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  • "Ready for BioData Management?" Data Stewardship program for the life sciences

    21 February - 31 October 2022

    Oeiras, Portugal

    "Ready for BioData Management?" Data Stewardship program for the life sciences https://tess.elixir-europe.org/events/ready-for-biodata-management-data-stewardship-program-for-the-life-sciences BioData.pt | ELIXIR Portugal, in collaboration with several other organizations has designed a program to train the first generation of Data Stewards for the life sciences, to support the implementation of data management, open science and FAIR data principles in Portuguese R&I organizations. It will unfold from February to October 2022, allowing trainees get some practice and consolidate the acquired knowledge. It will comprise an introductory module covering the basic concepts of Data Stewardship followed by two assignments and end with a hands-on course for knowledge consolidation. 2022-02-21 09:00:00 UTC 2022-10-31 17:00:00 UTC BioData.pt | ELIXIR Portugal Online and F2F (See details in training documentation), Oeiras, Portugal Online and F2F (See details in training documentation) Oeiras Portugal FAIR data Data submission, annotation, and curation Bioinformatics Data management Biodata.pt - Elixir's portuguese node of the european projec info@biodata.pt ELIXIR Life Science Researchers 24 workshops_and_courses registration_of_interest data managementData management plandata stewardshipdata annotationlife sciencestraining

  • Core Statistics using R (ONLINE LIVE TRAINING)

    29 June - 14 July 2022

    Cambridge, United Kingdom

    Elixir node event
    Core Statistics using R (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/core-statistics-using-r-online-live-training-1bdf4c7a-2283-4160-b3e3-4a8e7385502d This [award winning](https://www.cctl.cam.ac.uk/teaching-prizes/tel-prize/2020) virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course: # Use R confidently for statistics and data analysis # Be able to analyse datasets using standard statistical techniques # Know which tests are and are not appropriate R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4180988&course-title=Core%20Statistics%20using%20R).'' 2022-06-29 08:30:00 UTC 2022-07-14 12:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individualsThis course is included as part of several DTP and MPhil programmesas well as other departmental training within the University of Cambridge (potentially under a different name) so participants who have attended statistics training elsewhere should check before applying. workshops_and_courses [] HDRUK

  • An Introduction to Machine Learning (ONLINE LIVE TRAINING)

    4 - 12 July 2022

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Machine Learning (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/an-introduction-to-machine-learning-online-live-training-f0d82528-636b-4d41-856d-71a7ec0f8672 Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4341268&course-title=An%20Introduction%20to%20Machine%20Learning).'' 2022-07-04 08:30:00 UTC 2022-07-12 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Data mining University of Cambridge Bioinformatics Training [] This is aimed at life scientists with little or no experience in machine learning and that are looking at implementing these approaches in their research.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

  • Single-cell Transcriptomics

    4 - 6 July 2022

    Bern, Switzerland

    Elixir node event
    Single-cell Transcriptomics https://tess.elixir-europe.org/events/single-cell-transcriptomics-be70d45c-e4dd-4319-866d-d0c192c60ccf Overview In contrast to the Bulk RNA sequencing used to quantify the abundance of gene and transcript expression at a whole population level, single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression profile at a single cell 2022-07-04 09:00:00 UTC 2022-07-06 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Advanced Python for Biologists 2022

    4 - 15 July 2022

    Elixir node event
    Advanced Python for Biologists 2022 https://tess.elixir-europe.org/events/advanced-python-for-biologists-2022 Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at people who already have a basic knowledge of Python and are interested in using the language to tackle larger problems. In it, we will look in detail at the parts of the language which are particularly useful in scientific programming, and at the tools Python offers for making development faster and easier. The workshop will use examples and exercises drawn from various aspects of bioinformatics work. After completing the workshop, students should be in a position to (1) take advantage of the advanced language features in their own programs and (2) use appropriate tools when developing software programs. This event will be delivered virtually via Zoom & Slack, see more details on the further information tab. Please see here for a detailed syllabus of the course. 2022-07-04 09:00:00 UTC 2022-07-15 17:00:00 UTC Earlham Institute [] [] [] [] [] []

  • Systems biology: from large datasets to biological insight

    4 - 8 July 2022

    United Kingdom

    Elixir node event
    Systems biology: from large datasets to biological insight https://tess.elixir-europe.org/events/systems-biology-from-large-datasets-to-biological-insight-d2a1656c-29ef-412d-9ddb-233bf139d811 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. 2022-07-04 09:00:00 UTC 2022-07-08 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] This course is aimed at advanced PhD students, post-doctoral researchers, and non-academic scientists who are currently working with large-scale omics datasets with the aim of discerning biological function and processes. Ideal applicants should already have some experience (ideally 1-2 years) working with systems biology or related large-scale (multi-)omics data analyses. Applicants are expected to have a working knowledge of the Linux operating system and the ability to use the command line. Experience of using a programming language (i.e. Python) is highly desirable, and while the course will make use of simple coding or streamlined approaches such as Python notebooks, higher levels of competency will allow participants to focus on the scientific methodologies rather than the practical aspects of coding and how they can be applied in their own research. We recommend these free tutorials: Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training Python tutorial: https://www.w3schools.com/python/ R tutorial: https://www.datacamp.com/courses/free-introduction-to-r Regardless of your current knowledge we encourage successful participants to use these to prepare for attending the course and future work in this area. Selected participants will also 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. 30 [] [] []

  • Constraint-based modeling: Introduction and advanced topics

    4 - 8 July 2022

    Wageningen Campus, Netherlands

    Elixir node event
    Constraint-based modeling: Introduction and advanced topics https://tess.elixir-europe.org/events/constraint-based-modeling-introduction-and-advanced-topics This course will introduce computational modeling of large (genome-scale) metabolic reaction networks through a scalable framework known as constraint-based modeling. Emphasis will be on the usage in both biotechnology and systems biomedicine. Main topics will be fundamental constraint-based modeling methods,… The post Constraint-based modeling: Introduction and advanced topics appeared first on Dutch Techcentre for Life Sciences. 2022-07-04 09:00:00 UTC 2022-07-08 00:00:00 UTC Wageningen Campus, The Netherlands, Wageningen Campus, Netherlands Wageningen Campus, The Netherlands Wageningen Campus Netherlands [] [] [] workshops_and_courses [] []

  • Stakeholder consultation workshop: Developing ELIXIR's next Scientific Programme

    6 July 2022

    Brussels, Belgium

    Stakeholder consultation workshop: Developing ELIXIR's next Scientific Programme https://tess.elixir-europe.org/events/stakeholder-consultation-workshop-developing-elixir-s-next-scientific-programme ELIXIR is currently developing it’s Scientific Programme for 2024-2028. This high-level workshop takes place at The Hotel in Brussels and will bring together senior representatives from different research communities to give their perspective on the future. A series of short presentations (10 minutes) from our high-level panelists will give context and inspiration to round-table discussions between the all the workshop participants - each table will then make some recommendations at the end of the debate. Agenda 8:30 - 9:30 Registration and Coffee 9:30 - 9:45 Welcome & Introduction Niklas Blomberg (ELIXIR) 9:45 - 10:15 View from the European Commission Anna Panagopolou (European Commission) 10:15 - 11:00 Data needs across the life sciences in 2028 Biodiversity Dimitris Koureas (Naturalis) Genomics and Disease Søren Brunak (University of Copenhagen) Molecular and Cellular Biology Christine Orengo (UCL) Plants and Agriculture Klaas Vandepoele (VIB) 11:00 - 11:30 Coffee break 11:30 - 12:15 Breakout sessions on Scientific Topics 12:15 - 13:00 Lunch 13:00 - 13:45 Enabling collaborations - ELIXIR in the European landscape Data Management Hilary Hanahoe (RDA) EOSC Per Öster (CSC) ESFRI landscape Dominik Sobczak (European Commission) Software Paul Richmond (University of Sheffield) 13:45 - 14:15 Breakout sessions on Enabling Collaborations 14:15 - 14:45 Coffee break 14:45 - 15:15 Feedback from breakouts 15:15 - 16:15 Towards 2028 - data in life sciences in European and beyond - Panel discussion Alfonso Valencia (BSC) Claire Skentelbery (EuropaBio) Hugh Laverty (IHI) Søren Brunak (University of Copenhagen) 16:15 - 16:30 Final Remarks Niklas Blomberg (ELIXIR) 17:00 - 18:30 Drinks Reception 2022-07-06 08:30:00 UTC 2022-07-06 08:30:00 UTC The Hotel, Brussels, Belgium The Hotel Brussels Belgium [] [] [] [] [] []

  • Introduction to working with UNIX and bash (ONLINE LIVE TRAINING)

    6 - 7 July 2022

    Cambridge, United Kingdom

    Elixir node event
    Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/introduction-to-working-with-unix-and-bash-online-live-training-b013c4ea-fc73-42d1-9ac5-b11435801e1b PLEASE NOTE The Bioinformatics Team are presently teaching many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands. Building on the techniques learnt so far, we will then construct bash scripts combining the commands and structures already learnt into more complex, reusable tools. We will look at how we can apply these scripts to common problems faced in UNIX environments such as: communicating with remote servers; managing custom software installations and integrating these tools into our simple pipelines. This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4316938&course-title=Introduction%20to%20working%20with%20Unix%20and%20bash).'' 2022-07-06 13:00:00 UTC 2022-07-07 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

  • Bioinformatics for T-Cell immunology

    11 - 15 July 2022

    United Kingdom

    Elixir node event
    Bioinformatics for T-Cell immunology https://tess.elixir-europe.org/events/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. 2022-07-11 09:00:00 UTC 2022-07-15 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] The course is aimed at wet-lab scientists working in the field of immunology who wish to learn more about available data and tools that can help them in their research. 15 places are reserved for early-stage researchers from the ENLIGHT-TEN+ project.   30 [] [] []

  • RNA-seq gene expression and pathway analysis

    12 - 14 July 2022

    Elixir node event
    RNA-seq gene expression and pathway analysis https://tess.elixir-europe.org/events/rna-seq-gene-expression-and-pathway-analysis RNA-seq gene expression and pathway analysis - 12&14 July 2022 RNA-Seq (aka whole transcriptomic shotgun sequencing) aims to determine the presence and quantity of RNA in a biological sample at a given moment in time. This allows you to determine the level of expression of these genes and therefore compare these expressions across different sample groups, i.e. Differential Gene Expression (DGE). At the end of this course you will be able to align the transcriptomes of samples to a reference genome to determine gene expression levels. Following this you will be able to carry out Differential Gene Expression analysis to determine which genes are up and down regulated between sample groups. Places are restricted to UK-based researchers and only 20 places are available so please only register if you intend on attending. The workshop will be held over two days on Tuesday 12 and Thursday 14 July 2022, 10am-4pm, with registration opening 9.30am on Tuesday. The deadline to register is Monday 27 June, 2 weeks before the course. You will hear later that week whether you have been invited and will need to confirm your attendance. Register to NEOF mailing list to hear first about future NEOF free bioinformatics courses: https://neof.org.uk/news/ 2022-07-12 09:00:00 UTC 2022-07-14 17:00:00 UTC [] [] [] [] [] []

  • Omics analyses: Pathways, Networks and Biomarkers

    12 - 14 July 2022

    Liverpool, United Kingdom

    Omics analyses: Pathways, Networks and Biomarkers https://tess.elixir-europe.org/events/omics-analyses-pathways-networks-and-biomarkers A CBF three-day face-to-face intense course for experimental biologists and clinicians Demystify computational biology and come to learn: -Functional & pathway enrichment -In-silico biomarker discovery using multivariate methods and machine learning -Identification of transcriptional hubs & master regulators via network analysis -Best experimental design practices -Dedicated time to talk about your data and experiments Theory and practice sessions. 1-1 support. Requirements All materials have been built using relevant life sciences/clinical examples. The course has been designed for delegates with some R experience (basics). A refresher of R from beginner level is included and all relevant code will be provided such as delegates will only have to run specific scripts. Administrative details A significantly reduced access fee of £225 is available to all academic delegates. Other delegates will be quoted upon request. 2022-07-12 09:00:00 UTC 2022-07-14 17:00:00 UTC Computational Biology Facility TBC, Liverpool, United Kingdom TBC Liverpool Merseyside United Kingdom L69 7ZX Experimental design and studies Machine learning Data visualisation Bioinformatics University of Liverpool CBF@liverpool.ac.uk Liverpool Shared Research FacilitiesComputational Biology Facility Experimental Researchers 20 workshops_and_courses first_come_first_served Systems biology, Pathway analysis, Network analysis, Microarray data analysis, Nanomaterialsmachine learningExperimental designProteomicsMetabolomicstranscriptomics

  • High Performance Computing: An Introduction (ONLINE LIVE TRAINING)

    13 - 14 July 2022

    Cambridge, United Kingdom

    Elixir node event
    High Performance Computing: An Introduction (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/high-performance-computing-an-introduction-online-live-training-2e94ddaf-6071-4664-9d5d-619b49b20888 PLEASE NOTE The Bioinformatics Team are presently teaching many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Have you heard about High Performance Computing, but are not sure what it is or whether it is relevant for your work? Would you like to use a HPC, but are not sure where to start? Are you using your personal computer to run computationally demanding tasks, which take long and slow down your work? Do you need to use software that runs on Linux, but don't have access to a Linux computer? If any of these questions apply to you, then this course might be for you! Knowing how to work on a High Performance Computing system is an essential skill for applications such as bioinformatics, big-data analysis, image processing, machine learning, parallelising tasks, and other high-throughput applications. In this course we will cover the basics of High Performance Computing, what it is and how you can use it in practice. This is a hands-on workshop, which should be accessible to researchers from a range of backgrounds and offering several opportunities to practice the skills we learn along the way. As an optional session for those interested, we will also introduce the (free) HPC facilities available at Cambridge University (the course is not otherwise Cambridge-specific). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4316957&course-title=High%20Performance%20Computing:%20An%20Introduction).'' 2022-07-13 13:00:00 UTC 2022-07-14 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] This course is aimed at students and researchers of any background.We assume no prior knowledge of what a HPC is or how to use it.It may be particularly useful for those who have attended other Facility Courses and now need to process their data on a Linux server. It will also benefit those who find themselves using their personal computers to run computationally demanding analysis/simulations and would like to learn how to adapt these to run on a HPC.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

  • Proteomics bioinformatics

    17 - 22 July 2022

    United Kingdom

    Elixir node event
    Proteomics bioinformatics https://tess.elixir-europe.org/events/proteomics-bioinformatics-e45e1bf8-c758-491b-817d-e236414eb179 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. 2022-07-17 09:00:00 UTC 2022-07-22 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] The course is aimed at research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff, as well as specialists in related fields. The practical elements of the course will take raw data from a proteomics experiment and analyse it. Participants will be able to go from MS spectra to identifying and quantifying peptides, and finally to obtaining lists of protein identifiers that can be analysed further using a wide range of resources. The final aim is to provide attendees with the practical bioinformatics knowledge they need to go back to the lab and process their own data when collected. 30 [] [] []

  • [ONLINE] Data Carpentry @ EPCC 18-21 July 2022

    18 - 21 July 2022

    [ONLINE] Data Carpentry @ EPCC 18-21 July 2022 https://tess.elixir-europe.org/events/online-data-carpentry-epcc-18-21-july-2022 Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The workshop will cover: (Monday morning) Data Organization in Spreadsheets. OpenRefine for Data Cleaning. (Tuesday morning) Introduction to R. (Wednesday morning) Continuation of R: Data analysis and Visualization. (Thursday morning) Data Management with SQL. Each session will run   09:30 - 13:00 BST https://events.prace-ri.eu/event/1406/ 2022-07-18 08:30:00 UTC 2022-07-21 12:00:00 UTC [] [] [] workshops_and_courses [] []

  • Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2022

    9 - 11 August 2022

    Heidelberg, Germany

    Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2022 https://tess.elixir-europe.org/events/tools-for-systems-biology-modeling-and-data-exchange-copasi-cellnetanalyzer-sabio-rk-fairdomhub-seek-2022 During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer and a demonstration of CNApy. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. 2022-08-09 09:00:00 UTC 2022-08-11 17:00:00 UTC de.NBI /ELIXIR-DE BioQUANT, Heidelberg, Germany BioQUANT Heidelberg Germany 69120 University of Heidelberg, BioQUANT Frank T. Bergmann (frank.bergmann@bioquant.uni-heidelberg.de) [] ResearcherModellerStudents workshops_and_courses [] []

  • Advanced Statistics: Statistical Modelling

    22 - 25 August 2022

    Lausanne, Switzerland

    Elixir node event
    Advanced Statistics: Statistical Modelling https://tess.elixir-europe.org/events/advanced-statistics-statistical-modelling-dc58174b-c34c-468a-a484-1fa4c7ed7957 Overview While the statistical models and tools presented in an introductory statistics course (such as linear regression) can be used to answer a wide range of questions in life sciences, many types of data can not be analyzed using these simple 2022-08-22 09:00:00 UTC 2022-08-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Integrative structural biology course

    22 August - 2 October 2022

    Lund, Gothenburg, Stockholm, Sweden

    Elixir node event
    Integrative structural biology course https://tess.elixir-europe.org/events/integrative-structural-biology-course Deadline for application: 23rd of May: https://www.lyyti.fi/reg/Integrative_Structural_Biology_Course_3770 The two week course is a joint effort between the three large-scale research infrastructures SciLifeLab, MAX IV and ESS and additional related platforms. The aim is to give an overview of the structural biology available at the research infrastructures in Sweden. The course will focus on understanding the sample requirements, the nature of structural information that can be obtained and how data from multiple structural biology methods can be combined using e.g. computational chemistry techniques. The course consists of lectures, key note speakers, modelling practicals and facility visits. In addition events allowing time for networking within the group of students, the teachers and other infrastructure personnel, contributing to an expanded professional network. Technologies/methods: *Macromolecular X-ray and neutron crystallography *Small angle X-ray and neutron scattering *Cryo-electron microscopy *Macromolecular nuclear magnetic resonance spectroscopy *Structural mass spectrometry *Modelling and Computational methods *Biophysical characterization Keynote speakers: We proudly present a number of exciting keynote speakers that will present scientific examples of how integrative structural biology techniques can be used to solve intriguing questions. Professor Poul Nissen, Aarhus University Professor Carmen Domene, University of Bath Postdoctoral researcher Hanna Barriga, Karolinska university Also we will be able to join in on the SciLifeLab “Annual lecture on Structural Biology” where Demis Hassabis will talk on using AI to accelerate scientific discovery. Lessons on modelling/computational methods: We will have several lectures on modelling and computational techniques for structural biology. Associate professor Lucie Delemotte, Integrating physics-based and evolutionary modelling to investigate the conformational dynamics of membrane proteins Professor Gunnar von Heijne, Different approaches to the study of cotranslational protein folding Professor Erik Lindahl, titel tbd Principal Research Engineer Claudio Mirabello, The protein structure prediction problem: from Anfinsen to AlphaFold. 2022-08-22 09:00:00 UTC 2022-10-02 17:00:00 UTC Infralife Onsite on three different locations across Sweden where the Swedish national Research Infrastructures, MaxIV, SciLifeLab and ESS are coming together to deliver a course on structural biology. The course will be held in Sweden, on site, between Aug 22 and Sept 2nd 2022. *Lund, 22 to 25 Aug *Gothenburg, 26 Aug *Stockholm, 29 Aug to 2 Sep, Lund, Gothenburg, Stockholm, Sweden Onsite on three different locations across Sweden where the Swedish national Research Infrastructures, MaxIV, SciLifeLab and ESS are coming together to deliver a course on structural biology. The course will be held in Sweden, on site, between Aug 22 and Sept 2nd 2022. *Lund, 22 to 25 Aug *Gothenburg, 26 Aug *Stockholm, 29 Aug to 2 Sep Lund, Gothenburg, Stockholm Sweden Sweden Sweden Structural biology Infralife Josefin Lundgren (Infralife coordinator), josefin.lundgren@scilifelab.se This InfraLife integrative structural biology course is organized with funding support from the Swedish research council, Lif, Excillum, NBIS, Xenocs, SwedNMR, Bruker and CryoNET. The course is open to scientists of all age from academia, health care and industry. Level approximately corresponding to PhD student or postdoc depending on experience. Applicants welcome from Sweden, the Nordics, and other countries. receptions_and_networkingworkshops_and_courses registration_of_interest Structural biologybioinformaticsTechnologycomputational methods

  • WORKSHOP: Single cell RNAseq analysis in R

    22 - 23 August 2022

    WORKSHOP: Single cell RNAseq analysis in R https://tess.elixir-europe.org/events/workshop-single-cell-rnaseq-analysis-in-r Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using[ Seurat](https://satijalab.org/seurat/index.html) - an R package for QC, analysis, and exploration of single-cell RNAseq data. We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. **Lead trainers:** Dr Sarah Williams, Senior Bioinformatician, QCIF Mr Nick Matigan, Biostatistician and Bioinformatician, QCIF Dr Ahmed Mehdi, Senior Biostatistician, QCIF **Format** This online workshop will take place over two half-day sessions. You must attend both sessions. Expert trainers will guide you through each of the topics and provide activities to help you put your new skills into action. **Date/Time:** 22 and 23 August 2022, 1-5pm AEST/ ACST/AWST **Location:** Online **Learning outcomes:** By the end of the workshop you should be able to: 1. Load gene counts into a Seurat format 2. Perform QC and select cells for further analysis 3. Filter and normalise scRNAseq data 4. Cluster cells and identify cluster markers 5. Visualise scRNAseq expression data **Who the workshop is for:** This workshop is for Australian researchers who have or will work on scRNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. This workshop will not teach you the basics of R. While you don’t need to be an expert, you require some basic familiarity with R. For example you should be able to work with tables of data, know how to load an R package, make basic plots (ideally with ggplot2). You should also have basic knowledge of single cell RNA sequencing technology. **How to apply:** This workshop is free but participation is subject to application with selection. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. Applications close at **11:59pm AEDT, Wednesday 10 August 2022**. **[Apply here](https://biocommons-scrnaseq.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/) and[ Queensland Cyber Infrastructure Foundation (QCIF)](https://www.qcif.edu.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons_ 2022-08-22 13:00:00 UTC 2022-08-23 17:00:00 UTC Australian BioCommons RNA-Seq Australian Biocommons training@biocommons.org.au [] [] 80 workshops_and_courses registration_of_interest Single Cell technologiesscRNAseqSeuratR software

  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://tess.elixir-europe.org/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are. In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here] (https://unimelb.zoom.us/webinar/register/WN_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Whole genome sequencing Sequencing Genomics Bioinformatics Workflows Australian Biocommons training@biocommons.org.au [] [] 500 workshops_and_courses first_come_first_served []

  • Advanced Programming with R

    29 - 31 August 2022

    Lausanne, Switzerland

    Elixir node event
    Advanced Programming with R https://tess.elixir-europe.org/events/advanced-programming-with-r Overview This 3-day advanced course is targeted at life scientists or bioinformaticians using the R statistical software who want to extend their knowledge. Lectures will be conducted in the morning, with practicals in the afternoon. 2022-08-29 09:00:00 UTC 2022-08-31 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Introduction to RNA-Seq: From quality control to pathway analysis

    1 - 2 September 2022

    Basel, Switzerland

    Elixir node event
    Introduction to RNA-Seq: From quality control to pathway analysis https://tess.elixir-europe.org/events/introduction-to-rna-seq-from-quality-control-to-pathway-analysis-d8c6ae2e-37f6-44fe-826e-a3348db94bd4 Overview This two-day course will present the theory and bioinformatics tools required to analyze RNA-seq gene expression data, The course will present the theory and bioinformatics tools required to analyse RNA-seq gene expression data, from the 2022-09-01 09:00:00 UTC 2022-09-02 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Summer School of Single Cell: From the Lab to Data Analysis

    7 - 14 September 2022

    Plzeň (=Pilsen!), Czechia

    Elixir node event
    Summer School of Single Cell: From the Lab to Data Analysis https://tess.elixir-europe.org/events/summer-school-of-single-cell-from-the-lab-to-data-analysis By: Charles University, University of West Bohemia, Medical University of Vienna, London South Bank University, University of Milan, University of Warsaw, Heidelberg University and University of Copenhagen We are inviting you to join our unique Single-cell summer school which covers all important steps during CAR-T preparation, sample preparation for single-cell sequencing and data analysis. This eight-day intensive hands-on school focuses on experiment design, sample selection and preparation, quality control, sequencing, understanding NGS data formats, sequence editing, read mapping, handling potential problems and finally data interpretation. 2022-09-07 08:00:00 UTC 2022-09-14 17:00:00 UTC Charles University, University of West Bohemia, Medical University of Vienna, London South Bank University, University of Milan, University of Warsaw, Heidelberg University and University of Copenhagen https://singlecell-pilsen2022.zcu.cz/location.html, Plzeň (=Pilsen!), Czechia https://singlecell-pilsen2022.zcu.cz/location.html Plzeň (=Pilsen!) Czechia Genomics [] [] [] workshops_and_courses [] []

  • Comparative Genomics

    12 - 14 September 2022

    Streamed or Lausanne, Switzerland

    Elixir node event
    Comparative Genomics https://tess.elixir-europe.org/events/comparative-genomics-d3e772d0-ca37-4239-8d74-2ac20f260036 Overview The aims of this course are to (i) explore key evolutionary concepts, (ii) examine different methodological approaches, and (iii) gain hands-on experience in eukaryotic comparative genomic analyses. 2022-09-12 09:00:00 UTC 2022-09-14 00:00:00 UTC SIB, Streamed or Lausanne, Switzerland SIB Streamed or Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Mathematics of life: modelling molecular mechanisms

    12 - 16 September 2022

    United Kingdom

    Elixir node event
    Mathematics of life: modelling molecular mechanisms https://tess.elixir-europe.org/events/mathematics-of-life-modelling-molecular-mechanisms-1b57c504-4751-4313-a48d-3ac2da24ab02 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. 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. 2022-09-12 09:00:00 UTC 2022-09-16 00:00:00 UTC European Bioinformatics Institute Hinxton, United Kingdom European Bioinformatics Institute Hinxton Cambridge United Kingdom CB10 1SD [] [] This course is aimed at experimental biologists, bioinformaticians and mathematicians who have just started in systems biology, are familiar with the basic terminology in this field and who are now keen on gaining a better knowledge of systems biology modelling approaches to understand biological and biomedical problems. An experience of using a programming language (e.g Python, R, Matlab) would be a benefit but is not mandatory. An undergraduate knowledge of molecular and cellular biology or some background in mathematics is highly beneficial. 30 [] [] []

  • ELIXIR at ECCB 2022

    12 - 21 September 2022

    Barcelona, Spain

    ELIXIR at ECCB 2022 https://tess.elixir-europe.org/events/elixir-at-the-eccb-2022 The 21st European Conference on Computational Biology (ECCB 2022) has the theme "Planetary Health and Biodiversity". This year the conference runs 12 - 21 September and is organised by the Spanish National Bioinformatics Institute (INB/ELIXIR-ES) and the Barcelona Supercomputing Center (BSC). 12 - 16 September: online workshops 18 - 21 September: a four-day conference, with keynote speakers, talks, posters and workshops ELIXIR will be present at this year's ECCB conference with the ELIXIR Communities Track on Monday and Tuesday 19 - 20 September, and workshops on Sunday 18 September. You can find details about the conference, including how to register, on the ECCB 2022 website. Submit your abstract to the ELIXIR Communities Track Track chair: Katharina Heil, ELIXIR We invite submissions of abstracts to the ELIXIR Communities Track at ECCB2022. The aim of the ELIXIR Communities Track is to showcase the latest outputs and services emerging from ELIXIR’s Communities. Submissions are open to ELIXIR Community members. They should highlight services and activities of the ELIXIR Community. Presentations should be 15 minutes and will be followed by a maximum of five-minute discussions. Presenters are encouraged to demonstrate concrete services and outputs and show clearly the benefit of their resource or activity to the ECCB audience. Accepted submissions will be presented in one of the four ELIXIR Communities Track sessions at the conference. Authors of accepted submissions will be invited to publish their presentations on the ELIXIR F1000Research Gateway. Submit your abstract via EasyChair Call opens: 16 May 2022 Call closes: 29 May 2022 Authors will be notified of acceptance by 2 June 2022. Review Criteria All submissions will be evaluated according to the following criteria: Relevance, interest, and value of the topic to conference attendees. Relevance to the overall themes of ECCB2022: Data, Genome, Genes, Proteins, Systems. Relevance to ELIXIR activities. The ultimate decision of acceptance for an ELIXIR Communities Track lies with the Track Chair and ELIXIR Programme Committee. Accepted presenters are required to deliver the presentation themselves, and must register to attend the conference. Contacts For the ELIXIR Communities Track: katharina.heil@elixir-europe.org For general questions about the conference: eccb2022@bcocongresos.com 2022-09-12 09:00:00 UTC 2022-09-21 17:00:00 UTC Hotel Meliã Sitges, Barcelona, Spain Hotel Meliã Sitges Barcelona Spain [] [] [] [] [] []

  • Introduction to high-performance computing (sciCORE cluster)

    14 September 2022

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to high-performance computing (sciCORE cluster) https://tess.elixir-europe.org/events/introduction-to-high-performance-computing-scicore-cluster-73ca4b1c-7185-4a0a-9ea7-17be4fe5f45b This course is susceptible to be streamed to the registered participants, depending on the evolution of the sanitary situation Overview This full-day course has a practical focus, where participants will learn how to use the Linux command line and 2022-09-14 09:00:00 UTC 2022-09-14 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Good practice in high-throughput experiments

    21 - 22 September 2022

    Zurich or streamed, Switzerland

    Elixir node event
    Good practice in high-throughput experiments https://tess.elixir-europe.org/events/good-practice-in-high-throughput-experiments-b5752b6c-f7ee-4865-8875-ff2ee12485eb Overview This course offers an overview of good practice in high-throughput experiments (e.g. next-generation sequencing or compound screening). Particularly we focus on pitfalls in the design of projects (e.g. 2022-09-21 09:00:00 UTC 2022-09-22 00:00:00 UTC SIB, Zurich or streamed, Switzerland SIB Zurich or streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • ELIXIR Innovation and SME Forum: Data driven innovation in healthcare diagnostics

    22 September 2022

    Barcelona, Spain

    ELIXIR Innovation and SME Forum: Data driven innovation in healthcare diagnostics https://tess.elixir-europe.org/events/elixir-innovation-and-sme-forum-data-driven-innovation-in-healthcare-diagnostics The Innovation and SME Forum on Data driven innovation in healthcare diagnostics is a one-day event, which will be organised in hybrid mode*. The Forum is co-located with ECCB2022 and aims to bring together researchers from large, medium and small companies and academia who work on services for data management and sharing, as well as people involved in national healthcare initiatives. This event contains a mix of high-level speakers from academia and industry and interactive sessions to discuss and interact with other companies and ELIXIR partners on the following themes: Scientific achievements in structural genetics, multigenetics, diagnostics of rare and infectious diseases Managing standards and ethics in new technologies Challenges in boosting Open Innovation in healthcare sector A specific session with Flash Talks, will give SMEs and Start-Ups the chance to introduce their work to a broad audience. Potential investment opportunities will be explored during the networking session. Aims: Give companies the chance to present technological advances in the field of healthcare diagnostics Provide a forum to discuss visionary ideas, bottlenecks and solutions to some of the major data-driven challenges  Inform participants about ELIXIR resources and create a space for networking between industry and academia. Target audience: Researchers in academia and industry Large and small companies that develop services for bio-data management and analysis Anyone interested in the data-driven health care sector Venture capital Preliminary programme: (detailed programme will be announced soon) Two Keynote talks Two Sessions of presentations from academia and industry Flash talk session Networking session *Virtual option: streaming of the talks and Slido questions for the first two sessions in the morning only. 2022-09-22 10:00:00 UTC 2022-09-22 19:00:00 UTC Hotel Meliã Sitges, Barcelona, Spain Hotel Meliã Sitges Barcelona Spain 08870 [] [] [] meetings_and_conferences [] []

  • First Steps with UNIX for Life Scientists

    26 September 2022

    Zurich, Switzerland

    Elixir node event
    First Steps with UNIX for Life Scientists https://tess.elixir-europe.org/events/first-steps-with-unix-for-life-scientists Overview With a constant evolution of technologies, life scientists (such as laboratory biologists) are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis. 2022-09-26 09:00:00 UTC 2022-09-26 00:00:00 UTC SIB, Zurich, Switzerland SIB Zurich Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

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