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132 events found
  • Introduction to the analysis of NGS data, online

    30 September - 14 October 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-fe44ff0a-a9a4-4d39-b81b-2648bbb12681 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 2021-09-30 09:00:00 UTC 2021-10-14 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Elearning: Basic statistics theory

    1 - 31 October 2021

    Elixir node event
    Elearning: Basic statistics theory https://tess.elixir-europe.org/events/elearning-basic-statistics-theory After this training, you should be able to: Understand basic statistical concepts and methods for statistical analysis of life sciences data Choose the correct statistical test for analyzing your data Create the appropriate graph for visualizing your data Interpret and critically assess the results of basic statistical analyses Topics handled: Which statistical test should you choose? How to describe your data? How to visualize your data? The do's and don'ts of reporting statistics  Tips and tricks to improve the power of your tests  Examples   2021-10-01 09:00:00 UTC 2021-10-31 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • [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. 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
  • Advanced Python for Biologists 2021

    4 - 15 October 2021

    Advanced Python for Biologists 2021 https://tess.elixir-europe.org/events/advanced-python-for-biologists-2021 This Advanced level workshop is ideal for researchers and technical workers with a background in biology and a basic knowledge of Python, to develop bigger or more complicated programs and increase skills and knowledge about the language, including object-oriented approaches to programming. 2021-10-04 09:00:00 UTC 2021-10-15 17:00:00 UTC Earlham Institute [] training@earlham.ac.uk [] [] [] [] []
  • 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
  • 2nd de.NBI Summer School 2021 - Microbial Community Analysis

    4 - 8 October 2021

    2nd de.NBI Summer School 2021 - Microbial Community Analysis https://tess.elixir-europe.org/events/2nd-de-nbi-summer-school-2021-microbial-community-analysis Educators: Dr. Dirk Benndorf (Magdeburg, BiGi), Prof. Dr. Alexander Goesmann (Giessen, BiGi), Dr. Sebastian Jaenicke (Giessen, BiGi), Prof. Dr. Stefan Janssen (JLU Giessen), Sebastian Jünemann (Bielefeld, BiGi), Dr. Nils Kleinbölting (Bielefeld, BiGi), Kay Schallert (Magdeburg, BiGi), Prof. Dr. Alexander Sczyrba (Bielefeld, BiGi), Dr. Daniel Wibberg (Bielefeld, de.NBI Administration office), Dr. Georg Zeller (Heidelberg, HD-HuB), Dr. Robert Heyer (Magdeburg, BiGi), Jakob Wirbel (Heidelberg, HD-Hub), Dr. Alessio Milanese (ETH Zürich) Date: 04. - 08.10.21 Location: Online Content: We are pleased to announce that the de.NBI Summer School 2021 on Microbial Community Data Analysis will take place from October 4th to 8th, 2021. The German Network for Bioinformatics Infrastructure (de.NBI) presents the Summer School on Microbial Community Data Analysis that is organized by the Bielefeld-Gießen (BiGi) Center for Microbial Bioinformatics. The BiGi center is specialized in the field of Omics data analysis for microbes and is well-known for its software platforms such as EMGB, MetaProtServ, or MGX. During the event, we will cover topics such as sequence data preprocessing, amplicon data analysis (metabarcoding), read- and assembly based metagenomics, and metaproteomics. Program: *All times refere to Central European Summer Time (CEST)! The program includes talks, lectures and hands-on trainings that the participants will conduct on their own computers/laptops. Monday, 04.10.2021 10:00-10:30 Welcome note (A. Goesmann) 10:30-11:00 Presentation of the de.NBI network (D. Wibberg) 11:00-12:00 Keynote by M. Ziegler 12:00-13:00 Lunch break 13:00-14:00 Keynote: Sequencing technologies (T. Hain) 14:00-14:15 Break 14:15-16:15 From raw data to feature tables (S. Janssen, S. Jaenicke) 16:15-17:00 Break 17:00-18:00 Keynote: Advancing microbiome research through Qiita (A. Gonzalez) Tuesday, 05.10.2021 10:00-12:00 Assessing biodiversity (alpha/beta) (S. Janssen) 12:00-13:00 Lunch break 13:00-13:30 Statistical testing (S. Janssen) 13:30-13:45 Break 13:45-15:00 Tools for taxonomic classification (S. Jaenicke) 15:00-16:00 MGX (S. Jaenicke) Wednesday, 06.10.2021 10:00-12:00 Metagenome assembly (A. Sczyrba, S. Jünemann, N. Kleinbölting) 12:00-13:00 Lunch break 13:00-14:00 Binning into MAGs (A. Sczyrba, S. Jünemann, N. Kleinbölting) 14:00-14:45 Annotation & evaluation of MAGs (A. Sczyrba, S. Jünemann, N. Kleinbölting) 14:45-15:00 Break 15:00-16:00 Keynote: Critical assessment of metagenome interpretation - CAMI2 (A. McHardy) Thursday, 07.10.2021 10:00-11:00 Keynote: Shinichi Sunagawa 11:00-11:15 Break 11:15-13:00 Taxonomic profiling of shotgun metagenomes (Georg Zeller, Alessio Milanese) 13:00-14:00 Lunch break 14:00-14:30 Taxonomic profiling of shotgun metagenomes (Georg Zeller, Alessio Milanese) 14:30-15:15 Comparative metagenome analysis (Georg Zeller) 15:15-15:30 Break 15:30-17:00 Comparative metagenome analysis (Jakob Wirbel) Friday, 08.10.2021 10:00-11:00 Introduction in analyzing microbial communities by metaproteomics (Dirk Benndorf) 11:00-12:00 Identification of mass spectrometry data using the MetaProteomeAnalyzer (Robert Heyer) 12:00-13:00 Lunch break 13:00-14:00 Taxonomic and functional comparison of human gut samples using the MetaProteomeAnalyzer (Robert Heyer) 14:00-15:00 Biostatistical data evaluation and data visualization (Robert Heyer) 15:00-15:15 Break 15:15-16:00 Keynote: Metaproteomics: where are we now? A community-driven evaluation of experimental and computational techniques (Thilo Muth) Keynote speakers: Dr. Maren Ziegler, Systematics and Biodiversity Lab, Justus Liebig University Giessen, Germany PD Dr. Torsten Hain, Medical Microbiology, Justus Liebig University Giessen, Germany PhD Antonio González Peña, University of California, San Diego, USA Prof. Dr. Alice McHardy, Helmholtz Centre for Infection Research, Braunschweig, Germany Prof. Dr. Shinichi Sunagawa, Department of Biology, ETH Zurich, Switzerland Dr. Thilo Muth, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany Prerequisites: Participants need: - Basic knowledge in Linux/CLI - Basic knowledge of executing programs on the command line (shell) - Working knowledge of R Registration: Please fill out the application form to sign up. The number of participants is limited to 20! The application deadline is September 12th. 2021-10-04 09:00:00 UTC 2021-10-08 17:00:00 UTC de.NBI [] [] [] [] [] []
  • 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
  • Basic statistics in R, online

    4 - 25 October 2021

    Elixir node event
    Basic statistics in R, online https://tess.elixir-europe.org/events/basic-statistics-in-r-ghent-3e7e335a-0b60-401a-94a2-94276fe61f26 This introduction to the use of the free statistical software language R is aimed at beginners.  The training covers data handling, graphics, and basic statistical techniques (t-tests, one-way ANOVA and non-parametric equivalents). A full overview of statistical analyses in R including regression, two-way ANOVA... will be given in follow-up trainings. By following this training you will: get an idea of what R and Rstudio is use R to handle data: creating, reading, reformatting and writing data use R to create graphics: bar charts, box, violin, scatter, PCA plots, heat maps and various other plots use basic statistical techniques in R : t-tests, wilcoxon tests, one-way ANOVA, Kruskal Wallis tests, chi square tests, correlations, survival analysis... write and use R scripts 2021-10-04 09:00:00 UTC 2021-10-25 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • 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 [] []
  • ELIXIR Fluxomics Training School

    4 - 8 October 2021

    ELIXIR Fluxomics Training School https://tess.elixir-europe.org/events/elixir-fluxomics-training-school The first ELIXIR Fluxomics Training School is organised 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 five-day course, will take place in virtual mode on 4-8  October 2021, from 9:00 to 17:00 Central European Time (CET). It 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 August 27 2021.  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. More information on the school can be found on the school website. 2021-10-04 09:00:00 UTC 2021-10-08 17:00:00 UTC [] [] [] [] [] []
  • Best practices in research data management and stewardship

    4 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 2021-10-04 00:00:00 UTC Online Online [] [] [] [] [] []
  • Introduction to biostatistics and machine learning – Online

    4 - 9 October 2021

    Elixir node event
    Introduction to biostatistics and machine learning – Online https://tess.elixir-europe.org/events/introduction-to-biostatistics-and-machine-learning-online #url:https://www.scilifelab.se/event/introduction-to-biostatistics-and-machine-learning-online/ 2021-10-04 09:00:00 UTC 2021-10-09 00:00:00 UTC [] nina.norgren@scilifelab.se [] [] [] [] []
  • 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
  • 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 [] []
  • LIFS Course - ILS 2021 & LipidomicsForum 2021

    5 October 2021

    Regensburg, Germany

    LIFS Course - ILS 2021 & LipidomicsForum 2021 https://tess.elixir-europe.org/events/lifs-course-ils-2021-lipidomicsforum-2021 Educators: Jacobo Miranda Ackerman, Daniel Krause, Nils Hoffmann (de.NBI, BioInfra.Prot / LIFS) Date: October 5th, 2021, 9:00 – 12:00 (CEST) & 13:00 – 17:00 (CEST) Deadline for Workshop Registration: Until capacity is reached. Location: On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise) Contents: In the first part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. In part four, we will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology. Morning 09:00 – 09:45 Welcome and Introduction 10:00 – 10:30 Targeted Lipidomics with LipidCreator and Skyline 10:30 – 12:00 LipidCreator and Skyline Exercises Afternoon 13:00 – 14:30 Shotgun Lipidomics with LipidXplorer 14:30 – 15:30 Quantification of Shotgun Lipidomics data with lxPostman 15:30 – 17:00 Lipidome comparison with LUX Score Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score Registration: Please select the “LIFS Training session I & II” in the Workshops section of the conference registration. Capacity is limited to 30 participants. 2G (vaccinated or fully recovered) - with either certificate of full vaccination or certificate of recovery / positive PCR test not older than six months. Nose+mouth protection - FFP2 mask or medical mouth nose protection have to be worn inside of buildings. 2021-10-05 09:00:00 UTC 2021-10-05 17:00:00 UTC de.NBI Regensburg, Regensburg, Germany Regensburg Regensburg Oberpfalz Germany [] [] [] [] [] []
  • Basic statistics in R, Leuven

    5 - 26 October 2021

    Elixir node event
    Basic statistics in R, Leuven https://tess.elixir-europe.org/events/basic-statistics-in-r-leuven-687bde82-456b-4676-92d3-0ccfae8c151f This introduction to the use of the free statistical software language R is aimed at beginners.  The training covers data handling, graphics, and basic statistical techniques (t-tests, one-way ANOVA and non-parametric equivalents). A full overview of statistical analyses in R including regression, two-way ANOVA... will be given in follow-up trainings. By following this training you will: get an idea of what R and Rstudio is use R to handle data: creating, reading, reformatting and writing data use R to create graphics: bar charts, box, violin, scatter, PCA plots, heat maps and various other plots use basic statistical techniques in R : t-tests, wilcoxon tests, one-way ANOVA, Kruskal Wallis tests, chi square tests, correlations, survival analysis... write and use R scripts 2021-10-05 09:00:00 UTC 2021-10-26 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • 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 [] []
  • Workflow4Experimenters (W4E) international course 2021

    11 - 16 October 2021

    Workflow4Experimenters (W4E) international course 2021 https://tess.elixir-europe.org/events/workflow4experimenters-w4e-international-course-2021 2021-10-11 09:00:00 UTC 2021-10-16 00:00:00 UTC [] Organizers [] [] [] [] []
  • Workflow4Experimenters (W4E) international course 2021

    11 - 16 October 2021

    Workflow4Experimenters (W4E) international course 2021 https://tess.elixir-europe.org/events/workflow4experimenters-w4e-international-course-2021-f9ce83a8-9473-4e2a-985a-589ea1e54410 2021-10-11 09:00:00 UTC 2021-10-16 00:00:00 UTC [] Organizers [] [] [] [] []
  • 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 [] []
  • Workflow4Experimenters

    11 - 15 October 2021

    Toulouse, France

    Workflow4Experimenters https://tess.elixir-europe.org/events/workflow4experimenters-b965b444-1a71-4fd0-952a-5c41b68d50bb During this one-week course, participants will learn how to use the W4M infrastructure to analyze their own dataset. Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring. 2021-10-11 12:00:00 UTC 2021-10-15 12:00:00 UTC Workflow4Metabolomics - IFB/ELIXIR-FR and MetaboHUB 180 chemin de Tournefeuille, Toulouse, France 180 chemin de Tournefeuille Toulouse Haute-Garonne France 31000 Metabolomics INRA contact@workflow4metabolomics.org ELIXIR-FR/IFBMetaboHUBRFMFGenotoul BiologistsChemists 20 workshops_and_courses registration_of_interest GalaxyMetabolomics
  • Introduction to Data Management Practices

    12 - 15 October 2021

    Uppsala University

    Elixir node event
    Introduction to Data Management Practices https://tess.elixir-europe.org/events/introduction-to-data-management-practices-29420eae-4e0c-4d6a-b4a0-bee55cf29fd2 #training #url:https://uppsala.instructure.com/courses/52280 Introduction to Data Management Practices National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. 2021-10-12 09:00:00 UTC 2021-10-15 00:00:00 UTC Uppsala University Uppsala University [] Niclas Jareborg - niclas.jareborg@scilifelab.se [] [] [] [] #trainingtraining
  • Docker and Singularity for reproducible research: getting started with containers

    14 October 2021

    Bern or streamed, Switzerland

    Elixir node event
    Docker and Singularity for reproducible research: getting started with containers https://tess.elixir-europe.org/events/docker-and-singularity-for-reproducible-research-getting-started-with-containers-c19857f6-7765-4f0a-822a-8c6c38a1f095 Overview Reproducible analysis in bioinformatics goes beyond good documentation and sharing code. Often, analyses depend on an entire environment with many different programs, libraries and settings. 2021-10-14 09:00:00 UTC 2021-10-14 00:00:00 UTC SIB, Bern or streamed, Switzerland SIB Bern or streamed Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

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