Job Dispatcher RESTful API show how to access our tools programmatically and integrate them into workflows...

Nandana Madhusoodanan

7 November - 10 November 2022

The neurovascular interface

In this symposium we bring together researchers from vascular biology and neurobiology to foster interdisciplinary exchange and new emerging concepts on how vascular and nervous systems crosstalk to maintain organ homeostasis and function...

Amparo Acker-Palmer, Ralf Adams, Chenghua Gu

6 November - 13 November 2022

Practical integrative structural biology

Tab 1 Tab 1...

2 November 2022

Finding and using publicly available data Q&A session

This Q A question and answer webinar will provide an opportunity for anyone who has completed Finding and using publicly available data A curated set of online courses to join some of EMBL EBI s experts and ask their own questions This session will focus on biocuration open data and accessing publicly available data The questions covered during the Q A webinar will depend on those asked by attendees however we will likely cover topics such as Data sharing and submission Restricted access to genetic phenotypic and clinical data Data management of biological data and open data Finding the right EMBL EBI resource for accessing data...

31 October - 4 November 2022

Genome-resolved metagenomics bioinformatics

Learn about the tools processes and analysis approaches used in the field of genome resolved metagenomics This course will cover the use of publicly available resources to manage share analyse and interpret metagenomics data focussing primarily on assembly based approaches The virtually delivered content will involve participants learning via pre recorded lectures and live presentations followed by live Q As with the trainers Practical experience will be developed in group activities and in computational exercises run using containerised tools on our virtual training infrastructure Participants will need to be available between the hours of 09 00 17 00 GMT each day of the course...

Shereen Pethania

30 October - 4 November 2022

The fundamentals of high-end cell sorting

OverviewSpeakers ProgrammePractical informationSponsors Overview Please see EMBL s COVID 19 safety policy for testing and other requirements to attend this on site course Course overview This course includes a robust theoretical part on the fundamentals of cell sorting delivered by world leading experts and practical sessions on using standard cuvette sorters In addition the course...

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

27 October 2022

A guide to UniProt for students

UniProt provides the scientific community with a comprehensive high quality and freely accessible resource of protein sequence and functional information This webinar will guide you through ways in which students and researchers at all career stages may take a structured approach to access the data in the UniProtKB and Proteomes sections of the UniProt protein function database The webinar will discuss the types of data that can be accessed and using sequence analysis tools how this data can be analysed to answer biological questions We will demonstrate how to find the function of a protein how the protein components of a pathway may be identified features of proteins of interest can be compared similar sections of sequence can be sought in other species and how whole data sets containing all the proteins expressed in an organism can be obtained By accessing sequence structural and functional data through UniProt we want researchers to be part of data s biological journey and support further work and adventures along the way...

Paul Denny

26 October - 29 October 2022

Plasticity across scales: from molecules to phenotypes

OverviewSpeakersProgrammePractical informationSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Please see EMBL s COVID 19 safety policy for testing and other requirements if attending the on site event Couldn t attend the event Check out our event reporters take on the meeting Six enlightening questions about plasticity across...

Ehab Abouheif, Alexander Aulehla, Axel Meyer, Sonia Sultan

24 October 2022

EMBL Open Science Workshop 2022

Overview to follow...

Sophie Spencer

17 October - 21 October 2022

Bioinformatics approaches to viruses

This workshop will provide training on the use of bioinformatics tools to understand viral pathogens sequencing data Trainees will receive training on viral genome assembly comparative viral genomics phylogenomics metaviromics and downstream applications of this data in research and applied contexts...

Sophie Spencer

17 October - 18 October 2022

Using fish models to explore the impact of Gene by Environment (GxE) 2022

This workshop is intended to present some aspects of Medaka fish research to the wider fish models community We have several projects supported by two key grants that make use of Medaka s high tolerance of inbreeding to perform gene by environment research across the Medaka Inbred Kiyosu Karlsruhe MIKK panel The workshop will run in a virtual format including a mixture of formal research talks lightning talks by students and post docs and social activities aimed to increase awareness and collaboration across the model fish community Through these two days of discussions we aim to present details and foster collaborative links on the use of key resources such as the MIKK panel for gene by environment projects in the community Virtual workshop Participants will attend virtual formal presentations and lightning talks from students and post docs followed by moderated Q A sessions Practical experience and workshop style sessions will be intermixed with virtual social events via GatherTown 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 00 17 30 BST each day of the workshop Moderators will be available to assist answer questions and provide further explanations during these times...

Charlotte Pearton and Meredith Willmott

17 October - 21 October 2022

Structural bioinformatics

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 virtual course explores bioinformatics data resources and tools for the investigation analysis and interpretation of both experimentally determined and predicted biomacromolecular structures It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts The course content will also cover predicting function and exploring interactions with other macromolecules This course 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 09 00 18 00 UTC 0 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...

Juanita Riveros

16 October - 21 October 2022

Metabolite and species dynamics in microbial communities

OverviewSpeakers ProgrammePractical informationSponsors Overview Course overview Metagenomics studies are rapidly uncovering the compositional richness of microbial communities in diverse habitats ranging from the oceans to the human gut While their fundamental role in our health and environment is undeniable there is an urgent need for unravelling molecular mechanisms underlying the...

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

12 October 2022

Introductory bioinformatics Q&A session: proteins and structures

This Q A question and answer webinar will provide an opportunity for anyone who has completed Introductory bioinformatics a curated set of EMBL EBI online courses to join some of EMBL EBI s experts and ask their own questions This session will focus on proteins and structures including the EMBL EBI resources UniProt and PDBe The questions covered during the Q A webinar will depend on those asked by attendees however we will likely cover topics such as Searching for protein sequence and functional information data with UniProt Protein structures with PDBe Data management of biological data and open data Finding the right EMBL EBI resource...

Emily Bowler-Barnett, Anna Swan, Deborah Harrus, David Armstrong

12 October - 15 October 2022

The complex life of RNA

OverviewSpeakersProgrammePractical informationSponsorsAboutPre conference workshop Overview Late registration for VIRTUAL participation is possible Please contact Diah Yulianti for more information This conference will take place at EMBL Heidelberg with the option to attend virtually Participants will be requested to show a proof of a negative COVID 19 from a supervised negative...

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

11 October 2022

Data protection and security aspects of running simulations on personal data with HPC

When processing health and genetic data in High Performance Computing HPC clusters researchers must consider the application of research ethics principles as well as the General Data Protection Regulation including issues of identifiability duties of confidentiality and security and accountability A Data Protection Impact Assessment can be a useful tool to identify and mitigate any risks to the rights and freedoms of data subjects patients and research participants In this webinar we will also highlight the risks of working with sensitive data on an HPC cluster and we will provide you guidelines and measures that can help you secure your data and its processing Additionally we will give a short overview of what you should look out for when selecting or developing software to work on this data About the speakers Sarah Peter studied Bioinformatics and worked for a few years as a researcher and data manager at the Max Planck Institute Now she works at the Luxembourg Centre for Systems Biomedicine UNILU as an Infrastructure Engineer in the R3 and IT Infrastructure team She is also the liaison for the HPC team Since GDPR has come into effect she spends some of her time doing risk analysis for the institute s IT infrastructure and the HPC cluster Adrian Thorogood is a lawyer and Research Development Specialist in the Bioinformatics Core Luxembourg Centre for Systems Biomedicine UNILU He works with the European 1 Million Genomes Project and other infrastructure projects to address ethical and legal issues that arise when sharing genomic and health related data cross border and internationally His research focuses on how genomic sequencing platforms information and networking technologies open science practices and patient empowerment movements are disrupting research and health care...

Laurence Calzone, Arnau Montagud

9 October - 14 October 2022

Genome engineering: CRISPR/Cas from cells to mice

This course will provide training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR Cas9 system...

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

5 October 2022

Introductory bioinformatics Q&A session: genes and gene expression

This Q A question and answer webinar will provide an opportunity for anyone who has completed Introductory bioinformatics a curated set of EMBL EBI online courses to join some of EMBL EBI s experts and ask their own questions This session will focus on genes and gene expression including the EMBL EBI resources Ensembl and Expression Atlas The questions covered during the Q A webinar will depend on those asked by attendees however we will likely cover topics such as Browsing genomes with Ensembl Discovering gene expression data with Expression Atlas Data management of biological data and open data Finding the right EMBL EBI resource...

Aleena Mushtaq, Sarah Morgan, Nancy George, Benjamin Moore, Anja Fullgrabe, Louisse Paola Mirabueno

5 October - 8 October 2022

Molecular mechanisms in evolution and ecology

OverviewSpeakersProgrammePractical informationSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Proof of COVID 19 vaccination or recovery is required for on site attendance Please see EMBL s COVID 19 safety policy for on site events For late registrations to attend the workshop onsite please contact Raili Pall Conference...

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

3 October - 7 October 2022

Single-cell RNA-seq analysis using R

This course covers the analysis of scRNA seq data using R and command line tools Participants will be guided through droplet based scRNA seq analysis pipelines from raw reads to cell clusters They will explore and interpret data using R as well as the Single Cell Expression Atlas Finally participants will put their knowledge into practice through a group challenge on the last two days of the course Please note that participants will not analyse their own data as part of the course There will however be ample opportunity to discuss their 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 participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 00 17 30 BST each day of the course Trainers will be available to assist answer questions and provide further explanations during these times...

Jane Reynolds

29 September 2022

Programmatic access to UniProt using Python

UniProt is a comprehensive expert led publicly available database of protein sequence function and variation information This webinar will give an overview of programmatic access to the UniProt database using Python and cover key aspects of protein entry searches data filtering batch downloads and give examples of further processing of downloaded target data Following a brief introduction to UniProt services where to find relevant documentation and help features the webinar will focus on worked examples These will include how to programmatically search and retrieve protein entries and sequences within the results we will then show how to align orthologous sequences and filter for features of interest The webinar will also cover programmatic examples of the UniProt Retrieve ID mapping service batch downloads processing filtering data by annotation type and retrieval of recently published proteomics derived post translational modification data...

Emily Bowler-Barnett, Aurelien Luciani

28 September 2022

Finding Pfam's protein families data in the InterPro website

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains Together with twelve other resources it is part of the InterPro member database consortium After 20 years of good and faithful service we have decided to retire the Pfam website We are still planning to do Pfam releases and the data will still be available through the InterPro website This webinar aims to ease the transition from Pfam to InterPro by showing different ways to search and access the Pfam annotations in the InterPro website...

27 September - 30 September 2022

Bioinformatics and functional genomics in zebrafish

Zebrafish are widely used to study development toxicity and disease and functional genomics is used throughout the field to identify new pathways and mechanisms and for comparison to other model systems and humans In this hands on course participants will learn how to design functional genomics experiments manage and analyse RNA seq datasets from zebrafish and compare results to other species The aim of the course is to equip researchers with tools to carry out functional analysis and data visualisation of RNA seq data that has already been mapped to the genome and been analysed for differential gene expression The course will be relevant to researchers working on a wide range of topics and will use real datasets from our lab for hands on analysis Please note that this course will not teach the initial steps of RNA seq analysis but instead start at the point that you have a list of differentially expressed genes View other EMBL EBI s courses cover the initial stages extensively for instance Introduction to RNA seq and functional interpretation 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...

Meredith Willmott

22 September 2022

A guided tour of the new and improved UniProt website

This webinar will provide an interactive introduction to the new and improved UniProt website Developed with our user community in mind the new website aims to allow users to access all data provided by the UniProt consortium while being adaptable enough to meet the evolving needs of our users Join us to find out how we ve revamped our website structure to enable users to better navigate and find content in our various databases Also discover the improvements we ve made to our tools BLAST Align Peptide search and ID mapping and about the creation of the new Tools results dashboard where the user can view and revisit their BLAST Align Peptide search or ID mapping jobs save them as favourites or resubmit them We hope that this interactive webinar will introduce you to all the new features and improvements we implemented into the new website...

Kate Warner

21 September 2022

An introduction to EMBL-EBI resources

EMBL EBI is the home of the world s most comprehensive range of freely available molecular databases and resources Our resources help researchers share and analyse data and perform complex queries in many different ways Join us for a tour of the core data resources at EMBL EBI During this webinar we will introduce the types of data available how you can search for data and the various ways of getting assistance We will also discuss the role of EMBL EBI in making data open and accessible and how you can include EMBL EBI data in your workflows We will also provide information on further online training to help you learn more about specific topics in bioinformatics and EMBL EBI resources including an introduction to the training collections The collections bring together training on a specific area and include those on Introductory bioinformatics and Chemical biology After completing one of these collections you may then join us at a related Question Answer webinar where you will have the opportunity to ask questions to EMBL EBI experts search our live webinars for any upcoming Q A webinars Overview of webinar recording start with the introduction to watch the whole recording or click a section to go directly to that part of the recording Introduction Data resources at EMBL EBI Navigating EMBL EBI data resources Data submission EMBL EBI Training...

Sarah Morgan

20 September - 23 September 2022

Integrative analysis of multi-omics data

Experimental designs in basic biology research and biomedicine increasingly involve the use of multiple omics technologies to characterise a set of samples e g genomic variants epigenetic marks transcriptome proteome metabolome functional assays imaging This is true for both bulk and single cell analyses Therefore data analysis techniques are required that are able to cope with such data in an efficient and generalisable manner Thus the proposed advanced course addresses one of the major data challenges scientists face today Its core objective is to convey the conceptual and mathematical foundations that underpin integrative multimodal data analysis strategies and the practical trade offs of different methods...

Wolfgang Huber, Oliver Stegle, Britta Velten

19 September - 24 September 2022

Imaging down to single-molecule resolution: STED and MINFLUX nanoscopy

OverviewSpeakers Programme Practical information Overview Proof of COVID 19 vaccination or recovery is required to attend this on site course Please see EMBL s COVID 19 safety policy for on site events Course overview The course aims to train biological microscopy users in two forms of super resolution light microscopy Stimulated Emission Depletion STED Microscopy and Minimal...

Marko Lampe, Julia Menzel, Christian Wurm, Timo Zimmermann

13 September - 16 September 2022

Reconstructing the human past: using ancient and modern genomics

The study of population genetic variation and the sequencing of ancient DNA represent promising new avenues for investigating human history and our evolutionary past Population scale sequencing projects investigating human diversity have provided us with more than a million genome wide datasets that allowed new insights into patterns of human variation and mobility while others have obtained genome wide data from thousands of ancient human skeletons allowing the investigation of human evolution in action and providing direct insights into population genetic dynamics in situ...

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

12 September - 16 September 2022

Mathematics of life: modelling molecular mechanisms

This course will provide participants with an introduction and hands on training on modelling approaches tools and resources used in systems biology as well as touch on network analysis Computer models are increasingly used to understand the essential processes of biology Researchers in academic institutions as well as the pharmaceutical industry use mathematical models to generate hypotheses on how complex biomolecular systems work Modelling of biochemical pathways deregulated in disease conditions can offer mechanistic insights into the pathology help to elucidate mechanisms behind drug action and predict the dose required for treatment thus facilitating fundamental research and drug discovery This course will provide a helpful brief introduction to key modelling concepts and hands on training to use popular tools and resources used in this scientific field Virtual course This course has now been moved to a virtual format 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 09 00 17 30 British Summer Time 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...

Juanita Riveros

11 September - 12 September 2022

Organisation and utilisation of hologenomic datasets

This course will cover the generation and application of large scale holo omic data sets such as those produced within the HoloFood project There is an increasing recognition that organisms do not exist in isolation but are actually holobionts composed of the host and the many microorganisms found on or in the individual The HoloFood project has developed significant multi omics datasets for both chicken and salmon with a view to understanding how different feeds impact the gut microbiota and in turn animal productivity This course covers how to access and utilise both raw and derived data products the workflow to achieve genome resolved metagenomics analysis of host variation generation and interpretation of metabolomic data and approaches to multi omic integration to understand links between traits and genomic information The HoloFood project represents a cornerstone of hologenomic research providing a blueprint for how data from such projects should be archived analysed and interlinked As such the motivation for this course is to highlight the availability and usability of the HoloFood data in further holo omic analyses either as reference sets to compare against or as source data for subsequent novel analysis Participants will be required to provide their own wi fi enabled laptops with an up to date browser e g Chrome v 98 or higher and the ability to install cloud client software approx 2GB space required to allow connection to the virtual machines that will be used for the course Specifics of all technical requirements will be communicated prior to the course The training course is running as a precursor to the Applied HoloGenomics Conference 13 15 September also in Bilbao Spain The course is organised by the HoloFood Innovation Action and has received funding from the European Union s Horizon 2020 research and innovation programme under grant agreement No 817729...

Charlotte Pearton

11 September - 18 September 2022

Synthetic biology in action: beyond standard metabolism

OverviewSpeakers trainers and staffProgrammePractical informationSponsors Overview Proof of COVID 19 vaccination or recovery is required to attend this on site course Please see EMBL s COVID 19 safety policy for on site events Course overview Synthetic Biology SynBio has become a rapidly developing area for tackling a large number of challenges in life science research This is due to...

Sven Panke, Vitor Pinheiro, Karen Polizzi, Elisabeth Zielonka

5 September - 8 September 2022

Chemical biology 2022

OverviewSpeakersProgrammePractical informationSponsorsPre conference workshop Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Proof of COVID 19 vaccination or recovery is required for on site attendance Please see EMBL s COVID 19 terms and conditions Conference overview The conference sets the stage for the dissemination and exchange of...

Yimon Aye, Claire Deo, Kai Johnsson, Edward Lemke

5 September - 12 September 2022

Membrane protein expression, purification and characterization (mPEPC2)

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4 September - 13 September 2022

Current methods in cell biology

The major aim of the course is to allow participants to experience modern cell biology at work not only to see but also to try out in practice how cutting edge technologies can be used to answer questions at the frontiers of cell biology It is a tradition that the entire faculty of the Cell Biology and Biophysics Unit of EMBL teaches the course to cover a broad spectrum of techniques...

Sara Cuylen-Häring, Simone Köhler

27 August - 30 August 2022

Transcription and chromatin

OverviewSpeakersProgrammePractical informationSponsors Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Proof of COVID 19 vaccination or recovery is required for on site attendance Please see EMBL s COVID 19 terms and conditions Conference overview The EMBL Transcription and Chromatin meeting has a long standing tradition in shaping the...

Karen Adelman, Eileen Furlong, Jürg Müller, Peter Verrijzer

21 August - 29 August 2022

Advances in cryo-electron microscopy and 3D image processing

This course provides the theoretical and practical foundations of advanced cryoEM techniques from sample preparation to data collection to image processing...

Julia Mahamid, Sebastian Eustermann, Simone Mattei, Lori Passmore, Henning Stahlberg

18 July - 22 July 2022

Proteomics bioinformatics

This course provides hands on training in the basics of mass spectrometry MS and proteomics bioinformatics 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 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...

Juanita Riveros

17 July - 20 July 2022

Innate immunity in host-pathogen interactions

OverviewSpeakersProgrammePractical informationSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Proof of COVID 19 vaccination or recovery is required for on site attendance Please see EMBL s COVID 19 terms and conditions For late registration please contact Maryann Heck Symposium overview This symposium provides a...

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

17 July - 23 July 2022

C. elegans: from genome editing to imaging

OverviewSpeakersProgrammePractical informationSponsors Overview Proof of COVID 19 vaccination or recovery is required to attend this on site course Please see EMBL s COVID 19 safety policy for on site events Course overview C elegans is a popular experimental model that combines transparency reproducible anatomy traceable cell lineage sequenced genome and facile genetics allowing to...

Henrik Bringmann, Simone Köhler, Georgia Rapti, Pavak Shah

11 July - 15 July 2022

Bioinformatics for T-Cell immunology

This course will introduce and explore a number of key bioinformatics tools and resources that can be applied to T cell immunological research Targeted at life scientists with a wet lab focus it will provide participants with an overview of best practice methods in applying bioinformatics approaches and enable them to become confident users of their own and public domain data The resources introduced during the course will cover a variety of data types from genomic data to computational models and biological pathways Participants will gain experience of the analysis pipelines for RNA Seq and flow cytometry experiments as well as data integration of omics data and basics concepts of machine learning approaches This course has been developed in collaboration with the ENLIGHT TEN project a consortium focused on developing early stage research expertise in T cell immunology and big data analysis 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...

Sophie Spencer

11 July - 13 July 2022

Microfluidics 2022

The EMBL Microfluidics Conference brings together top researchers and emerging research leaders to spark scientific exchange and create community Topics spanning from fundamental physics chemistry to device design and nascent biological applications will be presented which should be of interest to everyone from experts in microfluidic design to users of the next generation of microfluidic tools and from academic scholars and trainees to industry colleagues...

Christoph Merten, Angela Wu

8 July - 15 July 2022

Super-resolution microscopy: time-resolved STED nanoscopy

This six day comprehensive microscopy course focuses on stimulated emission depletion microscopy STED and its application to biological questions It covers the fundamentals of STED microscopy different technical implementations and has a strong emphasis on sample preparation including choice of fluorophores and refractive index matching as well as image acquisition strategies for fixed samples and living cells Students will have the opportunity for exercises on state of the art STED microscopes in which they will acquire high quality nanoscopy data Through lectures tutorials demonstrations and practical workshops the course provides in depth knowledge on all aspects of STED Nanoscopy...

Marco Lampe, Rainer Pepperkok, Ulf Schwarz

4 July - 8 July 2022

Systems biology: from large datasets to biological insight

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 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...

Meredith Willmott

4 July - 15 July 2022

Visualising life – interdisciplinary approaches to biology

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29 June - 1 July 2022

Timing mechanisms linking development and evolution

OverviewSpeakersProgrammePractical InformationSponsors Overview This conference will take place at EMBL Barcelona Proof of COVID 19 vaccination recovery or negative test is required for on site attendance Please see EMBL s COVID 19 safety policy for on site events Conference Overview Time is inherent to biological processes It determines the order of events and the speed at...

James Briscoe, Megan Davey, Miki Ebisuya, Pierre Vanderhaeghen

28 June 2022

Impact of AlphaFold on research and development

This is the third and last webinar of the series about the impact of AlphaFold on training and research in life sciences This webinar will focus on the impact of AlphaFold on research and development in life sciences by highlighting a variety of case studies from academia as well as industries In this webinar we had the following panel of speakers Jan Kosinski AlphaFold has revolutionised structural biology by enabling the modelling of monomeric proteins and small complexes at accuracy similar to experimental structures However to model large complexes it still needs to be integrated with experimental data such as cryo electron microscopy maps I presented how such an integrative combination enabled us to model the human nuclear pore complex at unprecedented completeness and precision I used this example to highlight the new opportunities for integrative structural biology Juan Carlos Mobarec Methods and software to obtain information about protein structures from amino acid sequences have been applied in the pharmaceutical industry over the span of decades Hence what can deliver the AI containing modelling workflows such as AlphaFold to early stage R D We have pioneered the application of AlphaFold in R D on multiple cases Here we reviewed use case examples of the latest automated workflow for protein structure prediction Juri Rappsilber Crosslinking mass spectrometry is now a well established experimental technique for investigating protein interactions structure and function Crosslinking MS also remains unparalleled in its ability to provide structural information in complex systems This is particularly relevant in the light of the most recent revolutionary advancement in structural biology Artificial intelligence program based predictions of protein structure e g by AlphaFold are having a wide ranging impact on our ability to model protein structures but also to study protein interactions that are yet to be fully understood Crosslinking mass spectrometry offers here highly relevant experimental data Using a crosslinking mass spectrometry study of Bacillus subtilis we have investigated different aspects of joining AlphaFold and crosslinking Particularly the validity of the ipTM score was probed by crosslinking mass spectrometry and we present the possibility of assembling larger complexes based on the pairwise data resulting from crosslinking mass spectrometry and the AlphaFold prediction of two protein interactions Ultimately our structural understanding of biology stands to gain much from combining AlphaFold and crosslinking data particularly in our drive towards building a structural and functional understanding of the cell Katja Luck AlphaFold s ability to predict the structure of folded regions of proteins and to identify disordered regions of proteins with unprecedented accuracy transforms experimental design in molecular biology First I discussed how AlphaFold can advance the design of functional and well expressed protein constructs for the study of protein interactions and protein binding regions Second I highlighted the potential possible approaches but also limitations of AlphaFold for the identification of protein protein interaction interfaces Panel discussion was chaired by Janet Thornton...

Jan Kosinski, Katja Luck, Juan Carlos Mobarec, Juri Rappsilber, Janet Thornton, Randy J Read

22 June 2022

An introduction to the COVID-19 Data Portal

The COVID 19 Data Portal was launched in April 2020 to bring together relevant datasets and tools for sharing and analysis in an effort to accelerate coronavirus research It enables researchers to upload access and analyse COVID 19 related reference data and specialist datasets This webinar will provide an introduction to the COVID 19 Data Portal discuss the kind of data that is made available and include a demonstration of how to access data...

Nadim Mahdi Rahman

21 June 2022

HPC boosts mathematical models’ promises of personalised medicine

Mathematical models of the biological processes that are deregulated in diseases show a high complexity not only because of the number of genes and pathways involved but also because of the numerous patients or samples to include in the simulations in order to be predictive One way to address these issues is to combine High Performance Computer HPC based methods to scale up the power of the computation with mechanistic and statistical modelling approaches In the context of the PerMedCoE project we have brought together computer scientists and modellers to define the needs and the methods that need to be developed to optimise the simulations of these computationally demanding models Two use cases were defined the first one describes a workflow that inputs omics data of cancer patients and outputs personalised combinations of drugs per patient based on a model of intracellular signalling pathways and the second one aims at uncovering COVID 19 related mechanisms that explain the differences in severity among patients using personalised agent based models of different cell types We will conclude by briefly discussing the possible clinical applications of such types of models About the speaker Dr Laurence Calzone is a research scientist at Institut Curie France She has published mathematical models using several formalisms including nonlinear ordinary differential equations and Boolean formalism to address specific biological questions related to cancer cell fate decision processes in response to cell death signals interplays between MAPK pathways metastasis process etc with the aim to provide personalised treatments She has experience in constructing these models based on published articles and in analysing patient data using these models She has participated in developing methods and tools to improve the simulations of the mathematical models she builds She is an active member of modelling communities such as CoLoMoTo and SysMod Dr Arnau Montagud is a research scientist at the Life Sciences department of the Barcelona Supercomputing Center During his last undergrad year Arnau participated in synthetic biology s iGEM competition where he dove into the use of models in Biology which pushed him to pursue a PhD in the Department of Applied Mathematics in the Technical University of Valencia His research on Metabolic Engineering of hydrogen in cyanobacteria led him to be a visiting researcher at Uppsala University Denmark Technical University and EMBL Heidelberg After graduating he decided to apply modelling techniques to Cancer using logical models agent based models and data deconvolution and integration...

Laurence Calzone, Arnau Montagud

21 June 2022

Impact of AlphaFold on teaching and training in life sciences

This is the second webinar of the series about the impact of AlphaFold on training and research in life sciences This webinar will focus on how AlphaFold is changing or will change the teaching training landscape in life sciences This will help us identify the gaps and opportunities for developing training materials for students and researchers To discuss the impact of AlphaFold on teaching and training in life sciences we had the following panel of speakers Alexandre Bonvin In my short talk I reflected on how we have been incorporating AlphaFold in the bachelor and master courses I am giving at Utrecht University for chemistry and molecular and cellular life sciences students I have been teaching molecular modelling for many years describing how to represent molecules and their energetics and model their structure and dynamics in silico The advanced master course also has a computer practical in which students do homology modelling run molecular dynamics of a peptide and use the output for modelling a protein peptide complex by docking Part of this practical was published as an educational article This year we introduced at the end an AlphaFold bonus module in which students model directly the protein peptide complex from sequence something which works extremely well in this particular case We are also using AlphaFold this year in the context of a second year bachelor project in which students investigate how well AlphaFold performs for the modelling of antibodies In both cases students have little knowledge of the machinery under the hood but only some general understanding of the role of AI in the process Still they manage to use this fantastic resource very efficiently Key factors here are in my opinion 1 the availability of Jupyter notebooks that make using the software extremely easy and 2 the free computational resources of Google Colab Without those it would simply be impossible to expose students to such methods as installing the software and more importantly the 2TB of data for the model is simply not doable on student s laptop or computer rooms managed by our university IT Panagiotis L Kastritis AlphaFold is revolutionising structural molecular and even cellular biology due to its unmatched accuracy for various protein targets In addition the recent AlphaFold Structure Database and ColabFold are fast tracking structural biology research via models to be utilised either as hypothesis generators or explanatory of previously perplexing experimental data However incorporating AlphaFold in teaching requires special attention because a fundamental understanding of machine learning is not trivial and b physicochemical principles of protein folding in the light of AlphaFold success must be harmonised with interpretable machine learning which is presently unavailable I conclude that practical aspects of AlphaFold are currently preferable for teaching both students and young researchers in combination with e g homology modelling docking and other structure building tools In this way students and young researchers critically assess their derived models and motivate themselves to deduce structure function correlations while furthering working hypotheses on a given system Ezgi Karaca I have been teaching in molecular biology and medicine departments My students usually come with a little knowledge in structural biology Thanks to the availability of the EMBL EBI AlphaFold AF Database I can show them the images of proteins to explain how a protein structure is related to its function Otherwise we have been using AF over the ColabFold service for modelling disease associated protein mutations isoforms The fact that AF provides a residue based confidence score has been very helpful to us in assessing whether our models are biologically relevant For large systems though a local installation of AF is required Beyond protein structure prediction the performance of AF on protein complexes are yet to be critically discussed For this we should wait for the outcome of the CASP15 experiment where I act as the assembly assessor Dina Schneidman I am teaching an advanced course on Structural Bioinformatics intended for Computational Biology and Computer Science students The course consists of lectures 5 exercises and a 2 day hackathon Several years ago the never changing course part on folding began to change We had to update the lectures and the exercises We have encountered several challenges First we realised we have to teach deep learning to students with insufficient background Second we had to make sure the homework assignments have reasonable training time and the students have access to GPUs Finally we had to think about hackathon projects that can be done within two days In this webinar I described how we addressed these challenges in the webinar...

Alexandre Bonvin, Ezgi Karaca, Panagiotis L. Kastritis, Dina Schneidman

20 June - 24 June 2022

Cancer genomics

This course will focus on the analysis of data from genomic studies of 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...

Jane Reynolds

19 June - 22 June 2022

Defining and defeating metastasis

OverviewSpeakersProgrammePractical informationSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Proof of COVID 19 vaccination or recovery is required for on site attendance Please see EMBL s COVID 19 terms and conditions Late on site registration is still possible For information please contact Maria Bacadare Symposium overview...

Johanna Joyce, Daniel Klimmeck, Joan Massagué, Charles Swanton

15 June 2022

PRIDE database: Proteomics data submission, access and visualisation

The webinar will provide an introduction to the PRIDE database and the proteomics data submission process This will also provide information about how to access public proteomics datasets including the PRIDE...

Deepti Jaiswal Kundu

14 June 2022

Scope and vision of AlphaFold

AlphaFold is an AI system developed by DeepMind that predicts protein 3D structure from its amino acid sequence It s been a year since the AlphaFold software and AlphaFold Protein Structure Database were made publicly available for users to explore and investigate their protein of interest We are running a webinar series to mark this occasion by highlighting the impact of AlphaFold on training and research in life sciences This is the first webinar of the series where the speaker will describe and discuss the scope and vision of AlphaFold Speakers Kathryn Tunyasuvunakool Machine learning models have the potential to become core tools in biology as recent progress in protein structure prediction illustrates In this webinar I gave an overview of AlphaFold how the system works how to obtain protein structure predictions and how to analyse them I then reviewed some ways in which the system has been built upon and discussed how to evaluate AlphaFold for a new application Randy Read Few areas of structural biology have been untouched by the recent dramatic increases in the power and accuracy of computational modelling of protein structure These changes have been wrought by the current version of AlphaFold with RoseTTAFold not far behind Experimental structural biology is still needed to resolve ambiguities in the predicted structures and to verify the details but the availability of high quality models is removing many of the bottlenecks in the experiments Even without an experimental structure the new models are sufficient to generate interesting hypotheses that can be tested experimentally such as assessing how variants associated with genetic disease actually cause disease Limitations in the models could potentially be addressed by adding explicit physics and chemistry to the pattern recognition used in the current algorithms and by actively exploiting even limited experimental observations Sergey Ovchinnikov I discussed the impact of AlphaFold on structural bioinformatics by highlighting a few large scale efforts and structure search tools developed to characterise the AlphaFold models...

Kathryn Tunyasuvunakool , Randy J Read, Sergey Ovchinnikov

13 June - 17 June 2022

Summer school in bioinformatics

This course organised in association with Wellcome Connecting Science provides an introduction to the use of bioinformatics in biological research giving participants guidance for using bioinformatics in their work whilst also providing hands on training in tools and resources appropriate to their research Participants will initially be introduced to bioinformatics theory and practice including best practices for undertaking bioinformatics analysis data management and reproducibility To enable specific exploration of resources in their particular field of interest participants will be divided into focused groups to work on a project set by resource and data experts from EMBL EBI and external collaborating institutes These projects will end with a presentation from each group on the final day of the course to bring together learnings from all participants Participants will be required to review some pre recorded material prior to the start of the course and will have an opportunity to meet other trainees in an induction session to be held virtually in the week before the course take place 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 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 mentors Priit Adler University of Tartu Hedi Peterson University of Tartu Genome variation across human populations Natural variation between individuals or between different human populations is a result of genome mutations throughout evolutionary history Some mutations may become fixed because of their beneficial effect while most drift among individuals During this project you will investigate genomic variation between two separate human populations of European and Asian descent Using sequence data from a number of individuals from each population you will use a range of bioinformatics tools to discover variants that exist between them In the second section of the project you will attempt to analyse the functional consequences of the variants you have identified linking them to phenotypes Project mentors Baron Koylass EMBL EBI 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 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 mentors David Armstrong EMBL EBI Preeti Choudhary EMBL EBI Analysis of intercellular interactions in healthy and diseased states Ulcerative colitis is an inflammatory bowel disease The exact pathomechanism of the disease is unknown However the interactions between the intestinal immune cells and the intestinal epithelial cells play a crucial role during the development of the disease Single cell RNA seq measurements can help us understand these complex interactions The expression data combined with protein protein interaction databases can shed light on the connections between cells in diseased and healthy states During this project you will use a single cell RNA seq dataset to build interactions between the various cells The dataset contains pre processed cell type classified data of biopsies from healthy inflamed and non inflamed UC colonic biopsies The interactions between cells will be downloaded from the OmniPath database You will use Python Notebooks to build up the intercellular networks map the single cell RNA seq expression data and visualise them The intercellular networks between various cell types can then be compared by Cytoscape Project mentors Dezso Modos Quadram Institute Marton Olbei Earlham Institute...

EMBL-EBI Training team

12 June - 17 June 2022

Humanized mice, personalized therapies and big data

This course will train early and experienced researchers and consolidate interactions of the international scientific community in the field of humanized mouse models...

Karl-Dimiter Bissig, Ernesto de la Cueva Bueno, Christian Münz, J.J. Schuringa, Leonard Shultz, Brian Soper, Renata Stripecke

12 June - 17 June 2022

BioExcel summer school on biomolecular simulations 2022

The summer school will include lectures and hands on sessions on the following topics Molecular dynamics simulations Biomolecular docking Free energy calculations Advanced sampling methods Metadynamics BioExcel Building Blocks BioBB Quantum mechanics molecular mechanics QM MM Machine learning During the hands on computer practicals you will make use of the BioExcel flagship software and tools e g GROMACS HADDOCK PMX BioBB and CP2K The trainers developers and or experts in the use of the software will provide guidance and support You can find more informatioan about the course on the BioExcel website https bioexcel eu events bioexcel summer school on biomolecular simulations 2022...

Jane Reynolds

9 June 2022

The PerMedCoE competency framework to guide training and career development

PerMedCoE aims at providing an efficient and sustainable infrastructure to support personalised medicine adapting cell level simulation methods to pre exascale systems to translate omics data into molecular disease models One of the activities to achieve this consists of a training programme to educate professionals in life sciences and HPC communities about the capabilities of PerMedCoE developments We created a competency framework to define the training needs and based on them implement our training programme A competency is an observable ability of any professional integrating multiple components such as knowledge skills and behaviours The PerMedCoE framework lists the competencies for professionals within the scope of the CoE developing cell level simulation tools with the long term vision of using them in the clinical context The competency framework enables the definition of different professional profiles which can help people identify the abilities needed for working in a specific role e g bioinformatician tool developer biomedical researcher and therefore inform their professional development We will present the structure of the PerMedCoE competency framework the first profiles created within it and how to explore it in the EMBL EBI Competency Hub About the speaker Vera Matser PhD is a Scientific Training Project Coordinator at EMBL EBI and leads a subteam that contributes to the training and dissemination activities for a number of EU funded projects To assess the training needs of the different research communities she coordinates the development of competency frameworks and training programmes In addition to her work graduated from the RItrain EMMRI Executive Masters in Management of Research Infrastructures in 2020 Marta Lloret Llinares PhD is a Scientific Project Manager within the training team at EMBL EBI Marta currently leads the training activities for H2020 grants BioExcel and PerMedCoE which run competency based training programmes Marta is the product owner of the EMBL EBI Competency Hub a repository of competency frameworks that define the abilities required by professionals in a specific field and relate them to training resources and career profiles...

Vera Matser, Marta Lloret Llinares

8 June 2022

Open-access to genetic variation data at the European Variation Archive

The European Variation Archive EVA is an open access database for archival and accessioning of genetic variants from any species RS ID s are assigned to variants submitted to the EVA and this data is made available periodically This webinar will cover various methods of data access including bulk download of accessioned variants and a detailed dive into the latest EVA data release 3 This is the first release to contain existing variants updated to a new genome build...

Baron Koylass

8 June - 10 June 2022

Bioinformatics for Principal Investigators

This course has been designed to provide Principal Investigators PI s working in the life sciences with an introduction to the challenges of working with biological data as a research leader Starting with a look at where bioinformatics and data science fits into their research teams the course will enable PI s to take a strategic look at the requirements for undertaking such work and how bioinformatics capacity can be developed from personnel through to computational needs It will additionally provide guidance on strategies for managing data and the importance of data sharing how to work with computational collaborators and what resources are available across the life sciences to support such work During this course we will not be teaching hands on bioinformatics analysis but we will be signposting appropriate training resources to upskill you and your team This course is organised in parallel with Managing a Bioinformatics Core Facility to maximise opportunities for networking Shared sessions are highlighted in bold in the course programme 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...

Juanita Riveros

8 June - 11 June 2022

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...

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

1 June 2022

Computer-assisted functional precision medicine in cancer

Biological mechanisms provide a link between anti cancer compounds and therapy responses Insight to biological mechanisms is central for tomorrow s clinical decision support systems and personalised cancer therapy I will present the NTNU DrugLogics software that combines cancer signalling prior knowledge and data measurements to provide models that can predict therapy responses We combine in silico generated predictions with in vitro observations in the PRESORT project where patient derived cancer cultures are subjected to drugs and drug combinations predicted for the given patient to appreciate the efficacy for individual patients Together with Institut Curie Charit BSC Uppsala University and ProtAtOnce we test integrated computational and experimental pipelines on historic cohorts of patients treated at the molecular tumour boards at Institut Curie and Charit Current precision medicine trials including the nation wide trial IMPRESS Norway typically rely on individual and static biomarkers like DNA mutations for prediction of drug responses For future iterations of clinical decision support computer simulations taking in a number of data points and analyzed together combined with validation in patient derived tumour samples will be paramount About the speaker Dr smund Flobak works in clinical oncology and research at the St Olavs University hospital and at the Norwegian University of Science and Technology He is Project leader for the ERA PerMed project OncoLogics and for the RCN project PRESORT His work combines both experiments in the wet lab cell lines drug screening xenograft experiments and in the dry lab building logical models for drug combination response prediction development of a pipeline in Java for drug synergy studies Dr Flobak is the lead developer of the DrugLogics pipeline for drug synergy and resistance predictions The pipeline produces models tailored to single samples for drug synergy simulation and prediction...

Åsmund Flobak

29 May - 3 June 2022

Whole transcriptome data analysis

OverviewOrganisersProgrammePractical informationSponsors Overview Proof of COVID 19 vaccination or recovery is required to attend this on site course Please see EMBL s COVID 19 safety policy for on site events 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...

Marco Beccuti, Vladimir Benes, Raffaele Calogero, Francesca Cordero

28 May - 4 June 2022

Characterization of macromolecular complexes by integrative structural biology

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26 May - 27 May 2022

EMBL in Italy 2022: Emerging approaches in human health and infectious diseases

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EMBL Alumni Relations

25 May 2022

Exploring sequence alignment tools with Job Dispatcher

The Job Dispatcher framework at the EBI provides free access to several sequence analysis tools This webinar will introduce a list of sequence alignment resources available in Job Dispatcher This will include both pairwise and multiple sequence alignment tools and provide some useful tips for using the tools In addition to accessing these tools via the web browser this webinar will also demonstrate accessing them by using the API...

Nandana Madhusoodanan

24 May - 27 May 2022

Introduction to metabolomics analysis

This course will provide an introduction to metabolomics using publicly available data software and tools Participants will become familiar with the current state of experimental design data acquisition LC MS GC MS MS imaging processing and modelling as well as community standards and sharing in metabolomics particularly through using the EMBL EBI s MetaboLights repository and Galaxy infrastructure There will be a practical component where participants will learn through hands on tutorials to use tools available for data analysis and data submission The course will be completed with an interactive session which will build on the week s learning to discuss how to employ a metabolomics workflow with a case study 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...

Meredith Willmott

23 May - 25 May 2022

BioMalPar XVIII: biology and pathology of the malaria parasite

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

R. Dzikowski, S. Reece, M. Mota, C. Moxon

16 May - 20 May 2022

Exploring human genetic variation

Do you want to understand 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 three 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 Participants will learn via a mix of lectures trainer Q A sessions and hands on training Practical experience will be developed through group activities and trainer led exercises Live sessions will be delivered using Zoom with additional support and communication via Slack This course will take place over three non consecutive days 16 18 and 20 May 2022 Selected participants will be sent materials prior to the course These might include pre recorded talks and required reading or online training that will be essential to fully understand the course Participants will need to be available between the hours of 09 00 17 30 BST each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Jane Reynolds

16 May - 20 May 2022

Advanced fluorescence imaging techniques

OverviewSpeakers and TrainersProgrammePractical InformationSponsors Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic We are delighted to announce that the course is going virtual and invite you to join us online Course Overview This practical course will cover advanced light microscopy techniques and...

15 May - 19 May 2022

Microscopy data analysis: machine learning and the BioImage Archive

This course will introduce programmatic approaches used in the analysis of bioimage data via the BioImage Archive The content will explore a variety of data types including electron microscopy cell and tissue microscopy and miscellaneous or multi modal imaging data Participants will cover contemporary biological image analysis with an emphasis on machine learning and advanced image analysis Further instruction will be offered using applications such as ZeroCostDL4Mic ilastik ImJoy the BioImage Model Zoo and CellProfiler Virtual course Participants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack Pre recorded material may be provided before the course starts that participants will need to watch read or work through to gain the most out of the actual training event In the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 00 17 30 BST each day of the course Trainers will be available to assist answer questions and provide further explanations during these times...

Juanita Riveros

15 May - 18 May 2022

Mechanobiology in development and disease

OverviewSpeakersProgrammePractical informationSponsorsAbout Overview This conference will take place at EMBL Heidelberg with the option to attend virtually Proof of COVID 19 vaccination or recovery is required for on site attendance Please see EMBL s COVID 19 safety policy for on site events Symposium overview Environmental mechanics impact the behaviour of cells which in turn...

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

11 May 2022

Selecting and evaluating preprints for Journal Club

Preprints enable researchers to rapidly share their work publicly before the formal peer review process This webinar will introduce preprints demonstrate how to select and evaluate preprints by using tools developed by Europe PMC and show you how to set up and run a preprint journal club based on the experience run by the Immunology departments at Mount Sinai Oxford Karolinska Europe PMC indexes preprints abstracts and full text COVID 19 preprints from 24 life science preprint servers Preprints in Europe PMC are linked to data and platforms that comment or evaluate preprints How to use the linked data and platforms to select and evaluate preprints will be addressed We will also explore how to set up and run a preprint journal club and share useful tips so you can build your own preprint journal club This can help you in building your critical thinking whilst promoting awareness of current research...

Summer Rosonovski, Ester Gea-Mallorquí

9 May - 13 May 2022

Attacking open chromatin with ATAC sequencing

The goal of this introductory course is to teach the entire workflow of an ATAC Seq experiment including library preparation sequencing data processing and downstream analysis by addressing a real biological question that will be answered at the end of the course...

V. Benes, U. Litzenburger, J. Zaugg

9 May - 12 May 2022

Cellular mechanisms driven by phase separation

Liquid phase separation is emerging as a common biophysical basis underlying many important cellular functions This conference will bring together scientists from soft matter polymer physics molecular un structural biologists and biologists working in cell developmental and neurobiology to increase the awareness for how important phase separation is for our understanding of many biological processes...

Simon Alberti, Dorothee Dormann, Edward Lemke, Tanja Mittag

9 May - 11 May 2022

Building networks: engineering in vascular biology

OverviewSpeakersProgrammePractical InformationSponsors Overview This conference will take place at EMBL Barcelona Proof of COVID 19 vaccination recovery or negative test is required for on site attendance Please see EMBL s COVID 19 safety policy for on site events Conference Overview Blood vessels arise during early development and are essential for the formation and maintenance of...

4 May 2022

PDBe-KB Aggregated Views: providing biological insights into 3D structures

The Protein Data Bank in Europe Knowledge Base PDBe KB https pdbe kb org is an open collaboration between world leading specialist data resources with a goal to provide biological insights to macromolecular structure data in Protein Data Bank PDB Since we described PDBe KB in 2019 there have been significant improvements in the variety of available annotation data sets and user functionality This webinar presents the up to date improved PDBe KB protein specific aggregated views which provide an overview of available structural and functional information for a protein of interest referenced by a UniProtKB accession...

Preeti Choudhary

2 May - 6 May 2022

Hands-on flow cytometry: learning by doing!

OverviewSpeakers and TrainersProgrammePractical InformationSponsors Overview Proof of COVID 19 vaccination or recovery is required to attend this on site course Please see EMBL s COVID 19 safety policy for on site events 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...

Andrew Filby, Diana Ordonez, Malte Paulsen, Steffen Schmitt

27 April 2022

Approaches for using protein-protein interaction networks for biological discovery

It is hard to think of a biological process in which protein protein interactions PPIs do not play an essential role Thus in collective efforts over the last two decades comprehensive sets of human PPIs have been curated from the scientific literature or identified in systematic proteome wide mapping efforts These resources build large PPI networks with an amazing potential to advance our understanding of individual gene function towards a systems understanding of cellular organisation This webinar will provide important insights into technical biases that should be considered when using PPI data for system wide analyses It will explain theory and practical considerations when performing statistical tests on PPI networks to determine whether selected proteins i e that share a disease association tend to interact with each other or for the prediction of gene function using guilt by association principles...

Katja Luck

26 April 2022

Mathematical modelling as knowledge mapping in PhysiCell: a guided tour

Tissues are complex multiscale biological systems where cells communicate to modulate their behaviour in response to dynamical microenvironmental conditions Small perturbations to cells such as injuries or therapy can have unanticipated ripple effects that percolate through the system We can use computational models as virtual laboratories to explore these complex systems In this talk we will introduce PhysiCell an open source agent based modelling platform that can simulate many individual cell agents as they interact in tissue with multiple diffusing chemical signals We will give examples drawn from hypoxic cancer invasion mechanics driven reawakening of dormant micrometastases and innate and adaptive immune responses to viral pathogens like SARS CoV 2 and tumour micrometastases We will close with new developments and a live demonstration to integrate knowledge mapping directly into the modelling process where expert driven biological hypotheses chemical signal X increases cell behaviour Y are directly transformed into mathematics and code In our vision multidisciplinary teams will curate biological knowledge to jointly develop mathematical models in real time to better evaluate our knowledge gaps and exploit our knowledge to treat disease About the speaker Paul Macklin is an Associate Professor of Intelligent Systems Engineering at Indiana University IU His team the Math Cancer Lab develops open source computational tools for multicellular systems biology such as BioFVM for multi substrate diffusion and PhysiCell for large scale agent based simulations in 3 D tissues He has worked closely with others to develop new capabilities for the PhysiCell platform The codes developed have been applied to diverse problems in cancer biology nanotherapy tissue engineering immunology cryobiology synthetic systems and microbiology...

Paul Macklin

25 April 2022

Exploring parasite biology through their protein annotation in UniProtKB

Parasitic infections cause a major global burden in terms of human health whilst also affecting livestock and agriculture Understanding their biology is essential to identify potential candidates for drug and vaccine development To support the scientific community in this effort the UniProt knowledgebase UniProtKB provides a comprehensive high quality and freely accessible resource of protein sequence and functional information for a wide range of species including parasites and their hosts and vectors This webinar part of a series covering various aspects of UniProt will give you an overview on what type of functional information we provide and how to search and retrieve it We will also describe the curation process including how we annotate sequence polymorphism the interaction between host and parasite proteins and how we highlight the potential biotechnological use of a protein To illustrate these various aspects we will use the parasite P falciparum the causative agent of malaria as an example...

Rossana Zaru

23 April - 29 April 2022

Methods for analysis of circRNAs: from discovery to function

Circular RNAs CircRNAs are a rediscovered class of RNA species that originate from back splicing events which have been reported across all domains of life Many circular RNAs are stable abundant and conserved between species They exhibit context dependent expression patterns which are often linked to disease states Validated circular RNA functions are numerous and range from regulation of transcription and splicing to RNA protein sponging and scaffolding...

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

20 April 2022

Methods in building and analysing biological networks

Cells are complex and dynamic systems able to modify their behaviour and their morphology in response to internal or environment induced cues Such response is achieved thanks to enzymatic reactions and physical interactions that occur between cellular components such as proteins genes and molecules Complex diseases e g cancer have proven to result from alterations in the capacity of cell components to interact and communicate During this webinar we will Introduce biological networks conceptual and intuitive framework to investigate visualise and understand this complex web of interactions Show applications of basic graph theory concepts to physical or signalling interaction networks Familiarise with open access repositories that capture organise and display physical and signalling interactions Introduce Cytoscape an open source software platform for querying public databases and for visualising and analysing networks...

Livia Perfetto

13 April 2022

SciELO Preprints in Europe PMC

SciELO Scientific Electronic Library Online Preprints are now searchable in Europe PMC an open database which contains collections from 16 countries predominantly in Latin America Join us for this live demo to learn how to find SciELO preprints in Europe PMC how to explore links to journal published versions citation information annotations how to claim preprints to your ORCID record and more...

Summer Rosonovski, Alex Mendonça

12 April 2022

Biocuration in industry

This webinar part of the biocuration series will provide an insight into biocuration in industry We will be joined by Rachael Huntley Senior Scientific Curator at SciBite and George Georghiou Information Manager at Novartis Both will provide an insight into their role and the projects they work on In addition they will shed light on how biocuration tasks and projects may differ in industry from a more academic setting and which skills are helpful for moving into industry In particular Rachael will highlight the major differences between working in her previous biocurator roles in non profit and academia with her current role in a commercial company She will provide examples of services that SciBite provides to customers and of community projects that SciBite has been involved with George will be discussing how his role as a biocurator helped him transition into an information scientist Using his experience working with ontologies data annotation and his knowledge of biology he helps deliver custom data solutions and consulting services for his colleagues at Novartis This webinar is the final one in our series of webinars on the topic of biocuration In a survey in 2019 which aimed at identifying training needs in biocuration the most commonly indicated were programming development and use of ontologies and database management In addition skills like programming and extracting data from literature were mentioned as decisive for a successful biocuration career With our webinar series we want to help to close this gap Bicourators from different backgrounds and institutes will share their experience on how they have acquired these relevant skills in their job how they apply these in their works and why they benefit from it The speakers will also point to helpful tools and resources they use...

Rachael Huntley, George Georghiou

7 April 2022

UniProt for proteomics scientists

UniProt is a comprehensive expert led publicly available database of protein sequence function and variation information This webinar will give a brief introduction to the new UniProt website and then highlight resources available that proteomics scientists or users with large protein datasets may find useful in analysing their data This will encompass our proteomes service how to convert and retrieve ID mappings and how to carry out a peptide search The webinar will then go on to introduce the UniProt Proteins API which allows researchers to access and download UniProt data alongside large scale genomic proteomics and variation data without needing prior in depth knowledge of programmatic languages Data is available for download and querying in a range of formats including XML FASTA and PEFF The API multi query search functions will be demonstrated and useful features such as searching entries by peptide and the new functionality of searching for proteomic peptides and modifications will be explained The UniProt Proteins API is available at www ebi ac uk proteins api doc...

Emily Bowler-Barnett

6 April 2022

Methods for rare-variant association analysis

Rare variants contribute to development of familial cancer Genes carrying rare variants may contribute to molecular mechanisms of sporadic cancers Historically many of the rare variants were discovered by co segregation with the disease in cancer families However recent progress in population scale sequencing opens new opportunities for using association analysis for detection of rare variants The standard methods of association analysis were developed for common variants While the standard regression framework and population stratification approaches hold in the rare variant analysis it may additionally require i aggregating of variants per gene or pathway ii weighting by biological significance and allelic frequency and iii applying permutation style tests for estimating statistical significance The webinar will discuss these features of rare variant analysis and illustrate their implementation using SKAT R library...

Alexey Larionov

6 April - 8 April 2022

Microbial infections and human cancer

OverviewSpeakersProgrammePractical InformationSponsorsAbout Overview Please note that this event will now take place virtually Symposium Overview Microbial host interaction has a profound impact on numerous biological systems including metabolism immunology DNA integrity and nutrition Pathobionts and pathogenic bacteria have developed specific abilities to gain growth advantage...

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

5 April 2022

Working with sensitive data

This webinar part of the biocuration series will introduce the concept of sensitive data for example data relating to individual patients It will also discuss how controlled data resources that contain sensitive data are able to archive and share the data with researchers and the best practices for assembling metadata for a rare disease submission To give an example of how controlled data resources work the European Genome phenome Archive EGA will be introduced The EGA is a resource that archives and shares all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects The webinar will discuss why restricted access to the EGA s data is required what information about the data can be viewed by anyone and how researchers can gain access to the data they need This webinar is the fourth in our series of webinars on the topic of biocuration In an ELIXIR survey in 2019 which aimed at identifying training needs in biocuration the most commonly indicated were programming development and use of ontologies and database management In addition skills like programming and extracting data from literature were mentioned as decisive for a successful biocuration career With our webinar series we want to help to close this gap Bicourators from different backgrounds and institutes will share their experience on how they have acquired these relevant skills in their job how they apply these in their works and why they benefit from it The speakers will also point to helpful tools and resources they use...

Marcos Casado Barbero, Dona Shaju

4 April - 8 April 2022

Data visualisation for biology

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

EMBL-EBI Training team

4 April - 8 April 2022

Gene expression at single-cell resolution

OverviewSpeakers and TrainersProgrammePractical InformationSponsors Overview The course will be held online Course overview The goal of this course is to provide participants with both the theory and practical skills required to design prepare run and analyse high throughput single cell transcriptomic experiments using the Chromium Single Cell Controller from 10x Genomics We will begin...

Vladimir Benes, Dirk Jürgensen, Elisabeth Zielonka

31 March 2022

Bringing it all together: human cohort standards, tools and applications

The CINECA webinar series continues with a presentation by Dr Melanie Courtot from the Ontario Institute for Cancer Research OICR The ability to integrate and harmonise diverse large human cohort data at scale promises exciting research perspectives and applications This webinar provides a high level introduction to some current standards for data representation and access and tools leveraging them Finally we explore how modular assembly of tools and standards enables deployment of Findable Accessible Interoperable and Reusable FAIR data and showcase applications that bring it all together The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis as well as distribute CINECA project results All CINECA webinars include an audience Q A session during which attendees can ask questions and make suggestions Please note that all webinars are recorded and available for posterior viewing...

Melanie Courtot

30 March 2022

Methods in genomic variant calling

Genomic variant calling entails identifying single nucleotide polymorphisms small insertions and deletion InDels and larger variants structural variants and copy number variants from next generation sequencing data This webinar will cover the basics of germline and somatic variant calling as well as their annotation and visualisation We will get to know workflows to perform variant calling look at relevant file formats and discuss some variant calling applications in rare diseases cancer genomics and population genomics...

Tobias Rausch

29 March 2022

Ontologies for biocuration

This webinar part of the biocuration series will introduce the concept of an ontology a type of controlled vocabulary that encompasses relationships between entities and will cover why ontologies are useful for describing biological data and biology The webinar will also discuss the role of biocurators and the relevance of ontologies to biocuration During this webinar the Gene Ontology a species agnostic classification scheme for gene function will be used to illustrate how ontology terms are composed and how terms are related within the ontology Then as an example of how a data resource uses an ontology the International Mouse Phenotyping Consortium will be introduced along with a description of the Mammalian Phenotype Ontology that it uses to describe identified phenotypes This webinar is the third in our series of webinars on the topic of biocuration In an ELIXIR survey in 2019 which aimed at identifying training needs in biocuration the most commonly indicated were programming development and use of ontologies and database management In addition skills like programming and extracting data from literature were mentioned as decisive for a successful biocuration career With our webinar series we want to help to close this gap Bicourators from different backgrounds and institutes will share their experience on how they have acquired these relevant skills in their job how they apply these in their works and why they benefit from it The speakers will also point to helpful tools and resources they use...

Gun Antonia Nilsson Lock, Violeta Munoz-Pomer Fuentes

25 March - 1 April 2022

BioExcel school on biomolecular simulations

The course will include lectures and hands on sessions on the following topics Molecular Dynamics simulations Biomolecular Docking Free energy calculations Advanced sampling methods Metadynamics BioExcel Building Blocks BioBB Quantum mechanics molecular mechanics QM MM During the hands on computer practicals you will make use of the BioExcel flagship software and tools e g GROMACS HADDOCK PMX BioBB and CP2K The trainers developers and or experts in the use of the software will provide guidance and support...

Marta Lloret Llinares

23 March 2022

Methods in bioimage analysis

Microscopy is a key technology driving biological discovery Nowadays microscopy based scientific findings must be substantiated by quantitative image analysis The discipline concerned with such quantification of biological microscopy images is called bioimage analysis This webinar will walk us through the main concepts of a typical bioimage analysis workflow including how to quantitatively interpret the content of microscopy images how to automatically detect objects in images and derive object based measurements It will emphasise the importance of visual inspection and quality control of automated image analysis Finally this webinar will also provide an overview of current bioimage analysis tools and communities...

Christian Tischer

22 March 2022

Text mining for biocuration

This webinar part of the biocuration series will introduce the topic of text mining and discuss why text mining is used by life sciences data resources in part of their biocuration efforts To illustrate its use in biocuration this webinar will discuss how text mining has recently been used by two data resources Open Targets and UniProt in their curation of biological data This webinar is the second in our series of webinars on the topic of biocuration In an ELIXIR survey in 2019 which aimed at identifying training needs in biocuration the most commonly indicated were programming development and use of ontologies and database management In addition skills like programming and extracting data from literature were mentioned as decisive for a successful biocuration career With our webinar series we want to help to close this gap Bicourators from different backgrounds and institutes will share their experience on how they have acquired these relevant skills in their job how they apply these in their works and why they benefit from it The speakers will also point to helpful tools and resources they use...

Shyamasree Saha, Michele Magrane

21 March - 25 March 2022

Introduction to multi-omics data integration and visualisation

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

Juanita Riveros

21 March - 23 March 2022

Inter-organ communication in physiology and disease

OverviewSpeakersProgrammePractical InformationSponsorsAbout Overview Please note that this event will now take place virtually Symposium Overview Like a machine any organism even the simplest is a functional unit coherent and integrated We are far from having elucidated in complex organisms the entire structure of these functional units A major outcome of research using model...

Gerard Karsenty, Irene Miguel-Aliaga, Miguel Soares

16 March 2022

Discovering biological information from mass spectrometry-based proteomics

Mass spectrometry based proteomics has revolutionised the analysis of proteins by enabling quantitative analysis of thousands of proteins and their properties including post translational modification PTM The resulting datasets are rich multidimensional and comprehensive The webinar will cover basics of peptide and PTM identification by mass spectrometry strategies for quantitation and introduce tools for the analysis of proteomic datasets...

Tony Ly

15 March 2022

Programming skills in biocuration

This webinar will be the first of our series of webinars on the topic of biocuration and discuss programming skills that can be beneficial in biocuration as well as provide advice on how to acquire them In an ELIXIR survey in 2019 which aimed at identifying training needs in biocuration the most commonly indicated ones were programming scripting coding development and use of ontologies and database management In addition skills like programming and extracting data from literature were mentioned as decisive for a successful biocuration career With our webinar series we want to help to close this gap Biocurators from different backgrounds and institutes will share their experience on how they have acquired these relevant skills in their job how they apply these in their works and why they benefit from it The speakers will also point to helpful tools and resources they use In this first webinar we will hear from two UniProt biocurators who will share their experience on how they acquired programming skills and show you some intuitive scripts in Python and SQL which they use to facilitate some of their curation tasks In addition we will introduce other helpful curation software like UniFire a functional protein annotation system Speakers Elena Speretta EMBL EBI Elena Speretta is a Biocurator in the Protein Function Content team of UniProt at EMBL EBI working on the curation of Drosophila proteins as well as the creation of rules for automatic annotation of protein function Prior to joining EMBL EBI she worked as a postdoctoral researcher at the University of Dundee UK She obtained her PhD from the University of Cambridge UK and undergraduate degree from the University of Trieste Italy Pedro Raposo EMBL EBI Pedro Raposo is a Bioinformatician in the Protein Function Content team of UniProt at EMBL EBI working on creation of rules for automatic annotation of protein function After obtaining his MSc in Bioinformatics he worked at the UK Stem Cell Bank on genomic data before joining EMBL EBI...

Elena Speretta, Pedro Raposo

15 March 2022

Virtual Ensembl REST-API Workshop, March 2022

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

Aleena Mushtaq

13 March - 18 March 2022

Extracellular vesicles: from biology to biomedical applications – Cancelled

This course is intended for PhD students and Postdoctoral researchers who are interested in learning how to work with extracellular vesicles and know more about their biomedical applications...

An Hendrix, Cecilia Lässer, Esther Nolte-’t Hoen, Guillaume Van Niel

13 March - 16 March 2022

From 3D light to 3D electron microscopy

OverviewSpeakers and OrganisersProgrammePractical InformationSponsors Overview Please note that this event will now take place virtually Conference Overview The event is jointly organised by EMBL ZEISS The Francis Crick Institute and the VIB Ghent Life happens in 3D and understanding biological context in the three dimensions has been a major driver in the past decades in both...

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

9 March 2022

Methods for exploring newly-annotated species in Ensembl Rapid Release

Newly sequenced genomes including those produced by the Darwin Tree of Life project are all added to Ensembl Rapid Release These genomes have minimal annotation with genes mapped onto the genome protein domain analysis and homologue predictions This webinar will guide you through the data available for newly annotated species in the Ensembl Rapid Release site and how to cross reference against more fully annotated genomes in the main Ensembl genome browser...

Benjamin Moore

8 March - 10 March 2022

Ensembl Browser Virtual Workshop, March 2022

Work with the Ensembl Outreach team to get to grips with the Ensembl browser accessing gene variation comparative genomics and regulation data and mine these data with BioMart...

Aleena Mushtaq