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85 events found

Event types: Workshops and courses 

  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    1 January - 31 December 2021

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-b178602b-e29f-4ac7-afbf-5deafd52f8dd # Overview * **Duration**: There is no longer a live period for this course, and there will be no live monitoring of the forums, but you can still join and complete the course throughout 2021. * Free * Certificate of achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (9 credits), Royal College of Nursing (9 credits)** ** ### Why join the course? The increase in resistance of harmful bacteria to antibiotics is a major global threat to health. Here we explore bacterial genomes and the use of genome sequencing to identify and track these drug resistant bacteria. Join us to discover how genome research is helping scientists and healthcare professionals track disease outbreaks and prevent the rise of antibiotic resistant ‘superbugs’. ### Who is the course for? This course will be of interest to scientists, healthcare professionals, biomedical researchers and bioinformaticians. The course offers all learners an opportunity to learn about genomes, disease, and antimicrobial resistance. You require no previous knowledge of genome science to complete the course. ### What do people say about this course? "_I would definitely point students to this resource. Text, videos, and figures were all very well done._" Pablo Tsukayama, Assistant Professor of Microbiology "_A highlight of the course was the introduction to whole genome sequencing – new information for me._" Christine Laws, Medical Doctor “_Exchanging genetic information quickly throughout the world is clearly going to revolutionise the ability to combat disease._” Prue van der Hoorn, Artist # Programme and start dates ### What topics will you cover? * Diseases caused by bacteria * What bacterial genomes look like * Genome sequencing technology * Mechanisms of transmission and resistance * Genomic epidemiology – tracking the spread of bacterial pathogens * Antimicrobial resistance ### What will you achieve? By the end of the course, you'll be able to... * Explain why some bacteria are pathogenic * Explore the structure of bacterial genomes * Describe the uses of different genome sequencing technologies * Investigate how genome data are used to track the spread of bacterial disease * Discuss the role of genome sequencing in stopping the spread of antimicrobial resistance # Educators ## **Lead Educators** **[Dr Adam Reid][1]** I am a senior staff scientist at the Wellcome Sanger Institute near Cambridge in the United Kingdom. I'm interested in using genomics and bioinformatics to better understand infectious diseases. **[Dr Josie Bryant][2]** I am a Henry Wellcome Postdoctoral Fellow in the University of Cambridge, Department of Medicine. I am working on bacterial genomics and evolution with a focus on within-patient microbial diversity ### Dr Francesca Short I am a scientist at the Wellcome Sanger Institute. I am interested in using functional genomics techniques to understand infections caused by the bacterium _Klebsiella pneumoniae_. ## **Programme Lead Educator** **[Professor Nicholas Thomson][3]** I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease. ### The course also features interviews with distinguished scientists, including: * **[Mathew Beale][4]** - Wellcome Sanger Institute * **[Daryl Domman][5]** - Wellcome Sanger Institute * **[Gal Horesh][6]** - Wellcome Sanger Institute * **[Catherine Ludden][7]** - London School of Hygiene and Tropical Medicine * **[Tapoka Mkandawire][8]** - Wellcome Sanger Institute * **[Julian Parkhill][9]** - Wellcome Sanger Institute * **Lindsay Pike** - Wellcome Sanger Institute * **[Michael Quail][10]** - Wellcome Sanger Institute * **[Susannah J. Salter][11]** - Wellcome Sanger Institute * **[Estee Torok][12]** - Addenbrooke’s Hospital and University of Cambridge [1]: http://www.sanger.ac.uk/people/directory/reid-adam-james [2]: https://www.infectiousdisease.cam.ac.uk/directory/josie-bryant [3]: http://www.sanger.ac.uk/people/directory/thomson-nicholas-robert [4]: http://www.sanger.ac.uk/people/directory/beale-mathew [5]: http://www.sanger.ac.uk/people/directory/domman-daryl [6]: http://www.sanger.ac.uk/people/directory/horesh-gal [7]: https://www.lshtm.ac.uk/aboutus/people/ludden.catherine [8]: http://www.sanger.ac.uk/people/directory/mkandawire-tapoka-t [9]: http://www.sanger.ac.uk/people/directory/parkhill-julian [10]: http://www.sanger.ac.uk/people/directory/quail-michael-andrew [11]: http://www.sanger.ac.uk/people/directory/salter-susannah-j [12]: https://www.infectiousdisease.cam.ac.uk/directory/et317@medschl.cam.ac.uk # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CDP Approval 2021-01-01 09:00:00 UTC 2021-12-31 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK
  • Introduction to FAIR Data Stewardship

    8 September - 3 November 2021

    Hogeschool Leiden online, Hogeschool Leiden online

    Elixir node event
    Introduction to FAIR Data Stewardship https://tess.elixir-europe.org/events/introduction-to-fair-data-stewardship Research – in general terms – produces ever more data. It is desirable that this research data remains usable for follow-up research. In practice, this proves difficult. The FAIR principles have been formulated to address this issue. Data must be… The post Introduction to FAIR Data Stewardship appeared first on Dutch Techcentre for Life Sciences. 2021-09-08 09:00:00 UTC 2021-11-03 00:00:00 UTC Hogeschool Leiden online, Hogeschool Leiden online, Hogeschool Leiden online Hogeschool Leiden online Hogeschool Leiden online Hogeschool Leiden online [] [] [] workshops_and_courses [] []
  • 1st de.NBI Summer School 2021 - Analysis and integration of Mass Spectrometry based omics data in Proteomics, Metabolomics and Lipidomics

    27 - 30 September 2021

    1st de.NBI Summer School 2021 - Analysis and integration of Mass Spectrometry based omics data in Proteomics, Metabolomics and Lipidomics https://tess.elixir-europe.org/events/de-nbi-summer-school-2021-proteomics-lipidomics TBA 2021-09-27 09:00:00 UTC 2021-09-30 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • ZIDAS 2021

    27 September - 1 October 2021

    ZIDAS 2021 https://tess.elixir-europe.org/events/zidas-2021 # ZIDAS 2021: switZerland’s Image and Data Analysis School - When: 27th September-1st October 2021 - Where: Online event - **Application deadline: 2021-07-01 (23:59 CET)** - Website: [https://2021.zidas.org](https://2021.zidas.org) ## About the school: This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples. ## Lectures on - Image Formation - Denoising - Segmentation - Reproducibility & Ethics ## Hands-ons with - ImageJ/Fiji Macros - GoogleColab for Python notebooks - ZeroCostDL4Mic - Ilastik ## Further tools and topics - Each day will feature 3 parallel sessions with demos of the awesome tools developed by the BioImage Analysis community such as #QuPath, #CLIJ, #CellProfiler, #TrackMate, #FigureJ, #StarDist and more! - This year will have a strong "work on your own project" component, so you can take advantage of all our great trainers to help you work with your own data! **_Find us at [https://2021.zidas.org](https://2021.zidas.org)_** 2021-09-27 09:00:00 UTC 2021-10-01 17:00:00 UTC ETHZ, EPFL ETH ZurichEPFL Center for Experimental and Clinical Imaging Technologies Zurich (EXCITE Zurich) Life Science ResearchersBiologists workshops_and_courses registration_of_interest image processingbioinformatics
  • EATRIS-Plus workshop on Theory and Practice of Industry and Academia Collaboration

    27 - 28 September 2021

    Online, Online

    Elixir node event
    EATRIS-Plus workshop on Theory and Practice of Industry and Academia Collaboration https://tess.elixir-europe.org/events/eatris-plus-workshop-on-theory-and-practice-of-industry-and-academia-collaboration The EATRIS-Plus workshop on Theory and Practice of Industry and Academia Collaboration. is a two-day workshop which will take place online on 27-28 September 2021. EATRIS-Plus workshop on Industry and Academia Collaboration has been developed within the framework of EATRIS-Plus H2020… The post EATRIS-Plus workshop on Theory and Practice of Industry and Academia Collaboration appeared first on Dutch Techcentre for Life Sciences. 2021-09-27 09:00:00 UTC 2021-09-28 00:00:00 UTC Online, Online, Online Online Online Online [] [] [] workshops_and_courses [] []
  • International Summer School on Rare Disease Registries and FAIRification of Data

    27 September - 1 October 2021

    International Summer School on Rare Disease Registries and FAIRification of Data https://tess.elixir-europe.org/events/international-summer-school-on-rare-disease-registries-and-fairification-of-data-3f5621f8-73b6-4de3-a069-a30b68e0ca3f The International Summer School on Rare Disease Registries and FAIRification of Data is a part of a series of training activities proposed by the European Joint Programme on Rare Diseases (EJP-RD). EJP-RD is a European Commission funded project with the goal “to create a comprehensive, sustainable ecosystem allowing a virtuous circle between research, care and medical innovation”. For more information about the EJP-RD, see https://www.ejprarediseases.org/ This course is composed of two training modules: – During the first three days module (27-29 September 2021), participants will learn (a) what resources are needed for the establishment/maintenance of a high-quality registry (b) the features of successful strategies to ensure (i) long-time sustainability of the registry, (ii) quality, (iii) legal and ethical issues in compliance with the EU (European Union) General Data Protection Regulation – During the second two days module “FAIRification of data”, (September 30 -October 1, 2021) participants will deepen their knowledge on the single steps of the FAIRification of data and will discover the potential of FAIR registries. In this part a time slot will be allocated to discuss FAIR data management and FAIR project planning. 2021-09-27 14:00:00 UTC 2021-10-01 17:10:00 UTC European Joint Programme on Rare Diseases (EJP-RD), Istituto Superiore di Sanità of Italy Istituto Superiore di Sanità claudio.carta@iss.it [] Cliniciansmedical specialistsregistry curatorsdatabase managershealthcare professionalsrare disease patients representatives 30 workshops_and_courses first_come_first_servedregistration_of_interest Rare DiseasesRegistryethical issues
  • The FAIR Principles Lecture (in Estonian)

    27 September 2021

    Tartu, Estonia

    The FAIR Principles Lecture (in Estonian) https://tess.elixir-europe.org/events/the-fair-principles-lecture In recent years, more attention is put on what researchers do with the data (and other resources) they produce. Especially in Europe, but also everywhere else. The main idea is that when researchers use taxpayers' money, the taxpayers themselves should also have access to the results, free of charge. This means that the research should be published in open access journals and data should be made publicly available. Good data management may help you with that, at least to make the process easier on the whole. If you think “how to manage your data” at the beginning and during the project and know what you plan to do with it at the end of the project, the process at the end will be easier. However, what is “good data management”, is up to debate. The FAIR Principles concentrates on making your data findable, accessible, interoperable and reusable, so this is a good start. And let’s be honest, some of these things you are probably already doing. In this course, we will be going over all the FAIR Principles and how they are applied in real life. This way, you will already know what to consider, while writing a grant, filling out your data management plan or doing your research. 2021-09-27 14:15:00 UTC 2021-09-27 17:00:00 UTC ELIXIR Estonia Auditorium 1019, Narva mnt 18 (UT Delta Centre), Tartu, Estonia Auditorium 1019, Narva mnt 18 (UT Delta Centre) Tartu Tartumaa Estonia 51009 FAIR data University of Tartu, Institute of Computer Science [] Graduate StudentsResearchersdata stewards 20 workshops_and_courses first_come_first_served FAIRdata FAIRnessdata management
  • Introduction to high-performance computing (sciCORE cluster)

    28 September 2021

    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-08f393f3-a813-4e56-a574-7e419ca77f34 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 2021-09-28 09:00:00 UTC 2021-09-28 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • ELIXIR UNIX Shell Courses - Basic

    28 September 2021

    Tartu, Estonia

    ELIXIR UNIX Shell Courses - Basic https://tess.elixir-europe.org/events/elixir-unix-shell-courses-basic Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have a click and point access to. As a general rule, these high-performance computer resources use Linux operating systems and are accessible only by a shell terminal and we are here to teach you to obtain skills to master the terminal in your future work. This course is aimed to provide basic survival skills in Linux and the terminal environment. We will teach you how to access files and folders, move around and hopefully shake off the fear of getting stuck somewhere along the way. Objectives: * Obtain basic knowledge on dealing with files using command line (Linux or Mac) * Learn how to use search over several text files, combine files, extract certain knowledge. * Tips and tricks for effective command line hacks that would save a lot of time. No prior knowledge expected. 2021-09-28 10:15:00 UTC 2021-09-28 16:00:00 UTC ELIXIR Estonia Auditorium 2005 (the Linux classroom), Narva mnt 18 (UT Delta Centre), Tartu, Estonia Auditorium 2005 (the Linux classroom), Narva mnt 18 (UT Delta Centre) Tartu Tartumaa Estonia 51009 University of Tartu, Institute of Computer Science [] Graduate StudentsResearchers 20 workshops_and_courses first_come_first_served Unix/LinuxCommand lineUnix Shell
  • First Steps with Python in Life Sciences - streamed

    29 September - 1 October 2021

    Streamed from Basel and Lausanne, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences - streamed https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences-streamed-fad56994-b647-446e-b022-090a6af0090b We are sorry but this course is oversubscribed, with a long waiting list. Sign up here to be informed of the next course. 2021-09-29 09:00:00 UTC 2021-10-01 00:00:00 UTC SIB, Streamed from Basel and Lausanne, Switzerland SIB Streamed from Basel and Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers

    29 September 2021

    Australia

    WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers https://tess.elixir-europe.org/events/webinar-launching-the-new-apollo-service-collaborative-genome-annotation-for-australian-researchers Genome annotation is crucial to defining the function of genomic sequences. Apollo is a popular tool for facilitating real-time collaborative curation and genome annotation editing. The technical obstacles faced by Australian researchers wanting to access and maintain this software have now been solved. The new Apollo Service can host your genome assembly and supporting evidence files, taking care of all the system administration so you and your team can focus on the annotation curation itself. The Australian BioCommons and partners at [QCIF](https://www.qcif.edu.au/) and [Pawsey](https://pawsey.org.au/) are now offering the [Apollo Service](https://apollo-portal.genome.edu.au/) free to use for [Australian-based](https://apollo-portal.genome.edu.au/termsofuse#AusUni) research groups and research consortia. As part of this launch, you’ll hear what’s possible from some of the early adopters who helped guide the development of the service. These Australian researchers will highlight the benefits that Apollo is bringing to their genome annotation and curation workflows. Join us to find out how you can get access to the Apollo Service. **Who the webinar is for** Anyone with an interest in genome annotation, editing and curation. **Presenters:** Dr Tiffanie Nelson, Australian BioCommons Featuring case studies from: - Dr Rahul Rane, CSIRO - Prof Sandie Degnan and Prof Bernie Degnan, University of Queensland - Dr Ramil ‘Mau’ Mauleon and Julia Voelker, Southern Cross University **Date/time:** 29 September 2021 12pm - 1 pm AEST / 11:30am - 12:30pm ACST / 10am - 11am 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_0bDQZvP9RJ2hqGK0R2ulxg)** 2021-09-29 12:00:00 UTC 2021-09-29 13:00:00 UTC Australian BioCommons Australia Australia Genomics [] Melissa Burke (melissa@biocommons.org.au) [] [] 500 workshops_and_courses first_come_first_served genome annotationgenome curation
  • Using the Ensembl Genome Browser (ONLINE TRAINING)

    30 September 2021

    Cambridge, United Kingdom

    Elixir node event
    Using the Ensembl Genome Browser (ONLINE TRAINING) https://tess.elixir-europe.org/events/using-the-ensembl-genome-browser-online-training-f8a26f20-facb-424d-9f7b-6fd21fdf3d5c 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. The [Ensembl Project](http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3997805&course-title=Using%20the%20Ensembl%20Genome%20Browser).'' 2021-09-30 08:30:00 UTC 2021-09-30 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Gene transcripts Gene structure Bioinformatics 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
  • [ONLINE] Hybrid CPU programming with OpenMP and MPI @ CSC

    4 - 5 October 2021

    [ONLINE] Hybrid CPU programming with OpenMP and MPI @ CSC https://tess.elixir-europe.org/events/online-hybrid-cpu-programming-with-openmp-and-mpi-csc This course will be delivered as an ONLINE COURSE for remote participation  due to the COVID-19 measures enforced by most European governments. THE COURSE IS FULLY BOOKED! Description The course introduces the basics of parallel programming with the OpenMP paradigm, and discusses how to combine OpenMP with MPI. OpenMP is a threading based approach which enables one to parallelize a program over a single shared memory machine, such as a single node in Mahti, Puhti or LUMI (CPU partition). By using OpenMP together with MPI, parallel scalability with large number of nodes can be improved. The course consists of lectures and hands-on exercises on parallel programming. This course is part of CSC Autumn of HPC 2021, a set of five two day modules teaching essential skills in parallel programming for modern GPU-accelerated supercomputers and organised by CSC – IT Center for Science Ltd (Finland) under PRACE Training Centres activity. Learning outcome After the course the participants should be able to write simple parallel programs and parallelize existing programs with basic features of OpenMP, combine OpenMP, and understand also more advanced OpenMP topics such as OpenMP Tasks. Prerequisites and content level The participants are assumed to have working knowledge of Fortran and/or C/C++ programming languages and skills discussed in the course "Parallel programming with MPI". The content level of the course is broken down as: beginner's - 60%, intermediate - 40%, advanced - 0%, community-targeted content - 0%. Preliminary agenda Day 1, Monday October 4 Introduction to OpenMP Data and work sharing Reductions and execution control Combining OpenMP with MPI Day 2, Tuesday October 5 OpenMP tasks Thread/process affinity Lecturers Jussi Enkovaara (CSC), Martti Louhivuori (CSC) Language:  English Price:           Free of charge (2 training days) REGISTRATION is OBLIGATORY since the details to access the online course will be provided to the registered and accepted attendees only. If you have registered to this course and you are not able to attend, please CANCEL your registration in advance by sending an email to patc@csc.fi https://events.prace-ri.eu/event/1225/ 2021-10-04 06:00:00 UTC 2021-10-05 13:30:00 UTC [] [] [] workshops_and_courses [] []
  • Ensembl REST API workshop (ONLINE TRAINING)

    4 October 2021

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API workshop (ONLINE TRAINING) https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-online-training-7f1575d1-0b50-4e85-b3ab-78e4fdd97932 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. The [Ensembl project](http://www.ensembl.org/) 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](http://rest.ensembl.org/), including understanding the major endpoints and how to write scripts to call them. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3997816&course-title=Ensembl%20REST%20API%20Workshop).'' 2021-10-04 08:30:00 UTC 2021-10-04 15:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Bioinformaticians and wet-lab biologists who can programGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • ELIXIR Fluxomics Training School 2021

    4 - 8 October 2021

    Elixir node event
    ELIXIR Fluxomics Training School 2021 https://tess.elixir-europe.org/events/elixir-fluxomics-training-school-2021 The 1st ELIXIR Fluxomics Training School is organized by ELIXIR-GR (FORTH/ICE-HT) in collaboration with ELIXIR-ES (UB) in the context of the ELIXIR Metabolomics Community-lead Implementation Study “Standardizing the fluxomics workflows”. This 5-day course, will take place in virtual mode on October 4-8 2021 from 9:00 to 17:00 Central European Time (CET) and will provide an introduction to the field of fluxomics and the experimental and computational methods used to estimate and predict metabolic fluxes. The course is addressed mainly to graduate students and junior post-docs, of either experimental or computational background. Learning outcomes include familiarity with the basic concepts, experimental techniques, data deposition standards and computational methods and software tools in fluxomics. The course includes hands-on experience in computational methods and software tools and mini team projects that will help the students apply the taught concepts. The course will involve up to 30 students and the selection will be made based on an application package submitted by designated application deadline. Sponsored by ELIXIR, the course is free of charge for personnel of academic/research/non-profit institutions in ELIXIR Nodes. Registration fees apply for the rest. ECTS credits may be granted to graduate students of European Institutions upon request after approval of the involved Graduate Programs. 2021-10-04 09:00:00 UTC 2021-10-08 17:00:00 UTC ELIXIR-GR (FORTH/ICE-HT) in collaboration with ELIXIR-ES (UB) FORTH/ICE-HT You may contact the organizers of the Fluxomics Training School either by phone at the school secretariat (Mrs Aggeliki KOSMATOU, +30-2610-965266) or preferably by e-mail at fluxomics_school@iceht.forth.gr ELIXIR Mainly graduate students and Junior post-docs, of either experimental or computational background, with basic training in life sciences, or (bio)chemistry, or physics, or mathematics, or engineering 30 workshops_and_courses registration_of_interest FluxomicsC13 Labeling Fluxomics MetabolomicsMetabolic Network Analysis Isotopic labelingGenome-scale Metabolic Modeling Systems biology Metabolic Reaction DatabasesMass Spectrometry - based fluxomicsNMR-based fluxomicsMetabolic flux analysisMetabolismMetabolic pathway
  • 3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding

    4 - 6 October 2021

    3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding https://tess.elixir-europe.org/events/3daroc21-3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php or http://www.aidenlab.org/data.html). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: 1D - Map paired-end sequences to generate Hi-C interaction matrices 2D - Normalize matrices and identify constitutive domains (TADs, compartments) 3D - Generate populations of structures which satisfy the Hi-C interaction matrices 4D - Compare samples at different time points Participants can bring specific biological questions and/or their own 3C-based data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyze Hi-C data. Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. 2021-10-04 09:00:00 UTC 2021-10-06 17:00:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt Oeiras Valley experimental researchers and bioinformaticians at the graduate and post-graduate levels 20 workshops_and_courses registration_of_interest TADbit
  • ELIXIR Fluxomics Training School 2021

    4 - 8 October 2021

    Online, Online

    Elixir node event
    ELIXIR Fluxomics Training School 2021 https://tess.elixir-europe.org/events/elixir-fluxomics-training-school-2021-54b48757-8f93-49b8-9e8b-ab7a5786492e The 1st ELIXIR Fluxomics Training School is organized by ELIXIR-GR (FORTH/ICE-HT) in collaboration with ELIXIR-ES (UB) in the context of the ELIXIR Metabolomics Community-lead Implementation Study “Standardizing the fluxomics workflows”. This 5-day course, will take place in virtual mode on October 4-8 2021 from 9:00 to 17:00 Central European Time (CET) and will provide an… The post ELIXIR Fluxomics Training School 2021 appeared first on Dutch Techcentre for Life Sciences. 2021-10-04 09:00:00 UTC 2021-10-08 00:00:00 UTC Online, Online, Online Online Online Online [] [] [] workshops_and_courses [] []
  • Best practices in research data management and stewardship

    4 - 7 October 2021

    Elixir node event
    Best practices in research data management and stewardship https://tess.elixir-europe.org/events/best-practices-in-research-data-management-and-stewardship-bee94f1f-b735-4d19-b140-81e31d594751 This course is aimed at researchers, data stewards in the biomedical sciences who wish to improve their skills on data management. The course will introduce the concepts of the FAIR principles for data, the concept and implementation of data stewardship as well as practical aspects of day to day data management and data management plans, which are required in many grant applications. 2021-10-04 09:00:00 UTC 2021-10-07 12:30:00 UTC Online Online Luxembourg Centre for Systems Biomedicine [] ResearchersPhD candidatesMasters studentsdata steward / data manager 30 workshops_and_courses first_come_first_served DMPDMP toolsdata protectionGDPRdata publicationmetadata
  • Introduction to Machine Learning with Python - streamed

    4 - 5 October 2021

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to Machine Learning with Python - streamed https://tess.elixir-europe.org/events/introduction-to-machine-learning-with-python This course is now full with a waiting list but will be given again in 2022. 2021-10-04 09:00:00 UTC 2021-10-05 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • EMBO Practical Course - Research to service: Planning and running a bioinformatics core facility

    4 - 8 October 2021

    Elixir node event
    EMBO Practical Course - Research to service: Planning and running a bioinformatics core facility https://tess.elixir-europe.org/events/embo-practical-course-research-to-service-planning-and-running-a-bioinformatics-core-facility-62ea6744-3a2b-4478-886d-69be519d5e25 Computational core facilities play a vital role in enabling molecular life science, and the number of such facilities has grown considerably. There are many relatively inexperienced managers of core facilities, who often have to juggle their own research projects with the development and operation of services. This can be exceptionally challenging, not least because scientific impact tends only to be recognised and rewarded for research. The "EMBO Practical Course | Research to Service: Planning and Running a Bioinformatics Core Facility" is aimed at newly appointed managers of bioinformatics core facilities, especially those with one foot in the research camp, or those managers willing to stabilize and grow their services. The training set will provide an opportunity to learn from experienced core facilities managers on how to build a framework for the future development, resourcing, operation and impact assessment of your core services. By the end of the course, participants will have learned how to: *Identify the strengths and limitations of their core facility and prioritise areas for improvement *Design bioinformatics services and training using a user-centred approach and assuring best practices *Estimate the computing and human resources required to operate their facility effectively *Support users to manage their data, including sensitive data 2021-10-04 12:00:00 UTC 2021-10-08 14:00:00 UTC Barcelona Supercomputing Center (BSC), EMBL-European Bioinformatics Institute (EMBL-EBI), Izmir Biomedicine and Genome Center (IBG), INCLIVA Health Research Institute, Spanish National Bioinformatics Institute (INB/ELIXIR-ES) Bioinformatics INB/ELIXIR-ESBSC BSC Organising Team: embo.bioinfocore@bsc.es [] Core Facility Managers 20 workshops_and_courses registration_of_interest managing skillsdata managementsustainabilityservice designcomputing resourcesstorage needs
  • Train the Trainer (TrT) online course

    4 - 7 October 2021

    Train the Trainer (TrT) online course https://tess.elixir-europe.org/events/train-the-trainer-trt-online-course The ELIXIR Training Platform is pleased to announce a Train the Trainer (TtT) event online, in collaboration with ELIXIR-IL and Weizmann Institute of Science. ELIXIR TtT courses aim to give new instructors tools and tips for providing an enriching learning experience to trainees, irrespective of the topic, and to include best-practice guidance on course and training material development. Course dates: 04-07 October, 2021, 13:30 – 17:00 (IDT) There is no course attendance fee. 2021-10-04 13:30:00 UTC 2021-10-07 17:00:00 UTC Weizmann Institute of Science [] Danny Ben-Avraham dan.ben-avraham@weizmann.ac.il [] [] 20 workshops_and_courses first_come_first_served Train the trainertraining
  • Swedish HPC Business Day

    5 October 2021

    Swedish HPC Business Day https://tess.elixir-europe.org/events/swedish-hpc-business-day ENCCS in collaboration with RISE and KTH/PDC is organising Swedish HPC Business Day on 5th of October at the KTH Campus. Are you a company having an AI solution on your laptop but eager to test on larger data amount? Or may be you are the one simulating market stocks predictions, air pollution progressions or training neural language models and wondering what is high performance computing (HPC) and how it is useful for you? Then we invite you to join us for the “Swedish HPC Business day”. A day full of experience, exchange and exploration of possibilities to use AI and HPC and support with improving your software solutions. For schedule and updated info please visit https://enccs.se/events/2021/10/hpc-business-day/ https://events.prace-ri.eu/event/1256/ 2021-10-05 07:00:00 UTC 2021-10-05 10:30:00 UTC [] [] [] workshops_and_courses [] []
  • Advanced OpenMP @ EPCC Online 5th and 8th October 2021

    5 - 8 October 2021

    Advanced OpenMP @ EPCC Online 5th and 8th October 2021 https://tess.elixir-europe.org/events/advanced-openmp-epcc-online-5th-and-8th-october-2021 This course will take place online on two days, with two rest days in between Tuesday, 5th October (0900-1700)  Friday, 8th October (0900-1700) OpenMP is the industry standard for shared-memory programming, which enables serial programs to be parallelised using compiler directives.This course is aimed at programmers seeking to deepen their understanding of OpenMP and explore some of its more recent and advanced features. This course will cover topics including nested parallelism, OpenMP tasks, the OpenMP memory model, performance tuning, hybrid OpenMP + MPI, OpenMP implementations, and recently added features in OpenMP. Hands-on practical programming exercises make up a significant, and integral, part of this course. Attendees should be familiar with the basics of OpenMP, including parallel regions, data scoping, work sharing directives and synchronisation constructs. Access will be given to appropriate hardware for all the exercises, although many of them can also be performed on a standard Linux laptop. Requirements Participants must have access to a laptop/pc/workstation with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They are also required to abide by the ARCHER2 Code of Conduct. https://events.prace-ri.eu/event/1258/ 2021-10-05 08:00:00 UTC 2021-10-08 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • ELIXIR UNIX Shell Courses - Advanced

    5 October 2021

    Tartu, Estonia

    ELIXIR UNIX Shell Courses - Advanced https://tess.elixir-europe.org/events/elixir-unix-shell-courses-advanced This course is aimed to streamline your skills in Linux and the terminal environment. We will teach you how to make your life easier by creating maintainable and flexible bash scripts for your commonly used workflows or SLURM jobs. Objectives: * Learn how to iterate operations over many input files with bash loops and conditions * Learn how to combine complicated command line based workflows into maintainable bash scripts * Add additional useful utility functions and tools to your toolbox Expected prior knowledge: Experience in using the basic commands covered in the Basics course (e.g. cd, ls, mkdir, mv, cp, head, cat, find, less, pwd) 2021-10-05 10:15:00 UTC 2021-10-05 16:00:00 UTC ELIXIR Estonia Auditorium 2005 (the Linux classroom), Narva mnt 18 (UT Delta Centre), Tartu, Estonia Auditorium 2005 (the Linux classroom), Narva mnt 18 (UT Delta Centre) Tartu Tartumaa Estonia 51009 University of Tartu, Institute of Computer Science [] Graduate StudentsResearchers 20 workshops_and_courses first_come_first_served Unix/LinuxCommand lineUnix ShellShell script
  • Version Control with Git - streamed

    6 - 8 October 2021

    Streamed from Lausanne, Switzerland

    Elixir node event
    Version Control with Git - streamed https://tess.elixir-europe.org/events/version-control-with-git This course will be streamed only for the registered participants, who will receive specific information directly from the respective course’s organizers. 2021-10-06 09:00:00 UTC 2021-10-08 00:00:00 UTC SIB, Streamed from Lausanne, Switzerland SIB Streamed from Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • [ONLINE] CUDA Workshop @ENCCS

    7 - 8 October 2021

    [ONLINE] CUDA Workshop @ENCCS https://tess.elixir-europe.org/events/online-cuda-workshop-enccs About the course These course materials are developed for those who wants to leark GPU programming with CUDA from the beginning. The course consists of lectures, type-along and hands-on sessions. During the first day, we will cover the architecture of the GPU accelerators, basic usage of CUDA, and how to control data movement between CPUs and GPUs. The second day focuses on more advanced topics, such as how to optimize computational kernels for efficient execution on GPU hardware and how to explore the task-based parallelism using streams and events. We will also briefly go through profiling tools that can help one to identify the computational bottleneck of the applications. After the course the participants should have the basic skills needed for using CUDA in new or existing applications. Who is the course for? This course is for students, researchers, engineers and programmers who would like to learn GPU programming with CUDA. The participants are assumed to have knowledge of C/C++ programming language. Since participants will be using HPC clusters to run the examples, fluent operation in a Linux/Unix environment is assumed. No prior knowledge of CUDA is needed. Agenda For updated agenda please visit https://enccs.se/events/2021/10/cuda-workshop/ https://events.prace-ri.eu/event/1259/ 2021-10-07 07:00:00 UTC 2021-10-08 11:00:00 UTC [] [] [] workshops_and_courses [] []
  • WORKSHOP: Hybrid de novo genome assembly

    7 October 2021

    Australia

    WORKSHOP: Hybrid de novo genome assembly https://tess.elixir-europe.org/events/workshop-hybrid-de-novo-genome-assembly It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality. In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a _Bacillus Subtilis_ strain. We will demonstrate two hybrid-assembly methods using the tools [Flye](https://github.com/fenderglass/Flye), [Pilon](https://github.com/broadinstitute/pilon/wiki), and [Unicycler](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595) to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly. All analyses will be performed using [Galaxy Australia](https://usegalaxy.org.au/), an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. **Date/time:** 2 - 5pm AEDT/ 1 - 4pm AEST/ 1:30 - 4:30pm ACDT/ 11am - 2pm AWST, Thursday 7 October 2021 **Lead Trainer:** Grace Hall, Melbourne Bioinformatics **Learning outcomes** By the end of this workshop you should be able to: 1. Describe how Nanopore and Illumina reads can be used together to produce a high quality assembly 2. Use genome assembly and polishing programs in Galaxy Australia 3. Assess the quality of a genome assembly with and without a reference genome 4. Assemble an unknown, previously undocumented genome to high-quality using Nanopore and Illumina reads The workshop will NOT provide an introduction to the basics of Galaxy. If you would like to learn about this topic there are several tutorials available via the[ Galaxy Training Network](https://training.galaxyproject.org/training-material/). **Who the workshop is for** This workshop is for Australian researchers who are or will perform hybrid genome assembly as part of their projects. To get the most out of the workshops you must have experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. It is recommended that you complete the tutorial[ Galaxy 101 for Everyone](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). No programming experience is required. **How to apply** This workshop is free but participation is subject to application with selection. **_Applications close at 11:59pm AEST Wednesday 29 September 2021._** You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 1 October 2021. Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://hybrid-assembly.eventbrite.com.au/)** This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/) and[ Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). To hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to the Australian BioCommons’ eNewsletter. 2021-10-07 14:00:00 UTC 2021-10-07 17:00:00 UTC Australian BioCommons Australia Australia Genomics [] Melissa Burke (melissa@biocommons.org.au) [] [] 50 workshops_and_courses registration_of_interest Hybrid genome assembly
  • [ONLINE] Parallel Programming Workshop (Train the Trainer) @ HLRS

    11 - 15 October 2021

    [ONLINE] Parallel Programming Workshop (Train the Trainer) @ HLRS https://tess.elixir-europe.org/events/parallel-programming-workshop-train-the-trainer-hlrs-b39fa26b-b9fb-4b05-99ca-236fefa49d57 The Train the Trainer Program is provided in conjunction with the regular course Parallel Programming with MPI and OpenMP and Advanced Parallel Programming. Whereas the regular course teaches parallel programming, this program is an education for future trainers in parallel programming. Too few people can provide parallel programming courses on the level that is needed if scientists and PhD students want to learn how to parallelize a sequential application or to enhance parallel applications. Within Europe, currently only six PATC centres and several other national centres provide such courses on an European or national level. We would like to assist further trainers and centres to also provide such courses for whole Europe or at least within their countries. Prerequisites You are familiar with parallel programming with MPI and OpenMP on an advanced level and skilled in both programming languages C and Fortran. Your goal: You want to provide MPI and OpenMP courses for other scientists and PhD students in your country, i.e., you would like to provide at least the first three days of the regular course as a training block-course to PhD students. Background: (a) Your centre supports you to provide such PhD courses in a course room at your centre. The course room is equipped at least with one computer/laptop per two (or three) students and has access to a HPC resource that allows MPI and OpenMP programming in C and Fortran. Or (b), you as a future trainer would like to co-operate with a centre with the necessary course infrastructure. What does this Train the Trainer Program provide? We provide you with all necessary teaching material on a personal basis, i.e., with the copyright to use it and to provide pdf or paper copies to the students in your PhD courses. We provide all exercise material. You will listen the lectures that you get familiar with the training material. During the exercises, you will help the regular students to correct their errors. The regular students are advised to request help if they were stuck for more than a minute. You will be trained to detect their problems as fast as possible (typically in less than a minute) and to provide the students with the needed help.   The Train the Trainer Program includes the curriculum from Monday until Friday according the course agenda. The Train the Trainer Program starts on Monday with a short introductory meeting at 8:15 am. On Thursday evening we will have an additional meeting and dinner for all participants of this TtT program. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/1248/ 2021-10-11 06:15:00 UTC 2021-10-15 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Parallel Programming Workshop (MPI, OpenMP and advanced topics) @ HLRS

    11 - 15 October 2021

    [ONLINE] Parallel Programming Workshop (MPI, OpenMP and advanced topics) @ HLRS https://tess.elixir-europe.org/events/parallel-programming-workshop-mpi-openmp-and-advanced-topics-hlrs-ed8d3c66-1b46-4436-b830-636be2b003dc Distributed memory parallelization with the Message Passing Interface MPI (Mon, for beginners – non-PRACE part): On clusters and distributed memory architectures, parallel programming with the Message Passing Interface (MPI) is the dominating programming model. The course gives an introduction into MPI-1. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the basic constructs of the Message Passing Interface (MPI). Shared memory parallelization with OpenMP (Tue, for beginners – non-PRACE part): The focus is on shared memory parallelization with OpenMP, the key concept on hyper-threading, dual-core, multi-core, shared memory, and ccNUMA platforms. This course teaches shared memory OpenMP parallelization. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the directives and other interfaces of OpenMP. Race-condition debugging tools are also presented. Intermediate and advanced topics in parallel programming (Wed-Fri – PRACE course): Topics are advanced usage of communicators and virtual topologies, one-sided communication, derived datatypes, MPI-2 parallel file I/O, hybrid mixed model MPI+OpenMP parallelization, parallelization of explicit and implicit solvers and of particle based applications, parallel numerics and libraries, and parallelization with PETSc. MPI-3.0 introduced a new shared memory programming interface, which can be combined with MPI message passing and remote memory access on the cluster interconnect. It can be used for direct neighbor accesses similar to OpenMP or for direct halo copies, and enables new hybrid programming models. These models are compared in the hybrid mixed model MPI+OpenMP parallelization session with various hybrid MPI+OpenMP approaches and pure MPI. Further aspects are domain decomposition, load balancing, and debugging. Hands-on sessions are included on all days. This course provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. Hands-on sessions are included on all days. This course provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/1247/ 2021-10-11 06:30:00 UTC 2021-10-15 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • Machine Learning for bioinformatics and systems biology

    11 - 15 October 2021

    Amsterdam, Netherlands

    Elixir node event
    Machine Learning for bioinformatics and systems biology https://tess.elixir-europe.org/events/machine-learning-for-bioinformatics-and-systems-biology-fbe0ed55-3252-4ea6-95b0-2a38db87d82f Date: 11-15 October 2021, Amsterdam (if COVID-19 restrictions are lifted, otherwise online) Course overview Modern biology is a data-rich science, driven by our ability to measure the detailed molecular characteristics of cells, organs, and individuals at many different levels. Interpretation… The post Machine Learning for bioinformatics and systems biology appeared first on Dutch Techcentre for Life Sciences. 2021-10-11 09:00:00 UTC 2021-10-15 00:00:00 UTC Amsterdam, Netherlands, Amsterdam, Netherlands Amsterdam, Netherlands Amsterdam Netherlands [] [] [] workshops_and_courses [] []

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