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  • CAS Personalized Molecular Oncology

    1 October 2018 - 31 July 2019

    Basel, Switzerland

    Elixir node event
    CAS Personalized Molecular Oncology https://tess.elixir-europe.org/events/cas-personalized-molecular-oncology The CAS in Personalized Molecular Oncology aims at providing a comprehensive and integrative view of the field, by covering all the aspects involved along the pipeline: (i) tumor biology and genetics, (ii) molecular pathology, (iii) clinical bioinformatics, and (iv) clinical oncology. First of its kind in Switzerland, it will focus on the methodologies used to generate, analyze and interpret patients’ molecular profiles, also touching upon the associated technical, regulatory and ethical challenges. As an important outcome, it will establish a common language between the wide range of professionals involved in the personalized oncology process, from biologists, bioinformaticians, pathologists to clinicians, enabling an efficient and better informed use of e.g. genomic data for both routine clinical practice and clinical research. Moreover, it should empower professionals to develop a vision for their own institution, by critically evaluating the potential benefits and limitations of current and future developments in personalized oncology. The CAS is organized jointly by the University Hospital of Basel, the University Hospital of Lausanne, and the SIB Swiss Institute of Bioinformatics. 2018-10-01 09:00:00 UTC 2019-07-31 17:00:00 UTC SIB Swiss Institute of Bioinformatics Pathologie Universitätsspital Basel, 40, Schönbeinstrasse, Basel, Switzerland Pathologie Universitätsspital Basel, 40, Schönbeinstrasse Basel Switzerland University Hospital of BaselSIB Swiss Institute of BioinformaticsUniversity Hospital of Lausanne Dr. Aitana Lebrand Clinical Bioinformatics SIB | Swiss Institute of Bioinformatics Ch. des Mines 9 CH-1202 Genève Tel. +41 (0)22 379 02 67 aitana.lebrand@sib.swiss [] Professionals involved in personalized molecular oncology, including laboratory managers, biologists, bioinformaticians, pathologists, geneticists, clinicians and pharmaceutical company employees. workshops_and_courses registration_of_interest Tumor biology and geneticsMolecular pathologyClinical BioinformaticsClinical oncology

  • Executive Masters in Management of Research Infrastructures

    13 November 2018 - 26 June 2020

    Milan, Italy

    Elixir node event
    Executive Masters in Management of Research Infrastructures https://tess.elixir-europe.org/events/executive-masters-in-management-of-research-infrastructures-12abb26e-f3b7-45ac-92c6-24008017292d This Masters development programme is aimed at current Research Infrastructures managers and leaders who wish to develop the competencies required to meet the needs of Research Infrastructures in the planning, construction and operation phases. 2018-11-13 12:00:00 UTC 2020-06-26 12:00:00 UTC University of Milano-Bicocca, Milan, Italy University of Milano-Bicocca Milan Italy 20126 [] Claire Johnson [] [] [] [] []

  • Software Carpentry - Vanderbilt University

    15 March - 19 April 2019

    Software Carpentry - Vanderbilt University https://tess.elixir-europe.org/events/software-carpentry-vanderbilt-university-edf7b74c-2dff-45cd-819f-4bb0d4e84388 Find out more at https://broadwym.github.io/2019-03-15-vanderbilt/ 2019-03-15 09:00:00 UTC 2019-04-19 00:00:00 UTC Software Carpentry Vanderbilt University Vanderbilt University [] [] [] workshops_and_courses [] []

  • Metabolomics Data Processing and Data Analysis

    18 March - 12 April 2019

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics Data Processing and Data Analysis https://tess.elixir-europe.org/events/metabolomics-data-processing-and-data-analysis This online course will explore the tools and approaches that are used to process and analyse metabolomics data, we will investigate the challenges that are typically encountered in the analysis of metabolomics data and provide solutions to overcome these problems. The course will be delivered using a combination of short videos, articles, discussions, and online workshops with step-by-step instructions and test data sets. 2019-03-18 09:00:00 UTC 2019-04-12 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []

  • Revolutionizing Next-Generation Sequencing (3rd edition)

    25 - 26 March 2019

    Antwerpen, Belgium

    Revolutionizing Next-Generation Sequencing (3rd edition) https://tess.elixir-europe.org/events/revolutionizing-next-generation-sequencing-3rd-edition After two successful editions (Jan 2015, Leuven and March 2017, Antwerp), VIB is proud to present the third edition of this Tools & Technologies conference. VIB believes that the revolutionary discoveries enabled by NGS are not yet at its zenith and that the technology can go much further. During this 3rd edition VIB will bring together over 30 top scientists and technology developers form both industry and academia. They will discuss emerging tools and approaches in several sessions such as: • Long reads, Genome Structure and Mapping • Epigenomics • Metagenomics • Spatial transcriptomics • Population Scale and Clinical Sequencing • Single Cell Sequencing • Emerging technologies In addition to a great scientific and technology program, the conference will provide ample opportunities to network during the breaks, poster sessions and the conference dinner. Also young scientists are encouraged to showcase their own work to the international research community by oral or poster presentation! Information for poster submissions: The format for your poster should be: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation Deadlines: • Early Bird: 11/02/2019 • Late Registration: 11/03/2019 • Abstract deadline: 21/01/2019 2019-03-25 08:00:00 UTC 2019-03-26 18:00:00 UTC VIB Conferences BluePoint Antwerpen, 9, Filip Williotstraat, Antwerpen, Belgium BluePoint Antwerpen, 9, Filip Williotstraat Antwerpen Antwerpen Belgium 2600 Mapping Population genomics Population genetics Sequencing Transcriptomics Metagenomic sequencing Metagenomics Epigenetics Epigenomics Genotyping experiment Genotype and phenotype Genomics [] Evy Vierstraete +32 9 244 66 11 conferences@vib.be BioradBiokeLexogenAnalisBio-techneBGI [] 350 meetings_and_conferences [] Genome Structure Genome MappingEpigenomicsMetagenomicsSpatial transcriptomicsPopulation Scale clinical sequencingSequencingSingle Cell Sequencing

  • Software Carpentry - Bigelow Laboratory for Ocean Sciences

    25 - 26 March 2019

    Software Carpentry - Bigelow Laboratory for Ocean Sciences https://tess.elixir-europe.org/events/software-carpentry-bigelow-laboratory-for-ocean-sciences Find out more at https://bigelowlab.github.io/2019-03-25-Bigelow-DataCarpentry/ 2019-03-25 09:00:00 UTC 2019-03-26 00:00:00 UTC Software Carpentry Bigelow Laboratory for Ocean Sciences Bigelow Laboratory for Ocean Sciences [] [] [] workshops_and_courses [] []

  • Genome Browsers and using UCSC genome Browser tools

    25 - 26 March 2019

    Melbourne, Australia

    Genome Browsers and using UCSC genome Browser tools https://tess.elixir-europe.org/events/genome-browsers-and-using-ucsc-genome-browser-tools-e7d28a75-046c-4e5d-9132-6880c7f35d67 2019-03-25 09:00:00 UTC 2019-03-26 00:00:00 UTC Melbourne Bioinformatics 187 Grattan St, 187, Grattan Street, Melbourne, Australia 187 Grattan St, 187, Grattan Street Melbourne Australia [] enquiries@melbournebioinformatics.org.au [] [] [] [] []

  • An Introduction to Solving Biological Problems with R

    25 - 26 March 2019

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with R https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-r-870b40ac-8d7c-4931-8051-302644c93d9f [R](https://www.r-project.org/) is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. The course website providing links to the course materials is [here](http://cambiotraining.github.io/r-intro/). Please note that although we will demonstrate how to perform statistical analysis in R, we will not cover the theory of statistical analysis in this course. Those seeking an in-depth explanation of how to perform and interpret statistical tests are advised to see the list of Related courses. Moreover, those with some programming experience in other languages (e.g. Python, Perl) might wish to attend the follow-on [Data Analysis and Visualisation in R](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-intR) course. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=2673375&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R).'' 2019-03-25 09:30:00 UTC 2019-03-26 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology 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 [] []

  • Advanced Fortran Programming @ CSC

    26 - 28 March 2019

    Advanced Fortran Programming @ CSC https://tess.elixir-europe.org/events/advanced-fortran-programming-csc-6da7e8e1-98f1-4b80-ba96-23f3f01c8238 Description This course covers the modern features of the Fortran programming language. Topics include object-oriented features, language interoperability and several other enhancements included in Fortran 2008 standard. In addition, a way to express distributed memory parallelism via Fortran coarrays will be discussed in detail. The course provides an overview on all relevant features of Fortran beyond the 95 standard. You will also be able to write parallel programs using the Fortran coarrays concept. Learning outcome The course provides an overview on all the relevant features of Fortran beyond the 95 standard. You also will be able to write parallel programs using the Fortran coarrays concept. Prerequisites Solid knowledge of Fortran 95/2003. The concepts discussed in the PATC introduction course Fortran Programming for Scientific Computing is the minimum. Knowledge on C will also be needed for understanding the topics on the language interoperability. Familiarity with parallel programming with message-passing interface (MPI) standard will be assumed when discussing the Fortran coarrays. In addition, some familiarity with object-oriented programming concepts will be assumed. Agenda Day 1: Tuesday, March 26 09.00-09.15  Course introduction 09.15-10.00  Useful new features beyond F95 10.00-10.15  Coffee break 10.15-11.00  Advanced topics in Fortran I/O 11.00-11.45  Exercises 11.45-12:00  Working with Fortran compilers 12.00-13.00  Lunch break 13.00-14.00  Interoperability with C 14.00-14.45  Exercises 14.45-15.00  Coffee break 15.00-16.00  Exercises Day 2: Wednesday, March 27 09.00-09.45  Introduction to Fortran coarrays 09.45-10.00  Coffee break 10.00-11.15  Exercises 11.15-12.00  More coarray features 12.00-13.00  Lunch break 13.00-14.00  Exercises 14.00-14.45  Advanced topics in coarrays 14.45-15.00  Coffee break 15.00-16.00  Exercises Day 3: Thursday, March 28 09.00-10.00  Additional capabilities of Fortran types, procedure pointers 10.00-10.15  Coffee break 10.15-11.00  Exercises 11.00-12.00  Type extensions, type-bound procedures 12.00-13.00  Lunch break 13.00-14.00  Exercises 14.00-14.45  More complex data structures with Fortran 14.45-15.00  Coffee break 15.00-16.00  Exercises Lecturers:  Sami Ilvonen (CSC), Peter Råback (CSC) Language:   English Price:          Free of charge https://events.prace-ri.eu/event/852/ 2019-03-26 07:00:00 UTC 2019-03-28 14:00:00 UTC [] [] [] workshops_and_courses [] []

  • Parallel visualization of scientific data using Blender @ IT4Innovations

    26 March 2019

    Parallel visualization of scientific data using Blender @ IT4Innovations https://tess.elixir-europe.org/events/parallel-visualization-of-scientific-data-using-blender-it4innovations Annotation The course will focus on visualization of large datasets that can come from simulations of different physical phenomena (e.g. fluid dynamics, structural analysis, etc.). To create visually pleasing outputs of such data a path tracing rendering method will be used. Most of the course aspects will be covered within the popular 3D creation suite Blender. We will work with the brand new version 2.8 and introduce our developed plug-in called Covise Nodes to work with the scientific data inside Blender. Within the course we will demonstrate some of the basics of Blender, followed by a data visualization example using the plug-in, and we will finish the course with rendering of the final scene on the Salomon cluster. The course will be mainly hands-on. Purpose of the course (benefits for the attendees) Attendees will learn how to visualize different simulation data in Blender and how to provide visually pleasing outputs. About the tutor(s) Petr Strakoš obtained his Ph.D. from CTU (the Czech Technical University in Prague) in Mechanical Engineering. Now he is a member of the Infrastructure Research Lab and the VaVR (Visualization and Virtual Reality) group, where he focuses on research in the area of visualization, image processing, and efficient utilization of these topics on a cluster. He also cooperates with partners from industry and other institutions in applied research. Milan Jaroš is a researcher in the Infrastructure Research Lab at IT4Innovations. He has nine years of experience in professional programming (C++, C#, Java, etc.). He has developed several pieces of commercial software (including mobile applications). In recent years he has been focusing on research in the area of HPC computing (including support of GPU and Intel Xeon Phi coprocessor), processing of medical images, and visualizations of engineering data (virtual reality, rendering, post-processing of CFD calculation, etc.). He is a co-developer of plugins for multiple pieces of software (Blender, COVISE/OpenCOVER, Unity, etc.). Alena Ješko is a researcher in the Infrastructure Research Lab at IT4Innovations. She has worked on mesh transformation topics for cranial orthosis design and photogrammetry for treating orbital fractures. She has recently started to work on AI and Machine Learning in Image Processing. https://events.prace-ri.eu/event/851/ 2019-03-26 08:30:00 UTC 2019-03-26 15:30:00 UTC [] [] [] workshops_and_courses [] []

  • Software Carpentry - UC Irvine Libraries

    26 - 27 March 2019

    Software Carpentry - UC Irvine Libraries https://tess.elixir-europe.org/events/software-carpentry-uc-irvine-libraries-d2a350f7-c79e-4804-b116-a4c1d368244f Find out more at https://uci-libraries.github.io/2019-03-26-UCI/ 2019-03-26 09:00:00 UTC 2019-03-27 00:00:00 UTC Software Carpentry UC Irvine Libraries UC Irvine Libraries [] [] [] workshops_and_courses [] []

  • Identification and linking of data related to AOPWiki

    26 March 2019

    Identification and linking of data related to AOPWiki https://tess.elixir-europe.org/events/identification-and-linking-of-data-related-to-aopwiki 2019-03-26 09:00:00 UTC 2019-03-26 00:00:00 UTC OpenRiskNet [] [] [] workshops_and_courses [] adverse outcome pathway

  • EMBL-EBI Workshop: Interactions and pathways for endocrine biology

    26 March 2019

    New Orleans, United States of America

    Elixir node event
    EMBL-EBI Workshop: Interactions and pathways for endocrine biology https://tess.elixir-europe.org/events/embl-ebi-workshop-interactions-and-pathways-for-endocrine-biology This course is aimed at giving life scientists and clinicians training on how to explore and use molecular interaction and pathway bioinformatics resources. 2019-03-26 09:00:00 UTC 2019-03-26 13:00:00 UTC New Orleans Ernest N. Morial Convention Center, New Orleans, United States of America New Orleans Ernest N. Morial Convention Center New Orleans United States of America 70130 [] Marina Pujol [] [] [] [] []

  • Introduction to Variant Calling with Galaxy & the GVL

    26 - 27 March 2019

    Melbourne, Australia

    Introduction to Variant Calling with Galaxy & the GVL https://tess.elixir-europe.org/events/introduction-to-variant-calling-with-galaxy-the-gvl 2019-03-26 09:00:00 UTC 2019-03-27 00:00:00 UTC Melbourne Bioinformatics 187 Grattan St, 187, Grattan Street, Melbourne, Australia 187 Grattan St, 187, Grattan Street Melbourne Australia [] enquiries@melbournebioinformatics.org.au [] [] [] [] []

  • Cryo-EM Course on Tomography

    26 - 28 March 2019

    Elixir node event
    Cryo-EM Course on Tomography https://tess.elixir-europe.org/events/cryo-em-course-on-tomography 2019-03-26 09:00:00 UTC 2019-03-28 00:00:00 UTC [] [] [] workshops_and_courses [] []

  • Introduction to RNA-Seq and Functional Interpretation

    26 - 29 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to RNA-Seq and Functional Interpretation https://tess.elixir-europe.org/events/introduction-to-rna-seq-and-functional-interpretation This course will provide an introduction to the technology, data analysis, tools and resources used in RNA sequencing and transcriptomics. 2019-03-26 12:00:00 UTC 2019-03-29 14:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] Johanna Langrish [] [] [] [] []

  • Software Carpentry - UC Davis

    27 - 28 March 2019

    Software Carpentry - UC Davis https://tess.elixir-europe.org/events/software-carpentry-uc-davis-b8f09bbe-6710-4ac2-8700-c7660a808fde Find out more at https://karenword.github.io/2019-03-27-ttt-uc_davis/ 2019-03-27 09:00:00 UTC 2019-03-28 00:00:00 UTC Software Carpentry UC Davis UC Davis [] [] [] workshops_and_courses [] []

  • HPC@UGent introduction

    27 March 2019

    Gent, Belgium

    Elixir node event
    HPC@UGent introduction https://tess.elixir-europe.org/events/hpc-ugent-introduction-458c998e-3de7-4d05-88c5-2fbc5787a83d b'Quick introductory training jump starting new researchers to work on the supercomputing infrastructure of Ghent University\n \n Wednesday Mar 27th 2019, 10am - 5pm\n \n see also \n https://www.ugent.be/hpc/en/training/materials/2019/introhpcugent\n \r\n\r\n \n' 2019-03-27 09:00:00 UTC 2019-03-27 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []

  • Introduction to Genomics and its application in different medical specialties and introduction to Galaxy project for analyzing genome sequences

    27 - 28 March 2019

    Introduction to Genomics and its application in different medical specialties and introduction to Galaxy project for analyzing genome sequences https://tess.elixir-europe.org/events/introduction-to-genomics-and-its-application-in-different-medical-specialties-and-introduction-to-galaxy-project-for-analyzing-genome-sequences 2019-03-27 09:00:00 UTC 2019-03-28 00:00:00 UTC [] Abdelazeem Abdelhameed Elhabyan [] [] [] [] []

  • Best practices in HPC (sciCORE cluster)

    27 March 2019

    Basel, Switzerland

    Elixir node event
    Best practices in HPC (sciCORE cluster) https://tess.elixir-europe.org/events/best-practices-in-hpc-scicore-cluster Overview This one-day course is a follow-up to the sciCORE course "Introduction to HPC (sciCORE cluster)". 2019-03-27 09:00:00 UTC 2019-03-27 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Introduction to RNA-seq data analysis

    27 - 29 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to RNA-seq data analysis https://tess.elixir-europe.org/events/introduction-to-rna-seq-data-analysis-5ad59a77-0bc1-444d-b42c-8f9d499d2ef4 The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=2673403&course-title=Introduction%20to%20RNA-seq%20data%20analysis).'' 2019-03-27 09:30:00 UTC 2019-03-29 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR RNA-Seq Data mining Transcriptomics Data visualisation Functional genomics 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 [] []

  • Software Carpentry - Claremont McKenna College

    28 - 29 March 2019

    Software Carpentry - Claremont McKenna College https://tess.elixir-europe.org/events/software-carpentry-claremont-mckenna-college Find out more at https://timothylwarren.github.io/2019-02-22-claremont/ 2019-03-28 09:00:00 UTC 2019-03-29 00:00:00 UTC Software Carpentry Claremont McKenna College Claremont McKenna College [] [] [] workshops_and_courses [] []

  • Open Targets Workshop

    28 March 2019

    EMBL-EBI

    Open Targets Workshop https://tess.elixir-europe.org/events/open-targets-workshop-55d54e1b-0a19-4e14-9719-6df0ad7054b9 In this workshop, we introduce Open Targets and its underlying projects for data integration for access and visualisation of biological data in drug target identification and discovery. 2019-03-28 09:00:00 UTC 2019-03-28 00:00:00 UTC EMBL-EBI, EMBL-EBI EMBL-EBI EMBL-EBI [] [] [] workshops_and_courses [] Open Targets

  • Efficient Parallel I/O @ EPCC at Imperial College London

    28 - 29 March 2019

    Efficient Parallel I/O @ EPCC at Imperial College London https://tess.elixir-europe.org/events/efficient-parallel-i-o-epcc-at-imperial-college-london Please note:  This course will take place at Imperial College London SALC 10,  Sherfield building, level 5, South Kensington Campus One of the greatest challenges to running parallel applications on large numbers of processors is how to handle file IO. Standard IO routines are not designed with parallelism in mind, and IO overheads can grow to dominate the overall runtime. Parallel file systems are optimised for large data transfers, but performance can be far from optimal if every process opens its own file or if all IO is funneled through a single master process. This hands-on course explores a range of issues related to parallel IO. It uses ARCHER and its parallel Lustre file system as a platform for the exercises; however, almost all the IO concepts and performance considerations are applicable to any parallel system. The IO part of the MPI standard gives programmers access to efficient parallel IO in a portable fashion. However, there are a large number of different routines available and some can be difficult to use in practice. Despite its apparent complexity, MPI-IO adopts a very straightforward high-level model. If used correctly, almost all the complexities of aggregating data from multiple processes can be dealt with automatically by the library. The first day of the course will cover the MPI-IO standard, developing IO routines for a regular domain decomposition example. It will also briefly cover higher-level standards such as HDF5 and NetCDF which are built on top of MPI-IO. The second day will concentrate on performance, covering how to configure the parallel file system and tune the MPI-IO library for best performance. Case studies from real codes will be presented. Prerequisites: The course assumes a good understanding of basic MPI programming in Fortran, C or C++. Knowledge of MPI derived datatypes would be useful but not essential. Timetable Day 1 09:30 - 10:15 : Parallel IO 10:15 - 11:00 : Practical : Basic IO 11:00 - 11:30 : Break 11:30 - 12:15 : Derived Datatypes for MPI-IO 12:15 - 13:00 : Practical: Derived Datatypes 13:00 - 14:00 : Lunch 14:00 - 14:45 : Basic MPI-IO Routines 14:45 - 15:30 : Practical: Basic MPI-IO 15:30 - 16:00 : Break 16:00 - 16:45 : MPI-IO Features and alternative libraries 16:45 - 17:30 : Practical : Alternative Libraries Day 2 09:30 - 10:15 : Lustre file system on ARCHER 10:15 - 11:00 : Practical: Lustre configuration 11:00 - 11:30 : Break 11:30 - 12:15 : Parallel IO libraries on ARCHER 12:15 - 13:00 : Practical: tuning parallel IO 13:00 - 14:00 : Lunch 14:00 - 14:45 : Case studies 14:45 - 15:30 : Individual consultancy session   Trainer David Henty David teaches on a wide range of EPCC's technical training courses, including MPI and OpenMP, and is overall course organiser for EPCC's MSc in High Performance Computing.     Course Material http://www.archer.ac.uk/training/course-material/2019/03/io-imp/index.php https://events.prace-ri.eu/event/846/ 2019-03-28 09:00:00 UTC 2019-03-29 17:30:00 UTC [] [] [] workshops_and_courses [] []

  • Data Manipulation and Visualisation

    29 March 2019

    Sheffield, United Kingdom

    Data Manipulation and Visualisation https://tess.elixir-europe.org/events/data-manipulation-and-visualisation R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. 2019-03-29 09:30:00 UTC 2019-03-29 17:00:00 UTC Bartolome House, Computer Room ALG04, Sheffield, United Kingdom Bartolome House, Computer Room ALG04 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []

  • Population genomics: Background, tools and programming

    30 March - 6 April 2019

    Italy

    Population genomics: Background, tools and programming https://tess.elixir-europe.org/events/population-genomics-background-tools-and-programming Study methods in population genomics have been profoundly reshaped in the last few years, fostered by a rapid growth of DNA sequence production and sharing. This unprecedented opportunity guided major steps forward in the field and calls for new approaches and computational skills to become routine in evolutionary genomics laboratories. The objectives of this EMBO Practical Course are to give an overview of the state of the art methods in population genomics, including programming, and to enable participants to run their project’s analyses with high confidence. The course combines lectures from outstanding experienced population geneticists with practice, both at individual and group level. All conceptual innovation will be presented in lectures and applied in practice. This EMBO Practical Course will cover coalescent, genetic diversity, natural selection, population demography in time and space, admixture, genetic clustering, and genome-wide association studies. Population genetics topics will be complemented by computational ones such as Python programming and machine learning techniques. This course aims at evolutionary biologists who already have basic bioinformatics skills. Ph.D. students and Postdoc researchers will benefit the most out of this course, but applications from all candidates will be evaluated in their context. 2019-03-30 09:00:00 UTC 2019-04-06 17:00:00 UTC EMBO Procida, Italy Procida Italy Population genomics [] Organizing Secretariat Scientific Communication srl info@jeangilder.it +39 081 2296460 EMBO Evolutionary BiologistsPhD Studentspost-docs workshops_and_courses [] []

  • Programming paradigms for GPU devices@Cineca

    1 - 3 April 2019

    Programming paradigms for GPU devices@Cineca https://tess.elixir-europe.org/events/programming-paradigms-for-gpu-devices-cineca-1dff73da-578e-4e79-89d6-7b12bc4c67b9 This course gives an overview of the most relevant GPGPU computing techniques to accelerate computationally demanding tasks on HPC heterogeneous architectures based on GPUs. The course will start with an architectural overview of modern GPU based heterogeneous architectures, focusing on its computing power versus data movement needs. The course will cover both a high level (pragma-based) programming approach with OpenACC for a fast porting startup, and lower level approaches based on nVIDIA CUDA and OpenCL programming languages for finer grained computational intensive tasks. A particular attention will be given on performance tuning and techniques to overcome common data movement bottlenecks and patterns. Topics: Overview of architectural trends of GPUs in HPC. GPGPU parallel programming in heterogeneous architectures. Basis of OpenACC, CUDA and OpenCL programming. Skills: By the end of the course, students will be able to: understand the strengths and weaknesses of GPUs as accelerators program GPU accelerated applications using both higher and lower level programming approaches overcome problems and bottlenecks regarding data movement between host and device memories make best use of independent execution queues for concurrent computing/data-movement operations Target Audience: Researchers and programmers interested in porting scientific applications or use efficient post-process and data-analysis techniques in modern heterogeneous HPC architectures. Prerequisites: A basic knowledge of C or Fortran is mandatory. Programming and Linux or Unix. A basic knowledge of any parallel programming technique/paradigm is recommended. Grant: The lunch for the three days will be offered to all the participants and some grants are available. The only requirement to be eligible is to be not funded by your institution to attend the course and to work or live in an institute outside the Roma area. The grant  will be 300 euros for students working and living outside Italy and 150 euros for students working and living in Italy (outside Roma). Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lectures. Further information about how to request the grant, will be provided at the confirmation of the course: about 3 weeks before the starting date. Coordinating Teacher: Dr. L.Ferraro   https://events.prace-ri.eu/event/830/ 2019-04-01 07:00:00 UTC 2019-04-03 16:00:00 UTC [] [] [] workshops_and_courses [] []

  • GPU Programming with CUDA @ JSC

    1 - 3 April 2019

    GPU Programming with CUDA @ JSC https://tess.elixir-europe.org/events/gpu-programming-with-cuda-jsc-5b4c9199-55c1-44b6-b1df-7b7f28804105 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 an NVIDIA GPU. The course will cover basic aspects of GPU architectures and programming. Focus is on the usage of the parallel programming language CUDA-C which allows maximum control of NVIDIA GPU hardware. 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 CUDA GPU libraries like CuBLAS and CuFFT Tools for debugging and profiling Performance optimizations Prerequisites: Some knowledge about Linux, e.g. make, command line editor, Linux shell, experience in C/C++ Application Registrations are only considered until 28 February 2018 due to available space, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructors: Dr. Jan Meinke, Jochen Kreutz, Dr. Andreas Herten, JSC; Jiri Kraus, NVIDIA Contact For any questions concerning the course please send an e-mail to j.meinke@fz-juelich.de https://events.prace-ri.eu/event/823/ 2019-04-01 07:00:00 UTC 2019-04-03 14:30:00 UTC [] [] [] workshops_and_courses [] []

  • Performance portability for GPU application using high-level programming approaches @ MdlS /Idris

    1 - 2 April 2019

    Performance portability for GPU application using high-level programming approaches @ MdlS /Idris https://tess.elixir-europe.org/events/performance-portability-for-gpu-application-using-high-level-programming-approaches-mdls-idris-e05a2681-bd72-4aea-9ea1-7fa210925446 When developing a numerical simulation code with high performance and efficiency in mind, one is often compelled to accept a trade-off between using a native-hardware programming model (like CUDA or OpenCL), which has become tremendously challenging, and loosing some cross-platform portability. Porting a large existing legacy code to a modern HPC platform, and developing a new simulation code, are two different tasks that may be benefit from a high-level programming model, which abstracts the low-level hardware details. This training presents existing high-level programming solutions that can preserve at best as possible performance, maintainability and portability across the vast diversity of modern hardware architectures (multicore CPU, manycore, GPU, ARM, ..) and software development productivity. We will  provide an introduction to the high-level C++ programming model Kokkos https://github.com/kokkos, and show basic code examples  to illustrate the following concepts through hands-on sessions: hardware portability: design an algorithm once and let the Kokkos back-end (OpenMP, CUDA, ...) actually derive an efficient low-level implementation; efficient architecture-aware memory containers: what is a Kokkos::view; revisit fundamental parallel patterns with Kokkos: parallel for, reduce, scan, ... ; explore some mini-applications. Several detailed examples in C/C++/Fortran will be used in hands-on session on the high-end hardware platform Ouessant (http://www.idris.fr/ouessant/), equipped with Nvidia Pascal GPUs. Prerequisites: Some basic knowledge of the CUDA programming model and of C++. https://events.prace-ri.eu/event/818/ 2019-04-01 07:30:00 UTC 2019-04-02 15:00:00 UTC [] [] [] workshops_and_courses [] []

  • Data Carpentry in R

    1 - 2 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Data Carpentry in R https://tess.elixir-europe.org/events/data-carpentry-in-r-119428f3-9bb8-44f1-9b63-ec1b787a40b9 In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analysing and sharing data. Data Carpentry workshops are designed to teach basic concepts, skills and tools for working more effectively with data, using a combination of tools with a main focus in R. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools. This course is organised in collaboration with [ElixirUK](http://www.elixir-uk.org/) and the [Software Sustainability Institute](https://www.software.ac.uk/). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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 by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2857971&course-title=Data%20Carpentry%20in%20R).'' 2019-04-01 08:30:00 UTC 2019-04-02 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
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