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223 events found

  • EMBL-EBI Training webinar series

    1 September - 31 December 2017

    Elixir node event
    EMBL-EBI Training webinar series https://tess.oerc.ox.ac.uk/events/embl-ebi-training-webinar-series The EMBL-EBI Training webinar series is taking a short break and will return in at the end of September with new webinars. Details of upcoming webinars will be posted here soon. 2017-09-01 13:00:00 UTC 2017-12-31 13:00:00 UTC [] Melissa Burke [] [] [] []
  • Executive Masters in Management of Research Infrastructures

    20 September 2017 - 15 March 2019

    Milan, Italy

    Elixir node event
    Executive Masters in Management of Research Infrastructures https://tess.oerc.ox.ac.uk/events/executive-masters-in-management-of-research-infrastructures 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. 2017-09-20 12:00:00 UTC 2019-03-15 12:00:00 UTC University of Milano-Bicocca, Milan, Italy University of Milano-Bicocca Milan Italy 20126 [] Claire Johnson [] [] [] []
  • The Genomics Era: the Future of Genetics in Medicine

    6 November - 11 December 2017

    The Genomics Era: the Future of Genetics in Medicine https://tess.oerc.ox.ac.uk/events/the-genomics-era-the-future-of-genetics-in-medicine-42e56020-ebf6-4289-9192-03b853874b20 Get an introduction to the growing role of genomics in healthcare, for patient diagnoses, treatment and disease prevention. 2017-11-06 09:00:00 UTC 2017-12-11 00:00:00 UTC St George's, University of London [] [] workshops_and_courses [] []
  • Linux for bioinformatics

    20 - 27 November 2017

    Gent, Belgium

    Elixir node event
    Linux for bioinformatics https://tess.oerc.ox.ac.uk/events/linux-for-bioinformatics 2017-11-20 09:30:00 UTC 2017-11-27 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] []
  • Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl

    23 - 24 November 2017

    Edinburgh, United Kingdom

    Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl https://tess.oerc.ox.ac.uk/events/introduction-to-chip-seq-data-analysis-and-visualisation-using-ensembl-6be6d59a-454c-4b69-bdc5-de20c9f01346 ChIP-seq (Chromatin ImmunoPrecipitation followed by Sequencing) is a popular high-throughput sequencing assay to identify binding sites of DNA-associated proteins and histone modifications. Determining how proteins interact with DNA and the epigenetic landscape is essential for elucidating the regulation of gene expression. The aim of this workshop is to familiarise the participants with the primary analysis of ChIP-seq data sets by providing a balanced set of lectures and practicals on analysis methodologies. Practicals include publicly available ChIP-seq datasets, processed using widely used and open-source software programs (e.g. FASTQC, BWA, samtools, bedtools, wiggletools, MACS2, MEME, TOMTOM, ngsplot) and visualised on the Ensembl genome browser. 2017-11-23 09:00:00 UTC 2017-11-24 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Bioinformatics ChIP-seq Genomics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] workshops_and_courses [] BioinformaticsChIP-seqGenomics
  • An Introduction to Solving Biological Problems with Python

    23 - 24 November 2017

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with Python https://tess.oerc.ox.ac.uk/events/an-introduction-to-solving-biological-problems-with-python-64e86759-6975-4b49-b913-afe675eb6fd2 This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs. Course materials are available [here](http://pycam.github.io). Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, [Working with Python: functions and modules](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-advpython/). 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=2234811&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python).'' 2017-11-23 09:30:00 UTC 2017-11-24 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics Biology University of Cambridge Bioinformatics Training Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • Analysis of public microarray data using Genevestigator

    24 November 2017

    Gent, Belgium

    Elixir node event
    Analysis of public microarray data using Genevestigator https://tess.oerc.ox.ac.uk/events/analysis-of-public-microarray-data-using-genevestigator 2017-11-24 09:30:00 UTC 2017-11-24 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] []
  • Debugging and Optimization of Scientific Applications@Cineca

    27 - 29 November 2017

    Debugging and Optimization of Scientific Applications@Cineca https://tess.oerc.ox.ac.uk/events/debugging-and-optimization-of-scientific-applications-cineca-c79ea0d8-d3df-4fca-9d56-9052e79a4756 The tipical approach to the art of programming from the point of view of a scientist only rarely permits to reach good results in terms of computational performances. The basic knowledge about how a computer machine really works permits even to a naif programmer to better write his own code and eventually to optimize properly any kind of scientific program. This knowledge is way more important in the field of High-Performance Computing where the correct exploitation of the modern architecures is crucial to the achievement of scientific results. This code is addressed to C and Fortran programmers that, even without notions of computer science, have necessities to learn tricks and techniques to quickly debug and optimize codes without restarting from scratch. Aim of this course is to guide the user to analyze and improve performances of his software, by introducing techniques and tools used in the HPC world. Software and hardware profilers will be presented and it will be showed how to find bottlenecks and how to fix them. Typical techniques of optimization (cache reuse, unrolling, inlining, vectorization) will be presented the use of mathematical libraries will be discussed. Furthermore, the use of compiler flags on different architectures and compilers will be introduced.   Topics:  Computer architectures: cache memory, cache coherency, cache padding, memory alignment, pipeline, branch prediction. Introduction to compilers: what is and how a compiler does work. Optimization techniques: aliasing, interprocedural analysis, inlining, loop unrolling, intrinsic functions Profiling and debugging tools. Scientific libraries.   Target audience:  Researchers and programmers interested to a quick and efficient debugging and to a knowledge of fundamental concepts of optimization. This course is particularly suitable for people approaching for the first time to issues of computer programming in the framework of scientific calculations.   Pre-requisites:  Knowledge of Fortran or C/C++. Elementary notions of Linux/Unix. 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 and live in an institute outside the Bologna 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 Bologna area). 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.   https://events.prace-ri.eu/event/660/ 2017-11-27 08:00:00 UTC 2017-11-29 17:00:00 UTC [] [] workshops_and_courses [] []
  • Introduction to Bioinformatics using NGS data, 2 hp

    27 November - 1 December 2017

    Uppsala

    Introduction to Bioinformatics using NGS data, 2 hp https://tess.oerc.ox.ac.uk/events/introduction-to-bioinformatics-using-ngs-data-2-hp-f905b9ab-268b-4ca5-9f2d-7f92b2eee5d6 2017-11-27 09:00:00 UTC 2017-12-01 00:00:00 UTC Uppsala Uppsala [] [] workshops_and_courses [] []
  • Workshop Metagenomics

    27 - 28 November 2017

    Leiden, Netherlands

    Elixir node event
    Workshop Metagenomics https://tess.oerc.ox.ac.uk/events/workshop-metagenomics Metagenomics is a relatively new field that studies the presence of microorganisms in a sample, for example in water or soil samples, and interactions between the microorganisms. Genetic material is isolated from the samples and used to determine the presence… The post Workshop Metagenomics appeared first on Dutch Techcentre for Life Sciences. 2017-11-27 09:00:00 UTC 2017-11-28 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] workshops_and_courses [] []
  • Introduction to Biopython

    27 - 28 November 2017

    Introduction to Biopython https://tess.oerc.ox.ac.uk/events/introduction-to-biopython-480479af-82f8-428d-95c6-60cfc13542d6 This course provides a short introduction to python programming and Biopython tool library 2017-11-27 09:00:00 UTC 2017-11-28 17:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] workshops_and_courses [] []
  • 3rd de.NBI Bioimage Analysis Workshop

    27 - 29 November 2017

    3rd de.NBI Bioimage Analysis Workshop https://tess.oerc.ox.ac.uk/events/3rd-de-nbi-bioimage-analysis-workshop 2017-11-27 09:00:00 UTC 2017-11-29 00:00:00 UTC [] [] [] [] []
  • Python as a second language-II

    27 - 30 November 2017

    Heverlee, Belgium

    Elixir node event
    Python as a second language-II https://tess.oerc.ox.ac.uk/events/python-as-a-second-language-ii The second part elaborates on the theme of data transformation and scientific programming by concentrating on regular expressions, various file formats used in a scientific context, how to parse and transform data, interact with databases and external programs. It also covers the libraries that are useful for scientific programming such as numpy, scipy, matplotlib and pandas.Hands-on sessions provide real world challenges with increasing levels of complexity. Detailed time/place info 27/11/2017 - 09.00 - 13.00 30/11/2017 - 09.00 - 13.00 2017-11-27 09:00:00 UTC 2017-11-30 00:00:00 UTC ICTS opleidingscentrum B, Heverlee, Belgium ICTS opleidingscentrum B Heverlee Belgium 3001 [] [] [] [] []
  • Ensembl REST API course – 27th-28th November 2017

    27 - 28 November 2017

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API course – 27th-28th November 2017 https://tess.oerc.ox.ac.uk/events/ensembl-rest-api-course-27th-28th-november-2017 Work with the Ensembl developers to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2017-11-27 09:30:00 UTC 2017-11-28 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Emily Perry [] [] [] []
  • An Introduction to Solving Biological Problems with R

    27 - 28 November 2017

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with R https://tess.oerc.ox.ac.uk/events/an-introduction-to-solving-biological-problems-with-r-24eeee1c-3604-4fea-9fc8-a8acfdd37fae [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. 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=2234782&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R).'' 2017-11-27 09:30:00 UTC 2017-11-28 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics Biology University of Cambridge Bioinformatics Training Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • OpenStack Cloud Hands-On

    28 November 2017

    OpenStack Cloud Hands-On https://tess.oerc.ox.ac.uk/events/openstack-cloud-hands-on 2017-11-28 09:00:00 UTC 2017-11-28 00:00:00 UTC [] [] [] [] []
  • Earth Sciences Simulation Environments @ BSC

    29 November - 1 December 2017

    Earth Sciences Simulation Environments @ BSC https://tess.oerc.ox.ac.uk/events/earth-sciences-simulation-environments-bsc-eab9b650-7a00-498f-ada9-b67017f2dd44 The registration to this course is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course conveners: Andrea Manrique and Louis-Philippe Caron Course lecturers: Francesco Benincasa, Miguel Castrillo, Neven Fučkar, Oriol Jorba Casellas, Joan López de la Franca, Domingo Manubens, Nicolau Manubens, Kim Serradell Maronda, Oriol Tinto Objectives: The objective of this PATC course is to cover the basics of a high performance computing (HPC) environment oriented towards earth science applications, specifically chemical weather modelling and climate modelling. More precisely, the course will cover: Introduction to earth science fundamentals and modelling; Basic usage of an HPC environment: shell, compilers, libraries, file systems, queuing system; Build and configure targeted earth science applications with the NMMB/BSC-CTM chemical transport model and with the EC-EARTH climate model; Execute and monitor numerical experiments using a workflow manager; Analyse and visualise model outputs with a wide set of tools. Learning outcomes: Participants will learn and gain experience in accessing an HPC facility, installing earth science numerical models and related utilities and libraries, running numerical simulations, monitoring the execution of supercomputing jobs, analysing and visualising model results. Level: (All courses are designed for specialists with at least 1st cycle degree or similar background experience) For trainees with some theoretical and practical knowledge Prerequisites: At least University degree in progress on Earth Sciences, Computer Sciences or related area Basic knowledge of UNIX Knowledge of C, FORTRAN, MPI or openMP is recommended Knowledge of Earth Sciences data formats is recommended (grib, netcdf, hdf,…) Agenda: Day 1 (Nov. 29) 10:00-11:30 Introduction to earth science fundamentals and modelling.    11:30-11:50 Coffee break 11:50-13:30 Introduction to Linux and HPC, BSC facilities, PRACE and RES    13:30-14:30 Lunch break 14:30-16:00 HPC hands-on tutorial. At the end of this tutorial, the students will be able to compile and execute jobs on Mare Nostrum 4.    16:00-16:20 Coffee break 16:20-18:00 Introduction to analysis and visualisation tools for model outputs (s2dverification, MapGenerator, CDO, NCO, panoply, ncview)    20:00 Social dinner (participants pay individually) Day 2 (Nov 30) 10:00-11:00 Lecture on the NMMB-MONARCH chemical transport model. 11:00-12:00 Lecture on setting up and running the model.    12:00-12:30 Coffee break 12:30-14:00 Model hands-on tutorial. Students will run a prepared case.    14:00-15:00 Lunch break 15:00-17:00 Analysis hands-on tutorial. Students will apply tools for analysis and visualisation to the outputs created in the morning. Day 3 (Dec 1) 10:00-11:00 Lecture on the EC-EARTH climate model. 11:00-12:00 Lecture on setting up and running the model with Autosubmit.     12:00-12:30 Coffee break 12:30-14:00 Model hands-on tutorial. Students will run with a prepared case.    14:00-15:00 Lunch break 15:00-17:00 Analysis hands-on tutorial. Students will apply tools for analysis and visualisation to the outputs created in the morning. 17:00-17:30 MareNostrum visit End of Course https://events.prace-ri.eu/event/642/ 2017-11-29 08:00:00 UTC 2017-12-01 17:00:00 UTC [] [] workshops_and_courses [] []
  • Proteogenomics and Immunopeptidomics

    29 November - 1 December 2017

    Lausanne, Switzerland

    Proteogenomics and Immunopeptidomics https://tess.oerc.ox.ac.uk/events/proteogenomics-and-immunopeptidomics This course is co-organised by the CUSO/StarOmics doctoral program. Priority is given to its members, but is open to everyone. Overview Proteogenomics is an area of research at the interface of proteomics and genomics. 2017-11-29 09:00:00 UTC 2017-12-01 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] workshops_and_courses [] []
  • Data Analysis and Visualisation in R

    29 November 2017

    Cambridge, United Kingdom

    Elixir node event
    Data Analysis and Visualisation in R https://tess.oerc.ox.ac.uk/events/data-analysis-and-visualisation-in-r-00b0647a-16ff-4576-92a9-0de0a4ed107f This course introduces some relatively new additions to the R programming language: dplyr and ggplot2. In combination these R packages provide a powerful toolkit to make the process of manipulating and visualising data easy and intuitive. Materials for this course can be found [here](http://bioinformatics-core-shared-training.github.io/r-intermediate/). 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=2234798&course-title=Data%20analysis%20and%20visualisation).'' 2017-11-29 09:30:00 UTC 2017-11-29 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics Biology Data visualisation University of Cambridge Bioinformatics Training Existing R users who are not familiar with dplyr and ggplot2Those with programming experience in other languages that want to know what R can offer themGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • Hands-on Introduction to HPC for Life Scientists

    29 November - 1 December 2017

    Elixir node event
    Hands-on Introduction to HPC for Life Scientists https://tess.oerc.ox.ac.uk/events/hands-on-introduction-to-hpc-for-life-scientists This course provides an introduction to High-Performance Computing (HPC) for researchers in the life sciences, using ARCHER as a platform for hands-on training exercises. The course is co-organised and funded by BioExcel (http://bioexcel.eu/) and PRACE (http://www.prace-ri.eu/), and delivered in collaboration with ARCHER – the UK national supercomputing service (http://archer.ac.uk). 2017-11-29 10:00:00 UTC 2017-12-01 15:00:00 UTC [] Vera Matser [] [] [] []
  • Hands-on Introduction to HPC for Life Scientists @ EPCC

    29 November - 1 December 2017

    Hands-on Introduction to HPC for Life Scientists @ EPCC https://tess.oerc.ox.ac.uk/events/hands-on-introduction-to-hpc-for-life-scientists-epcc This course provides an introduction to High-Performance Computing (HPC) for researchers in the life sciences, using ARCHER as a platform for hands-on training exercises. The course is organised and funded by BioExcel - the Centre of Excellence for Computational Biomolecular Research (http://bioexcel.eu) and PRACE, and delivered in collaboration with ARCHER - the UK national supercomputing service (http://archer.ac.uk). Overview High-performance computing (HPC) is a fundamental technology used to solve a wide range of scientific research problems. Many important challenges in science such as protein folding, the search for the Higgs boson, drug discovery, and the development of nuclear fusion all depend on simulations, models and analyses run on HPC facilities to make progress.   This course introduces HPC to life science researchers, focusing on the aspects that are most important for those new to this technology to understand. It will help you judge how HPC can best benefit your research, and equip you to go on to successfully and efficiently make use of HPC facilities in future. The course will cover basic concepts in HPC hardware, software, user environments, filesystems, and programming models. It also provides an opportunity to gain hands-on practical experience and assistance using an HPC system (ARCHER, the UK national supercomputing service) through examples drawn from the life sciences, such as biomolecular simulation. Registration Registration is on a first-come, first-served basis via https://events.prace-ri.eu/event/626/registration/ Learning outcomes On completion of the course, we expect that attendees will understand and be able to explain:       • Why HPC? - What are the drivers and motivation? Who uses it and why?     • The UK & EU HPC landscape - HPC facilities available to researchers     • HPC hardware - Building blocks and architectures     • Parallel computing - Programming models and implementations     • Using HPC systems         • Access         • Batch schedulers & resource allocation         • Running jobs         • Dealing with errors         • Compiling code         • Using libraries         • Performance     • The Future of HPC Pre-requisites This course follows on naturally from the BioExcel Summer School on Foundation skills for HPC in computational biomolecular research (http://bioexcel.eu/events/bioexcel-summer-school/) Familiarity with basic Linux commands (at the level of being able to navigate a file system) is recommended. You may find a Linux 'cheat sheet' such as http://www.archer.ac.uk/documentation/user-guide/linux.php#quickref useful if you are less familiar with Linux. No programming skills or previous HPC experience is required. Desktop computers running Windows will be available, however you are encouraged to bring your own laptop (running Windows, Linux, or macOS) as you will find it useful to learn how to set this up to connect to ARCHER (with assistance from course helpers if needed) and perform the hands-on practicals. Bursaries BioExcel will be providing a limited number of fixed amount travel bursaries for this event. If you would like to be considered for a travel bursary email Vera Matser (matser [at] ebi.ac.uk). Eligibility criteria and conditions for the travel grants are available at http://bioexcel.eu/wp-content/uploads/2017/01/BioExcelTravelGrant.pdf   Timetable Wednesday November 29th 10:00 - Welcome, introduction, and course overview Review of HPC skills and competencies framework Familiarisation with fellow attendees 11:00 - LECTURE - What is HPC? 11:25 - PRACTICAL - Connecting to ARCHER 11:30 - BREAK - Coffee & Tea 12:00 - PRACTICAL - Sequence Alignment 13:00 - BREAK - Lunch 14:00 - LECTURE - Parallel Computing Patterns 14:30 - LECTURE - Measuring Parallel Performance 15:00 - PRACTICAL - Sequence Alignment (continued) 15:30 - BREAK - Coffee & Tea 16:00 - PRACTICAL - Sequence Alignment (continued) 16:15 - LECTURE - Building Blocks - Software (Operating System, Processes and Threads) 16:45 - LECTURE - Building Blocks - Hardware (Processors & cores, Memory, Accelerators) 17:15 - Review of the day 17:30 - Finish Thursday November 30th 9:30 - Summary of day 1 9:45 - LECTURE - Parallel Models 10:30 - PRACTICAL - Fractal 11:00 - BREAK - Coffee & Tea 11:30 - PRACTICAL - Fractal (continued) 12:00 - LECTURE - HPC Architectures 12:30 - LECTURE - Batch Systems & Parallel Application Launchers 13:00 - BREAK - Lunch 14:00 - PRACTICAL - Molecular Dynamics 15:00 - LECTURE - Compilers and Building Software 15:30 - BREAK - Coffee & Tea 16:00 - PRACTICAL - Molecular Dynamics (continued) 16:30 - LECTURE - Parallel libraries 17:00 - Review of the day 17:15 - Finish 19:00 - Dinner at Amber restaurant Friday December 1st 9:30 - Summary of day 2 9:45 - LECTURE - Pipelines and workflows 10:15 - PRACTICAL - t.b.c. 11:00 - LECTURE - The UK & EU HPC Landscape 11:30 - BREAK - Coffee & Tea 12:00 - LECTURE - The Future of HPC 12:30 - LECTURE - "Where next?" and things to remember 13:00 - Lunch 14:00 - Individual consultations, course review and feedback / competency survey 15:00 - Finish Course Materials www.archer.ac.uk/training/course-material/2017/11/intro-epcc/index.php   Dinner The course dinner will be held at the Amber restaurant, located at the Scotch Whisky Experience near Edinburgh Castle, on Thursday 30th November at 19:00. For location and travel information see https://www.scotchwhiskyexperience.co.uk/plan-your-visit       https://events.prace-ri.eu/event/626/ 2017-11-29 10:00:00 UTC 2017-12-01 15:00:00 UTC [] [] workshops_and_courses [] []
  • Ensembl Bite-Sized November 2017

    29 November 2017

    Cambridge, United Kingdom

    Elixir node event
    Ensembl Bite-Sized November 2017 https://tess.oerc.ox.ac.uk/events/ensembl-bite-sized-november-2017 Work with the Ensembl team to get to grips with fungal, protist and bacterial species in the Ensembl Genomes browser and data. 2017-11-29 12:00:00 UTC 2017-11-29 12:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Benjamin Moore [] [] [] []
  • Connecting proteins to genes programmatically with UniProt

    29 November 2017

    Elixir node event
    Connecting proteins to genes programmatically with UniProt https://tess.oerc.ox.ac.uk/events/connecting-proteins-to-genes-programmatically-with-uniprot Learn how to use the Proteins REST API providing UniProt data for connecting proteins and protein annotations (e.g. domains, variants) to the corresponding genome coordinates. Learn about navigating through protein isoforms, gene transcripts and exon boundaries to right data relationships. 2017-11-29 16:00:00 UTC 2017-11-29 17:00:00 UTC [] Melissa Burke [] [] [] []
  • Node-Level Performance Engineering @ LRZ

    30 November - 1 December 2017

    Node-Level Performance Engineering @ LRZ https://tess.oerc.ox.ac.uk/events/node-level-performance-engineering-lrz-cdd5f555-d34c-4c9a-a571-57e77a2bcc52 This course teaches performance engineering approaches on the compute node level. "Performance engineering" as we define it is more than employing tools to identify hotspots and bottlenecks. It is about developing 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. Once the architectural requirements of a code are understood and correlated with performance measurements, the potential benefit of optimizations can often be predicted. We introduce a "holistic" node-level performance engineering strategy, apply it to different algorithms from computational science, and also show how an awareness of the performance features of an application may lead to notable reductions in power consumption. The course is a PRACE Advanced Training Center event. Introduction Our approach to performance engineering Basic architecture of multicore systems: threads, cores, caches, sockets, memory The important role of system topology Tools: topology & affinity in multicore environments Overview likwid-topology and likwid-pin Microbenchmarking for architectural exploration Properties of data paths in the memory hierarchy Bottlenecks OpenMP barrier overhead Roofline model: basics Model assumptions and construction Simple examples Limitations of the Roofline model Pattern-based performance engineering Optimal use of parallel resources Single Instruction Multiple Data (SIMD) Cache-coherent Non-Uniform Memory Architecture (ccNUMA) Simultaneous Multi-Threading (SMT) Tools: hardware performance counters Why hardware performance counters? likwid-perfctr Validating performance models Roofline case studies Dense matrix-vector multiplication Sparse matrix-vector multiplication Jacobi (stencil) smoother Optional: The ECM performance model https://events.prace-ri.eu/event/632/ 2017-11-30 08:00:00 UTC 2017-12-01 16:00:00 UTC [] [] workshops_and_courses [] []
  • Introduction to RNA-seq Data Analysis

    30 November - 1 December 2017

    Edinburgh, United Kingdom

    Introduction to RNA-seq Data Analysis https://tess.oerc.ox.ac.uk/events/introduction-to-rna-seq-data-analysis-995275ae-2661-4b94-b238-9844d6a0d8aa RNA sequencing (RNA-seq) is quickly becoming the method of choice for transcriptome profiling. Nevertheless, it is a non-trivial task to transform the vast amount of data obtained with high-throughput sequencers into useful information. Thus, RNA-seq data analysis is still a major bottleneck for most researchers in this field. The ability of correctly interpreting RNA-seq results, as well as knowledge on the intrinsic properties of these data, are essential to avoid incorrect experimental designs and the application of inappropriate analysis methodologies. The aim of this workshop is to familiarise researchers with RNA-seq data and to initiate them in the analysis by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs will be used. 2017-11-30 09:00:00 UTC 2017-12-01 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Bioinformatics Genomics RNA-Seq Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] workshops_and_courses [] BioinformaticsGenomicsRNA-seq
  • Introduction to metabolomics for the clinical scientist

    1 December 2017

    Birmingham, United Kingdom

    Elixir node event
    Introduction to metabolomics for the clinical scientist https://tess.oerc.ox.ac.uk/events/introduction-to-metabolomics-for-the-clinical-scientist-03088b2e-2054-4760-a172-a8bfceab7207 The 1-day course in partnership with the Phenome Centre Birmingham will provide clinicians with an overview of the metabolomics pipeline highlighting the benefits of this technique to the medical field and an introduction to the Phenome Centre Birmingham and the MRC-NIHR National Phenome Centre. The course will provide a suitable introduction to metabolomics prior to taking additional training courses at either the Birmingham Metabolomics Training Centre or the Imperial International Phenome Training Centre. 2017-12-01 09:00:00 UTC 2017-12-01 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] []
  • Hackathon – Fiji, ImageJ, and KNIME development 2017

    3 - 16 December 2017

    Hackathon – Fiji, ImageJ, and KNIME development 2017 https://tess.oerc.ox.ac.uk/events/hackathon-fiji-imagej-and-knime-development-2017 2017-12-03 09:00:00 UTC 2017-12-16 00:00:00 UTC [] [] [] [] []
  • GPU Programming with OpenACC @ CSC

    4 - 5 December 2017

    GPU Programming with OpenACC @ CSC https://tess.oerc.ox.ac.uk/events/gpu-programming-with-openacc-csc-dd9e1461-d241-4c5f-a35d-22ac85686ded Description This course gives a thorough introduction to programming GPUs using the directive based OpenACC paradigm. The course consists of lectures and hands-on exercises. Topics of this course include the basic usage of OpenACC, as well as some more advanced issues related to profiling, performance and interoperability with CUDA. Learning outcome After the course the participants should have the basic skills needed for utilizing OpenACC in new, or existing programs. Prerequisites The participants are assumed to have working knowledge of Fortran and/or C programming languages. In addition, fluent operation in a Linux/Unix environment will be assumed. Agenda Day 1, Monday 4.12 09:00 - 12:00 SESSION 1 & Coffee break Introduction to accelerators​ Introduction to OpenACC Exercises 12:00 - 13:00 Lunch 13:00 - 16:00 SESSION 2 & Coffee break Data movement Exercises Day 2, Tuesday 5.12 09:00 - 12:00 SESSION 3 & Coffee break Profilling Performance considerations Exercises 12:00 - 13:00 Lunch 13:00 - 16:00 SESSION 4 & Coffee break Asynchronous operations and pipelining Interoperability with CUDA and GPU-Accelerated libraries Exercises   Lecturers:   Sami Ilvonen (CSC), Fredrik Robertsén (CSC)  Language:  EnglishPrice:          Free of charge https://events.prace-ri.eu/event/670/ 2017-12-04 07:00:00 UTC 2017-12-05 14:00:00 UTC [] [] workshops_and_courses [] []
  • Cryo-EM image handling

    4 - 8 December 2017

    Stockholm

    Cryo-EM image handling https://tess.oerc.ox.ac.uk/events/cryo-em-image-handling 2017-12-04 09:00:00 UTC 2017-12-08 00:00:00 UTC Stockholm Stockholm [] [] workshops_and_courses [] []
  • Cryo-EM image processing

    4 - 8 December 2017

    Stockholm

    Cryo-EM image processing https://tess.oerc.ox.ac.uk/events/cryo-em-image-processing 2017-12-04 09:00:00 UTC 2017-12-08 00:00:00 UTC Stockholm Stockholm [] [] workshops_and_courses [] []

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