Events archive

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

7 October 2022

Federated data analysis

This learning pathway is intended for end users interested in working with synthetic cohorts datasets and in learning how to use these datasets in federated analysis Following this pathway you can learn about tools for finding and accessing data from synthetic cohorts how the metadata of a synthetic cohort is harmonised how to use a workflow to carry out a federated data analysis and finally the main ELSI considerations when working with a synthetic cohort The aim is to give you a broad understanding of the procedure and point you towards different resources...

Daniel Thomas Lopez

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 - 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

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

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...

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 - 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

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

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 - 15 July 2022

Visualising life – interdisciplinary approaches to biology

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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

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...

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 series will comprise 3 webinars Overview scope and vision of AlphaFold This webinar took place on Tuesday 14 June at 13 30 BST Click on the Watch video button on this page to listen to the webinar How AlphaFold is changing the teaching training landscape in life sciences Tuesday 21 June 13 30 BST Click here to find more information and the recording for this webinar Impact of AlphaFold on research and development in life sciences Tuesday 28 June 13 30 BST Click here to find more information and the recording for this webinar To discuss the overview scope and vision of AlphaFold we had the following panel of 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 - 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

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

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

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...

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

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

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

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 - 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...

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

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

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

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

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 multiomics data integration and visualisation

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

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 - 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

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

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

7 March - 11 March 2022

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 for mammalian and plant genomes Please note that although participants will not be able to use their own data during the course practicals there will be ample time to discuss their research and ideas with both course participants and trainers As part of this participants will present lightning talks on their research topics Near the end of the course participants will engage in small group discussions about their research challenges and problems with each other and the trainers at the Talk with trainers Virtual course Participants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and communication via Slack Pre recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 00 17 00 GMT each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Sophie Spencer

6 March - 11 March 2022

Analysis and integration of transcriptome and proteome data – Cancelled

During this course participants will gain theoretical insight in the structure of sequencing and proteomic data and they will receive training in data analysis for the annotation quantification and statistical analysis of gene and protein expression using various computational tools...

Vladimir Benes, Raffaele Calogero, Jeroen Krijgsveld, Lennart Martens

6 March - 9 March 2022

Biological oscillators: design, mechanism, function

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 Conference Overview Are you interested in oscillatory phenomena and biological dynamics At...

Alexander Aulehla, Hanspeter Herzel, Eve Marder, Ueli Schibler

3 March 2022

Identifying tumor cells at the single cell level through machine learning

Tumours are highly complex tissues composed of cancerous cells surrounded by a heterogeneous cellular microenvironment A tumor s response to treatments is governed by an interaction of the cancer cell s intrinsic factors with external influences of the tumor microenvironment Disentangling the heterogeneity within a tumor is a crucial step in the development and utilisation of effective cancer therapies The single cell sequencing technology enables an effective molecular characterisation of single cells within the tumor This technology can help deconvolute heterogeneous tumor samples and thus revolutionise personalised medicine However a governing challenge in cancer single cell analysis is cell annotation that is the assignment of a particular cell type or a cell state to each sequenced cell The identification of tumor cells within single cell or spatial sequencing experiments remains a critical and limiting step for research clinical and commercial applications In this webinar we will discuss these challenges and a novel machine learning pipeline aimed at performing automatic annotation and distinguishing tumor cells from normal cells at the single cell level About the speaker Altuna Akalin is a bioinformatics scientist and the head of Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology Max Delbr ck Center MDC in Berlin He has developed computational methods for analysing and integrating large scale genomics data sets since 2002 He uses machine learning and statistics to uncover biological patterns for example those related to disease state and type In his current work he uses complex molecular signatures to provide decision support systems for disease diagnostics and biomarker discovery Additionally he is actively involved in organising and teaching at computational genomics courses...

Altuna Akalin

2 March 2022

Exploring Gene Ontology, GO annotations, tools and resources

The Gene Ontology GO resource is the world s most comprehensive source of information about the function of gene products proteins and non coding RNAs The GO consists of two main components an ontology of terms that describe biological phenomena and annotations that connect gene products to ontology terms In addition GO develops tools to help researchers make use of the GO in their analyses This webinar will provide an overview of what GO terms are and how they relate within the structure of the ontology It will also describe how annotations are created and highlight some of the limitations of the GO Lastly it will introduce some freely available bioinformatic resources used for accessing the GO and methods used in GO analysis...

Antonia Lock

21 February - 25 February 2022

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 communication via Slack Pre recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 30 16 00 GMT each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Meredith Willmott

21 February - 2 March 2022

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 This course will take place from 21 to 23 February and on 2 March 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 the afternoon of 22 February For an introduction to the concept of web services and how you can use them to access the tools and data available programmatically please watch this EMBL EBI programatically webinar You will be provided exercises for each resource that you will work through on your own in the following week with remote trainer support available if needed We will then meet again on 2 March to discuss issues that occurred while working through the material in more detail All participants will be asked to pre record a short presentation three minutes about their research work as part of the course These will provide an opportunity to share your research with the other participants and provide a forum for discussion Further details will be provided to participants once registrations have closed This course will be run virtually and delivered over Zoom with additional text communication over Slack In order to make the most out of the course you should make sure to have a stable internet connection throughout the course...

Jane Reynolds

17 February 2022

Social Media in Science Communication

In this session you will hear from Michelle on the increasing demand for researchers to build a digital presence and the role of social media in science communication She will cover examples of scientific organisations and researchers using innovative approaches to promote their research on social media with insights on how BioExcel Centre of Excellence used Twitter to build a successful computational biomolecular research community She will also provide tips on how to optimise your use of social media platforms along with the dos and don ts of building a digital presence...

Michelle Mendonca

15 February 2022

Ensembl REST API workshop, University of Cambridge

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

14 February 2022

Ensembl browser workshop, University of Cambridge

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

14 February - 18 February 2022

CABANA Workshop: Bioinformatics approaches to viruses and genomic surveillance

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 including public health and policy...

Juanita Riveros

9 February 2022

Exploring genotype-phenotype data using the GWAS Catalog

The GWAS Catalog is the primary resource of genotype phenotype associations identified through genome wide association studies GWAS Catalog data are publicly available in a consistent searchable and visualisable format which is easily integrated with other resources Uses for the data include prioritising candidate loci exploring disease mechanisms predicting risk of disease identifying new drug targets gathering statistics on traits or populations of interest and downloading full summary data for use in downstream analyses This webinar will include a brief introduction to the GWAS Catalog and a demonstration of our web based search interface focusing on the most common use cases...

Maria Cerezo

9 February - 11 February 2022

The epitranscriptome

OverviewSpeakersProgrammePractical InformationSponsorsPre conference Webinar Overview Conference Overview The regulation of the transcriptome is key to cellular processes that underpin cell biology development and tissue function All classes of cellular RNA are subject to post transcriptional modification be it by direct chemical modification editing or non templated nucleotide...

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

3 February 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 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, Hermann Zellner

2 February 2022

MetaboLights: the home for metabolomics experiments and derived information

MetaboLights is a database for metabolomics experiments and derived information The database is cross species cross technique and covers metabolite structures and their reference spectra as well as their biological roles locations and concentrations and experimental data from metabolic experiments It is the recommended metabolomics data repository for several leading journals This webinar will introduce metabolomics data and the MetaboLights resource including how to submit access and search relevant data...

Thomas Payne

31 January - 4 February 2022

SymbNET: from metagenomics to metabolic interactions

Run jointly with SymbNET this virtual course will introduce and discuss state of the art tools for understanding microbial communities metagenomics and discovering and analysing species interactions in gut microbial communities with a particular focus on metabolic interactions The goal will be to enable users to integrate experimental results with the latest computational methods to move from correlative analyses of host microbiome systems towards mechanistic understanding using a combination of introductory lectures and hands on training materials Virtual course Participants will learn via a mix of pre recorded lectures live presentations trainer Q A sessions and hands on training Live sessions will be delivered using Zoom with additional support and communication via Slack Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their 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 further explain the analysis during these times About SymbNET SymbNET is a European network for host microbe interactions research funded by the European Union s Horizon 2020 research and innovation programme The project coordinated by FCG IGC Instituto Gulbenkian de Ci ncia Portugal brings together the world leading research institutions EMBL European Molecular Biology Laboratory Germany CAU Christian Albrechts Universit t zu Kiel Germany and UNIL Universit de Lausanne Switzerland and a local widening partner ITQB NOVA Instituto de Tecnologia Qu mica e Biol gica Portugal This project has received funding from the European Union s Horizon 2020 research and innovation programme under grant agreement N 952537...

Jane Reynolds

31 January - 2 February 2022

PATC: 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 The course is organised and funded by PerMedCoE the HPC Exascale Centre of Excellence in Personalised Medicine and BioExcel the Centre of Excellence for Computational Biomolecular Research http bioexcel eu using MareNostrum part of the Spanish supercomputing network https www bsc es marenostrum marenostrum...

Daniel Thomas Lopez

31 January - 4 February 2022

Exploratory analysis of biological data: data carpentry

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

Renato Alves, Fotis E. Psomopoulos, Christian Schudoma

26 January 2022

Guide to exploring genes and genomes with Ensembl

This webinar will provide a brief overview to the Ensembl browser and demonstrate how you can access information about genes or genomes of your interest We will also showcase the data types and tools available at Ensembl which can help your research...

Aleena Mushtaq

26 January - 27 January 2022

The next generation in infection biology

OverviewOrganisers and SpeakersParticipating OrganisationsProgrammePractical InformationSponsors Overview Conference Overview Infectious diseases are among the most prevalent causes of human illness and death in the world Pathogens infect humans and all life forms on Earth being able to cross species barriers thereby adversely impacting human and planetary health Fundamental research...

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

20 January 2022

Logic modelling of signalling networks – CellNOpt and CARNIVAL

Reconstruction of signaling networks has been widely utilised in the past for example to understand aberrations in diseased cells or to figure out mechanism of drug actions With the development of high throughput data platforms it is possible to infer these networks from the data alone alternatively we could reuse existing knowledge about possible mechanisms reported in literature and interaction databases The prior knowledge network PKN describes the possible interactions among the signaling molecules and connects the perturbations to the measured molecular markers Different formalisms build different types of models from the PKN ranging from boolean networks to differential equations It is then possible to train the models to the measured data using optimisation methods CellNOpt uses different logic formalisms which include boolean fuzzy probabilistic and ordinary differential equations models which are trained against phosphoproteomic data On the other hand similar approaches are used to extract mechanistic insights from multi omics data using CARNIVAL to train signaling networks from gene expression data using integer linear programming to infer causal paths linking signaling drives with downstream transcripts levels In this webinar we introduce CellNOpt and CARNIVAL and show how each can be used to build models of signalling networks About the speaker Dr Pablo Rodriguez Mier is a Postdoctoral Researcher at Julio Saez Rodriguez s group at the Joint Research Center for Computational Biomedicine He has a background in Computer Science and Artificial Intelligence Prior to this he was a Postdoctoral Researcher at the Food Toxicology Research Center of the French National Institute for Agricultural Research INRAE in Toulouse in a project funded by the French National Cancer Institute INCA He was in charge of developing new computational methods to understand metabolic dysregulations in cancer due to mutations in the p53 gene and also in key target genes combining previous biological knowledge with experimental data...

Pablo Rodriguez Mier

20 January 2022

Uncovering protein function with UniProt

This webinar will discuss 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

17 January - 21 January 2022

Deep learning for image analysis

This is a blended learning course on Deep Learning for Image Analysis...

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

16 December - 17 December 2021

The big picture – zooming into life

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

2021 EMBL PhD Symposium Organising Committee

14 December 2021

Biomedicine, supercomputers and simulations: in silico experiments and its applications in cancer research

Computational simulations of cellular processes e g metabolism gene expression signal transduction are critical tools to formulate mechanistic explanations that facilitate the interpretation of experimental results However complex biological processes such as tumour evolution span across different time space scales For instance a population level description is needed to account for genetic heterogeneity and phenotypic variability due to environmental noise whereas intracellular models such as cell signalling networks need to address the effect of mutated genes In this context multi scale models are ideal tools to address systems biology questions as they can consider several time space scales by combining different approaches into a hybrid simulation PhysiCell is an open source agent based extensible multi scale modelling framework that allows simulating complex multicellular systems such as healthy tissues and tumours At the lowest scale PhysiCell uses BioFVM solver to simulate the chemical microenvironment using partial differential equations which model the diffusion uptake and secretion of substrates and signalling molecules At the cell scale PhysiCell uses mechanical equations to model individual cell movement cell cell interactions as well as interactions between cells and the microenvironment s physical components e g as extracellular matrix Additionally different cells types and heterogeneous populations can be defined by using different submodels for cell growth death as well as user defined custom behaviours Furthermore PhysiCell can be extended to provide cell agents with more complex intracellular networks such as signalling and metabolism For instance PhysiBoSS is an addon based extension that provides cell agents with individual Boolean models of regulatory networks which are simulated using the MaBoSS algorithm The Boolean model inputs can be connected to different cell variables and their outputs can be used to trigger changes in the cell behaviour Altogether PhysiBoSS bridges intracellular dynamics to the population level Because of its flexibility the PhysiCell Framework can be applied to a broad range of biological problems related to cancer immunology infectious diseases and microbial ecology among others In this webinar we will introduce the basic concepts of the PhysiCell PhysiBoSS modelling framework and its HPC based implementation using different biological examples focusing on applications to treatment optimisation in models of tumour growth About the speaker Miguel Ponce de Le n is a recognized postdoctoral researcher at the Computational Biology Group at the Life Science Department of the Barcelona Supercomputing Center BSC His area of expertise is in the field of systems biology and scientific computation where most of his research has been on reconstruction and simulation of biological networks His line of research at BSC is the development of systems biology approaches to personalized medicine with a particular focus on cancer He uses different modelling approaches to integrate heterogeneous sources of information with two main objectives 1 developing tools to assist in the decision making process of choosing the most adequate therapy for specific patients given their unique genetic background and 2 improving the knowledge of basic cancer biology...

Miguel Ponce de León

14 December - 16 December 2021

Virtual Ensembl REST-API Workshop, 14th-16th December

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 December - 17 December 2021

CABANA Workshop: Plant bioinformatics - analysis of crop genomics data

This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping During the course participants will learn about genotyping experimental design variant calling comparative genomics using Ensembl analyse variation data with Ensembl Variant Effect Predictor and explore concepts of genome wide association studies GWAS The content will explain how to make use of existing public data retrieve submit and share your data with the community Trainers will cover the basics of diversity analysis using R before analyzing various genomes to assess diversity investigating gene phenotype relationships and microsatellites The course will be delivered through a combination of hands on training sessions and lectures This course will be a virtual event The content will be delivered over Zoom In order to make the most out of the course you should make sure to have a stable internet connection throughout the week Computational practicals will be run on EMBL EBI s virtual training infrastructure this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course...

Juanita Riveros

7 December - 9 December 2021

Ensembl Browser Virtual Workshop, December 2021

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 December - 9 December 2021

IITM-EMBL-EBI Winter School 2021

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

IBSE Workshop Team

1 December 2021

The BioImage Archive: Home for life sciences microscopy data

The BioImage Archive is EMBL EBI s open access image archive accepting molecular biology imaging data associated with peer reviewed publications This webinar will provide an introduction to the archive including an overview of the data preparation and submission process data retrieval and future development plans...

Matthew Hartley

1 December - 3 December 2021

CABANA Virtual Workshop: Managing a Bioinformatics Core Facility

This introductory knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities in both formal and informal positions to learn from various core facility managers across Latin America and EMBL EBI from each other and from potential users of their services These facilities play an essential role in enabling research in the molecular life sciences The landscape is constantly evolving as new research tools emerge as experiments become increasingly data intensive and as their clients experimental researchers become more exposed to the power of data driven biology The workshop 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 lectures live and pre recorded and active sessions to learn from managers of bioinformatics facilities hear how others have tackled common problems and work together to design core services Please note this course will NOT provide any bioinformatics training...

Rebeca Campos

29 November - 1 December 2021

Recent advances in structural biology of membrane proteins

Integral membrane proteins IMPs are encoded by 20 30 of genes in a genome and provide key functions in the cell Due to their hydrophobic nature they are structurally and biochemically difficult to study Traditionally IMPs have been extracted using detergents which are a poor mimic of the lipid membrane and have been shown to denature membrane proteins However newly developed lipid nanodisc approaches enable structural and functional studies of IMPs in a detergent free near native membrane environment Therefore a central theme of this workshop is highlighting the importance of lipids in MP research and how they can be preserved...

Panagiotis Kastritis, Sandro Keller, Christian Löw, Cristina Paulino

24 November 2021

Analysing publications and funding with the Europe PMC REST API

Europe PMC is a database of life science publications and preprints Articles in Europe PMC are enriched with additional resources such as author funding and affiliation information citations and links to data peer reviews and more In this webinar we will explain how to programmatically access publications and related information using the Europe PMC Articles RESTful API Michael Parkin Data Scientist at Europe PMC will demonstrate how to access the API using the browser and provide some scripting examples in Python R He will outline different API methods rules for filtering and pagination as well as output formats Following on Antonio Campello Senior Data Scientist at the Wellcome Trust will explain how Wellcome uses Europe PMC APIs to gain insights into the outputs of the research they fund He will discuss several use cases including charting Wellcome s research portfolio developing novel technologies to link grants to academic publications and tracking which grants have been influential to the COVID 19 literature Additional reading Linking academic publications to grants with machine learning Which research fields have emerged in the last years A machine learning approach...

Michael Parkin, Antonio Campello

22 November - 24 November 2021

Cancer genomics

This conference will provide an opportunity to learn about and keep up to date with the rapidly progressing area of cancer genomics It will cover presentations from cancer genome projects the areas of cancer functional genomics systems biology cancer immunogenomics and epigenomics cancer mouse models and the translation and clinical impact of scientific results obtained The meeting will bring together leading scientists from across these areas for a unique opportunity to interact and stimulate further integration of these efforts...

Jan Korbel, Núria López-Bigas, Seishi Ogawa, Elli Papaemmanuil

18 November 2021

Introduction to qualitative modelling with MaBoSS

Boolean modelling uses a simple representation of biological entities as either active or inactive and describes their relations with logical formulas MaBoSS extends Boolean modelling by adding a notion of continuous time with the introduction of rates of in activation This enable the representation of physical time and of processes with different time scales MaBoSS simulate multiple stochastic trajectories and produces trajectories of the probabilities of the system state This webinar will introduce the concepts of boolean modelling and MaBoSS continuous time boolean modelling and will then demonstrate the use of WebMaBoSS a web interface designed for easily simulating MaBoSS models About the speaker Dr Vincent No l M is a postdoctoral student at the Computational Systems Biology of Cancer team of the U900 in Institut Curie His research interests concern modelling of biological systems where he has experience in both construction and analysis of these models He did his PhD in applied mathematics studying simplifications of ODE models and then did his first postdoc within a molecular biology unit building a model of Ras Mapk signaling in Y1 tumor cells He also developed tools to simplify the construction and analysis of models and the reproducibility of this work He has a good experience in the optimisation of numerical simulation workflows and has been working on MaBoSS for more than three years...

Vincent Noël

17 November - 20 November 2021

Metabolism meets epigenetics

Metabolism and epigenetics are intricately linked playing a key role in development cancer immune signalling and ageing This symposium brings together world leading researchers and young scientists to explore this nexus with a particular focus on how metabolites and metabolic networks impact gene regulation on recently discovered roles of metabolites in disease and how this opens novel therapeutic avenues...

Theodore Alexandrov, Andreas Ladurner, Jane Mellor, Erika Pearce

10 November 2021

A guide to accessing ChEMBL and UniChem through an API

ChEMBL is a database of bioactivity data that links drug like compounds to their biological targets UniChem is a database that produces cross references between chemical structure identifiers from different databases Both ChEMBL and UniChem can be accessed through an interactive interface as well as programmatically via web services This webinar will provide an overview of programmatic strategies that can be used to extract data from ChEMBL and UniChem alongside examples to illustrate the applications...

Fiona Hunter, James Alan Blackshaw

9 November - 11 November 2021

Virtual Ensembl Plants REST API Workshop

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

Michal Szpak

8 November - 12 November 2021

Metagenomics bioinformatics

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

Juanita Riveros

8 November - 9 November 2021

CABANA Virtual Workshop: Introducción a R y Bioconductor para análisis genómicos

Este taller introducir el lenguaje de programaci n de R la utilizaci n de la interfaz gr fica RStudio y el empleo de Bioconductor para trabajar con datos provenientes de bases de datos gen micos como Ensembl y Ensembl Genomes Adem s de introducir las funciones b sicas de R y Bioconductor se aplicar n herramientas espec ficas para este tipo de datos Se explorar tambi n el v nculo de R con bases de datos gen micas p blicas como Ensembl y Ensembl Genomes...

A2B2C Courses

8 November - 12 November 2021

CABANA Virtual Workshop: Exploring biological networks and its application in health and disease

This workshop will introduce open source tools for creating visualizing and analyzing biological networks oriented towards the study of pathogens Training will be provided on computational tools and databases such as Reactome Cytoscape Gephi for graph visualization and analyses MetaFlux Pathway Tools BioCyc for reconstruction of pathway genome databases using omics data and Target Pathogen for the discovery of targets using integrative approaches The main principles of network analysis will be covered as well as its applications to health and disease...

Dario Fernandez Do Porto

8 November - 12 November 2021

CABANA Virtual Workshop: Innovative methods for viral detection and discovery in genomic and metagenomic data

Emerging viruses can cause new diseases in humans and animals and proper epidemiological surveillance is essential to detect and characterize such viruses Given the enormous impact of the COVID 19 pandemics this course will cover the assembly of the SARS CoV 2 genome from human patients characterization of viral variants and identification of variants of concern VOCs The course will also present some innovative methods that can improve the detection of evolutionarily remote viruses Among other methods the course will cover the construction of profile HMMs and their application to screening metagenomic datasets for both known and novel viruses Virtual machines All students will receive an account in a virtual machine VM The VMs will be running Linux and all programs used throughout the course will be available to students Access to the VMs will be granted throughout the entire duration of the course No programs are needed on the local computer except Zoom...

Arthur Gruber

3 November 2021

Getting gene and genome data programmatically: Ensembl REST API

This webinar will provide a brief introduction to what the Ensembl REST API is the types of data available and how to get started with using it...

Emily Perry

2 November - 4 November 2021

Virtual Ensembl Plants Browser Workshop

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

Michal Szpak

29 October 2021

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

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

Renato Alves, Anthony Burdett, Mariia Levchenko, Sandra Orchard

28 October 2021

A walk through the new 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 used information from our users to revamp our website structure so users can 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 including the creation of a 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 The new website is currently in its first beta release so we hope that this interactive webinar will introduce you to all the new features and improvements we implemented into the new website and encourage your feedback to assist user guided development of the website If you would like to formally sign up for testing the new website and or participate in future user research please register your interest here https forms gle BhYmSz6bRwU85s9N8 This webinar is part of a series covering various aspects of UniProt view other upcoming webinars here...

Kate Warner, Aurelien Luciani

28 October - 29 October 2021

Microglia 2021

Microglia are a resident macrophage of the central nervous system at the intersection of immunology and neuroscience They have gained increasingly more attention over the past decade as more research shows that they are key contributors to neural circuit development and function There is also increasing evidence that microglia are also important in the etiology of many nervous system diseases This workshop will highlight the many important functions of microglia to nervous system physiology and function the newest and most exciting literature and will bring together researchers using state of the art imaging genomics and molecular biology to study these enigmatic cells...

Sonia Garel, Florent Ginhoux, Dorothy Schafer, Amada Sierra

27 October 2021

Open access: publications and preprints

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

Mariia Levchenko

25 October - 3 November 2021

Solution scattering from biological macromolecules

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M. Gräwert, A. Kikhney, D. Svergun

21 October 2021

Analysis of huge metabolic models with COBREXA.jl

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

Miroslav Kratochvil

20 October 2021

Open access: Finding and accessing open data

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

Ugis Sarkans, Anna Swan

20 October - 22 October 2021

Bringing molecular structure to life: 50 years of the PDB

In 1971 the structural biology community established the single worldwide archive for macromolecular structure data the Protein Data Bank PDB It is one of the oldest surviving archives in any biomedical field From its inception the PDB has embraced a culture of open access leading to its widespread use by the research community with nowadays more than 1 million unique users worldwide and by more than 400 biomedical data resources...

Stephen Cusack, Gerard Kleywegt, Christoph Mueller, Christine Orengo, Janet Thornton, Sameer Valenkar, Matthias Wilmanns

20 October - 21 October 2021

Introduction to the EMBL-EBI bioinformatics tools framework

The EMBL EBI provides free access to a wide range of core bioinformatics sequence analysis applications via the web and via programmatic access This course is split into two main sessions running over two days The first session focuses on learning about the bioinformatics applications provided and how to use them in conjunction with a range of biological databases There will be a focus on sequence alignment e g Clustal Omega and MAFFT and sequence similarity search NCBI BLAST and FASTA tools The second session focuses on alternative approaches to accessing the tools beyond the website We will explore the Tools APIs and various examples of how the tools can be accessed on the command line and integrated into workflows...

Ajay Mishra

18 October 2021

Using the Ensembl genome browser to interrogate disease-associated variants

A hands on workshop introducing the principles of interrogating genetic variants using the Ensembl genome browser and using the Ensembl Variant Effect Predictor to map variants onto Ensembl GENCODE transcripts and other genomic features to determine their likely functional effects...

Michal Szpak

14 October 2021

Sight, vision and UniProt proteins

Join us on World Sight Day to find out about our ongoing curation project at UniProt to annotate proteins involved in eye development and disease Globally around 2 2 billion people have a near or distance vision impairment of whom at least 1 billion have a condition that could have been prevented or is yet to be treated WHO World report on vision 2019 One of the many curation efforts at UniProt aims to support biomedical research into eye health and treatment by focusing on curating proteins in human and model organisms that have an involvement in eye formation maintenance and or health This webinar will demonstrate how we selected these proteins then collected interpreted and integrated information from a range of sources to provide comprehensive and high quality overview of their sequence and functional information It will also discuss how we also annotate photoreceptor cell and eye proteins in non human organisms to help scientists understand common components and regulatory mechanisms that underly the formation and maintenance of visual systems This webinar is part of a series covering various aspects of UniProt view other upcoming webinars here...

Kate Warner, Emily Bowler-Barnett

13 October 2021

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

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

Renato Alves, Brice Letcher

13 October - 15 October 2021

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...

Irene Bozzoni, V. Narry Kim, Gisela Storz, Igor Ulitsky

11 October - 15 October 2021

From specimens to genomes

This course will cover the entire arc of a reference genome project from sample acquisition and shipping through nucleic acid extraction sequencing assembly curation and annotation in public databases It will promote the use and reuse of aquatic genomic data build a community of researchers able to exploit these new data types and introduce them to the theory and practice of reference quality genome sequencing and assembly The course content will connect participants to researchers at the forefront of the biodiversity genomics revolution and meet with others worldwide who also aim to apply these new approaches to their study systems Participants will develop bioinformatics skills to quality assess raw genomic sequence data identify co bionts assemble data into a genome build assess and then annotate the model with biological significance Symbiosis lies at the heart of the origins of the eukaryotic cell and new symbiosis events today shape much of the natural world playing key roles in ecosystem engineering and in colonisation of extreme habitats such as hydrothermal vents Biological understanding of symbiosis will be hugely enhanced through the deep analysis of the genomes of the interacting partners and the Aquatic Symbiosis Genomics project is working globally to generate reference genomes for many symbints from marine and freshwater habitats Virtual course Participants will learn via a mix of lectures technical presentations group work and discussion sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and communication via Slack Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 09 45 17 30 GMT each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Lucie Smith

11 October - 15 October 2021

Structural bioinformatics

Structural biology determining the three dimensional shapes of biomacromolecules and their complexes can tell us a lot about how these molecules function and the roles they play within a cell Data derived from structure determination experiments enables life science researchers to address a wide variety of questions 2021 marks 50 years of the Protein Data Bank PDB the single worldwide archive of experimental biomacromolecular structures highlighting the depth of knowledge available for understanding molecular structure and function This course explores bioinformatics data resources and tools for the investigation analysis and interpretation of biomacromolecular structures It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts The course content will also cover predicting protein structure and function and exploring interactions with other macromolecules as well as with low MW compounds There will also be a short session covering the new AI predicted protein structures database AlphaFold DB This course will be a virtual event delivered via a mixture of live streamed sessions pre recorded lectures and tutorials with live support We will be using Zoom to run the live stream sessions all fully password protected with automated English closed captioning and transcription with support and networking opportunities provided by Slack In order to make the most out of the course you should make sure to have a stable internet connection throughout the week There will also be networking and short social activities throughout the course and efforts will be made to make these accessible at different time zones across the week Selected participants will be sent materials prior to the course These might include pre recorded talks and required reading or online training that will be essential to fully understand the course...

Meredith Willmott

7 October - 14 October 2021

Liquid Biopsies

Liquid biopsies have the advantage of being largely non invasive and providing a vast amount of information for the detection and monitoring of diseases such as cancer This course will provide hands on experience in the several techniques to detect and analyse circulating tumor cells CTCs cell free tumor DNA ctDNA cell free tumor RNA ctRNA and proteins Participants will have the opportunity to learn all aspects ranging from proper sampling through error free sequencing to data analysis Lectures will also cover extracellular vesicles and clinical aspects using liquid biopsies especially in the field of cancer diagnostics...

Vladimir Benes, Anders Ståhlberg

6 October 2021

Open access: Data sharing and submission

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

Tony Burdett, Birgit Meldal

5 October - 8 October 2021

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 place emphasis on methods that are able to capture the dynamics of life spanning the whole range from molecular resolution to imaging of whole organisms...

Jan Ellenberg, Jennifer Lippincott-Schwartz, Atsushi Miyawaki

4 October 2021

Ensembl REST API workshop, University of Cambridge

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

Michal Szpak

30 September 2021

Ensembl browser workshop, University of Cambridge

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...

Michal Szpak

27 September - 1 October 2021

Bioinformatics for Immunologists

Run jointly with Wellcome Connecting Science this course will provide participants with an introduction to a range of bioinformatics resources and approaches applicable to immunological research The resources introduced during the course will cover a variety of data types from genomic and proteomic data to computational models biological pathways and reaction information Participants will gain experience of the analysis pipelines for NGS experiments relevant to immunology and will be led through an exploration of this data to identify information of interest Additionally participants will be introduced to how data from several sources can be integrated to provide a wider view of their research thereby enabling them to be more confident users of their own data and that from public sources Virtual course Participants will learn via a mix of pre recorded lectures live presentations trainer Q A sessions and hands on training Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and communication via Slack Pre recorded material will be made available to registered participants before the start of the course Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their machines Participants will need to be available between the hours of 09 00 17 30 BST each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Wellcome Connecting Science

27 September - 1 October 2021

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 introduction to tools and resources used in this scientific field The course will involve participants learning via pre recorded lectures live presentations trainer Q A sessions and hands on tutorials The content will be delivered over Zoom with additional text communication over Slack In order to make the most out of the course you should make sure to have a stable internet connection throughout the week Computational practicals will be run on EMBL EBI s virtual training infrastructure this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course Trainers will be available to provide support answer questions and further explain the analysis during these practicals Selected participants will be sent materials prior to the course These might include pre recorded talks and required reading that will be essential to fully understand the course Participants will need to be available between the hours of 09 30 17 15 BST each day of the course...

Jane Reynolds

26 September - 3 October 2021

Genome Engineering: CRISPR/Cas from Cells to Mice

This course will provide hands on training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR Cas9 system Participants will learn design of CRISPR targets using bioinformatics tools generation of gene knock outs knock ins and target validation using the most current technologies The course will be split into two groups mammalian cells OR mice based on participants expertise...

Neil Humphreys, Birgit Koch, Premnath Rajakannu, Elisabeth Zielonka

23 September 2021

The future of preprint peer review

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

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

22 September 2021

Retrieving biological data from EMBL-EBI resources using Dbfetch

Dbfetch provides a single point of access to retrieve biological data entries from various databases at EMBL EBI This webinar will provide a brief overview of the Dbfetch service and illustrate various output formats of data retrievable via Dbfetch In addition to the web browser based applications of Dbfetch we will also demonstrate accessing Dbfetch using the API...

Nandana Madhusoodanan, Fabio Madeira

16 September 2021

Exascale-ready cell-level simulations for European Personalised Medicine

Personalised Medicine PerMed opens unexplored frontiers to treat diseases at the individual level combining clinical and omics information However the performances of the current simulation software are still insufficient to tackle medical problems such as tumour evolution or patient specific treatments The challenge is to develop a sustainable roadmap to scale up the essential software for the cell level simulation to the new European HPC Exascale systems Simulation of cellular mechanistic models are essential for the translation of omic data to medical relevant actions and these should be accessible to the end users in the appropriate environment of the PerMed specific big confidential data The goal of PerMedCoE is to provide an efficient and sustainable entry point to the HPC Exascale upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance It will accomplish so by Optimising four core applications for cell level simulations to the new pre exascale platforms Integrating PerMed into the new European HPC Exascale ecosystem by offering access to HPC Exascale adapted and optimised software Running a comprehensive set of PerMed use cases including simulations of tumour evolution and drug combinations for cancer treatment Building the basis for the sustainability of the PerMedCoE by coordinating PerMed and HPC communities and reaching out to industrial and academic end users with use cases training expertise and best practices The PerMedCoE cell level simulations will fill the gap between the molecular and organ level simulations from the other CoEs with which this project is aligned at different levels It will connect method developers with HPC HTC and HPDA experts Finally PerMedCoE will work with biomedical consortia and pre exascale infrastructures including a substantial co design effort About the speaker Alfonso Valencia is a Spanish biologist ICREA Professor current director of the Life Sciences department at Barcelona Supercomputing Center BSC and of Spanish National Bioinformatics Institute INB ISCIII He received his PhD in molecular biology in 1988 from the Autonomous University of Madrid From 1989 to 1994 he was a Postdoctoral Fellow in the laboratory of Chris Sander at the European Molecular Biology Laboratory EMBL in Heidelberg studying the evolution of protein function using sequence and structure based approaches In 1994 Valencia formed the Protein Design Group at the Spanish National Center for Biotechnology CNB He was leader of the Structural and Computational Biology Group at Spanish National Cancer Research Center CNIO From 2015 2018 he was President of the International Society for Computational Biology ISCB As computational biologist the focus of his work is the mechanistic understanding of biological systems including cancer and other diseases with a combination of Bioinformatics Network Biology and Machine Learning approaches His group has developed systems in the areas of protein structure prediction protein interactions and protein networks systems biology text and data mining with applications in epigenetic cancer genomics and disease comorbidity All these activities converge into the general topic of Personalised Medicine with particular interest in the interface with Artificial intelligence and High Performance Computing...

Alfonso Valencia

15 September 2021

Getting started with the Open Targets Platform GraphQL API

The Open Targets Platform 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 overview of the GraphQL API that powers the Open Targets Platform The API provides multiple endpoints that support language agnostic queries for a single entity or target disease association Users can also browse the schema to see available API fields and run sample queries using the API playground During the webinar participants will have access to interactive walkthroughs and API queries that can be run directly in their browser There will also be sample Python and R scripts that they can run to test different endpoints...

Andrew Hercules, Helena Cornu

15 September - 17 September 2021

Multiomics to Mechanisms: Challenges in Data Integration

The current speed at which high throughput data are produced and the growing number of studies that use not only one but multiple omics technologies on the same samples offers tremendous opportunities for enhancing our molecular understanding of biological systems One of the biggest challenges in the era of multiomics is the integration and interpretation of the diverse large scale omics data in a way that provides biological insights This requires the development of statistical mathematical and computational tools and equally important experimental strategies to follow up on hypotheses generated by large scale data Together these computational and experimental tools will enable us to address novel questions and identify biological mechanisms...

Nevan Krogan, Uwe Sauer, Judith Zaugg

14 September - 16 September 2021

Virtual Ensembl REST-API Workshop, 14th-16th Sept

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

Ben Moore

8 September 2021

How to interpret AlphaFold structures

This webinar will introduce AlphaFold system for prediction and interpretation of protein structures This webinar is designed for experimental biologists who wish to understand the strengths and limitations of AlphaFold and use the models to guide their experimental studies In this webinar we will provide an overview for the AlphaFold method and statistics that can be used to understand the reliability of the models We will also introduce the AlphaFold Database which provides hundreds of thousands of ready made models across the tree of life as well as highlight the AlphaFold Open Source and Colab notebooks that can be used to generate structures of sequences not yet available within the AlphaFold Database We will conclude by demonstrating a range of use cases followed by a question and answer session with all the presenters...

Alex Bateman, Sameer Velankar, Kathryn Tunyasuvakool, Sergey Ovchinnikov, Pedro Beltrao, Bálint Mészáros

7 September - 9 September 2021

Virtual Ensembl Browser Workshop, 7th-9th Sept

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...

Michal Szpak

7 September - 10 September 2021

Protein Synthesis and Translational Control

The regulation of mRNA translation is a process required to maintain cell homeostasis and its malfunction can lead to disease In recent years advances in high throughput and microscopy methods have revealed findings that challenge hitherto established dogmas such as extensive translation in untranslated regions of a transcript pervasive initiation from non AUG codons heterogeneity and specialization of the ribosome or specialized roles for general translation factors The influence of epitranscriptomics and physical transitions in translation or the molecular mechanisms underlying ribosome quality control are just examples where rapid progress is impacting our view of translation...

Fátima Gebauer, Matthias W. Hentze, Jerry Pelletier, Christian Spahn

6 September - 10 September 2021

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, Paolo Ronchi, Martin Schorb

29 August - 1 September 2021

Gene Expression at Spatial Resolution

This course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics The Visium Spatial Gene Expression Solution incorporates unbiased high throughput total mRNA analysis for intact tissue sections with morphological context offering a previously inaccessible view of tissue biology These two complementary methods to study tissue come together on Visium Spatial Gene Expression slides Through both theoretical sessions as well as extensive hands on practical work the participants will learn the entire workflow of sample preparation of fresh frozen tissue samples fixation and optimisation of tissue permeabilisation and sequencing library preparation Utilising the 10x Genomics Loupe Browser pipeline the participants will also have hands on training of spatial transcriptomics data analysis...

V. Benes, K. Danielski, E. Zielonka

29 August - 1 September 2021

The Mobile Genome: Genetic and Physiological Impacts of Transposable Elements

Although often disparaged as junk DNA it is now undeniable that transposable element TE activity has significantly shaped the structure and function of all genomes ranging from bacteria to humans TEs are major drivers of genetic diversity and contribute to human disease Remarkably recent research has shown that TE derived sequences also can be co opted by the host to play important roles in gene expression early development immunity neuronal diversification and perhaps aging The goal of this conference is to assemble 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 It will provide a venue for cross disciplinary discussions with the goal of catalysing inter disciplinary collaborations to address emerging questions in these scientific fields...

Orsolya Barabas, Julius F. Brennecke, Jose L. Garcia-Perez, John V. Moran

23 August - 27 August 2021

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...

P. Barthelemy, J. Delgado, A. Halavatyi, S. Marawske, S. Reither

2 August - 10 August 2021

CABANA Workshop: Genomic and transcriptomic resources for eukaryotic species

This course is intended to be a gentle introduction to the computational resources available for analysis of omics data in eukaryotic species Specifically we will cover 1 an optional Linux crash course 2 file formats commonly used in NGS data analysis 3 web resources available for the analysis of eukaryotic omics data 4 common bioinformatics pipelines used to analyse genomic transcriptomic data from eukaryotic species sequence alignment phylogenetic tree reconstruction variant detection RNA Seq and data visualization in genome browsers Live components of the course will run around 09 00 12 00 BRT and you are encouraged to use the afternoon to practice using a specified forum or communication method to ask for support Support will end around 17 00 BRT each day...

Francisco Lobo

25 July - 29 July 2021

FISHing for RNAs: Classical to Single Molecule Approaches

This course aims to highlight three powerful RNA visualisation techniques in histological tissue samples During this course the participants will learn to validate the cellular localisation of candidate genes from transcriptome studies through conventional ISH and the more recent cutting edge smFISH Single Molecule Fluorescent ISH and HCR ISH Hybridization Chain Reaction based RNA ISH hybridisation methods Additionally the course will also cover essential tissue embedding protocols that are adapted for use in visually interrogating RNA transcripts in mammalian tissues...

I. Gaspar, E. Perlas, E. Zielonka

19 July - 30 July 2021

Basics to Advanced Genome Annotations at Ensembl and REST Application Programming Interfaces (APIs)

We are organising this high quality workshop for the participants interested in the genomics bioinformatics and genome annotations In this workshop one of the trainers from European Bioinformatics Institute EMBL EBI United Kingdom will provide the hands on training sessions of Ensembl Genome browser and Ensembl REST Application Programming Interfaces APIs This workshop will cover the topics from basics to advanced techniques of genome annotations This workshop will be equally useful for the researchers working with any domain of life e g microbes animals fungus and plants At the successful completion of this workshop participants will be become expert of all the modules of Ensembl Genome browser and Ensembl REST Application Programming Interfaces APIs for their research...

NextGenHelper

12 July - 16 July 2021

Microscopy data analysis: Machine learning and the BioImage Archive

Develop programmatic skills for the analysis of bioimage data 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 the BioImage Model Zoo and CellProfiler The organisers welcome applications from scientists who have specific research questions that look to use publicly available data held in the BioImage Archive and can demonstrate use cases for the resource 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 30 17 30 BST each day of the course Trainers will be available to assist answer questions and provide further explanations during these times...

Marina Pujol

12 July - 16 July 2021

Proteomics bioinformatics

Hands on training in the basics of mass spectrometry proteomics bioinformatics and related methods and resources Run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences this popular course provides hands on training in the basics of mass spectrometry MS and proteomics bioinformatics approaches search engines and post processing software quantitative proteomics approaches and related statistical concepts MS proteomics data repositories and public data re use how to employ existing databases for protein analysis perform the annotation of subsequent protein lists and the incorporation of information from molecular interaction and pathway databases 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 two weeks 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 further explain the analysis during these times...

Advanced courses

11 July - 15 July 2021

Super-Resolution Microscopy: Time-Resolved STED Nanoscopy

This five day advanced course on fluorescence super resolution microscopy will cover the theory and practical application of current super resolution microscopy techniques to biological questions...

M. Lampe, R. Pepperkok, U. Schwarz

7 July 2021

A guide to EBI Search

This webinar will introduce the EBI Search service EBI Search is a text search engine that provides easy and uniform access to the biological data resources hosted at EMBL EBI It provides up to date search results across all of the stored datasets as well as simple intra domain navigation via internal cross references In addition to the web front end there is a RESTful API interface allowing the search engine to be queried programmatically The webinar will illustrate both the web application and take a brief look at the RESTful interface...

Matt Pearce

6 July - 8 July 2021

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...

30 June 2021

A guide to analysing binding sites in protein structures

This webinar gives an introduction to the information required to effectively interpret ligand binding sites in protein structures It will highlight tools available at the Protein Data Bank in Europe PDBe and PDBe Knowledge Base PDBe KB to analyse ligand binding pockets and interactions It will also highlight how this information can be used for the design of new inhibitors through a specific case study...

David Armstrong, James Tolchard

28 June - 2 July 2021

Advanced methods in bioimage analysis

The course focuses on the highly interdisciplinary topic of metagenomics During the course participants will receive an overview of state of the art genomic technologies and bioinformatic tools A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines...

R. Haase, A. Klemm, S. Nørrelykke, P. Paul-Gilloteaux, C. Tischer, C. Wahlby

28 June - 2 July 2021

Summer school in bioinformatics

This virtual course organised in association with Wellcome Genome Campus Scientific Conferences and Advanced Courses 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 small project set by EMBL EBI resource and research staff ending in a presentation from each group on the final day of the course to bring together learnings from all participants The course includes training and mentoring by experts from EMBL EBI and external institutes 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 17 30 BST each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times Group projects 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 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 silco 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 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 implement this process programmatically 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 Multiomics analysis of human disease In this project you will explore the benefits of multiomics data integration to investigate the onset and progression of human disease You will analyse plasma proteomics and metabolomics data from patients and healthy controls to identify immunological and physiological changes that are associated with disease severity You will exploit differential analysis dimensionality reduction methods and multiomics integration tools to identify features that distinguish different patient groups perform functional enrichment analysis and visualise metabolomics and proteomics correlation networks in Cytoscape Finally you will build basic machine learning models to predict the course of disease and to propose therapeutic interventions that are likely to be most effective at different disease stages Posters All participants are expected to provide a poster for the course We expect the posters to provide other delegates and trainers with information on your research and to act as a talking point They should give an idea of the work you are engaged in what you are planning to do next any challenges you have experienced in your research and anything of interest that might be useful for other delegates Further information about posters will be provided following application selections...

Scientific conferences

23 June 2021

A guide to proteomics data analysis using UniProt and InterPro

This webinar will give a brief introduction to the UniProt and InterPro websites and highlight resources available that proteomic scientists or other users with protein datasets may find useful to analyse their data This will encompass searching by protein sequence identifying protein peptides and retrieving sequence specific features and functional information both curated and predicted The UniProt database aims to provide a high quality comprehensive publicly available protein database annotated by expert curators It contains detailed information on protein function interactions pathways protein sequences and isoforms disease variants and post translational modifications InterPro is a database that helps users to understand the possible functions of protein sequences by identifying what family it belongs to or what domains and motifs it contains InterPro provides the world s most comprehensive predictions by combining predictions from 13 member databases Both databases are freely available resources that are actively maintained with bi monthly data updates additionally all data is available through intuitive user interfaces APIs and data downloads...

Typhaine Paysan-Lafosse, Emily Bowler-Barnett, Paul Denny

21 June 2021

Preprints 101 for authors

Joint webinar with ASAPbio Sumeet Pal Singh and Europe PMC Preprints enable researchers to rapidly share their work publicly before the formal peer review process In this webinar you will learn more about preprints and their benefits for the research community from ASAPbio Accelerating Science and Publication in biology will hear an author s perspective on posting preprints from Sumeet Pal Singh a group leader at IRIBHM ULB and will find out how to incorporate preprints in your literature search routine by using the preprint discovery tools developed by Europe PMC ASAPbio is a scientist driven nonprofit that promotes the productive use of preprints in the life sciences ASAPbio coordinates a global community of researchers and stakeholders interested in preprints and develops resources to advance best practices and help researchers make informed decisions about communicating their work via preprints Iratxe Puebla Associate Director at ASAPbio will provide an overview of preprints and their growth in the life sciences and cover things researchers should consider before posting a preprint Sumeet Pal Singh is a group leader at IRIBHM ULB and an ASAPbio fellow Sumeet will describe the journey of publishing his first senior author paper from a preprint to a peer reviewed article as well as the details related to the timing of posting a preprint and its relationship to the peer review process He will outline a new path provided by Review Commons that allows the authors to receive peer reviews for their manuscript prior to a journal submission as well as post the reviewer s comments and the authors response on preprint server bioRxiv Europe PMC indexes over 300 000 preprints abstracts and full text COVID 19 preprints from 20 life sciences preprint servers alongside published journal articles Preprints in Europe PMC are linked to citations data community peer reviews and more In this part of the talk we will demonstrate how to find relevant preprints cite and track preprint citations claim preprints to ORCID or discover relevant resources...

Iratxe Puebla, Sumeet Pal Singh, Maria Levchenko

21 June - 25 June 2021

Curso Internacional: Estrategias bioinformáticas para el estudio de enfermedades tropicales desatendidas (ETDs)

Este curso ofrecer entrenamiento en herramientas y estrategias bioinform ticas para el estudio de enfermedades tropicales desde una perspectiva molecular Las sesiones cubrir n el an lisis de datos provenientes de m ltiples repositorios micos con informaci n relacionada sobre los pat genos causantes de las enfermedades El objetivo principal es explorar metodolog as para el descubrimiento de blancos moleculares e inhibidores que sirvan para modularlos usando una perspectiva traslacional de los hallazgos computacionales Informaci n estructural de las prote nas y redes de interacci n prote na prote na ser n cubiertas en detalle adem s de otros recursos disponibles en la web El curso ser transmitido via Zoom Los participantes deben asegurar que teng n activo y funcionando el sistema de audio para escuchar y hablar durante el evento...

Rodrigo Ochoa

21 June - 25 June 2021

Systems biology: From large datasets to biological insight

This course run with Wellcome Connecting Science covers the use of multi omics data and methodologies in systems biology The content will explore a range of approaches ranging from network inference to machine learning 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 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 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 however a small app will need to be installed to access the compute infrastructure Participants will need to be available between the hours of 09 30 17 30 BST each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Advanced Courses

16 June 2021

A guide to the maintenance of life science data by biocurators

The aim of this webinar is to introduce you to the principles of how biological data is archived curated maintained and updated by expert biocurators and how you can contribute...

Claire O’Donovan, Deborah Harrus, Birgit Meldal, Rossana Zaru

15 June - 17 June 2021

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...

Jane Reynolds

15 June - 17 June 2021

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...

Michal Szpak

13 June - 15 June 2021

Predicting Evolution

The conference will explore the evolution of biological systems at different levels from genes and molecules to organism development and ecology As such we have invited leaders in their respective fields across various scales of evolution molecular network microbial developmental and community Particular emphasis for this conference will be placed on understanding evolution through mechanistic biology We will explore recent advances in experimental and theoretical approaches to study how genetic and non genetic changes drive and constrain evolution...

9 June 2021

A guide to sequence similarity search for biomolecular sequences

This webinar aims to provide an introduction to basic concepts in sequence similarity search with a focus on the similarity search tools and databases provided by EMBL EBI In this webinar we will also provide useful tips on which tools and databases to use and explore some examples of use cases using BLAST...

Nandana Madhusoodanan

8 June - 10 June 2021

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...

Michal Szpak

4 June - 11 June 2021

BioExcel summer school on biomolecular simulations 2021

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 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...

Michelle Mendonca

2 June 2021

A guide to multiomics pathway analysis

In this webinar we will discuss how to perform comparative multiomics pathway analyses using the ReactomeGSA pathway analysis system We will be comparing independent studies that use different omics approaches as well as different omics measurements from the same study Additionally we will be looking at simple to use methods to integrate public datasets into one s own analysis Finally we will use the ReactomeGSA R package to improve the annotations of single cell RNAseq data During the webinar we will use Reactome s web interface as well as the ReactomeGSA Bioconductor R package...

Johannes Griss

26 May 2021

A guide to molecular interactions

During this webinar we will give you an introduction to molecular interactions and how to find these through the molecular interaction database IntAct We will show you examples of how you can search for interaction data how to create molecular interaction networks using our network viewer based on Cytoscape js and how to download this data for further analysis We will also have a quick look at two other resources PSICQUIC and IMEx that integrate molecular interactions from several sources...

Birgit Meldal, Kalpana Panneerselvam

25 May 2021

PsyArXiv preprints in Europe PMC

Psychological sciences preprints from PsyArXiv are now searchable in Europe PMC an open database of life sciences literature Join us for this live demo to learn how to find PsyArXiv preprints in Europe PMC how to explore links to data citations comments or open peer reviews how to claim preprints to your ORCID record and more...

Maria Levchenko, Jack Arnal

25 May - 27 May 2021

BioMalPar XVII: Biology and Pathology of the Malaria Parasite

The 17th BioMalPar conference will address fundamental questions on the biology of the malaria parasite its vector the immune response of the host the disease that it causes and the latest technological approaches The conference will emphasise training and networking with a focus on allowing speaking opportunities for early career researchers...

25 May - 27 May 2021

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...

Emily Perry

19 May 2021

A guide to identifying and prioritising drug targets with the Open Targets Platform

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 overview of the Open Targets Platform which is a freely available resource that is actively maintained with bi monthly data updates All data is available through an intuitive user interface a GraphQL API and data downloads Likewise the pipeline and infrastructure codebases are open source and can be used to create a self hosted private instance of the Platform with custom data...

Helena Cornu, Andrew Hercules

18 May - 20 May 2021

Ri.Logistica

The RI Logistica conference is an online event designed for research infrastructures RIs their users and collaborators companies in the supply chain management and governmental authorities to discuss all aspects of logistics critical for research facilities and laboratories...

18 May - 20 May 2021

Managing a bioinformatics core facility

This virtual knowledge exchange workshop is an opportunity for managers of bioinformatics core facilities to learn from EMBL EBI s service teams from each other and from potential users of their services These facilities play an essential role in enabling research in the molecular life sciences The landscape is constantly evolving as new research tools emerge as experiments become increasingly data intensive and as their clients experimental researchers become more exposed to the power of data driven biology Virtual workshop The workshop 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 Live sessions will include both group and individual activities alongside optional social and networking opportunities Participants will need to be available between the hours of 08 45 15 30 BST each day Programme may be subject to slight changes before registration...

Marina Pujol

18 May - 20 May 2021

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...

Michal Szpak

17 May - 20 May 2021

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...

17 May - 21 May 2021

Cancer genomics

This course will focus on the analysis of data from genomic studies of cancer Lectures 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 lecturers 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 BST each day of the course...

Jane Reynolds

16 May - 24 May 2021

Measuring Translational Dynamics by Ribosome Profiling

Regulation of translation is a key layer in the control of gene expression playing a critical role in many biological and pathophysiological settings In the last decade methodological advances have provided comprehensive insights into cellular transcriptomes and proteomes however the systems wide analysis of translation has remained an unsolved experimental challenge The recent advent of ribosome profiling has provided the methodological basis for comprehensive transcriptome wide analyses of translation at sub codon resolution by the precise and high throughput determination of ribosomal positions on mRNA Its application in a variety of organisms yielded novel insights into protein synthesis and its dynamic regulation significantly advancing our understanding of the post transcriptional regulation of gene expression This practical course will combine theoretical sessions with hands on experimentation and computation emphasising the key steps of the protocol and computational quality control...

13 May 2021

EMBL-EBI workshop: The Open University, 2021 (Virtual)

This workshop will introduce participants to the publicly available data resources provided by EMBL EBI It will serve to introduce the organisation the role it plays in the wider life science data landscape and provide a high level overview of the data resources and basic tools available to researchers Participants will have the opportunity to ask questions spend time exploring data of interest and providing feedback that will help plan for future workshops that will offer a more in depth explanation of key resources...

Tom Hancocks

12 May 2021

A guide to exploring drug-like compounds and their biological targets using ChEMBL

ChEMBL is a widely used database of bioactivity data that links drug like compounds to their biological targets and has applications in drug discovery This webinar will provide an overview of the ChEMBL web interface data types within ChEMBL and how ChEMBL can be used to answer questions relevant to medicinal chemistry and drug discovery...

Emma Manners, Fiona Hunter

10 May - 12 May 2021

AQUA-FAANG: Bioinformatic analysis of regulatory elements

This course will provide training on two bioinformatic pipeline core assays defined by the FAANG initiative for the study of regulatory elements in fish genomes The content will cover the use of ChIP seq chromatin immunoprecipitation sequencing and ATAC seq assay for transposase accessible chromatin sequencing Participants will be introduced to key bioinformatic steps involved in data analysis and interpretation from raw sequence data through to peak calling interpretation of data quality and data integration including by use of genome segmentation methods The concept of software containers and their use for reproducible pipeline deployment will also be explored Please visit the AQUA FAANG website for more information on the project...

Juanita Riveros

6 May 2021

Contributing to the UniProt Knowledgebase: how you can help

This webinar will present how the research community can contribute both literature references and annotation to the UniProt database of protein sequence and function www uniprot org First we will provide an overview of the resource and then we will focus on describing the functionality to add publications and knowledge to protein entries including a demo In this webinar you will also learn how your domain knowledge contribution improves the resource for the general community and how it can be used as an alternative metric of your research output given that UniProt uses ORCID a unique identifier for each researcher as a mechanism for user validation and credit for these contributions...

Cecilia Arighi

5 May 2021

A guide to organising data associated to a publication using BioStudies

The goal of the BioStudies database is to facilitate transparency and reproducibility of research by aggregating all the outputs of a study a data package in a single place A data package may include links to parts of data deposited into specialised community databases at EMBL EBI and elsewhere as well as data that have no other natural home such as supplemental data In this webinar we will look at a range of examples for data submission and access including large image datasets...

Ugis Sarkans

4 May - 7 May 2021

The Identity and Evolution of Cell Types

Cell types are the fundamental units of multicellular life which have diversified during animal evolution Single cell genomics transcriptomics technologies and new insights into the molecular mechanisms specifying cell type identity allow us to explore this process in unprecedented detail Our second EMBO EMBL Symposium on the identity and evolution of cell types will re assemble the growing community of scientists pushing forward the limits of this exciting new field Based on the very positive feedback on the first symposium we will keep session topics such as the cell type tree of life and genetic and epigenetic mechanisms of cell type differentiation in development We have also identified exciting new areas in our rapidly growing field such as molecular mechanisms of cell type origination in evolution the evolutionary assembly of cellular modules different aspects of neuronal identity and sensory cell type diversification in vertebrates For this meeting we will also provide extended discussion time within and between sessions and organize a final discussion...

D. Arendt, C. Baker, M.A. Tosches, G. Wagner

2 May - 6 May 2021

Quantitative Proteomics: Strategies and Tools to Probe Biology

This course will provide both theoretical and practical training in the use of quantitative proteomics approaches Participants will learn the principles of current methodologies including label free SILAC and TMT as well as targeted proteomics and they will be trained in the use of bioinformatic tools for data analysis...

26 April - 28 April 2021

EIROforum Conference: Grand Challenges in AI and Data Science

Overview Organisers Overview Registration is not yet open for this event If you are interested in receiving more information please register your interest Conference Overview More information about this conference will follow shortly Organisers Iva Gavran Course and Conference Officer EMBL Heidelberg Germany...

J. Korbel, J. McEntyre

26 April - 30 April 2021

Single-cell RNA-seq & network analysis using Galaxy and Cytoscape

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 cell cluster comparisons In addition to running a basic pipeline participants will explore single cell networks using Cytoscape Please note that although participants will not be able to use their own data during the course practicals there will be ample time to discuss their research and ideas with both course participants and trainers As part of this participants will present lightning talks on their research topics Near the end of the course participants will engage in small group discussion about their research challenges and problems with each other and the trainers at the Talk with Trainers Virtual course Participants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and trainer led computational exercises Live sessions will be delivered using Zoom with additional support and communication via Slack Pre recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session Computational practicals will run on EMBL EBI s virtual training infrastructure meaning participants will not require access to a powerful computer or install complex software on their own machines Participants will need to be available between the hours of 08 00 17 30 GMT each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Meredith Willmott

22 April 2021

UniProtKB: Increasing our understanding of neurodegenerative disorders through data curation

This webinar will give an overview on how molecular data of proteins associated with neurodegenerative diseases is provided in UniProtKB including information on molecular protein function protein protein interactions sequence variants pathways and drug candidates...

Yvonne Lussi

21 April 2021

A guide to RNA families

Rfam is a database of RNA families that currently contains almost 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 be joined by a guest speaker Prof Sam Griffiths Jones University of Manchester who founded Rfam in 2002 and is now responsible for miRBase the microRNA registry We will discuss the ongoing efforts to synchronise the microRNA families between Rfam and miRBase...

Anton Petrov, Sam Griffiths-Jones, Nancy Ontiveros-Palacios, Eric Nawrocki

15 April 2021

Ethics/ELSI considerations - From FAIR to fair data sharing

The FAIR principles standing for Findability Accessibility Interoperability and Reusability have become the guiding principles for the wider sharing of research data in the life sciences While FAIR provides guidance for the management of data as well as tools and workflows the institutional conditions and organizational challenges associated with data sharing need to be taken into account to ensure responsible and fair data practices This requires considering the context of legal requirements for instance the principle of fairness and transparency in GDPR expectations of research participants data subjects societal aspects and the ethics work that is an integral part of data flows as well as fairness equity and benefit sharing within transnational collaborations which is of utmost importance This webinar will from the perspective of ethical legal and societal implications ELSI discuss this broader context of responsible and fair data sharing associated with FAIR The How FAIR are you webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software training materials and cohort data to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis...

Melanie Goisauf

14 April 2021

A guide to exploring genes and genomes with Ensembl

Ensembl is a genome browser that provides a single point access to annotated gene and genomes This webinar will provide a brief overview to the Ensembl browser and demonstrate how you can access information about genes or genomes of your interest We will also showcase the data types and tools available at Ensembl which can help your research...

Aleena Mushtaq

12 April - 19 April 2021

Microbial Metagenomics: A 360º Approach

Organisers V Benes G D Auria J E Gonz lez Pastor E Zielonka The course focuses on the highly interdisciplinary topic of metagenomics During the course participants will receive an overview of state of the art genomic technologies and bioinformatic tools A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines...

31 March 2021

Submitting your genome wide association study data to the GWAS Catalog

The GWAS Catalog is a comprehensive and highly accessed resource for GWAS data including full summary statistics We encourage authors to submit their data to us to make them accessible and reusable by the wider GWAS community This webinar provides a step by step guide to the submission process including setting up your account converting your summary statistics to our standard format providing metadata and receiving accession numbers to cite in publications...

Elliot Sollis

30 March - 11 May 2021

SAXS (Small Angle X-Ray Scattering) for Biomolecules

Small angle X ray scattering SAXS is a powerful method to obtain information on size and shape of macromolecules in solution In this introductory course we will cover basics of SAXS instrumentation sample preparation modelling techniques and complementary use with other methods The course is aimed at students researchers interested in structural biology methods Time will be spent in understanding how to read interpret SAXS sections of integrated structural biology research papers...

28 March - 29 March 2021

Strategy for Future EMBL Research Infrastructures in the Life Sciences in Hamburg

The workshop s main aim is to consult with leading experts and stakeholders about the synergistic use of the future X ray infrastructures with complementary structural and computational methods It is planned to review possible future needs and strategies for EMBL infrastructures at and around PETRA IV and to discuss how the interests of the research communities worldwide and in particular those in the EMBL member states could be best taken into account...

25 March 2021

Integrating knowledge of proteins and small molecules with UniProtKB

A complete understanding of biological systems requires integration of knowledge of the regulation and function of small molecule metabolites the metabolome with that of genes transcripts and proteins the genome transcriptome and metabolome The UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive high quality and freely accessible resource of protein sequences and functional information UniProtKB integrates interprets and standardizes data from a range of sources including the scientific literature tools for protein sequence analysis other knowledge resources and databases and automatic annotation systems to provide a detailed overview of the available protein knowledge This webinar will provide an introduction into how UniProtKB captures and represents knowledge of small molecule metabolites using the Rhea knowledgebase of biochemical reactions based on the chemical ontology ChEBI and how UniProt users can access and exploit that knowledge...

Alan Bridge

24 March 2021

Mol*: Improved molecular visualisation at PDBe

This webinar will focus on the use of the online molecular visualisation tool Mol at PDBe We will show basic usage observation of electron density maps and EM volumes interrogation of ligand structures and the visualisation of sequence annotations We will also highlight the advantages to using Mol in comparison to other tools and show the different ways the Mol viewer is presented and accessed on PDBe s pages...

James Tolchard

23 March - 25 March 2021

VIZBI 2021: Visualizing Biological Data

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...

23 March - 25 March 2021

Ensembl API virtual workshop, 23rd-25th March 2021

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

22 March - 26 March 2021

Introduction to metabolomics analysis

EMBL EBI plans to deliver the majority of its 2021 events face to face with a small number of virtual events Please note that some events that are currently listed as on site might need to be delivered virtually depending on the prevailing status of the pandemic at the time More courses will be added to this programme as our plans develop further...

18 March 2021

How to make training FAIR

There is a wealth of training content developed and delivered across the globe each year there will be many similar sessions on similar topics all delivered to similar audiences At the same time there will be trainers looking for inspiration and ideas on how to approach new topics or on new ways to teach old topics as well as trainees looking for materials to further their own knowledge Many trainers or lecturers educators etc do not share their materials or if materials are shared they are not easily found or re used by others During this webinar we will give you some tips and suggestions on how you can make more of the training materials you produce and encourage others to do the same FAIR is not just for data we can make our training materials FAIR too Join us to find out the benefits of sharing your FAIR materials and some simple ways you can make it easy for others to use your materials in their teaching or as aids for individuals to learn more The How FAIR are you webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software training materials and cohort data to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis...

Anna Swan, Sarah Morgan

17 March 2021

BioSamples: a FAIR sample metadata archive

BioSamples is the EMBL EBI archive which records and supplies metadata about biological samples and connects sample records across EBI databases to the corresponding experimental data BioSamples aims to improve metadata quality through ontology annotation metadata curation data validation and certification In this webinar we will briefly introduce BioSamples and highlight specific use cases from current collaborations and features deployed to increase FAIRness Findability Accessibility Interoperability Reusability of the data Ongoing collaboration with major consortia rely on and drive addition of new features to BioSamples Ability to walk an ontology hierarchy such as disease for the Global Alliance for Genomics and Health GA4GH Synthetic dataset and linking to human controlled access data for the Common Infrastructure for National Cohorts in Europe Canada and Africa CINECA Metrics and automated processes for FAIRplus...

Fuqi Xu

16 March - 18 March 2021

Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture

Synthetic morphogenesis is a novel and exciting field that requires collaboration among traditionally distinct scientific communities from developmental biologists to chemists theoreticians and computational modellers This symposium will bring together scientists from these different disciplines to discuss the extent to which cells tissues organs can be built de novo starting from isolated components...

16 March - 19 March 2021

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 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 17 30 GMT each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Meredith Wilmott

16 March - 18 March 2021

Virtual Ensembl Browser workshop, 16th-18th March

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

Michal Szpak

10 March 2021

Introduction to exploring genome-phenome data with EGA

European Genome phenome Archive EGA is a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects This webinar aims to cover a quick introduction to EGA by exploring topics ranging from searching and accessing data in EGA to interpreting Data Use Ontology DUO codes We will also demonstrate downloading data with an EGA test account...

Dona Shaju, Giselle Kerry

8 March - 11 March 2021

Friend or Foe: Transcription and RNA Meet DNA Replication and Repair

RNA biology is intimately interlinked with DNA metabolism on multiple levels and the crosstalk between the two nucleic acids involves potential for both conflicts as well as cooperative relationships On the one hand gene expression poses a considerable risk for genome maintenance and vice versa On the other hand the machineries involved in RNA and DNA transactions are known to cooperate in several important aspects of nuclear biology This symposium will bring together scientists studying genome maintenance and the DNA damage response with those investigating the biology of transcription and RNA biology in order to discuss these mutual interactions of DNA and RNA metabolism...

4 March 2021

Practically FAIR

This webinar will focus on practical applications of the FAIR data principles particularly in the context of clinical bioinformatics We will highlight several example projects that have put the FAIR principles in practice and discuss the advantages and some of the challenges involved ELIXIR Galaxy community elixir europe org communities galaxy promotes the use of Galaxy projects that enhance the FAIRness in data analysis We will demonstrate the Galaxy services that deliver practical FAIR data analysis with Single Sign On capability provided by ELIXIR AAI The aim is to provide medical researchers with the practicalities of implementing and using FAIR principles in the context of the CINECA project as applied to translational research at Erasmus University Medical Center The How FAIR are you webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software training materials and cohort data to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis...

Andrew Stubbs

3 March 2021

Annotating your own variation data with the Ensembl Variant Effect Predictor (VEP)

The Ensembl VEP is a powerful tool that allows you to input a list of genetic variants and determines which genes are affected and how In this webinar you ll learn how to use the online VEP tool which is suitable for analysing short lists of genetic variants and the offline tool which allows you to annotate whole genome variant calls...

Emily Perry (Pritchard)

2 March - 3 March 2021

Life at the Periphery: Mechanobiology of the Cell Surface

The cell surface comprising the plasma membrane the underlying cortical cytoskeleton and in many cell types a cell wall is a central integrator of cell form and function Its physico chemical properties are rapidly modulated to accommodate or drive changes in shape or behaviour and to exchange matter and information with the environment This symposium will bring together researchers from different communities interested in processes occurring at the cell surface across kingdoms It will focus on new technologies that empower studies of cell wall actin and membrane biology such as advanced imaging in in vitro and in vivo systems as well as approaches combining molecular biology with computational and biophysical approaches...

1 March - 5 March 2021

Data visualisation for biology: A practical workshop on design, techniques and tools

Please note this course is under review and the dates are likely to change to later in 2021 Please email courses ebi ac uk if you have any questions...

1 March - 4 March 2021

NEUcrest: "Big Data" workshop

This course will introduce participants to the concept of big data in relation to biology bioinformatics and life science data It will explore data resources and bioinformatics tools from the European Bioinformatics Institute and the Wellcome Sanger Institute The course content will also cover the fundamentals of bulk and single cell sequencing of RNA samples and provide practical instruction in basic analytical approaches...

Tom Hancocks

1 March - 11 March 2021

CABANA workshop: Analysis of crop genomics data

Please note this course was postponed in 2020 due to the COVID 19 pandemic and will take place virtually in 2021 This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping During the course participants will learn about genotyping experimental design variant calling comparative genomics using Ensembl analyse variation data with Ensembl Variant Effect Predictor and the European Variation Archive and explore concepts of genome wide association studies GWAS The content will explain how to make use of existing public data retrieve submit and share your data with the community It will also provide training on using R in genomics applications for crop genotyping Trainers will cover the basics of diversity analysis using R before analyzing various genomes to assess diversity This will include hierarchical clustering correlating genomic data with geographic and phenotypic information and investigating gene phenotype relationships and microsatellites This course will use genomic data of wheat maize and potato as training datasets throughout the week The course will be delivered through a combination of hands on training sessions and lectures Please note The course will use genomic data from crop plant species throughout the week It will not explore in detail methods for assembling genomes...

Marco Cristancho, Derrin Crawte, Marina Pujol

28 February - 5 March 2021

Attacking Open Chromatin with ATAC Sequencing

V Benes U Litzenburger J Zaugg...

22 February - 26 February 2021

Introduction to multiomics data integration and visualisation

Identify the challenges strategies and resources for multiomics data integration using biological examples The virtual course will focus on the use of public data resources and open access tools for enabling integrated working with an emphasis on data visualisation Working with public domain data can provide added value to data derived through a researcher s own work and additionally inform experimental design This course is highly relevant in the current research scenario where an increased volume of data across the whole spectrum of biology has created both more opportunities and challenges to identifying novel perspectives and answering questions in the life sciences This course will focus on issues around data integration but will not include systems biology modelling or machine learning approaches A major element of this course is a group project where participants will be organised in small groups to work together on a challenge set by trainers from EMBL EBI data resource and research teams 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 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 17 30 GMT each day of the course...

Jane Reynolds

16 February 2021

Ensembl API workshop, University of Cambridge, 16.02.2021

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

15 February - 19 February 2021

Next generation sequencing bioinformatics

A guide to the technology analysis workflows tools and resources for next generation sequencing data analysis This virtual course will provide insights into how biological knowledge can be derived from genomics experiments and explain different approaches in analysing such data The main focus will be on assembly re sequencing and variant calling during the analysis of higher eukaryotes with a particular 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 17 30 GMT each day of the course Trainers will be available to assist answer questions and further explain the analysis during these times...

Marina Pujol

11 February 2021

Ensembl Browser workshop, University of Cambridge, 11.02.2021

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

10 February 2021

Exploring non‐coding RNAs in RNAcentral

RNAcentral is a database of non coding RNA sequences that provides a unified view of 40 specialised databases This webinar will give an overview of the data found in RNAcentral as well as the RNAcentral website The team will share tips on how to efficiently explore the data using text and sequence similarity search how to visualise RNA secondary structure and how to access the bulk data in the FTP archive More advanced functionality including the programmatic data access and public Postgres database will also be discussed Join the webinar to also learn what s new in RNAcentral or ask any questions you may have...

Blake Sweeney, Carlos Ribas, Anton Petrov

8 February - 12 February 2021

Immune Profiling of Single Cells

V Benes K Danielski D Ordonez E Zielonka...

8 February - 12 February 2021

Deep Learning for Image Analysis

The advent of deep learning has brought a revolution in the field of computer vision including most tasks and research questions concerned with microscopy image analysis Neural networks have been successfully used for image restoration classification and segmentation for the detection of objects and characterisation of their morphology for high throughput imaging and large scale processing in 3D Despite these advances training and deployment of such neural networks remains difficult for practitioners of image analysis The aim of our course is to close this gap and teach the participants in the most hands on way possible to apply deep learning based methods to their own data and image analysis problems...

1 February - 5 February 2021

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 final two days 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...

Meredith Willmott

1 February - 11 February 2021

EMBL-EBI workshop: University of Pavia, 2021 (Virtual)

This series of workshops will explore EMBL EBI data resources for genomics transcriptomics protein sequences structures and interactions and chemical biology Each half day workshop will introduce participants to browsing searching retrieving and conducting a basic analysis of a wide range of biological data types Two workshops will cover the Ensembl genome browser where researchers can explore annotated genomes and features of interest including genes transcripts and variants Participants will also be introduced to the Variant Effect Predictor VEP tool and BioMart for bulk data download Functional genomics resources Array Express Expression Atlas will introduce public data derived from transcriptomics experiments and provide instruction on how to begin investigating biological functions Participants will also cover the Single cell Expression Atlas and the expression data from individual cell sequencing Three workshops will explore resources dedicated to protein data covering UniProt the PDBe IntAct the Complex Portal and Reactome These topics will provide overviews of protein sequence structure and interactions allowing participants to gain a greater understanding of the role played by proteins in the cell The final workshop will cover the EBI s chemical biology resources ChEBI and MetaboLights Participants will learn how to access information on chemical entities of biological interest and the myriad metabolites found in metabolomics experiements Virtual workshop Participants will learn via a mix of pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through trainer led demonstrations and personal exercises on each resource Live sessions will be delivered using Zoom with additional support and communication from the host trainer and resource specialists in the chat stream...

Claudia Binda

30 January - 5 February 2021

Analysis and Integration of Transcriptome and Proteome Data

V Benes R Calogero J Krijgsveld L Martens...

27 January 2021

Preprints discovery 101: Tips & tricks for authors

Preprints enable researchers to rapidly share their work publicly before the formal peer review process This webinar will demonstrate how to incorporate preprints in your literature search routine by using the discovery tools developed by Europe PMC Europe PMC indexes preprints abstracts and full text COVID 19 preprints from many life sciences preprint servers alongside published articles Preprints in Europe PMC are linked to data and platforms that comment on or peer review preprints We will demonstrate how to find the data behind preprints as well as comments and reviews associated with a given preprint We will also share useful tips for posting your pre prints claiming a pre print to your ORCID and tracking your pre prints citations revisions or recommendations by readers To learn more about using Europe PMC in your research try our Europe PMC Quick tour or our webinar Using Europe PMC for effective literature research...

Dayane Rodrigues Araujo

24 January - 28 January 2021

Exploratory Analysis of Biological Data: Data Carpentry

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

10 January - 14 January 2021

Drosophila Genetics and Genomics

The fruit fly Drosophila has played a leading role in the discovery and dissection of basic biological processes uncovering general principles of development evolution and disease Almost a century of research has generated a powerful genetic toolbox that provides a unique arsenal of methods that can tackle almost any biological question This combined with exciting new technologies developed in recent years have changed the way Drosophila research is conducted enabling biologists to address questions that were impossible to study before...

7 December - 11 December 2020

CABANA: Genomic data for surveillance of communicable disease (Cancelled)

This course has been cancelled We apologise for any inconvenience caused This course will develop skills in the analysis of field collected microbial genomes samples and how to use data this genomic in the surveillance of communicable diseases...

6 December - 8 December 2020

In situ Structural Biology: From Cryo-EM to Integrative Modelling – Virtual

OverviewSpeakers and OrganisersProgramme Overview Conference Overview There is an increasing awareness that mechanistic structural information on molecular machines is ideally generated within the context of intact cells in order to fully grasp how they function in a complex native environment Recent technological advances have nurtured the development of such in situ structural biology...

4 December - 10 December 2020

Design Thinking: Approaches for Chronic Disease Management – Virtual

OverviewSpeakers Trainers and OrganisersProgramme Overview Course Overview This workshop will bring together young professionals and students to learn and apply state of the art design thinking techniques Over the course of three days small interdisciplinary teams will co create innovative healthcare solutions for chronic disease management Each team will take on a specific pre defined...

2 December 2020

Introduction to the Complex Portal

This webinar will introduce the Complex Portal an encyclopaedic database for information on macromolecular complexes In this webinar we will explain the coverage and curation priorities of the Complex Portal show how to search for complexes using a variety of accession numbers keywords and how to use the organism search We will also demonstrate examples of complex details pages that include visualisation tools and link outs to related database...

Birgit Meldal

1 December - 4 December 2020

CABANA workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 pandemic

This workshop will provide training on the use of bioinformatic tools for the design and analysis of research and diagnostic molecular assays Trainees will receive training on viral genome assembly comparative viral genomics and downstream applications of this data in research and applied contexts Trainers will focus practical sessions on the analysis of Illumina SARS CoV 2 sequences This online workshop will be delivered on Zoom and comprise a blend of live lectures and hands on practicals delivered by trainers across Latin America Certificates will be provided to mark successful completion of this workshop Sessions on Friday 4th December will be livestreamed on YouTube and made freely available on the platform thereafter There will be an opportunity to deliver a short presentation about your work to other trainees...

Marina Pujol

30 November - 4 December 2020

CABANA: Bioinformatics for plant biology (Postponed until 2021)

Please note this course will be postponed to 2021 and as further information about the course becomes available we will update this page By registering your interest using the button above we will inform you applications open for the course For details of previous courses hosted at EMBL EBI please look at our 2019 onsite listing...

Marina Pujol

26 November - 28 November 2020

The Roaring 20s: A New Decade for Life Sciences - Virtual

PhD Students...

26 November 2020

Sequence analysis tools in UniProt: BLAST and Align

BLAST and multiple sequence alignments 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 a comprehensive resource of protein sequence and function 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...

Rossana Zaru

25 November 2020

Discovering scientific evidence using Europe PMC SciLite annotation

For readers of life sciences journal articles annotations make it easier to scan an article and get a quick overview find key concepts and discover evidence such as gene disease associations or molecular interactions This webinar will demonstrate how to use the power of text mining to find evidence in scientific literature...

Dayane Rodrigues Araujo

24 November 2020

Technologies for Extracellular Vesicles Research: Q&A

A Hendrix C L sser E Noltet Hoen G Van Niel...

23 November - 27 November 2020

Structural bioinformatics (Virtual)

Structural biology determining the three dimensional shapes of biomacromolecules and their complexes can tell us a lot about how these molecules function and the roles they play within a cell Data derived from structure determination experiments enables life science researchers to address a wide variety of questions This course explores bioinformatics data resources and tools for the investigation analysis and interpretation of biomacromolecular structures It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts The course content will also cover predicting protein structure and function and exploring interactions with other macromolecules as well as with low MW compounds This course will be a virtual event delivered via a mixture of live streamed sessions pre recorded lectures and tutorials with live support We will be using Zoom to run the live stream sessions all fully password protected with support provided by Slack In order to make the most out of the course you should make sure to have a stable internet connection throughout the week There will also be networking and short social activities throughout the course 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...

Meredith Willmott

18 November 2020

MGnify API: accessing microbiome data computationally

This webinar will provide an overview of the MGnify API MGnify offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional metabolic potential of environmental samples Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository The webinar will include how to utilise the API using a browser where to find documentation how to use filtering and pagination available output formats and scripting examples in Python...

Martin Beracochea

17 November - 20 November 2020

Basics to advanced genome annotation at Ensembl and REST Application Programming Interfaces (APIs)

Introduction to the Ensembl Genome Browser and REST API in collaboration with NextGenHelper...

16 November - 19 November 2020

From Functional Genomics to Systems Biology – Virtual

OverviewSpeakers and OrganisersProgramme Overview Conference Overview Recent advances in genomics and proteomics technologies have transformed our ability to study diverse molecular processes We can now use these technologies to study and understand mechanisms regulating transcription translation protein abundance protein protein protein metabolites and protein drug interactions at a...

12 November 2020

Understanding proteomes

A proteome is the set of proteins thought to be expressed by an organism Through the Proteomes portal UniProt provides a large collection of proteomes for organisms whose genomes have been sequenced and annotated Currently our database contains more than 300 000 proteomes spanning eukaryotes bacteria archea and viruses This webinar will show you how to retrieve proteomes of interest and download the corresponding datasets We will also cover where proteomes come from and the features available to help users find the right dataset for their work...

Ramona Britto

11 November 2020

MGnify today: analysing microbiome data

This webinar will describe how MGnify can assist you in your microbiome research by providing a broad overview of resources available in MGnify MGnify offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional metabolic potential of environmental samples Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository During this webinar we will cover what types of microbiome data are included improvements we have made to our analysis pipeline as well as ways to search for data...

Varsha Kale

11 November 2020

CABANA train the trainer workshop for XMXP20

This highly interactive virtual workshop takes place within the X meeting eXperience 2020 organized by AB3C It will provide new trainers with knowledge skills guidance and tips for developing and delivering training Trainees will explore a range of methods to enable and encourage learning examine the requirements for a successful course and acquire appropriate feedback The workshop itself will depend on trainee participation in group activities The workshop will provide guidance on general training techniques and appropriate use of methods based on learner needs including some general DO s and DO NOTs for successful training provide a framework for successful curriculum design and further development to enable trainers to build a course appropriate to their learners needs The workshop will take place virtually via Zoom...

Piraveen Gopalasingam, Mindy Stephania Miranda, Nicole Scherer

9 November - 10 November 2020

Ensembl Browser workshop, University of California San Francisco, 9-10 November 2020

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...

4 November 2020

Variant submission and data access at the European Variation Archive

This webinar will cover how to access data using the EVA UI API and the methodology of variant data submission to the EVA specifically focusing on data transformation and formats With a new version of the variant ID data release now available this webinar will also cover what has been updated and what to expect from future releases...

Baron Koylass

4 November - 5 November 2020

Our House is Burning: Scientific and Societal Responses to Mass Extinction – Virtual

OverviewSpeakers and OrganisersProgramme Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic We are delighted to announce that the symposium is going virtual and invite you to join us online The virtual symposium includes talks from invited speakers short talk presenters digital poster sessions and networking...

Lucia von Bredow

3 November 2020

Europe PMC: Programmatic access

Europe PMC is an open repository providing access to worldwide biomedical literature including articles preprints books patents and clinical guidelines This webinar will introduce the Europe PMC Articles RESTful API and show how to programmatically access publications and related information such as citations references data links or text mined terms...

Dayane Rodrigues Araujo

2 November - 6 November 2020

Metagenomics bioinformatics (Virtual)

Gain knowledge of the tools processes and analysis approaches used in the field of metagenomics This course will cover the metagenomics data analysis workflow from the point of newly generated sequence data Participants will explore the use of publicly available resources and tools to manage share analyse and interpret metagenomics data The content will include issues of data quality control and how to submit to public repositories While sessions will detail marker gene and whole genome shotgun WGS approaches the primary focus will be on assembly based approaches Discussions will also explore considerations when assembling genome data the analysis that can be carried out by MGnify on such datasets and what downstream analysis options and tools are available Virtual course The course content will involve participants learning via pre recorded lectures live presentations and trainer Q A sessions Practical experience will be developed through group activities and computational exercises Sessions will be delivered over Zoom with additional text communication over Slack Trainers will be available to assist answer questions and further explain the analysis during these times Computational practicals will be run in Docker containers operating 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 Participants will need to be available between the hours of 09 00 17 00 GMT each day of the course...

Marina Pujol

29 October 2020

Introducing the new UniProt Disease Portal

This webinar will provide an interactive introduction to the new UniProt Disease Portal a single centralised resource of UniProt disease centric information which has been developed with the help of our users to better serve the needs of the research community and facilitate protein discoverability The UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive high quality and freely accessible resource of protein sequence and functional information To do this UniProt integrates interprets and standardises data from a range of sources including scientific literature protein sequence analysis tools other databases and automatic annotation systems to provide a detailed overview of the available protein knowledge This webinar will introduce you to the UniProt Disease Portal which aims to help researchers explore and access current genomic disease related data from the UniProtKB database but in a single centralised resource The portal incorporates UniProt functional annotations protein network visualisations genomic variant and drug related data and organises in a way that allows users to easily visualise and compare data to identify similarities using variants protein interactions diseases and drug data The Disease Portal is currently in its first beta release so we hope that this interactive introduction will give you an understanding of how to access disease centric protein data in UniProt and encourage your feedback to assist ongoing development of the Portal to further suit the requirements of our users...

Kate Warner, Emily Bowler-Barnett

28 October 2020

The PRIDE database: storing, disseminating and integrating proteomics data in the public domain

This webinar will provide an introduction to proteomics approaches and the PRIDE database followed by more detailed examples of PRIDE public data re use including big data approaches...

Juan Antonio Vizcaino

28 October - 30 October 2020

Neuroepigenetics: From Cells to Behaviour and Disease – Virtual

OverviewSpeakers and TrainersProgramme Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic We are delighted to announce that the symposium is going virtual and invite you to join us online The virtual symposium includes talks from invited speakers short talk presenters digital poster sessions and networking...

23 October 2020

Open with purpose: How and why to make your data open

As part of EMBL EBI s celebration of Open Access week this special one off webinar will give you insight into the benefits of open access data alongside guidance and tips on managing your data Featuring four members of EMBL EBI s resource teams from BioSamples ENA IntAct Complex Portal Europe PMC you ll get an overview of Open and FAIR data insights into submission processes and support the importance of open literature and some hints tips and tricks for ensuring your data can easily be made available to others You ll also get an opportunity to ask live questions to all four of our speakers and find out where you can learn more...

Fuqi Xu, Sam Holt , Birgit Meldal, Dayane Araujo

22 October - 23 October 2020

CABANA train the trainer workshop for ISCB-Latin America 2020

This virtual workshop takes place within the ISCB LA SoIBio BioNetMX 2020 symposium It will provide new trainers with knowledge skills guidance and tips for developing and delivering training Participants will explore a range of methods to enable and encourage learning examine the requirements for a successful course and acquire appropriate feedback The workshop will provide guidance on general training techniques and appropriate use of methods based on learner needs including some general DO s and DO NOTs for successful training provide a framework for successful curriculum design and further development to enable trainers to build a course appropriate to their learners needs The workshop will take place virtually via Zoom...

Patricia Carvajal Lopez, Maria Trinidad Bernardi, Mindy Stephania Miranda

21 October 2020

Multiomics comparative pathway analysis with ReactomeGSA

The webinar will demonstrate how to perform multiomics comparative pathway analyses using ReactomeGSA This will cover the web interface and R package We will demonstrate how to use ReactomeGSA to quickly derive novel biological knowledge by combining multiple datasets In addition we will also cover the function of ReactomeGSA for investigating scRNA seq cell clusters at the pathway level...

Johannes Griss

21 October - 24 October 2020

Organoids: Modelling Organ Development and Disease in 3D Culture – Virtual

OverviewSpeakers and TrainersProgramme Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic We are delighted to announce that the symposium is going virtual and invite you to join us online The virtual symposium includes talks from invited speakers short talk presenters digital poster sessions and networking...

20 October 2020

Data visualisation at PDBe

This webinar will introduce some of the data visualisations available from PDBe how to add these to your own website and how to customise them for your own requirements There will also be specific case studies that demonstrate how these visualisations can be used and implemented This webinar is part of a 6 part PDBe API webinar series introducing different levels of programmatic access at PDBe The series will range from basic data retrieval and search using the PDBe API to more advanced features including access and reuse of PDBe data visualisation components...

Mandar Deshpande

19 October - 23 October 2020

Computing Skills For Reproducible Research: Software Carpentry – Virtual

OverviewSpeakers and TrainersProgramme Overview Course Overview Computation is an integral part of today s research as data has grown too large or too complex to be analysed by hand An ever growing fraction of science is performed computationally and many wet lab biologists spend part of their time on the computer Many scientists struggle with this aspect of research as they have not...

14 October - 16 October 2020

Exploring biological sequences

We are currently developing the course programme for 2020 and as further information about the course becomes available we will update this page...

13 October 2020

PDBe tools in GitHub

This webinar will show you how to access some of the software packages created at PDBe used to generate the data displayed on our website This will include a walkthrough of our github repositories highlighting the types of packages available how to access them and some examples of how they can be used This webinar is part of a 6 part PDBe API webinar series introducing different levels of programmatic access at PDBe The series will range from basic data retrieval and search using the PDBe API to more advanced features including access and reuse of PDBe data visualisation components...

Lukas Pravda

13 October - 15 October 2020

Gender Roles and their Impact in Academia – Virtual

OverviewSpeakers and TrainersProgramme Overview Conference Overview Women are not rising to the higher echelons of any career in the numbers expected based on the number of women entering universities and the workforce Debates have focused on biology and societal structures as explanations for this phenomenon With this conference we want to explore our understanding of how gender roles...

12 October - 16 October 2020

Summer school in bioinformatics (Virtual)

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 be divided into focused groups to work on a small project set by EMBL EBI resource and research staff ending in a presentation from each group on the final day of the course to bring together learnings from all participants The course includes training and mentoring by experts from EMBL EBI and external institutes 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 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 This year s projects are as follows Networks and pathways This project will make use of gene expression data RNA seq to build protein protein interaction networks which can be used to explore functional relationships between the potentially expressed protein products You will use Cytoscape to visualise protein networks identify key regulators of biological pathways and explore biological function through network analysis integration and co visualisation of additional data and ontology functional enrichment analysis helping to build a better view of the wider biological context 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 computational models of signalling pathways from a recent publication using COPASI and how to reproduce the simulation results Furthermore you will learn how to annotate models and re use pre existing models from open repositories such as BioModels 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 Metabolic network engineering using a systems model based approach Metabolic pathway analysis helps to identify the structure and dynamics of a metabolic network and thereby also allow us to have an insight into cell physiology which is the foundation of metabolic engineering You will work with a curated model related to a metabolism network chosen from BioModels and learn how to carry out computational analyses to find common patterns in the networks These might include computing feasible pathways through the network and minimal reactions to knock out specific metabolic functions along with visualisation and exploration to gain a further insight into the results Finding and interpreting publicly available structural data This project will introduce you to the wealth of publicly available structural data and give you the opportunity to investigate how this data can be used to analyse macromolecular structures You will firstly explore the search and entry pages at PDBe to identify the type of data available for analysis Then using this knowledge you will discover how to access this data programmatically and analyse a subset of your results to interpret biological relevance Functional annotation of proteins Functional annotation refers to discovering the functions of proteins Participants will annotate a protein of interest which has not been annotated previously either manually or by any UniProt automatic system Participants will use different ways to discover the function of their protein of interest from alignment to machine learning You will learn the different annotation types in UniProtKB and how to use the UniProt resources for their investigation You will also learn how to build machine learning models from dataset construction to prediction...

Scientific conferences

7 October - 9 October 2020

Advancement Summit for Life Sciences

M Hentze M Rayner...

7 October 2020

The Ensembl Rapid Release genome browser

This webinar will introduce you to the data available in the Ensembl Rapid Release site a new lightweight genome browser designed to allow quick release of the latest genome annotation for a large number of vertebrate and non vertebrate species...

Benjamin Moore

7 October - 9 October 2020

The Complex Life of RNA – Virtual

OverviewSpeakers and TrainersProgramme Overview Symposium Overview Before the genetic information stored in DNA can be used to direct cell growth and metabolism it has to be transferred into RNA Messenger RNAs mRNAs that code for proteins and noncoding RNAs are key components in the transmission of genetic information in all life forms from viruses to complex mammalian organisms...

6 October 2020

Using the PDBe graph API

This webinar will introduce the PDBe graph API which is generated from the PDBe graph database and contains an even richer level of data than our standard API We will highlight how this API supports our PDBe KB aggregated views with specific case studies that demonstrate the possibilities through this API This webinar is part of a 6 part PDBe API webinar series introducing different levels of programmatic access at PDBe The series will range from basic data retrieval and search using the PDBe API to more advanced features including access and reuse of PDBe data visualisation components...

Sreenath Nair

5 October - 9 October 2020

CZI-CABANA Joint Workshop: Microbiome Bioinformatics with QIIME 2

Members of the QIIME 2 team will teach a five day online workshop on bioinformatics tools for microbiome science This workshop will provide attendees with the foundation needed to begin using QIIME 2 to advance their own microbiome research projects This will be accomplished by providing detailed in depth theory lectures hands on interactive tutorials guided discussion and general question and answer sessions The workshop will include lectures covering QIIME 2 usage and theory and interactive work with QIIME 2 to perform microbiome analysis from raw sequence data through publication quality statistics and visualizations This workshop will also feature several opportunities for attendees to network with other researchers in the field as well as with QIIME 2 developers and other experts...

Greg Caporaso, Matthew Ryan Dillon

30 September 2020

Reproducibility in Systems Biology Modelling: BioModels' role

This webinar will give an overview of BioModels a popular repository of curated systems biology models It will also provide a brief introduction to BioModels Parameters a sub resource within BioModels that provides model parts followed by discussion of a study carried out to assess how reproducible systems biology models are the reasons why mathematical models fail to reproduce simulation results and the solution we propose to tackle lack of reproducibility...

Rahuman Sheriff

30 September - 2 October 2020

Molecular Mechanisms in Evolution and Ecology – Virtual

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

29 September 2020

Creating complex PDBe API queries

This webinar will demonstrate how to create more complex queries by combining the PDBe search API with numerous other calls By introducing specific case studies we will highlight the scope of PDBe programmatic access This webinar is part of a 6 part PDBe API webinar series introducing different levels of programmatic access at PDBe The series will range from basic data retrieval and search using the PDBe API to more advanced features including access and reuse of PDBe data visualisation components...

Nurul Nadzirin

28 September - 2 October 2020

Mathematics of life: Modelling molecular mechanisms (Virtual)

Computer models are increasingly used to understand 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 participants with an introduction to modelling resources tools and approaches used in systems biology as well as touch on network analysis This course will be a virtual event delivered via a mixture of live streamed sessions pre recorded lectures and tutorials with live support We will be using Zoom to run the live stream sessions all fully password protected with support provided by Slack In order to make most out of the course you should make sure to have a stable internet connection throughout the week Selected participants will be sent materials prior to the course These might include pre recorded talks and required reading that will be essential to fully understand the course...

Rebecca Nicholl

28 September - 5 October 2020

Genome Engineering: CRISPR/Cas from Cells to Mice – Virtual

OverviewSpeakers Trainers and OrganisersProgramme Overview Course Overview This course will provide training in genome editing and cell engineering in mammalian cells and mouse embryos using the highly efficient CRISPR Cas9 system Participants will learn design of CRISPR targets using bioinformatics tools generation of gene knock outs knock ins and target validation using the most current...

25 September 2020

Ensembl Browser workshop, IGMM, University of Edinburgh, 25 September 2020

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...

23 September 2020

Investigating genotype-phenotype data using the GWAS Catalog

This webinar will include a brief introduction to the GWAS Catalog followed by hands on demonstrations and exercises covering different methods for accessing GWAS Catalog data focusing on the most common use cases This will include our web based search interface with a number of different tools for data access and visualisation and download of filtered datasets We will also briefly introduce and describe how to submit your own data...

Laura Harris

22 September 2020

Searching with the PDBe API

This webinar will introduce the PDBe search API a powerful Solr based query system that underlies the PDBe search pages The breadth of search options will be highlighted along with specific case studies that demonstrate what is possible through the search API This webinar is part of a 6 part PDBe API webinar series introducing different levels of programmatic access at PDBe The series will range from basic data retrieval and search using the PDBe API to more advanced features including access and reuse of PDBe data visualisation components...

John Berrisford

16 September 2020

The International Mouse Phenotyping Consortium (IMPC): a large-scale functional catalogue of mammalian genes

The IMPC is an international research infrastructure comprised by 21 of the leading mouse genetics centres worldwide that is systematically identifying the function of every protein coding gene in the mouse genome Despite having sequenced the entire genomes of many species the exact function of most genes remains unknown To address this the IMPC is coordinating the production of a knockout mouse strain per protein coding gene which are then characterised using a standardised broad based phenotyping pipeline giving insights into the function for genes for which very little is known Our open access database now includes phenotyping data for nearly 6 500 mouse genes This webinar will discuss some of the exciting discoveries in genetic disease development and sexual dimorphism that biologists and clinical researchers are making using IMPC resources The IMPC strives to generate data that ultimately help understand human health and disease and identify new targets for therapeutic intervention This data is also useful for research focusing on other mammalian species including evolutionary research studies seeking to understand adaptation All IMPC data is freely available to use and can be accessed at www mousephenotype org The IMPC would like to encourage researchers to get in touch via the IMPC website if they are interested in using IMPC data and would like further guidance on how to use our data...

Violeta Munoz Fuentes, Hamed Haseli

15 September 2020

Introduction to PDBe programmatic access

This webinar will give an introduction to programmatic access at PDBe highlighting the type of data that is available and how this can be utilised This webinar is part of a 6 part PDBe API webinar series introducing different levels of programmatic access at PDBe The series will range from basic data retrieval and search using the PDBe API to more advanced features including access and reuse of PDBe data visualisation components...

David Armstrong

14 September - 16 September 2020

The Molecular Basis and Evolution of Sexual Dimorphism – Virtual

OverviewSpeakers and OrganisersProgramme Overview EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic We are delighted to announce that the conference is going virtual and invite you to join us online The virtual conference includes talks from invited speakers short talk presenters digital poster sessions online group...

11 September - 18 September 2020

Liquid Biopsies – Virtual

OverviewSpeakers Trainers and OrganisersProgramme Overview Course Overview Liquid biopsies have the advantage of being largely non invasive and providing a vast amount of information for the detection and monitoring of diseases such as cancer This course will provide an overview in the several techniques to detect and analyse circulating tumour cells CTCs cell free tumor DNA ctDNA...

8 September 2020

EurOPDX IT tools to support cancer research with patient-derived xenograft models

The new EurOPDX Research Infrastructure RI funded by the European Union Horizon 2020 programme aims to improve cancer drug development success rates through the enablement of collaborative cancer research using patient derived xenograft PDX models In particular we are developing efficient and user friendly IT tools to optimise access to and data searching of the collection of PDX models and their clinical molecular and pharmacological annotations Following a first webinar in October 2019 introducing the new EurOPDX Data Portal we will present the latest data and functionalities added to the repository and associated IT tools to browse molecular data associated with the models the EurOPDX instance of the well known cBioPortal and the GenomeCruzer for 3D interrogation of data The webinar will in particular support the last applicants to our PDX access grant programme last deadline on 18th September 2020 https www europdx eu europdxri ta...

Emilie Vinolo, Enzo Medico

3 September - 5 September 2020

Chemical Biology 2020 – Virtual

OverviewSpeakers and OrganisersProgramme Overview Conference Overview The conference sets the stage for the dissemination and exchange of new developments in diverse hot fields within chemical biology It is the largest and longest standing conference in the field being a platform for inspiration collaboration and networking for researchers in academia and industry We aim to provide...

2 September 2020

Ensembl API workshop, University of Cambridge (Virtual)

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website The workshop covers how to use the Ensembl REST APIs including understanding the major endpoints and how to write Python Perl R scripts to call them Feedback from previous courses Wish I had taken the course long time ago Didn t know before how good and powerful APIs are API workshop EMBL EBI January 2016 I really enjoyed the course and the ENSEMBL API will become a very relevant part of my toolset API workshop Cambridge December 2013 If you think you d like to host a similar course at your institute you can find out more on the Ensembl workshops page...

Michal Szpak

1 September 2020

Ensembl Browser workshop, University of Cambridge (Virtual), 01.09.2020

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...

1 September - 4 September 2020

Gene Expression at Spatial Resolution – Virtual