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129 events found
  • ELIXIR 3D-Bioinfo Community Webinar: Development of models for protein-ligand interactions

    19 October 2021

    ELIXIR 3D-Bioinfo Community Webinar: Development of models for protein-ligand interactions https://tess.elixir-europe.org/events/elixir-3d-bioinfo-community-webinar-development-of-models-for-protein-ligand-interactions   Programme Vincent Zoete: Development of models for protein-ligand interactions Ute Röhrig: Development of reliable Benchmark Sets for Structure-Based Drug Design: Focus on Metalloproteins and Covalent Interactions ​Each presentation will last around 20 minutes followed by questions. There will be an opportunity for a wider discussion at the end.  This is the third of a series of 10 webinars organised by the ELIXIR 3D-BioInfo Community. The series will present the five major aims of the Community around protein structural annotations, protein complexes, protein ligand interactions, protein nucleic acid interactions and protein engineering. See the webinar series page for details. 2021-10-19 15:00:00 UTC 2021-10-19 16:00:00 UTC [] [] [] [] [] []
  • Experimental Design (Online)

    20 October 2021

    Cambridge, United Kingdom

    Elixir node event
    Experimental Design (Online) https://tess.elixir-europe.org/events/experimental-design-online-9bdf4bdf-ddbe-4574-bf7c-6fa46b49475d PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Modern technologies are able to deliver an unprecedented amount of data rapidly. However, without due care and attention early in the experimental process, such data are meaningless if they cannot adequately answer the intended research question. This course is aimed at those planning high-throughput experiments and highlights the kinds of questions they should be asking themselves. The course consists of a lecture and small-group discussions led by a member of the Genomics or Bioinformatics Cores. This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at [CRUK Cambridge Institute](http://www.cruk.cam.ac.uk/). 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=4024508&course-title=Experimental%20Design).'' 2021-10-20 08:30:00 UTC 2021-10-20 15:30:00 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
  • Basic git training

    20 October 2021

    Elixir node event
    Basic git training https://tess.elixir-europe.org/events/basic-git-training-8c0c9072-f1b4-4e8b-869f-2c6744cbe0ef Are you coding regularly? Do you want to assure quality of your code and learn about the version control software git? Git keeps records of all changes that you make in your scripts, facilitates collaborative development, and most importantly, allows you to revert to previous states when you did something wrong. This absolute beginner’s training course on git teaches you the basics to get started and assure high-quality of your code! 2021-10-20 09:00:00 UTC 2021-10-20 00:00:00 UTC Online Online [] [] [] [] [] []
  • [ONLINE] Advanced Deep Learning with Transformers @ENCCS&RISE

    21 October 2021

    [ONLINE] Advanced Deep Learning with Transformers @ENCCS&RISE https://tess.elixir-europe.org/events/online-advanced-deep-learning-with-transformers-enccs-rise Overview In recent years, Graph Neural Networks (GNNs) and Transformers have led to numerous break-through achievements in a variety of fields such as Natural Language Processing (NLP), chemistry and physics. By doing away with the need for fixed-size inputs, these architectures significantly extend the scope of problems in which deep learning can be applied. Preliminary Agenda This workshop will take you from the representation of graphs and finite sets as inputs for neural networks to the implementation of full GNNs for a variety of tasks. You will learn about the central concepts used in GNNs in a hands-on setting using Jupyter Notebooks and a series of coding exercises. While the workshop will use problems from the field of chemistry as an example for applications, the skills you learn can be transferred to any domain where finite set or graph-based representations of data are appropriate. From GNNs, we will make the leap to Transformer architectures, and explain the conceptual ties between the two. The workshop is free of charge and will be conducted fully online using zoom. Prerequisites To successfully participate in this workshop, you should have a good understanding of basic linear algebra and core concepts of deep learning such as CNNs, stochastic gradient descent, and supervised learning. You should also be familiar with the implementation of neural networks using PyTorch. A basic conceptual understanding of mathematical graphs is recommended but not a prerequisite. Agenda For updated agenda you can follow this link https://enccs.se/events/2021/10/advanced-deep-learning/ Contact person Apostolos Vasileiadis apostolos.vasileiadis@it.uu.se https://events.prace-ri.eu/event/1260/ 2021-10-21 07:00:00 UTC 2021-10-21 10:30:00 UTC [] [] [] workshops_and_courses [] []
  • Mining enzyme data in UniProtKB using Rhea - streamed

    22 October 2021

    Streamed from Grenoble and Geneva, Switzerland

    Elixir node event
    Mining enzyme data in UniProtKB using Rhea - streamed https://tess.elixir-europe.org/events/mining-enzyme-data-in-uniprotkb-using-rhea-streamed This course will be streamed only for registered participants. Registered participants will receive information from the course organizer in due time. 2021-10-22 09:00:00 UTC 2021-10-22 00:00:00 UTC SIB, Streamed from Grenoble and Geneva, Switzerland SIB Streamed from Grenoble and Geneva Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Mining enzyme data in UniProtKB using Rhea - streamed

    22 October 2021

    Streamed from Grenoble and Geneva, Switzerland

    Elixir node event
    Mining enzyme data in UniProtKB using Rhea - streamed https://tess.elixir-europe.org/events/mining-enzyme-data-in-uniprotkb-using-rhea-streamed-370e6f56-32fb-4f0e-9fa3-f973225a7879 This course will be streamed only for registered participants. Registered participants will receive information from the course organizer in due time. 2021-10-22 09:00:00 UTC 2021-10-22 00:00:00 UTC SIB, Streamed from Grenoble and Geneva, Switzerland SIB Streamed from Grenoble and Geneva Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Functional Plant Bioinformatics (PLAZA)

    25 - 26 October 2021

    Zwijnaarde, Belgium

    Elixir node event
    Functional Plant Bioinformatics (PLAZA) https://tess.elixir-europe.org/events/functional-plant-bioinformatics-plaza-6cf34ba3-39b5-47da-b820-f337f736a3db Introduction plant comparative genomics (genes and gene families) + introduction PLAZA platform Functional characterization of plant genes (Gene families, GO, InterPro) Synteny analysis in polyploid cereals Gene set analysis for different plant -omics data sets: Functional interpretation of RNA-Seq and ChIP-Seq genes using the PLAZA Workbench Comparing gene sets between different di/polyploidy crop species 2021-10-25 09:00:00 UTC 2021-10-26 00:00:00 UTC VIB Bioinformatics Core UGent-VIB Research Building FSVM, Zwijnaarde, Belgium UGent-VIB Research Building FSVM Zwijnaarde Belgium 9052 [] [] [] [] [] []
  • Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)

    25 - 30 October 2021

    Elixir node event
    Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE) https://tess.elixir-europe.org/events/epigenomics-data-analysis-from-bulk-to-single-cell-online #url: https://www.scilifelab.se/event/epigenomics-data-analysis-from-bulk-to-single-cell-online/ 2021-10-25 09:00:00 UTC 2021-10-30 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Next Generation Sequencing Platforms and Bioinformatics Analysis (ONLINE LIVE TRAINING)

    26 - 27 October 2021

    Cambridge, United Kingdom

    Elixir node event
    Next Generation Sequencing Platforms and Bioinformatics Analysis (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/next-generation-sequencing-platforms-and-bioinformatics-analysis-online-live-training-e3757e4e-fa87-48a9-b5bf-256dd59b045b PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Day 1 will introduce you to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, quality control. This session will include an introduction to Galaxy. [Galaxy](https://galaxyproject.org/) is an open, web-based platform for data-intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses. Day 2 will be hands-on practicals on using Galaxy to explore sequencing quality control, before and after removal of low quality samples. This forms the core of all NGS analyses and this day will conclude with how this data pipes into gene expression studies, variant calling and genome assemblies. 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=4036128&course-title=NGS%20Platforms%20and%20Bioinformatics%20Analysis).'' 2021-10-26 08:00:00 UTC 2021-10-27 11:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Biologistswet-lab scientistsbioinformatics and other life scientists planning to work with next-generation sequencing data.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • [ONLINE] Directive-based GPU programming with OpenACC @ JSC

    27 - 29 October 2021

    [ONLINE] Directive-based GPU programming with OpenACC @ JSC https://tess.elixir-europe.org/events/online-directive-based-gpu-programming-with-openacc-jsc-cc1f4c22-ba41-4772-9cc5-ced2b4f659b7 GPU-accelerated computing drives current scientific research. Writing fast numeric algorithms for GPUs offers high application performance by offloading compute-intensive portions of the code to the GPU. The course will cover basic aspects of GPU architectures and programming. Focus is on the usage of the directive-based OpenACC programming model which allows for portable application development. Examples of increasing complexity will be used to demonstrate optimization and tuning of scientific applications. Topics covered will include: Introduction to GPU/Parallel computing Programming model OpenACC Interoperability of OpenACC with GPU libraries (like cuBLAS and cuFFT) and CUDA Multi-GPU Programming with MPI and OpenACC Tools for debugging and profiling Performance optimization The course consists of lectures and interactive hands-on sessions in C or Fortran (the attendee’s choice). This course will take place as an online event. The link to the online platform will be provided to the registrants only. Prerequisites: Some knowledge about Linux, e.g. make, command line editor, Linux shell (see for instance this overview), a little experience in C/Fortran Application Registrations are only considered until 1 October  2021, the maximal number of participants is limited. Applicants will be notified three weeks before the course, whether they are accepted for participation. The link to the course platform will be sent shortly before the course. Instructors: Dr. Andreas Herten, Dr. Thorsten Hater, Dr. Kaveh Haghighi-Mood, JSC; Markus Hrywniak, Jiri Kraus, NVIDIA Contact For any questions concerning the course please send an e-mail to a.herten@fz-juelich.de https://events.prace-ri.eu/event/1253/ 2021-10-27 07:00:00 UTC 2021-10-29 11:00:00 UTC [] [] [] workshops_and_courses [] []
  • New Horizons in Alzheimer's Disease (Hybrid edition)

    27 - 28 October 2021

    Leuven, Belgium

    Elixir node event
    New Horizons in Alzheimer's Disease (Hybrid edition) https://tess.elixir-europe.org/events/new-horizons-in-alzheimer-s-disease-hybrid-edition Alzheimer’s Disease research is accelerating with exciting new insights into molecular and cellular mechanisms. This upcoming conference brings together some of the thought leaders in the field with young investigators to stimulate discussion and interaction. We anticipate further insights into the triangle amyloid, Tau and neuroinflammation and how these might provide novel therapeutic approaches. The following topics will be the focus of this conference: - Genes and environment - Synapse and circuitry - Mechanisms and models of disease - Seeds and spreading of disease Next to an inspiring scientific program, conference participants will have ample networking opportunities (both live and virtual) during the breaks, poster sessions and the conference dinner. **Information for poster submissions** The format for your poster should be: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation. The best fourteen abstracts will be given a short talk slot in the plenary program. No registration is needed before submitting a abstract. The deadline for abstracts is 27 August 2021. All accepted poster submissions will have a chance to win one of the two SAO Poster Prizes. **SAO sponsored Travel grants and registration waive** SAO will sponsor 10 poster presenters (PhD or postdoc) for a travel grant plus registration fee waive. Submit your motivation below by clicking on the 'Apply for a grant' button before 30 July 2021. The organizing committee will notify you of your travel grant acceptance by the end of August. **Speaker line-up** *Session 1: Genes and environment* - Lucía Chávez Gutiérrez VIB-KU Leuven Center for Brain & Disease Research, BE - Christopher Glass University of California, San Diego, US - Steven A. Goldman University of Rochester Medical Center, US - Henne Holstege Amsterdam UMC & Amsterdam Alzheimer Center, NL - Christine Van Broeckhoven VIB-UAntwerp Center for Molecular Neurology, BE - Sangram S. Sisodia Department of Neurobiology, University of Chicago, US - Steven A. Goldman University of Rochester Medical Center, US *Session 2: Synapse and circuitry* - Marc Aurel Busche UK Dementia Research Institute at UCL, UK - Inna Slutsky Tel Aviv University, IL - Tara Spires-jones The University of Edinburgh and UK Dementia Research Institute, UK - Li-Huei Tsai The Picower Institute for Learning and Memory & MIT, US - Matthijs Verhage Vrije Universiteit & Amsterdam University Medical Center, NL Evening keynote: Roger M Nitsch CEO, Neurimmune, CH *Session 3: Mechanisms and models of disease* - Philip L. De Jager Division of Neuroimmunology & Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, US - Jerome Mertens Salk Institute for Biological Studies, US & University of Innsbruck, AT - Anne Rovelet-Lecrux University of Rouen, Inserm UMR1245, FR - Beth Stevens FB Kirby Neurobiology Center; Boston Children's Hospital & Broad Institute Member, US - Tony Wyss-Coray Stanford University, US - Henrik Zetterberg University of Gothenburg, SE and UK Dementia Research Institute, UK. *Session 4: Seeds and spreading of disease* - Luc Buée University of Lille, Inserm, CHU-Lille, FR - Bart De Strooper VIB-KU Leuven Center for Brain & Disease Research, BE & UK Dementia Research Institute, UK - Karen E. Duff UK Dementia Research Institute at UCL, UK - Mathias Jucker The Hertie Institute for Clinical Brain Research (HIH) & German Center for Neurodegenerative Diseases (DZNE), DE - Maiken Nedergaard University of Rochester, Medical Center, US 2021-10-27 08:50:00 UTC 2021-10-28 18:10:00 UTC VIB Conferences KU Leuven, Promotion & Jubileumzaal, Leuven, Belgium KU Leuven, Promotion & Jubileumzaal Leuven Vlaams-Brabant Belgium 3000 Neurology Neurobiology VIB conferences@vib.be Stichting Alzheimer Onderzoek [] 300 receptions_and_networkingmeetings_and_conferences [] Alzheimer's DiseaseGenes and environmentSynapse and circuitryMechanisms and models of diseaseSeeds and spreading of diseasetriangle amyloidTauneuroinflammation
  • [ONLINE] Shared memory parallelization with OpenMP @ VSC Vienna

    28 - 29 October 2021

    [ONLINE] Shared memory parallelization with OpenMP @ VSC Vienna https://tess.elixir-europe.org/events/online-shared-memory-parallelization-with-openmp-vsc-vienna-6a1f95a7-ee21-4079-9033-8d906aed3059 This course will be delivered as an ONLINE COURSE (using Zoom) for remote participation. REGISTRATION is strictly NECESSARY since the details to access the online course will be provided to the registered and accepted attendees only. Registration follows the "first come – first served" principle. For the online course we can take a maximum of 40 persons. Additional registrations will be added to a waiting list. Furthermore, accepted participants will be contacted a few days before the course and asked to do a short PRE-ASSIGNMENT that has to be completed before the course starts. For doing the HANDS-ON LABS all you need is a C/C++ or Fortran compiler that supports OpenMP. Participants can choose between using their own laptops or any system they have access to that provides an OpenMP enabled compiler, it's even possible to do the exercises in Google Colab. Alternatively, participants can ask for a training user account at the VSC for the duration of the course. Overview The focus of this 2 days course is on shared memory parallelization with OpenMP for dual-core, multi-core, shared memory, and ccNUMA platforms. This course teaches OpenMP starting from a beginners level. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the OpenMP directives, environment variables, and library routines. Race-condition debugging tools are also presented. Content Levels: Beginners = 6:00h (50%) + Intermediate = 4:00h (33%) + Advanced = 2:00h (17%) This course is a PRACE training event. It is organized by the VSC Research Center, TU Wien, in cooperation with the High-Performance Computing-Center Stuttgart (HLRS). Agenda & Content 1st day 08:45  Join online 09:00    Welcome 09:10    Introduction to modern hardware (talk) 10:10    An overview of OpenMP (talk) 10:35   Coffee 10:50    OpenMP programming and execution model (talk+practical) 12:30   Lunch 13:30    OpenMP worksharing directives (talk+practical)  15:00   Coffee 15:15    More OpenMP (talk+practical) 16:00    Summary (talk) + Q & A 16:30   End of first day 2nd day 08:45  Join online 09:00    How to write correct OpenMP programs (talk) 09:30    Intel Inspector XE (demo+practical) 10:30   Coffee 10:45    How to write efficient OpenMP programs (talk) 11:00    Heat equation (talk+practical) 12:30   Lunch 13:30    Heat equation (practical — continued) 14:00    Vectorization with OpenMP (talk) 14:25    Thread affinity in OpenMP (talk) 15:00   Coffee 15:15     The taskloop directive (talk+practical) 16:30   End of second day (course) https://events.prace-ri.eu/event/1250/ 2021-10-28 06:45:00 UTC 2021-10-29 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • DNA Methylation: Design to Discovery 2021

    28 - 29 October 2021

    DNA Methylation: Design to Discovery 2021 https://tess.elixir-europe.org/events/dna-methylation-design-to-discovery-2021 Educators: Abdulrahman Salhab, Epigenetics Department @ Saarland University (de.NBI-Epi / HD-HuB) Date: 28-29 October 2021 Location: Online Contents: This course aims to convey basic knowledge on the bioinformatic processing of DNA methylation data. Following the outline of a standard experiment we discuss qualities of various assays and when they are beneficial. In the first half there will be a slight focus on sequencing data. We will prepare raw sequence reads for alignment, methylation calls and identification of differentially methylated sites or regions. Throughout, we consider how experimental settings interact and influence the results and how quality control can be used to understand generated data and might improve on subsequent experiments. The second half will focus on how to evaluate the data and connect it to public resources to further understanding of the results. Presentations will be interleaved with practical sessions Learning goals: • Understand the bioinformatic processing of DNA methylation • Preparation and description of raw read files • Basic generation of methylation calls and differentially methylated regions • How to evaluate DNA methylation data Prerequisites: The course requires basic skills in: • Linux/bash • R Keywords: DNA methylation Tools: nf-core/methylseq, RnBeads, methylSeekR 2021-10-28 09:00:00 UTC 2021-10-29 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Research Data Management and Data Management Plan

    28 - 29 October 2021

    Lausanne, Switzerland

    Elixir node event
    Research Data Management and Data Management Plan https://tess.elixir-europe.org/events/research-data-managment-and-data-management-plan We are sorry but this course is oversubscribed, with a long waiting list. You are welcome to register to the SIB courses mailing list to be informed of all future courses, as well as all important deadlines using the form here. 2021-10-28 09:00:00 UTC 2021-10-29 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • HPC and NIRD toolkit user course

    2 - 5 November 2021

    Elixir node event
    HPC and NIRD toolkit user course https://tess.elixir-europe.org/events/hpc-and-nird-toolkit-user-course HPC and NIRD toolkit user course November 2021 In November 2021, the Norwegian Research Infrastructure Services NRIS (formerly known as the Metacenter) partners Sigma2, UiB, UiO & UiT are jointly offering a hands-on course for current and future users of national HPC systems (Saga, Fram, Betzy) and the NIRD Toolkit. The course is open to all users and free of charge. For individual sessions we list recommended prerequisites. The participants can choose which session they want to attend and you’re certainly welcome to just attend all sessions you are interested in. On each course day, we will start at 09:00 and conclude at around 13:00. Each “morning” will include presentations and hands-on time on one of the actual HPC systems or the NIRD Toolkit. We recommend that participants use the afternoon on each day to repeat examples from the morning to get more experience on the systems. Practical Information This is an online course via zoom. Participants require access to a computer (not provided by the course organisers) with internet connectivity and pre-installed programs to participate in the video meeting of the course (zoom, might work from a browser), to access the HPC systems (e.g., ssh or Putty), to transfer data to/from an HPC system (e.g., scp or WinSCP) and to access the NIRD Toolkit (web browser). Note Those who do not have an account on one of the HPC machines or NIRD (storage, Toolkit, …) yet need to apply for an account. The application page is available here and documentation for the application procedure is available here. You are applying for an HPC account. For the project, please select “NN9987K: Course Resources as a Service #3” (the Project manager will be filled in automatically), choose Saga under Resources, set the Account start date to 2021-10-26 and the Account end date to one week after the course, that is 2021-11-12. In order to use the NIRD Toolkit during the course you will need either a Feide account or a Feide OpenIDP guest account. You can create a Feide OpenIDP guest account at https://openidp.feide.no/. See your eduPersonPrincipalName (eduPPN) at http://innsyn.feide.no . You can always contact us by sending an email to support@metacenter.no. If you want to receive further information about training events, and other announcements about IT resources and services for researchers, there are a couple of information channels you can subscribe to: users at University of Bergen and affiliated institutes: register to hpcnews@uib.no users of Sigma3 services: subscribe to Sigma2’s newsletter Dates: 2021 November 2, 3, 4 and 5 Time: each day 09:00-13:00 with short breaks Location: Video meeting (zoom), we use HackMD for asking questions (information will be send to registered participants via email). Note, sessions will be recorded and made publicly available after the course! Participants may choose the lectures which they are interested in. Registration The course is free of charge and is organised by the NRIS partners Sigma2, UiB, UiO & UiT. Registration deadline for the course is October 20th. Register your participation here Code of Conduct All participants in our course are expected to show respect and courtesy to others. We follow carpentry code of conduct. If you believe someone is violating the Code of Conduct, we ask that you report it either to Radovan Bast or Dhanya Pushpadas 2021-11-02 08:50:00 UTC 2021-11-05 13:00:00 UTC Sigma2 - NRIS University of BergenUniversity of OsloUniversity of TromsøSigma2 radovan.bast@uit.no Dhanya.Pushpadas@uib.no Sigma2 HPC users workshops_and_courses [] HPCstorage
  • 3D-Bioinformatics 2021 Annual Workshop

    2 - 4 November 2021

    3D-Bioinformatics 2021 Annual Workshop https://tess.elixir-europe.org/events/3d-bioinformatics-2021-annual-workshop ELIXIR Communities enable the participation of communities of practice in different areas of the life sciences in the activities of ELIXIR, which underpin the evolution of a data, tools, interoperability, compute and training infrastructure for European life science informatics (see www.elixir-europe.org/use-cases). Structural bioinformatics has a broad impact across the life sciences and provides tools to archive, visualise, analyse, annotate, and predict molecular structures. Structural bioinformatics is traditionally very strong in Europe offering many software tools, methodologies, and databases, as well as community-wide prediction challenges. Its applications cover research activities from structural biology to drug discovery and personalised medicine that are all well represented within the national ELIXIR nodes. The meeting will be virtual this year due to the COVID-19 pandemic. Details of a Zoom link will be sent closer to the time.  Submission of abstracts for posters is encouraged, as researchers with accepted posters will be offered the opportunity to pre-record short talks for their poster. Authors of selected poster talks will be invited to give longer talks during the main meeting sessions.   To find out more about the 3D-BioInfo Community, please go to the website: www.elixir-europe.org/communities/3d-bioinfo   Overview of Programme: The meeting will start with a brief overview of the aims of the 3DBioInfo Community. This will be followed by Breakout sessions for each of the major 3D-BioInfo Activities described below. These breakout sessions will be held sequentially, allowing participants to attend any number of sessions they want. Next will come a Plenary session, at which coordinators of the different Activities will present their reports. Some slots for short presentations and posters will be available for some of the activities. If you are interested in contributing, please submit an abstract together with your application. The application deadline is: September 15th (for poster/short talk) and October 31st (for attendance only). Some slots for short presentations and posters will be available for some of the activities. If you are interested in contributing, please submit an abstract together with your regsitration or send an email to our Communities Coordinator Katharina Heil: katharina.heil@elixir-europe.org The application deadline is: 27th September (for poster/short talk) and 1st November (for attendance only). All the sessions and talks will be recorded, with the recordings made available after the event. 2021-11-02 13:00:00 UTC 2021-11-04 17:00:00 UTC [] [] [] [] [] []
  • 3D-BioInfo 2021 Annual Meeting

    2 - 4 November 2021

    3D-BioInfo 2021 Annual Meeting https://tess.elixir-europe.org/events/3d-bioinfo-2021-annual-meeting ELIXIR Communities enable the participation of communities of practice in different areas of the life sciences in the activities of ELIXIR, which underpin the evolution of a data, tools, interoperability, compute and training infrastructure for European life science informatics (see https://elixir-europe.org/communities). Structural bioinformatics has a broad impact across the life sciences and provides tools to archive, visualise, analyse, annotate, and predict molecular structures. Structural bioinformatics is traditionally very strong in Europe offering many software tools, methodologies, and databases, as well as community-wide prediction challenges. Its applications cover research activities from structural biology to drug discovery and personalised medicine that are all well represented within the national ELIXIR nodes. The meeting will be virtual this year due to the COVID-19 pandemic. Details of a Zoom link will be sent closer to the time.  Submission of abstracts for posters is encouraged, as researchers with accepted posters will be offered the opportunity to pre-record short talks for their poster. Authors of selected poster talks will be invited to give longer talks during the main meeting sessions.   To find out more about the 3D-BioInfo Community, please go to the website: www.elixir-europe.org/communities/3d-bioinfo.   Overview of Programme: The meeting will start with a brief overview of the aims of the 3DBioInfo Community. This will be followed by Breakout sessions for each of the major 3D-BioInfo Activities described below. These breakout sessions will be held sequentially, allowing participants to attend any number of sessions they want. Next will come a Plenary session, at which coordinators of the different Activities will present their reports. Some slots for short presentations and posters will be available for some of the activities. If you are interested in contributing, please submit an abstract together with your application. Abstracts shall be submitted as a pdf document, maximum of one page; text, including references/figure if desired.    The application deadline is: 27th September (for poster/short talk) and 1st November (for attendance only). Or you can send an email to our Communities Coordinator Katharina Heil: katharina.heil@elixir-europe.org. All the sessions and talks will be recorded, with the recordings made available to meeting attendees after the event. 2021-11-02 13:00:00 UTC 2021-11-04 17:00:00 UTC [] [] [] [] [] []
  • NGS - Quality control, Alignment, Visualisation

    3 - 5 November 2021

    Bern, Switzerland

    Elixir node event
    NGS - Quality control, Alignment, Visualisation https://tess.elixir-europe.org/events/ngs-quality-control-alignment-visualisation-bc83a158-63bc-43f4-9c62-a8a9b4bd1545 Please be aware that to comply with recent federal and cantonal recommendations, you will most probably have the obligation to present a COVID certificate to be able to attend the course. Take this into consideration before applying to this course. 2021-11-03 09:00:00 UTC 2021-11-05 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • [ONLINE] SYCL Workshop @ENCCS

    8 - 9 November 2021

    [ONLINE] SYCL Workshop @ENCCS https://tess.elixir-europe.org/events/sycl-workshop Overview Welcome to this ENCCS workshop, in collaboration with CSC Finland and Izum, Slovenia. The training will run on the EuroHPC JU Vega system. SYCL_ is a C++ abstraction layer for programming heterogeneous hardware with a single-source approach. SYCL_ is high-level, cross-platform, and extends standard ISO C++17. You will learn to: Use the hipSYCL_ compiler to generate executable for multiple hardware targets. Write hardware-agnostic code to express parallelism using the queue, command group, and kernel abstractions. Use buffer and accessors to handle memory across devices. Evaluate drawbacks and advantages of unified shared memory. Agenda For updated agenda, please visit https://enccs.se/events/2021/11/sycl-workshop/ https://events.prace-ri.eu/event/1257/ 2021-11-08 08:00:00 UTC 2021-11-09 11:10:00 UTC [] [] [] workshops_and_courses [] []
  • A tour of machine learning: classification

    8 - 9 November 2021

    Gent, Belgium

    Elixir node event
    A tour of machine learning: classification https://tess.elixir-europe.org/events/a-tour-of-machine-learning-classification-ef0d581e-647b-4565-a0a8-cfc496bb61f4 At the end of the workshop you will be able to compute and evaluate prediction models from your data using the Scikit-Learn Python library. You will also be able to understand current advances in Machine Learning such as Deep Learning.  2021-11-08 09:00:00 UTC 2021-11-09 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • TMex Winter School – Translational Medicine Explained

    8 - 12 November 2021

    Online, Online

    Elixir node event
    TMex Winter School – Translational Medicine Explained https://tess.elixir-europe.org/events/tmex-winter-school-translational-medicine-explained The TMex  5-day online workshop is intended for PhD students in the second half of their PhD, early postdocs and other young scientists involved in biomedical research. For the second time, the course will take place online, allowing more flexibility… The post TMex Winter School – Translational Medicine Explained appeared first on Dutch Techcentre for Life Sciences. 2021-11-08 09:00:00 UTC 2021-11-12 00:00:00 UTC Online, Online, Online Online Online Online [] [] [] workshops_and_courses [] []
  • BioHackathon Europe 2021

    8 - 12 November 2021

    Barcelona, Spain

    BioHackathon Europe 2021 https://tess.elixir-europe.org/events/biohackathon-europe-2021 Each November ELIXIR organises BioHackathon Europe, which brings together bioinformaticians from around the world. The event takes place in different locations around Europe. This year it will be at the Campus La Mola near Barcelona. The BioHackathon offers an intense week of hacking, with over 160 international participants who work on diverse and exciting projects. This year there will be 37 hacking projects. For details of this year's event see the BioHackathon website. To find out what happened in previous BioHackathons, see the BioHackathon Europe page. 2021-11-08 09:00:00 UTC 2021-11-12 17:00:00 UTC Campus La Mola, Barcelona, Spain Campus La Mola Barcelona Spain [] [] [] [] [] []
  • Single-cell Transcriptomics - streamed

    8 - 10 November 2021

    Bern or streamed, Switzerland

    Elixir node event
    Single-cell Transcriptomics - streamed https://tess.elixir-europe.org/events/single-cell-transcriptomics-streamed-2d5e78ee-bc2b-4093-b3d7-57ccb1835353 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 2021-11-08 09:00:00 UTC 2021-11-10 00:00:00 UTC SIB, Bern or streamed, Switzerland SIB Bern or streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • UNIX scripting for Life Scientists

    8 - 9 November 2021

    Lausanne or streamed, Switzerland

    Elixir node event
    UNIX scripting for Life Scientists https://tess.elixir-europe.org/events/unix-scripting-for-life-scientists-ce31f453-1655-4860-ab78-672cc3d7dcf4 Overview Scripting allows shell users to automate repetitive tasks, thus improving reproducibility, reducing the risk of errors, freeing time, and avoiding boredom. 2021-11-08 09:00:00 UTC 2021-11-09 00:00:00 UTC SIB, Lausanne or streamed, Switzerland SIB Lausanne or streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Metagenomics bioinformatics

    9 - 12 November 2021

    Cambridge, United Kingdom

    Elixir node event
    Metagenomics bioinformatics https://tess.elixir-europe.org/events/metagenomics-bioinformatics-57053a63-9889-4fee-bb77-70394c57f080 EMBL-EBI plans to deliver the majority of its 2021 events face-to-face with a small number of virtual events. Please note that some events that are currently listed as ‘on-site’ might need to be delivered virtually, depending on the prevailing status of the pandemic at the time. More courses will be added to this programme as our plans develop further. 2021-11-09 09:00:00 UTC 2021-11-12 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Galaxy Pre-conference Workshops

    9 - 11 November 2021

    Galaxy Pre-conference Workshops https://tess.elixir-europe.org/events/galaxy-pre-conference-workshops 2021-11-09 09:00:00 UTC 2021-11-11 00:00:00 UTC [] Galaxy India Community [] [] [] [] []
  • Metagenomics bioinformatics (Virtual)

    9 - 12 November 2021

    Cambridge, United Kingdom

    Elixir node event
    Metagenomics bioinformatics (Virtual) https://tess.elixir-europe.org/events/metagenomics-bioinformatics-virtual-24fa1698-1f9b-4529-893a-8fe88b17b165 Gain knowledge of the tools, processes and analysis approaches used in the field of metagenomics. This course will cover the metagenomics data analysis workflow from the point of newly generated sequence data. Participants will explore the use of publicly available resources and tools to manage, share, analyse and interpret metagenomics data. 2021-11-09 09:00:00 UTC 2021-11-12 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • [ONLINE] Earth Sciences Simulation Environments @ BSC

    9 - 11 November 2021

    [ONLINE] Earth Sciences Simulation Environments @ BSC https://tess.elixir-europe.org/events/online-earth-sciences-simulation-environments-bsc The registration to this course will open soon. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course conveners: Herve Petetin and Vladimir Lapin This training will be online via zoom. Course lecturers: Earth Sciences Department researchers involved in the group of Computational Earth Sciences, Atmospheric Composition, Climate Prediction and Earth System Services. Final lectures TBA. Objectives: The objective of this PATC course is to cover the basics of a high performance computing (HPC) environment oriented towards earth science applications, specifically chemical weather modelling and climate modelling. More precisely, the course will cover: Introduction to earth science fundamentals and modelling; Basic usage of an HPC environment: shell, compilers, libraries, file systems, queuing system and parallel computing. Build and configure targeted earth science applications with the NMMB/BSC-CTM chemical transport model and with the EC-EARTH climate model; Execute and monitor numerical experiments using a workflow manager; Analyse and visualise model outputs with a wide set of tools. Learning outcomes: Participants will learn and gain experience in accessing an HPC facility, installing earth science numerical models and related utilities and libraries, running numerical simulations, monitoring the execution of supercomputing jobs, analysing and visualising model results. Level: (All courses are designed for specialists with at least 1st cycle degree or similar background experience) For trainees with some theoretical and practical knowledge Prerequisites: At least University degree in progress on Earth Sciences, Computer Sciences or related area Basic knowledge of UNIX Knowledge of C, FORTRAN, MPI or openMP is recommended Knowledge of Earth Sciences data formats is recommended (grib, netcdf, hdf,…) Knowledge of R and Python Agenda: Agenda: Day 1 (Nov. 09) – 4.5h 10:00-10:15 Welcome and introduction of the BSC Earth Sciences Department. (Francisco Doblas-Reyes, Head of BSC-ES Department) 10:15-10:30 Technical and logistic information. (Hervé Petetin and Vladimir Lapin) 10:30-11:00 Introduction to earth science fundamentals and modelling. (Eleftheria Exarchou) 11:00-11:30 Break 11:30-13:00 Introduction to Linux and HPC, BSC facilities, PRACE and RES + preparation/checks for hands-on tutorial after lunch break (Mario Acosta) 13:00-14:00 Lunch break 14:00-16:00 HPC hands-on tutorial. At the end of this tutorial, the students will be able to compile and execute jobs on Mare Nostrum 4. (Mario Acosta, Miguel Castrillo and Hervé Petetin and Vladimir Lapin) Day 2 (Nov 10) – 3.5h 9:30-10:00 Lecture on the EC-EARTH climate model. (Eleftheria Exarchou) 10:00-10:30 Lecture on the NMMB-MONARCH atmosphere chemistry model. (Enza di Tomaso and Jan Mateu) 10:30-11:00 Lecture on setting up and running the NMMB-MONARCH model with Autosubmit. (Francesca Macchia and Gilbert Montane) 11:00-11:30 Break 11:30-13:30 Model hands-on tutorial. Students will run a prepared case. (Francesca Macchia, Gilbert Montane, Hervé Petetin and Vladimir Lapin) Day 3 (Nov 11) – 3h 10:00-11:00 Introduction to analysis and visualisation tools for model outputs (s2dverification, MapGenerator, CDO, NCO, panoply, ncview). (Francesco Benincasa) 11:00-11:30 Break 11:30-13:30 Analysis hands-on tutorial. Students will apply tools for analysis and visualisation to the outputs created the day before. (Amalia Vradi, An-Chi Ho, Nuria Perez, Hervé Petetin and Vladimir Lapin)   END of COURSE https://events.prace-ri.eu/event/1231/ 2021-11-09 09:00:00 UTC 2021-11-11 12:30:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to Statistical Analysis (Online)

    9 November 2021

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Statistical Analysis (Online) https://tess.elixir-europe.org/events/introduction-to-statistical-analysis-online-296374b8-5b8c-4190-a0dc-86057641cd04 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. This course provides a refresher on the foundations of statistical analysis. The emphasis is on interpreting the results of a statistical test, and being able to determine the correct test to apply. Practicals are conducted using a series of online apps, and we will not teach a particular statistical analysis package, such as R. For courses that teach R, please see the links under "Related courses" . This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at [CRUK Cambridge Institute](http://www.cruk.cam.ac.uk/). 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 Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4007755&course-title=Introduction%20to%20Statistical%20Analysis).'' 2021-11-09 09:30:00 UTC 2021-11-09 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Introduction to high-performance computing (sciCORE cluster)

    10 November 2021

    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-258314f5-c22d-4dcf-97e4-9efff8baa9aa 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 2021-11-10 09:00:00 UTC 2021-11-10 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

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