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128 events found
  • FAIR data (session 2)

    15 - 18 November 2021

    Elixir node event
    FAIR data (session 2) https://tess.elixir-europe.org/events/fair-data The training is four half-days. It is delivered in French. 2021-11-15 09:00:00 UTC 2021-11-18 12:30:00 UTC Institut Français de Bioinformatique (IFB) Open science FAIR data Biology Bioinformatics Data management [] [] BiologistsbioinformaticiansBiomedical researchers health professionals workshops_and_courses [] metadataData management plandata organisationstoragelife science standardslicensing
  • RNA-seq data analysis ONLINE

    15 - 20 November 2021

    Elixir node event
    RNA-seq data analysis ONLINE https://tess.elixir-europe.org/events/rna-seq-data-analysis-online-e3625416-9488-4abe-852b-9a8b97438dc9 #url: https://www.scilifelab.se/event/rna-seq-data-analysis-online/ 2021-11-15 09:00:00 UTC 2021-11-20 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Reproducible research and data analysis using Nextflow pipelines

    15 - 18 November 2021

    Streamed from Lausanne and Barcelona, Switzerland

    Elixir node event
    Reproducible research and data analysis using Nextflow pipelines https://tess.elixir-europe.org/events/reproducible-research-and-data-analysis-using-nextflow-pipelines Overview Nextflow is a powerful polyglot workflow language that, provides a robust, scalable and reproducible way to run computational pipelines. 2021-11-15 09:00:00 UTC 2021-11-18 00:00:00 UTC SIB, Streamed from Lausanne and Barcelona, Switzerland SIB Streamed from Lausanne and Barcelona Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Introduction to the analysis of NGS data, online

    18 - 25 November 2021

    Leuven, Belgium

    Elixir node event
    Introduction to the analysis of NGS data, online https://tess.elixir-europe.org/events/introduction-to-the-analysis-of-ngs-data-online-05f80e0e-ba8e-481e-92b6-ce0d07a27547 This training is an introduction to a series of trainings on the analysis of Next Generation Sequencing data. This training is intended for newbies to the field and will teach them all background knowledge required to successfully complete the advanced NGS analysis trainings. To this end the training will give an overview of: - The Illumina platform - NGS data formats and file handling - Quality control of NGS data - Mapping of NGS data - Supporting IT: Galaxy platform 2021-11-18 09:00:00 UTC 2021-11-25 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • [ONLINE] Data Science and Deep Learning with Python @ Cineca

    22 - 26 November 2021

    [ONLINE] Data Science and Deep Learning with Python @ Cineca https://tess.elixir-europe.org/events/online-data-science-and-deep-learning-with-python-cineca Description: The increasing amount of data collected through sensors or computational simulations can take advantage of new techniques for being processed in order to extract new insights out of raw data. The purpose of this course is to present researchers with data science methods and techniques. The course includes theoretical lectures followed by practical sessions on data manipulation, visualisation, machine learning and deep learning.  A specific session on how to use HPC resources is included. Participants will utilize Python on their personal computers as well as Cineca HPC resources for practical projects. Topics: -Introduction to data analytics -Machine Learning theory (supervised/unsupervised) -Data Manipulation with Numpy and Pandas -Data visualization with Matplotlib, Seaborn, Bokeh -Machine learning with sci-kit learn -Deep learning with Tensorflow and Keras -Introduction to Cineca HPC facilities Target Audience: Students and researchers from academia and industry with different backgrounds who are looking for technologies and methods to analyse large amounts of data. Prerequisites: Participants must have basic knowledge in statistics, fundamentals of computer programming with Python and use of GNU/Linux-based systems. The number of participants is limited to 25 students. Applicants will be selected according to their experience, qualification and scientific interest BASED ON WHAT WRITTEN IN THE "Reason for participation" FIELD OF THE REGISTRATION FORM.  APPLICATION DEADLINE OCT 29th, 2021.  STUDENTS WILL BE NOTIFIED ON THEIR ADMISSION OR NOT WITH AN EMAIL ON MONDAY NOV 9th.  Attendance is FREE.    https://events.prace-ri.eu/event/1261/ 2021-11-22 08:00:00 UTC 2021-11-26 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Translational Immunology

    22 - 23 November 2021

    Gent, Belgium

    Elixir node event
    Translational Immunology https://tess.elixir-europe.org/events/translational-immunology The organizing committee is looking forward to organize the postponed edition of this event on 22 - 23 November 2021 in Ghent, Belgium. The aim of this conference is to bridge the translational gap in immunopathology, bringing together clinicians, research scientists and industry partners to discuss prominent advances from the bench to the clinic. Internationally renowned speakers will present their latest findings during 5 plenary sessions: Making the most of your antibodies T Cell activation and exhaustion Bugs and drugs in immunology From drug to market Tissue immunity 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 three abstracts were given a short talk slot in the plenary program. The 2 best posters will win the Poster prize sponsored by Elsevier's journal "Cellular Immunology"! Travel grants We offer 5 travel grants to international attendees, which will reimburse travel costs up to 400 Euros. Are you interested in attending Translational Immunology and want to have a chance on a travel grant? Submit your motivation below by clicking on the 'Apply for a grant' button before 30 August 2021. The organizing committee will notify you of your travel grant acceptance by the end of March. 2021-11-22 09:00:00 UTC 2021-11-23 17:00:00 UTC VIB De Bijloke, Jozef Kluyskensstraat 2, 9000 Gent, Gent, Belgium De Bijloke, Jozef Kluyskensstraat 2, 9000 Gent Gent Oost-Vlaanderen Belgium 9000 Immunology Translational medicine VIB conferences@vib.be [] PhD StudentsAcademicsPhysiciansIndustry [] first_come_first_served Immunologytargeted therapeuticstherapeutic application
  • 3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon

    22 - 24 November 2021

    Lutherstadt Wittenberg, Germany

    3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon https://tess.elixir-europe.org/events/3rd-de-nbi-elixir-de-metarbolomics-hackathon de.NBI Organisers: Marr / Schmidt / Meier / Neumann Date: 22.11. - 24.11.2021 Location: Leucorea, Lutherstadt Wittenberg Information on travel and accommodation: https://docs.google.com/document/d/1tM9mzGmTNT11p3cYRdHjm-CT3gb-yEDbZ-xoAUKixGs Workshop goals: Aim of the workshop is to improve the interoperability of packages (e.g. using common data structures and interfaces), combine efforts (use single implementation of common functions), create and demonstrate complex workflows by integrating existing tools, identify gaps in the metaRbolomics ecosystem that need to be covered. We will also have enough discussion time to ponder challenges of the future, taking metaRbolomics into the next decade. Prerequisites: Laptop, understanding in Metabolomics, R language skills Keywords: Metabolomics, mass spectrometry, R, Bioconductor, data processing, metabolite annotation, metabolite identification 2021-11-22 09:00:00 UTC 2021-11-24 17:00:00 UTC de.NBI Lutherstadt Wittenberg, Lutherstadt Wittenberg, Germany Lutherstadt Wittenberg Lutherstadt Wittenberg Germany [] [] [] workshops_and_courses [] []
  • Applied Metaproteomics Workshop Magdeburg 2021

    22 - 26 November 2021

    Magdeburg, Germany

    Applied Metaproteomics Workshop Magdeburg 2021 https://tess.elixir-europe.org/events/applied-metaproteomics-workshop-magdeburg-2021 Educators: Dirk Benndorf, Stephan Fuchs, Robert Heyer, Kay Schallert (BiGi/MetaProtServ) Date: 22.11.2021 – 26.11.2021 Location: Magdeburg, Germany (Universitätsplatz 2, Building 28.205) Contents: Microbiome research is rapidly increasing. Meta-Omics data provide insights into microbial community influencing human health and biochemical cycle. Metaproteomics focusses on proteins representing the expressed genes and functions. In contrast to metagenomics or metatranscriptomics, the extraction and the analysis of proteins from human or environmental samples is challenging. The de.NBI course on Applied Metaproteomics trains the participants to apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Maximum 10 participants are strongly encouraged to analyze their own samples to start their own metaproteomics project. The workshop takes place at chair of bioprocess engineering at Otto-von-Guericke University Magdeburg. The team of microbial communities head by Dr. Dirk Benndorf is well experienced in metaproteomics. The samples will be measured on newly purchased timsTOF Pro MS. His group devellopes the MetaProteomAnalyzer service facilitating the analysis of of metaproteomic data. The provision of service is supported by the German Network for Bioinformatics Infrastructure - de.NBI. Monday 09:00-10:00 Arrival 10:00-11:00 Introduction to metaproteomics (lecture: Dirk Benndorf) 11:00-12:00 Design of experiments and sample preparation (lecture: Robert Heyer) 12:00-13:00 Lunch 13:00-18:00 Sample preparation I (protein extraction, protein quantification: Robert Heyer) during the afternoon short presentations of participant´s about their samples (each participant max. 10 min) Tuesday 08:00-11:00 Sample preparation II (FASP digest, SDS-PAGE: Robert Heyer) 11:00-13:00 Introduction to high resolution mass spectrometry (lecture: Dirk Benndorf) 13:00-14:00 Lunch 13:00-14:00 Sample preparation II (peptide extraction: Robert Heyer) 14:00-16:00 Introduction to the MPA 2.0 (lecture: Kay Schallert) non-stop: measurement of participant’s samples I Wednesday non-stop: measurement of participant’s samples I: Dirk Benndorf, Patrick Hellwig 09:00-11:00 MPA 2.0 exercise I (working with a small reference dataset, db searching, metaprotein concept: Kay Schallert, Robert Heyer) 11:00-13:00 MPA 2.0 exercise II (loading user db, BLAST search of unknown hits, quantitative comparison of datasets, visualization and data export: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Prophane workflow (lecture and training: Stefan Fuchs, external speaker) Thursday 09:00-13:00 MPA 2.0 exercise III (analyzing own data: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Training at MS (calibration, setup of LC-MS methods, solvent exchange, trouble shooting, Patrick Hellwig) Friday 08:00-10:00 MPA 2.0 exercise IV (visualization of data: Robert Heyer) 10:00-12:00 Individual discussion of results and preparation of presentations (Dirk Benndorf, Robert Heyer, Kay Schallert) 12:00-13:00 Short presentations of participant‘s results and conclusion 13:00 Lunch and departure Learning goals: To apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Prerequisites: Fee: 70 € -> The so-called “3G rule” (the course is only open to those that are vaccinated, recovered, or tested - geimpft, genesen, getestet) will be applied! Keywords: Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer, Tools: MetaproteomeAnalyzer 2021-11-22 09:00:00 UTC 2021-11-26 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Sachsen-Anhalt Germany [] [] [] workshops_and_courses [] []
  • Deep learning in biology

    22 - 23 November 2021

    Elixir node event
    Deep learning in biology https://tess.elixir-europe.org/events/deep-learning-in-biology Large amounts of data and compute resources have enabled the development of high-performance machine learning models. This is particularly due to deep learning techniques. By looking at many data samples, these models can find structure in the data that is useful for predictive and explorative analysis: e.g. classification, clustering, data generation, dimensionality reduction, etc. The most popular applications within biotechnology are concerned with image segmentation, diagnostics, sequence analysis, etc. However, deep learning models are far from straightforward to implement correctly due to the many different hyperparameter settings, optimization procedures, architecture choices, etc. In this course, we will make use of Jupyter Notebook and PyTorch, which are both based on Python, to apply deep learning techniques on both bio informatics and bio image informatics data. We aim to work towards applications that participants would like to study. 2021-11-22 09:00:00 UTC 2021-11-23 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • Recombinant Protein Expression

    22 November 2021

    Elixir node event
    Recombinant Protein Expression https://tess.elixir-europe.org/events/recombinant-protein-expression The training will start with an introduction on the available recombinant protein expression systems, with their advantages and limitations, from which to choose for your favorite protein. Also, high-throughput protein expression, expression in plant cells, antibody and nanobody expression and a difficult-to-express protein case will be discussed. A next session will focus on strategy design to optimize protein purification and how to address quality assurance of the purified proteins. For clinical use of a protein-based biological stability and production yields are critical issues that come on top of the desired therapeutic efficacy. Why and how to deal with these critical aspects will be addressed as well during the training. Furthermore, also the key steps that are required for optimal protein formulation will be reviewed. We plan to end the day with a keynote talk from a pharma industry speaker illustrating the issues that need to be considered when engineering recombinant proteins for clinical applications. 2021-11-22 09:00:00 UTC 2021-11-22 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • Introduction to bioinformatics using NGS data – ONLINE

    22 - 27 November 2021

    Elixir node event
    Introduction to bioinformatics using NGS data – ONLINE https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-online-060ce494-27a0-4f5e-bc94-13f4d1e25d81 #url: https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online-2/ 2021-11-22 09:00:00 UTC 2021-11-27 00:00:00 UTC [] nina.norgren@scilifelab.se [] [] [] [] []
  • [ONLINE] ChEESE Advanced Training on HPC for Computational Seismology @ BSC

    23 - 25 November 2021

    [ONLINE] ChEESE Advanced Training on HPC for Computational Seismology @ BSC https://tess.elixir-europe.org/events/parallel-programming-workshop-bsc-c0c4f034-83ff-4b55-b1bd-caab3b02034b The registration to this course will open soon. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course Convener: To be determined Location: Online via Zoom Objectives: Are you interested in numerical wave simulations but feel like there are too many codes and methods out there and don’t know which option is right for you? Or perhaps you just want to refresh your knowledge and gain some practical experience with the different possibilities? Either way, this fully virtual workshop is for you! This training course will present introductory hands-on tutorials for ExaHyPE, Salvus, SeisSol, and SPECFEM3D, which are four different high-performance computational seismology software packages focused on waveform modeling and inversion. The course will provide you with an overview of their similarities, differences, and areas of applicability. Unique and in-depth half-day practicals will be provided for each package, with computational resources provided by BSC. Participants will also be encouraged to present their own work and/or motivation as a one-minute lightning-talk during the wrap-up session of the workshop.   This training event is hosted by ChEESE, the Center of Excellence for Exascale in Solid Earth.   Requirements: - Basic knowledge of computational seismology (e.g., familiarity with the elastic wave equation) - Basic knowledge of Python and Jupyter notebooks - Optional: basic programming skills (C/C++, only for the ExaHyPE course module) Learning Outcomes: - A basic introduction to waveform physics modeling - Hands-on experience with four different wave propagation codes Agenda: To be determined   https://events.prace-ri.eu/event/904/ 2021-11-23 08:30:00 UTC 2021-11-25 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Advanced Fortran Topics @ LRZ

    23 - 26 November 2021

    [ONLINE] Advanced Fortran Topics @ LRZ https://tess.elixir-europe.org/events/online-advanced-fortran-topics-lrz-a524a65e-54e4-45a8-a557-56e13b64dc0e Overview This online course is targeted at scientists who wish to extend their knowledge of Fortran to cover advanced features of the language. Topics covered include (still preliminary) Best Practices global objects and interfaces abstract interfaces and the IMPORT statement object based programming Object-Oriented Programming type extension, polymorphism and inheritance binding of procedures to types and objects generic type-bound procedures abstract types and deferred bindings IEEE features and floating point exceptions Interoperability with C mixed language programming patterns Fortran 2003 I/O extensions OO Design Patterns: application of object-oriented programming creation and destruction of objects polymorphic objects and function arguments interacting objects dependency inversion: submodules and plugins Coarrays PGAS concepts and coarray basics dynamic entities advanced synchronization parallel programming patterns recent enhancements: collectives, events, teams, atomic subroutines performance aspects of coarray programming The course combines lectures and hands-on sessions. Prerequisites Course participants should have good knowledge of the Fortran 95 standard (such as covered in the February course at LRZ), and also basic UNIX/Linux knowledge (e.g. shell commands, simple scripts, editors like vi or emacs). Hands-On Please use your own laptop or institute cluster for the hands-on sessions. On your laptop or PC you should run either a Linux distribution, or a Microsoft Linux for Windows subsystem. A recent version of the gfortran compiler should be installed. Alternatively, an evaluation version of the NAG compiler (version 7.0) can be used. The latter can be obtained from https://www.nag.com/content/software-trials?product=NAG%20Compiler. Finally, the GSL (GNU scientific library) and its header files should be installed. Language English Lecturers Dr. R. Bader, Dr. G. Brietzke (LRZ) Prices and Eligibility The course is open and free of charge for people from academia and industry. Registration Via https://events.prace-ri.eu/event/1244/registrations/913/ Please register with your official e-mail address to prove your affiliation. Withdrawal Policy See Withdrawal https://events.prace-ri.eu/event/1244/ 2021-11-23 09:00:00 UTC 2021-11-26 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • First Steps in Parallelization with OpenMP

    24 November 2021

    Basel, Switzerland

    Elixir node event
    First Steps in Parallelization with OpenMP https://tess.elixir-europe.org/events/first-steps-in-parallelization-with-openmp-ad9c6e36-8ddc-47b8-98e7-33547b450196 This course is susceptible to be streamed to the registered participants, depending on the evolution of the sanitary situation Overview We currently live in the era of multicore computers, where almost every computing machine has many CPUs. 2021-11-24 09:00:00 UTC 2021-11-24 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First Steps in Parallelization with OpenMP - streamed

    24 November 2021

    Streamed from Basel, Switzerland

    Elixir node event
    First Steps in Parallelization with OpenMP - streamed https://tess.elixir-europe.org/events/first-steps-in-parallelization-with-openmp-45b442fd-4698-42c9-af20-13586a4e31ac Overview We currently live in the era of multicore computers, where almost every computing machine has many CPUs. In order to benefit from this computational power, we need to devise programs explicitly written for parallel machines. 2021-11-24 09:00:00 UTC 2021-11-24 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Deep Learning for Life Sciences - fundamentals and applications

    25 November 2021

    Streamed, Switzerland

    Elixir node event
    Deep Learning for Life Sciences - fundamentals and applications https://tess.elixir-europe.org/events/deep-learning-for-life-sciences-fundamentals-and-applications Overview The aim of this course is to familiarise the participants with the deep learning model and some of its applications in life sciences. 2021-11-25 09:00:00 UTC 2021-11-25 00:00:00 UTC SIB, Streamed, Switzerland SIB Streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Multivariate analysis for -omics data integration: principles and applications

    29 November - 2 December 2021

    Lyon, Switzerland

    Elixir node event
    Multivariate analysis for -omics data integration: principles and applications https://tess.elixir-europe.org/events/multivariate-analysis-for-omics-data-integration-principles-and-applications This course will take place in Lyon with rules complying to COVID situation (distances and hygiene), but in the event of restrictions preventing the event to take place in person, the participants will be informed about a probable streamed version. 2021-11-29 09:00:00 UTC 2021-12-02 00:00:00 UTC SIB, Lyon, Switzerland SIB Lyon Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Multivariate analysis for -omics data integration: principles and applications

    29 November - 2 December 2021

    Lyon, Switzerland

    Elixir node event
    Multivariate analysis for -omics data integration: principles and applications https://tess.elixir-europe.org/events/multivariate-analysis-for-omics-data-integration-principles-and-applications-1316ecac-0dfc-4839-b5e9-fcea597e96a3 This course will take place in Lyon with rules complying to COVID situation (COVID certificate, distances and hygiene). More details in the Additional Information section below. 2021-11-29 09:00:00 UTC 2021-12-02 00:00:00 UTC SIB, Lyon, Switzerland SIB Lyon Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • [ONLINE] Node-Level Performance Engineering @ LRZ

    1 - 3 December 2021

    [ONLINE] Node-Level Performance Engineering @ LRZ https://tess.elixir-europe.org/events/online-node-level-performance-engineering-lrz-5b04463a-1fa4-44e4-92ad-c37fd2f4b0a0 This online course organised in cooperation with NHR@FAU covers performance engineering approaches on the compute node level. Even application developers who are fluent in OpenMP and MPI often lack a good grasp of how much performance could at best be achieved by their code. This is because parallelism takes us only half the way to good performance. Even worse, slow serial code tends to scale very well, hiding the fact that resources are wasted. This course conveys the required knowledge to develop a thorough understanding of the interactions between software and hardware. This process must start at the core, socket, and node level, where the code gets executed that does the actual computational work. We introduce the basic architectural features and bottlenecks of modern processors and compute nodes. Pipelining, SIMD, superscalarity, caches, memory interfaces, ccNUMA, etc., are covered. A cornerstone of node-level performance analysis is the Roofline model, which is introduced in due detail and applied to various examples from computational science. We also show how simple software tools can be used to acquire knowledge about the system, run code in a reproducible way, and validate hypotheses about resource consumption. Finally, once the architectural requirements of a code are understood and correlated with performance measurements, the potential benefit of code changes can often be predicted, replacing hope-for-the-best optimizations by a scientific process. The course is a PRACE training event. Introduction Basic architecture of multicore systems: pipelines, SIMD, caches, sockets, memory The important role of system topology Tools: topology & affinity in multicore environments likwid-topology and likwid-pin, alternatives Roofline model basics          Model assumptions and construction Simple examples Limitations of the Roofline model Tools: hardware performance counters Why hardware performance counters? likwid-perfctr Validating performance models Optimal use of parallel resources Single Instruction Multiple Data (SIMD) Cache-coherent Non-Uniform Memory Architecture (ccNUMA) Roofline case studies Tall & skinny dense matrix-matrix multiplication Sparse matrix-vector multiplication Jacobi (stencil) smoother Basics of performance engineering PE process Code profiling Proper benchmarking Reproducibility and documentation Beyond Roofline: The ECM performance model (optional) Prerequisites You have to be able to handle a Linux command line and file editing remotely. Basic knowledge of C, C++, or Fortran programming and of OpenMP is required. Hands-On Exercises will be done on a cluster at NHR@FAU. For the exercises you need an SSH client on your local computer. Language English Lecturers Prof. Gerhard Wellein, Dr. habil. Georg Hager (RRZE, Uni. Erlangen) Prices and Eligibility The course is open and free of charge for people from academia and industry. Withdrawal Policy See Withdrawal Legal Notices This course is offered in cooperation with NHR@FAU. Some of your personal data will be transferred to NHR@FAU (title, first name, surname, institution, country, email, course) to create the course accounts. The legal basis is in accordance with Article 6(1)(b) GDPR. Please see also our data protection notice (in German: https://www.lrz.de/datenschutzerklaerung/). https://events.prace-ri.eu/event/1249/ 2021-12-01 08:00:00 UTC 2021-12-03 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] High Performance Bioinformatics@CINECA

    1 - 3 December 2021

    [ONLINE] High Performance Bioinformatics@CINECA https://tess.elixir-europe.org/events/online-high-performance-bioinformatics-cineca-cc74092e-a7db-4dbd-a99f-f769dc572523 We live in a big-data era and simple serial bioinformatic pipelines can’t efficiently handle huge input datasets. Hence, High Performance Computing (HPC) can represent a good solution for researchers who need to analyze and address new biological questions with their data.  This course is both theoretical and practical and is addressed to bioinformaticians who want to scale up their analysis on a cluster machine. It mainly focuses on the development and execution of automated data analysis pipelines. On the first day, students will become confident with a cluster machine (e.g. hardware, software, module environment, data storage) and will learn how to submit a single batch scripts via the SLURM scheduler. On the second day, partecipants will be introduced to the world of Next Generation Sequencing (NGS) and will learn how to build a fully automated RNA-seq pipeline able to handle large input datasets, focusing on job concatenations and HPC request resource optimization. On the last day students will be introduced to cloud computing and to the world of snakemake, a python workflow management system tool able to create reproducible and scalable data analyses, with particular attention to scaling workflows on cluster and cloud without modifyng the workflow definition. Ad-hoc hands-on sessions, aimed at applying the concepts explained during the course, will be held every afternoon. Skills: By the end of the course each student should be able to: - Know all the conventions and opportunities offered by CINECA for accessing HPC resources; - Download datasets from public repositories and/or transfer input files from the user’s local computer to the CINECA clusters; - Navigate through the software environment set up by CINECA; - Run single-step jobs on a supercomputer via SLURM scheduler; - Combine several bioinformatics applications into a fully automated pipeline able to run on a supercomputer; - Learn how to iterate through samples in order to manage huge input datasets; - Have an overview of how to take advantage of snakemake to build a portable, scalable and fully automated pipeline. Target audience: Biologists, bioinformaticians and computer scientists interested in approaching large-scale NGS-data analysis. Course prerequisites: Good knowledge of python and shell command line. A very basic knowledge of R and biology is recommended but not strictly required. https://events.prace-ri.eu/event/1262/ 2021-12-01 08:00:00 UTC 2021-12-03 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • Enrichment Analysis

    3 December 2021

    Lausanne or Streamed, Switzerland

    Elixir node event
    Enrichment Analysis https://tess.elixir-europe.org/events/enrichment-analysis-d41a6c02-b748-45e0-913a-b349661ead77 Overview Experiments designed to quantify gene expression often yield hundreds of genes that show statistically significant differences between two classes (two biological states, two phenotype states, two experimental conditions, etc). 2021-12-03 09:00:00 UTC 2021-12-03 00:00:00 UTC SIB, Lausanne or Streamed, Switzerland SIB Lausanne or Streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Analysing RNA-Seq data

    3 December 2021

    Analysing RNA-Seq data https://tess.elixir-europe.org/events/creating-scientific-figures For more details please see https://www.bioinformatics.babraham.ac.uk/cgi-bin/public/course_dates.cgi. Course status: Spaces Available. 2021-12-03 09:30:00 UTC 2021-12-03 17:00:00 UTC Babraham Campus Babraham Campus CB22 3AT [] mailto:babraham.bioinformatics@babraham.ac.uk [] [] [] [] []
  • Managing your Research Data (Online)

    3 December 2021

    Cambridge, United Kingdom

    Elixir node event
    Managing your Research Data (Online) https://tess.elixir-europe.org/events/managing-your-research-data-online-76810eb7-4087-4495-8dab-9322044fe215 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. How much data would you lose if your laptop was stolen? Have you ever emailed your colleague a file named 'final_final_versionEDITED'? Have you ever struggled to import your spreadsheets into R? Would you be able to write a Data Management Plan as part of a grant proposal? As a researcher, you will encounter research data in many forms, ranging from measurements, numbers and images to documents and publications. Whether you create, receive or collect data, you will certainly need to organise it at some stage of your project. This workshop will provide an overview of some basic principles on how we can work with data more effectively. We will discuss the best practices for research data management and organisation so that our research is auditable and reproducible by ourselves, and others, in the future. Course materials are available [here](https://datachampcam.github.io/avoid-data-disaster/) 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=4011883&course-title=Managing%20your%20Research%20Data).'' 2021-12-03 10:00:00 UTC 2021-12-03 16:00:00 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)

    8 December 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-1113385d-e02b-4d19-a4bf-c94f67c30812 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 2021-12-08 09:00:00 UTC 2021-12-08 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • [ONLINE] CUDA 4 Dummies @ VSC Vienna

    9 - 10 December 2021

    [ONLINE] CUDA 4 Dummies @ VSC Vienna https://tess.elixir-europe.org/events/online-cuda-4-dummies-vsc-vienna-b6d97f62-473e-44ea-9a0c-100c00d4a5b9 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. The HANDS-ON LABS will be done on VSC-3, all participants will get a training user account at the VSC for the duration of the course. Overview CUDA is the standard API for code development targeting the GPU and a number of impressive examples have already been given in diverse areas from particle physics to computational biology. CUDA allows simple extensions of standard C/C++/Fortran code with GPU-specific functions. In this way thousands of cores available on the GPU can be leveraged to work in parallel and thus carry out significant fractions of the computational workload on the device rather than the CPU. There is also a vast set of auxiliary tools available to the developer including libraries, code templates, building blocks, analysis tools, developmental frameworks and in general a vivid community making up the CUDA Developer Zone. It is often for this multifaceted support environment that the interested beginner is feeling overwhelmed and unsettled about which particular first steps should best be taken to gain a straightforward introduction into the subject. For exactly this reason the present course is offering a systematic step-by-step introduction into GPU computing from the perspective of the newcomer. Basic design principles will be established, central programming techniques acquired and a number of state-of-the-art workflows examined that efficiently employ the GPU and are frequently used in scientific computing. This course provides lectures, demos, and hands-on labs. This course is a PRACE training event. It is organized by the VSC Research Center, TU Wien. Agenda & Content (tentative) 1st day – 9 December 2021 Basic design principles, getting started with simple CUDA routines, mastering the CUDA environment; Memory Hierarchy with a focus on CUDA managed unified memory; Practical exercise: all the pitfalls one can run into when porting a dummy code to CUDA. 08:45 - 09:00    join online 09:00 - 13:00    lectures and hands-on labs (with breaks: 10:45-11:00) 13:00 - 14:00    lunch break 14:00 - 17:00    lectures and hands-on labs (with breaks: 15:20-15:35) 2nd day – 10 December 2021 Selected examples to demonstrate CUDA capabilities and GPU operation, e.g., bandwidthTest, simpleAssert, simpleStreams, etc.; CUDA libraries, CUBLAS, CUSolver, considering numerical precision, gaining insight into the runtime; Practical exercise: CUDA in everyday life (of a scientist). 08:45 - 09:00    join online 09:00 - 13:00    lectures and hands-on labs (with breaks: 10:45-11:00) 13:00 - 14:00    lunch break 14:00 - 17:00    lectures and hands-on labs (with breaks: 15:20-15:35) https://events.prace-ri.eu/event/1251/ 2021-12-09 07:05:00 UTC 2021-12-10 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Statistics and Machine Learning for Life Sciences - streamed

    9 - 10 December 2021

    Streamed from Basel, Switzerland

    Elixir node event
    Statistics and Machine Learning for Life Sciences - streamed https://tess.elixir-europe.org/events/statistics-and-machine-learning-for-life-sciences-6cd03f39-e452-420b-afb2-8212be992b1a Overview Statistics are an integral aspect of scientific research, and in particular of life sciences that heavily rely on quantitative methodologies. 2021-12-09 09:00:00 UTC 2021-12-10 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Heads of Nodes teleconference

    9 December 2021

    Heads of Nodes teleconference https://tess.elixir-europe.org/events/heads-of-nodes-teleconference-0d88b72a-dc49-4e00-b647-52002b23af26 The ELIXIR Heads of Nodes Teleconference is scheduled to take place on Thursday, 9 December 2021 from 10:00 - 13:00 (GMT) / 11:00 - 14:00 (CET) / 12:00 - 15:00 (EET). This is a closed meeting and intended for ELIXIR Heads of Nodes. 2021-12-09 10:00:00 UTC 2021-12-09 10:00:00 UTC [] [] [] [] [] []
  • Initiation to Linux command line

    10 December 2021

    Ghent, Belgium

    Elixir node event
    Initiation to Linux command line https://tess.elixir-europe.org/events/initiation-to-linux-command-line-b5770ec7-60d2-48f5-9ce4-78647de489f8 After this training you will: feel comfortable using Linux command line use bash to execute commands in Linux and know your way around the file system 2021-12-10 09:00:00 UTC 2021-12-10 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • Integrated modeling and optimization

    13 - 17 December 2021

    Wageningen Campus, Netherlands

    Elixir node event
    Integrated modeling and optimization https://tess.elixir-europe.org/events/integrated-modeling-and-optimization Course date 13-17 December 2021, Wageningen Course coordinator Natal van Riel, Eindhoven University of Technology Lecturers Prof. Natal van Riel, Eindhoven University of Technology (course coordinator) Dr. Aalt-Jan van Dijk, Wageningen University & Research Prof. Jaap Molenaar, Wageningen University &… The post Integrated modeling and optimization appeared first on Dutch Techcentre for Life Sciences. 2021-12-13 09:00:00 UTC 2021-12-17 00:00:00 UTC Wageningen Campus, Netherlands, Wageningen Campus, Netherlands Wageningen Campus, Netherlands Wageningen Campus Netherlands [] [] [] workshops_and_courses [] []
  • Ligand-protein docking, and computer-aided drug design

    13 - 15 December 2021

    Basel, Switzerland

    Elixir node event
    Ligand-protein docking, and computer-aided drug design https://tess.elixir-europe.org/events/ligand-protein-docking-and-computer-aided-drug-design-streamed Overview This workshop aims to present basics on molecular visualization, ligand-protein docking and several computer-aided drug design tools developed at SIB. Numerous case examples are taken from different therapeutic fields. 2021-12-13 09:00:00 UTC 2021-12-15 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

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