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91 events found

Event types: Workshops and courses 

  • eLife Innovation Leaders 2020

    1 February - 30 June 2020

    eLife Innovation Leaders 2020 https://tess.elixir-europe.org/events/elife-innovation-leaders-2020 *eLife Innovation Leaders* is a 14-week mentorship and open leadership training programme designed for innovators developing open-source tools and projects for open research communication. Key takeaways: - A personalised experience with one-on-one mentorship - A shared co-learning journey - Theory and practice in project design, community engagement, and more - Opportunities to be supported beyond the programme The programme will take place between February and June 2020. We invite you to find out more and apply by December 8 here: [elifesci.org/innovationleaders](https://elifesci.org/innovationleaders) If you have any specific requirements to enable your participation, please don't hesitate to let us know through the application form or through email, we're happy to discuss potential arrangements. 2020-02-01 09:00:00 UTC 2020-06-30 23:59:00 UTC Emmy Tsang, Innovation Community Manager @ eLife [] Emmy at innovation [at] elifesciences [dot] org [] research software engineers and research data managers working with ELIXIR-supported tools and resourcestool authorssoftware developers, bioinformaticians workshops_and_courses [] Open scienceopen sourceCommunication
  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    9 March - 12 July 2020

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-9b6d1f32-b676-422b-93fe-ad935f02bf74 # Overview * **Duration**: 3 weeks, 3 hours per week * Free * Certificate of achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (9 credits), Royal College of Nursing (9 credits) * **Start Date**: The course is run ‘live’ for 3 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? The increase in resistance of harmful bacteria to antibiotics is a major global threat to health. Here we explore bacterial genomes and the use of genome sequencing to identify and track these drug resistant bacteria. Join us to discover how genome research is helping scientists and healthcare professionals track disease outbreaks and prevent the rise of antibiotic resistant ‘superbugs’. ### Who is the course for? This course will be of interest to scientists, healthcare professionals, biomedical researchers and bioinformaticians. The course offers all learners an opportunity to learn about genomes, disease, and antimicrobial resistance. You require no previous knowledge of genome science to complete the course. ### What do people say about this course? "_I would definitely point students to this resource. Text, videos, and figures were all very well done._" Pablo Tsukayama, Assistant Professor of Microbiology "_A highlight of the course was the introduction to whole genome sequencing – new information for me._" Christine Laws, Medical Doctor “_Exchanging genetic information quickly throughout the world is clearly going to revolutionise the ability to combat disease._” Prue van der Hoorn, Artist # Programme and start dates ### Course start dates This course is repeated twice a year. ### What topics will you cover? * Diseases caused by bacteria * What bacterial genomes look like * Genome sequencing technology * Mechanisms of transmission and resistance * Genomic epidemiology – tracking the spread of bacterial pathogens * Antimicrobial resistance ### What will you achieve? By the end of the course, you'll be able to... * Explain why some bacteria are pathogenic * Explore the structure of bacterial genomes * Describe the uses of different genome sequencing technologies * Investigate how genome data are used to track the spread of bacterial disease * Discuss the role of genome sequencing in stopping the spread of antimicrobial resistance # Educators ## **Lead Educators** **[Dr Adam Reid][1]** I am a senior staff scientist at the Wellcome Sanger Institute near Cambridge in the United Kingdom. I'm interested in using genomics and bioinformatics to better understand infectious diseases. **[Dr Josie Bryant][2]** I am a Henry Wellcome Postdoctoral Fellow in the University of Cambridge, Department of Medicine. I am working on bacterial genomics and evolution with a focus on within-patient microbial diversity ### Dr Francesca Short I am a scientist at the Wellcome Sanger Institute. I am interested in using functional genomics techniques to understand infections caused by the bacterium _Klebsiella pneumoniae_. ## **Programme Lead Educator** **[Professor Nicholas Thomson][3]** I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease. ### The course also features interviews with distinguished scientists, including: * **[Mathew Beale][4]** - Wellcome Sanger Institute * **[Daryl Domman][5]** - Wellcome Sanger Institute * **[Gal Horesh][6]** - Wellcome Sanger Institute * **[Catherine Ludden][7]** - London School of Hygiene and Tropical Medicine * **[Tapoka Mkandawire][8]** - Wellcome Sanger Institute * **[Julian Parkhill][9]** - Wellcome Sanger Institute * **Lindsay Pike** - Wellcome Sanger Institute * **[Michael Quail][10]** - Wellcome Sanger Institute * **[Susannah J. Salter][11]** - Wellcome Sanger Institute * **[Estee Torok][12]** - Addenbrooke’s Hospital and University of Cambridge [1]: http://www.sanger.ac.uk/people/directory/reid-adam-james [2]: https://www.infectiousdisease.cam.ac.uk/directory/josie-bryant [3]: http://www.sanger.ac.uk/people/directory/thomson-nicholas-robert [4]: http://www.sanger.ac.uk/people/directory/beale-mathew [5]: http://www.sanger.ac.uk/people/directory/domman-daryl [6]: http://www.sanger.ac.uk/people/directory/horesh-gal [7]: https://www.lshtm.ac.uk/aboutus/people/ludden.catherine [8]: http://www.sanger.ac.uk/people/directory/mkandawire-tapoka-t [9]: http://www.sanger.ac.uk/people/directory/parkhill-julian [10]: http://www.sanger.ac.uk/people/directory/quail-michael-andrew [11]: http://www.sanger.ac.uk/people/directory/salter-susannah-j [12]: https://www.infectiousdisease.cam.ac.uk/directory/et317@medschl.cam.ac.uk # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CDP Approval 2020-03-09 09:00:00 UTC 2020-07-12 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK
  • Introduction to high throughput screening

    24 March - 31 December 2020

    Elixir node event
    Introduction to high throughput screening https://tess.elixir-europe.org/events/introduction-to-high-throughput-screening-791e68be-3d9a-424b-b170-8fcf71b03139 2020-03-24 09:00:00 UTC 2020-12-31 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    20 April - 16 August 2020

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-92c9e794-2186-4766-8435-3273e0756322 # Overview * **Duration**: 2 weeks, 5 hours per week * Free * Certificate of Achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (10 credits) * **Start Date**: The course is run ‘live’ for 2 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Join us in our quest to discover what makes microbes dangerous. Use bioinformatics to probe genomes, to explore and represent DNA and protein sequences. Then, use databases to find protein sequences’ conserved domains and investigate their functions. ### Who is the course for? The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, biomedical researchers, microbiologists, healthcare professionals and all those who are interested in learning about the underlying mechanisms of bacterial disease, DNA sequences and protein data, or how to use online analytical tools to probe genomes. The topics covered in this course are applicable to the genomes of all organisms. It is not essential to have previous knowledge or experience in bioinformatics. Scientific terminology is explained. The opportunity to use online computational tools in the context of bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students. ### What do people say about this course? "_Clear introduction of the – often viewed as complex – field of bioinformatics_." Mqondisi Tshabalala, PhD student, Institute for Cellular and Molecular Medicine, University of Pretoria, South Africa "_Highlights of the course were the investigations with the databases - these reinforced the learning._" Dr. Alan McLintic, Anaesthesiologist, Faculty of Medicine and Health Scientists, University of Auckland, New Zealand # Programme and start dates ### Course start dates This course will be repeated: Next start dates: * September 2019 (date TBC) ### What topics will you cover? * Bioinformatics tools, DNA and protein sequences * Retrieving DNA and protein sequences from repositories * Databases for protein annotation * Inferring function from sequence ### What will you achieve? By the end of the course, you'll be able to... * assess DNA representations and protein sequences * perform searches in primary databases (repositories) and retrieve gene/protein data * interpret different repository submission formats * investigate biological databases for research * identify the putative function of proteins based on their conserved domains # Educators ## **Lead Educators** ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ## **Educator** ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## **Programme Lead Educator** ### Professor Nicholas Thomson Group Leader at the Wellcome Sanger Institute, interested in bacterial evolution and the spread of infectious disease; provides scientific oversight for this course. The course also features interviews with two distinguished experts: ### Dr Rob Finn Team Leader of EMBL-EBI Sequence Families Team ### Dr Claire Chewapreecha Sir Henry Wellcome Fellow and Lecturer, University of Cambridge, UK, and King Mongkut University of Technology, Thailand. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CPD Approval 2020-04-20 09:00:00 UTC 2020-08-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK
  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    20 April - 16 August 2020

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-58453edc-686a-4baa-87e1-e8f5dbab3cb1 # Overview * **Duration**: 2 weeks, 5 hours per week * Free * Certificate of Achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (10 credits) * **Start Date**: The course is run ‘live’ for 2 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Join us in our quest to discover what makes microbes dangerous. Use bioinformatics to probe genomes, to explore and represent DNA and protein sequences. Then, use databases to find protein sequences’ conserved domains and investigate their functions. ### Who is the course for? The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, biomedical researchers, microbiologists, healthcare professionals and all those who are interested in learning about the underlying mechanisms of bacterial disease, DNA sequences and protein data, or how to use online analytical tools to probe genomes. The topics covered in this course are applicable to the genomes of all organisms. It is not essential to have previous knowledge or experience in bioinformatics. Scientific terminology is explained. The opportunity to use online computational tools in the context of bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students. ### What do people say about this course? "_Clear introduction of the – often viewed as complex – field of bioinformatics_." Mqondisi Tshabalala, PhD student, Institute for Cellular and Molecular Medicine, University of Pretoria, South Africa "_Highlights of the course were the investigations with the databases - these reinforced the learning._" Dr. Alan McLintic, Anaesthesiologist, Faculty of Medicine and Health Scientists, University of Auckland, New Zealand # Programme and start dates ### Course start dates This course will be repeated: Next start dates: * September 2019 (date TBC) ### What topics will you cover? * Bioinformatics tools, DNA and protein sequences * Retrieving DNA and protein sequences from repositories * Databases for protein annotation * Inferring function from sequence ### What will you achieve? By the end of the course, you'll be able to... * assess DNA representations and protein sequences * perform searches in primary databases (repositories) and retrieve gene/protein data * interpret different repository submission formats * investigate biological databases for research * identify the putative function of proteins based on their conserved domains # Educators ## **Lead Educators** ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ## **Educator** ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## **Programme Lead Educator** ### Professor Nicholas Thomson Group Leader at the Wellcome Sanger Institute, interested in bacterial evolution and the spread of infectious disease; provides scientific oversight for this course. The course also features interviews with two distinguished experts: ### Dr Rob Finn Team Leader of EMBL-EBI Sequence Families Team ### Dr Claire Chewapreecha Sir Henry Wellcome Fellow and Lecturer, University of Cambridge, UK, and King Mongkut University of Technology, Thailand. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CPD Approval 2020-04-20 09:00:00 UTC 2020-08-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK
  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    20 April - 16 August 2020

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-f8f943e2-2214-43f4-80a9-0215800cbed1 # Overview * **Duration**: 2 weeks, 5 hours per week * Free * Certificate of Achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (10 credits) * **Start Date**: The course is run ‘live’ for 2 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Join us in our quest to discover what makes microbes dangerous. Use bioinformatics to probe genomes, to explore and represent DNA and protein sequences. Then, use databases to find protein sequences’ conserved domains and investigate their functions. ### Who is the course for? The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, biomedical researchers, microbiologists, healthcare professionals and all those who are interested in learning about the underlying mechanisms of bacterial disease, DNA sequences and protein data, or how to use online analytical tools to probe genomes. The topics covered in this course are applicable to the genomes of all organisms. It is not essential to have previous knowledge or experience in bioinformatics. Scientific terminology is explained. The opportunity to use online computational tools in the context of bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students. ### What do people say about this course? "_Clear introduction of the – often viewed as complex – field of bioinformatics_." Mqondisi Tshabalala, PhD student, Institute for Cellular and Molecular Medicine, University of Pretoria, South Africa "_Highlights of the course were the investigations with the databases - these reinforced the learning._" Dr. Alan McLintic, Anaesthesiologist, Faculty of Medicine and Health Scientists, University of Auckland, New Zealand # Programme and start dates ### Course start dates This course will be repeated twice a year. ### What topics will you cover? * Bioinformatics tools, DNA and protein sequences * Retrieving DNA and protein sequences from repositories * Databases for protein annotation * Inferring function from sequence ### What will you achieve? By the end of the course, you'll be able to... * assess DNA representations and protein sequences * perform searches in primary databases (repositories) and retrieve gene/protein data * interpret different repository submission formats * investigate biological databases for research * identify the putative function of proteins based on their conserved domains # Educators ## **Lead Educators** ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ## **Educator** ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## **Programme Lead Educator** ### Professor Nicholas Thomson Group Leader at the Wellcome Sanger Institute, interested in bacterial evolution and the spread of infectious disease; provides scientific oversight for this course. The course also features interviews with two distinguished experts: ### Dr Rob Finn Team Leader of EMBL-EBI Sequence Families Team ### Dr Claire Chewapreecha Sir Henry Wellcome Fellow and Lecturer, University of Cambridge, UK, and King Mongkut University of Technology, Thailand. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CPD Approval 2020-04-20 09:00:00 UTC 2020-08-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK
  • Data Science in Python (ONLINE LIVE TRAINING)

    1 - 2 June 2020

    Cambridge, United Kingdom

    Elixir node event
    Data Science in Python (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/data-science-in-python-online-live-training PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes. Note: this course is the continuation of the [Introduction to Solving Biological Problems with Python](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-python/); participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python. 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=3414283&course-title=Data%20Science%20in%20Python).'' 2020-06-01 08:30:00 UTC 2020-06-02 15:30:00 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 [] HDRUK
  • Data Manipulation and Visualisation

    1 June 2020

    United Kingdom

    Data Manipulation and Visualisation https://tess.elixir-europe.org/events/data-manipulation-and-visualisation-588646eb-6b41-45a6-96da-c00750c9f120 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. 2020-06-01 08:30:00 UTC 2020-06-01 16:00:00 UTC Bartolome House, Seminar Room EG03, United Kingdom Bartolome House, Seminar Room EG03 United Kingdom S10 2HQ [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Data Carpentry - SADiLaR (online)

    1 - 5 June 2020

    South Africa

    Data Carpentry - SADiLaR (online) https://tess.elixir-europe.org/events/data-carpentry-sadilar Data Carpentry trains researchers in the core data skills for efficient, shareable, and reproducible research practices. We run accessible, inclusive training workshops; teach openly available, high-quality, domain-tailored lessons; and foster an active, inclusive, diverse instructor community that promotes and models reproducible research as a community norm. 2020-06-01 09:00:00 UTC 2020-06-05 00:00:00 UTC SADiLaR (online), South Africa SADiLaR (online) South Africa South African Centre for Digital Language Resources (SADiLaR) [] [] workshops_and_courses [] []
  • [POSTPONED] Basic Parallel Programming with MPI and OpenMP @SURFsara

    2 - 3 June 2020

    [POSTPONED] Basic Parallel Programming with MPI and OpenMP @SURFsara https://tess.elixir-europe.org/events/basic-parallel-programming-with-mpi-and-openmp-surfsara NOTE: this is the basic part of a 4-day course at SURFsara. If you wish to attend the full course, you should also register for the advanced part separately. Please check here the advanced part.   This 2-day basic course is focused on providing an introduction to parallel programming using the most widely used approaches: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP). You will start exploring the benefits (and limitations) of parallel programming, and then you will explore the possibilities that task and data parallelism offer to develop multi-core and multi-node programs. Each session includes hands-on exercises to facilitate the understanding of the different constructs.   As a participant, you have already some familiarity with C or Fortran programming, and in these two days you will be able to start the development of your own parallel application. Moreover, right after this short course you will have the opportunity to continue exploring advanced topics on parallel programming and everyday use of MPI/OpenMP. For this you'll need to register for the advanced course too. https://events.prace-ri.eu/event/1004/ 2020-06-02 07:00:00 UTC 2020-06-03 15:35:00 UTC [] [] [] workshops_and_courses [] []
  • Statistical Analysis of Biological Data in R

    2 June 2020

    United Kingdom

    Statistical Analysis of Biological Data in R https://tess.elixir-europe.org/events/statistical-analysis-of-biological-data-in-r-8763da73-bed8-4cf7-8b11-dc61e09e7d32 This course provides a refresher on the foundations of statistical analysis. 2020-06-02 08:30:00 UTC 2020-06-02 16:00:00 UTC Bartolome House, Seminar Room EG03, United Kingdom Bartolome House, Seminar Room EG03 United Kingdom S10 2HQ [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Cryo-EM sample preparation and data collection (POSTPONED)

    2 - 4 June 2020

    Elixir node event
    Cryo-EM sample preparation and data collection (POSTPONED) https://tess.elixir-europe.org/events/cryo-em-sample-preparation-and-data-collection-4921cece-9b6d-460f-a1b2-1bce618fb3d6 2020-06-02 09:00:00 UTC 2020-06-04 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • First steps with R in Life Sciences - streamed

    3 - 4 June 2020

    Streamed from Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences - streamed https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-4ddd6df7-e4ed-4f77-a73f-8540aae27887 This course will be streamed, and accessible only for the registered participants. The course is now full with a waiting list. Application is now closed. There will be other sessions next year. Thank you for your understanding. 2020-06-03 09:00:00 UTC 2020-06-04 00:00:00 UTC SIB, Streamed from Lausanne, Switzerland SIB Streamed from Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Introduction to high-performance computing (sciCORE cluster) - streamed

    3 June 2020

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to high-performance computing (sciCORE cluster) - streamed https://tess.elixir-europe.org/events/introduction-to-high-performance-computing-scicore-cluster-17743d87-92b4-473f-9591-384d43fe776d This course will be streamed only for the registered participants. Registered participants will receive specific information directly from the respective course’s organizers. This course is currently over-subscribed with a waiting list. 2020-06-03 09:00:00 UTC 2020-06-03 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • [POSTPONED] MPI and OpenMP in Scientific Software Development @SURFsara

    4 - 5 June 2020

    [POSTPONED] MPI and OpenMP in Scientific Software Development @SURFsara https://tess.elixir-europe.org/events/advanced-parallel-programming-with-mpi-and-openmp-surfsara NOTE: this is the advanced part of a 4-day course at SURFsara. If you wish to attend the full course, you should also register for the basic part separately. Please check here the basic part.   This 2-day advanced course describes different everyday challenges that developers of parallel code have to face in everyday work, and provides working solutions for them. Here you will see how to deal with parallel profiling and explore the knobs and dials that make your code exploit the best possible performance, just like domain decomposition techniques and parallel I/O. Each of these sessions includes hands-on exercises to facilitate the understanding of the different constructs. Moreover, you will also obtain some insight on useful parallel libraries and routines for scientific code development, like ParMETIS and PETSc.   As a participant for these two days, you already have basic knowledge on parallel programming with MPI and OpenMP using the C or Fortran programming languages, which are covered in our basic course. If you are not very familiar with these basic concepts, please register for the basic course and then you can also register for this advanced part! https://events.prace-ri.eu/event/1005/ 2020-06-04 07:00:00 UTC 2020-06-05 15:35:00 UTC [] [] [] workshops_and_courses [] []
  • Data Carpentry - ONLINE

    4 - 5 June 2020

    United Kingdom

    Data Carpentry - ONLINE https://tess.elixir-europe.org/events/data-carpentry-online-03216c87-bcbe-428e-ba6b-ad69d32ccd2e Data Carpentry trains researchers in the core data skills for efficient, shareable, and reproducible research practices. We run accessible, inclusive training workshops; teach openly available, high-quality, domain-tailored lessons; and foster an active, inclusive, diverse instructor community that promotes and models reproducible research as a community norm. 2020-06-04 09:00:00 UTC 2020-06-05 00:00:00 UTC ONLINE, United Kingdom ONLINE United Kingdom University of Edinburgh [] [] workshops_and_courses [] []
  • Course Data analysis for Metabolomics

    4 - 5 June 2020

    Wageningen, Netherlands

    Elixir node event
    Course Data analysis for Metabolomics https://tess.elixir-europe.org/events/course-data-analysis-for-metabolomics Metabolomics experiments based on mass spectrometry (MS) or nuclear magnetic resonance (NMR) produce large and complex data sets. This course will introduce approaches to process and analyse data and design high-quality experiments. Through hands-on workshops and lectures highlighting the different… The post Course Data analysis for Metabolomics appeared first on Dutch Techcentre for Life Sciences. 2020-06-04 09:00:00 UTC 2020-06-05 00:00:00 UTC Wageningen, Netherlands, Wageningen, Netherlands Wageningen, Netherlands Wageningen Netherlands [] [] [] workshops_and_courses [] []
  • RaukR, Advanced R for Bioinformatics, Summer course (CANCELLED)

    7 - 18 June 2020

    Elixir node event
    RaukR, Advanced R for Bioinformatics, Summer course (CANCELLED) https://tess.elixir-europe.org/events/raukr-advanced-r-for-bioinformatics-summer-course-53c91aeb-5cb1-4a8c-8a91-03076abd6403 2020-06-07 09:00:00 UTC 2020-06-18 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • [POSTPONED] High-performance computing with Python @ JSC

    8 - 10 June 2020

    [POSTPONED] High-performance computing with Python @ JSC https://tess.elixir-europe.org/events/high-performance-computing-with-python-jsc-8f572b9d-fe3d-4357-a015-1be3342e47a8 This course was postponed to autumn 2020. The exact date will be fixed later. Python is increasingly used in high-performance computing projects. It can be used either as a high-level interface to existing HPC applications and libraries, as embedded interpreter, or directly. This course combines lectures and hands-on sessions. We will show how Python can be used on parallel architectures and how to optimize critical parts of the kernel using various tools. The following topics will be covered: Interactive parallel programming with IPython Profiling and optimization High-performance NumPy Just-in-time compilation with numba Distributed-memory parallel programming with Python and MPI Bindings to other programming languages and HPC libraries Interfaces to GPUs This course is aimed at scientists who wish to explore the productivity gains made possible by Python for HPC. Prerequisites: Good working knowledge of Python and NumPy Application Registrations are only considered until 7 May 2020 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, Dr. Olav Zimmermann, JSC Contact For any questions concerning the course please send an e-mail to j.meinke@fz-juelich.de https://events.prace-ri.eu/event/982/ 2020-06-08 07:00:00 UTC 2020-06-10 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] HPC code optimisation workshop @ LRZ

    8 - 10 June 2020

    [ONLINE] HPC code optimisation workshop @ LRZ https://tess.elixir-europe.org/events/hpc-code-optimisation-workshop-lrz-8793a2fd-4991-4524-97f3-e424f669005a          This course will be delivered as an ONLINE COURSE for remote participation because of the COVID-19 measures enforced by most European governments. REGISTRATION is strictly NECESSARY since the details to access the online course will be provided to the registered and accepted attendees only. The AGENDA is still subject to be adopted to online training. Please mind that the time has been changed to 10:00-12:00 & 13:00-16:00 CEST.   Contents In the ever-growing complexity of computer architectures, code optimization has become the main route to keep pace with hardware advancements and effectively make use of current and upcoming High Performance Computing systems. Have you ever asked yourself: Where does the performance of my application lay? What is the maximum speed-up achievable on the architecture I am using? Is my implementation matching the HPC objectives? In this workshop, we will answer these questions and provide a unique opportunity to learn techniques, methods and solutions on how to improve code, how to enable the new hardware features and how to use the roofline model to visualize the potential benefits of an optimization process. We will begin with a description of the latest micro-processor architectures and how the developers can efficiently use modern HPC hardware, in particular the vector units via SIMD programming and AVX-512 optimization and the memory hierarchy. The attendees are then conducted along the optimization process by means of hands-on exercises and learn how to enable vectorization using simple pragmas and more effective techniques, like changing data layout and alignment. The work is guided by the hints from the Intel® compiler reports, and using Intel® Advisor. Besides Intel® Advisor, the participants will also be guided to the use of Intel® VTune™ Amplifier, Intel® Application Performance Snapshot and LIKWID as tools for investigating and improving the performance of a HPC application. We further cover the Intel® Math Kernel Library (MKL), in order to show how to gain performance through the use of libraries. We provide an N-body code, to support the described optimization solutions with practical hands-on. You can ask Intel in the Q&A session about how to optimise your code. Please provide a description of your code in the registration form. Learning Goals Through a sequence of simple, guided examples of code modernization, the attendees will develop awareness on features of multi and many-core architecture which are crucial for writing modern, portable and efficient applications. A special focus will be dedicated to scalar and vector optimizations for the latest Intel® Xeon® Scalable processor, code-named Skylake, utilized in the SuperMUC-NG machine at LRZ. The workshop interleaves frontal and practical sessions. Here is a preliminary outline: Day 1 Introduction to systems and software Code modernization approach Scalar optimization Compiler autovectorization Data layout from AoS to SoA Memory access optimization SDLT (Intel® SIMD Layout Templates) / Explicit vectorization / Skylake optimization Day 2 Introduction to roofline model Intel® Advisor analysis Intel® Math Kernel Library (MKL) and other libraries Day 3 Introduction to Intel® VTune™ Amplifier Introduction to Intel® Application Performance Snapshot (APS) LIKWID ( “Like I Knew What I’m Doing.”)  Performance Tools Q&A Session Please use your own laptop or PC (with X11 support and an ssh client installed) for the hands-on sessions. For GUI applications we require the installation of vncviewer (https://www.realvnc.com/en/connect/download/viewer/ )”. The workshop is a PRACE training event organized by LRZ in cooperation with Intel and RRZE. About the Lecturers Fabio Baruffa is a senior software application engineer at Intel. He provides customer support in the high-performance computing (HPC) area and artificial intelligence software solutions at large scale. He collaborates with several research institutes in Europe to develop prototypes of quantum computing algorithm simulations running on current HPC systems. Prior at Intel, he has been working as HPC application specialist and developer in the largest supercomputing centers in Europe, mainly the Leibniz Supercomputing Center and the Max-Plank Computing and Data Facility in Munich, as well as Cineca in Italy. He has been involved in software development, analysis of scientific code and optimization for HPC systems. He holds a PhD in Physics from University of Regensburg for his research in spintronics devices and quantum computing. Gennady Fedorov is a Technical Consulting Engineer supporting technical and Intel Performance Libraries ( IPP, MKL and DAAL) within the Intel Architecture, Graphics and Software Group at Intel in Russia. His focus areas are Image Processing, Crypto, Compressing techniques, High Performance Computing and Artificial Intelligence. Thomas Gruber (né Röhl) collected experience with all kinds of clustering approaches during his apprenticeship at the Erlangen Regional Computing Center (RRZE), the IT service provider for the Friedrich-Alexander-University Erlangen-Nuernberg (FAU). Afterwards, he studied Computer Science at RWTH Aachen University with emphasis on parallel programming and operating system kernel development. At the same time, he worked as a research assistant for the HPC group of the RWTH IT center. After receiving his M. Sc. degree, he went back to RRZE to work for the HPC group. Thomas Gruber leads the development of the performance tool suite LIKWID, which comprises easy-to-use tools for hardware performance monitoring, affinity control and micro-benchmarking. He also works on projects involving monitoring and analysis of hardware performance data. Carla Guillen works as a researcher in the application support group at the LRZ. She obtained her PhD in computer science at the Technische Universitaet Muenchen in 2015. She joined the LRZ in 2009, and has been working in the fields of system-wide performance monitoring and energy optimization of large scale clusters. Gerald Mathias works in the application support for the HPC systems at LRZ since 2015 and leads the Biolab@LRZ. After his PhD in Computational Biopyhsics at the LMU Munich he joined the chair of Theoretical Chemistry at the RUB in Bochum afterwards as a postdoc. He is experienced in the development and optimization of highly parallel ab initio and force field based molecular dynamics codes, both in Fortran and C. Michael Steyer is a Technical Consulting Engineer supporting technical and High Performance Computing segments within the Intel Architecture, Graphics and Software Group at Intel in Germany. His focus areas are High Performance Computing and Artificial Intelligence. Igor Vorobtsov has more than 11 years of experience in the areas of C/C++ and Fortran compilers, application tuning and developer support. Igor got a Master of Science degree in Applied Mathematics. Since joining Intel in 2008, Igor has worked as a Technical Consulting Engineer supporting software developers throughout EMEA region. Igor has a broad array of application experience, including enterprise applications and high performance computing environments. https://events.prace-ri.eu/event/1003/ 2020-06-08 08:00:00 UTC 2020-06-10 14:00:00 UTC [] [] [] workshops_and_courses [] []
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    8 June - 9 August 2020

    Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-34117159-0fd6-4263-8a2c-9882b99f2572 # Overview * **Duration**: 3 weeks, 5 hours per week * Free * Certificate of achievement available on satisfactory completion * **Start Date**: The course is run ‘live’ for 3 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Disease outbreaks are still a big problem in our modern world. Comparison between two or more bacterial genomes can help improve understanding of the causes of pathogenicity and outbreaks of disease caused by bacteria. On this course you will learn how to use the free Artemis Comparison Tool (ACT). Developed at the Wellcome Sanger Institute, ACT will help you to visualise the comparison of genomes and analyse the results. ### Who is the course for? This course would benefit those interested in learning how to use tools to investigate and research bacterial genomes, and acquire bioinformatics skills to evaluate the role of microbial genes in disease. Learners will gain experience in comparative genomics, using the Artemis Comparison Tool to probe, visualise and compare genomes, and analyse the results. This course will be of interest to anyone interested in microbiology, including undergraduates, post-graduates, biomedical researchers, microbiologists, bioinformaticians, teachers, and healthcare professionals. The opportunity to gain experience in using the Artemis Comparison Tool, a computational tool designed for comparative genomics, will also be of interest to all those who have studied our pre-requisite courses: those with an interest in genomics and disease outbreaks, teachers and their 16-18-year-old science and computing students. Ideally, you will have completed [Bacterial Genomes: From DNA to Protein Function Using Bioinformatics][1] and [Bacterial Genomes: Accessing and Analysing Microbial Genome Data][2] before joining this course. [1]: /our-events/bacterial-genomes-dna-protein-function-bioinformatics-online-sep19/ [2]: /our-events/bacterial-genomes-accessing-analysing-microbial-genome-data-feb19/ # Programme ### What topics will you cover? Week 1 * Introduction to comparative genomics * Introduction to ACT Week 2 * Analyse available data * Generate your own comparison files * Make your own comparisons in ACT Week 3 * Identify pseudogenes in Mycobacterium leprae using ACT * Peer review project: Comparative genomics on two clinically relevant plasmids from Shigella ### What will you achieve? By the end of the course, you'll be able to... * Explain the advantages of comparative genomics * Explore basic tools of ACT * Interpret results from already generated comparison files * Produce new comparisons and analyse results * Develop hypothesis based on results observation ### What software or tools do you need? This course will give you an opportunity to learn about and use Artemis Comparison Tool (ACT), a free tool used to display pairwise comparisons between two DNA sequences. To run this software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of ACT requires version 11 of Java to run successfully. Java 11 can be downloaded from [this link][1]. Older versions of ACT require Java 8 to run successfully. Java 8 can be downloaded from [this link][2]. [1]: https://www.oracle.com/technetwork/java/javase/downloads/jdk11-downloads-5066655.html [2]: https://www.java.com/en/download/ # Educators ## Lead Educators ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ### Dr. Ulrike Böhme I am a researcher in parasitology at the Wellcome Sanger Institute where I work as biocurator for Plasmodium genomes. ### Dr. Pablo Tsukayama I am a professor of microbiology at Universidad Peruana Cayetano Heredia and a visiting research scholar at the Wellcome Sanger Institute. I study how pathogen populations evolve and spread in Peru. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## Programme Lead Educator ### Professor Nicholas Thomson I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible 2020-06-08 09:00:00 UTC 2020-08-09 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • Analyse Next Generation Sequencing (NGS) data

    8 June 2020

    Leiden, Netherlands

    Elixir node event
    Analyse Next Generation Sequencing (NGS) data https://tess.elixir-europe.org/events/analyse-next-generation-sequencing-ngs-data Deze tweedaagse workshop geeft toepasbare up to date informatie over NGS. Verschillende platforms, de werking van sequencers en nucleïnezuur isolatie komen uitvoerig aan bod. De analyse van NGS data bij DNA en RNA sequencing wordt geïntroduceerd. Verschillende toepassingen zoals genoom… The post Analyse Next Generation Sequencing (NGS) data appeared first on Dutch Techcentre for Life Sciences. 2020-06-08 09:00:00 UTC 2020-06-08 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    8 June - 9 August 2020

    Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-78fb77a6-ce29-4ed5-a32b-56b7f46a5d8e # Overview * **Duration**: 3 weeks, 5 hours per week * Free * Certificate of achievement available on satisfactory completion * **Start Date**: The course is run ‘live’ for 3 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Disease outbreaks are still a big problem in our modern world. Comparison between two or more bacterial genomes can help improve understanding of the causes of pathogenicity and outbreaks of disease caused by bacteria. On this course you will learn how to use the free Artemis Comparison Tool (ACT). Developed at the Wellcome Sanger Institute, ACT will help you to visualise the comparison of genomes and analyse the results. ### Who is the course for? This course would benefit those interested in learning how to use tools to investigate and research bacterial genomes, and acquire bioinformatics skills to evaluate the role of microbial genes in disease. Learners will gain experience in comparative genomics, using the Artemis Comparison Tool to probe, visualise and compare genomes, and analyse the results. This course will be of interest to anyone interested in microbiology, including undergraduates, post-graduates, biomedical researchers, microbiologists, bioinformaticians, teachers, and healthcare professionals. The opportunity to gain experience in using the Artemis Comparison Tool, a computational tool designed for comparative genomics, will also be of interest to all those who have studied our pre-requisite courses: those with an interest in genomics and disease outbreaks, teachers and their 16-18-year-old science and computing students. Ideally, you will have completed [Bacterial Genomes: From DNA to Protein Function Using Bioinformatics][1] and [Bacterial Genomes: Accessing and Analysing Microbial Genome Data][2] before joining this course. [1]: /our-events/bacterial-genomes-dna-protein-function-bioinformatics-online-sep19/ [2]: /our-events/bacterial-genomes-accessing-analysing-microbial-genome-data-feb19/ # Programme ### What topics will you cover? Week 1 * Introduction to comparative genomics * Introduction to ACT Week 2 * Analyse available data * Generate your own comparison files * Make your own comparisons in ACT Week 3 * Identify pseudogenes in Mycobacterium leprae using ACT * Peer review project: Comparative genomics on two clinically relevant plasmids from Shigella ### What will you achieve? By the end of the course, you'll be able to... * Explain the advantages of comparative genomics * Explore basic tools of ACT * Interpret results from already generated comparison files * Produce new comparisons and analyse results * Develop hypothesis based on results observation ### What software or tools do you need? This course will give you an opportunity to learn about and use Artemis Comparison Tool (ACT), a free tool used to display pairwise comparisons between two DNA sequences. To run this software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of ACT requires version 11 of Java to run successfully. Java 11 can be downloaded from [this link][1]. Older versions of ACT require Java 8 to run successfully. Java 8 can be downloaded from [this link][2]. [1]: https://www.oracle.com/technetwork/java/javase/downloads/jdk11-downloads-5066655.html [2]: https://www.java.com/en/download/ # Educators ## Lead Educators ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ### Dr. Ulrike Böhme I am a researcher in parasitology at the Wellcome Sanger Institute where I work as biocurator for Plasmodium genomes. ### Dr. Pablo Tsukayama I am a professor of microbiology at Universidad Peruana Cayetano Heredia and a visiting research scholar at the Wellcome Sanger Institute. I study how pathogen populations evolve and spread in Peru. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## Programme Lead Educator ### Professor Nicholas Thomson I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible 2020-06-08 09:00:00 UTC 2020-08-09 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • [ONLINE] Parallel Programming with OpenMP and MPI @ VSC Belgium & SURFsara

    9 - 12 June 2020

    [ONLINE] Parallel Programming with OpenMP and MPI @ VSC Belgium & SURFsara https://tess.elixir-europe.org/events/online-parallel-programming-with-openmp-and-mpi-vsc-belgium-surfsara Overview The Flemish Supercomputing Center (VSC, Belgium) and SURFsara (The Netherlands) are organizing this online course on parallel programming using OpenMP and MPI. The materials of this course have been developed by Dr. Rolf Rabenseifner (HLRS, Stuttgart). Course format The training sessions will be provided online using the Blackboard Collaborate system. More information on how to access the system for the training sessions and how to follow the course will be provided soon. Course level Basic content: 40 % Intermediate content: 40 % Advanced content: 20 % After every day there will be a round of "Questions and Answers". Indicative timetable Tue 9th of June 09:00    Welcome and presentation 09:10    Introduction to parallel computing 10:00    An overview of OpenMP: execution model 10:30    Coffee break 10:45    Worksharing directives 12:30    Lunch break 13:30    Data environment and combined constructs 15:00    Coffee break 15:15    Optimization and pitfalls 16:00    Summary / Questions and Answers    16:30    End of first day Wed 10th of June 09:00   MPI Overview 10:30   Coffee break 10:45   MPI Process Model 11:30   Messages and Point-to-Point Communication 12:30   Lunch break 13:30   Messages and Point-to-Point Communication (cont.) 14:00   Non-Blocking Communication 15:00   Coffee break 15:15   Error handling and new Fortran module 16:00   Summary / Questions and Answers    16:30   End of second day Thu 11th of June 09:00   Collective Communication 10:30   Coffee break 10:45   Groups & Communicators 12:30   Lunch break 13:30   Virtual Topologies 15:00   Coffee break 15:15   Derived Datatypes 16:00   Summary / Questions and Answers 16:30   End of third day Fri 12th of June 09:00   One-sided Communication 10:30   Coffee break 10:45   Shared Memory 12:30   Lunch break 13:30   MPI + Threads 14:15   Parallel I/O 15:00   Coffee break 15:15   Best practices 16:00   Summary / Questions and Answers   16:25   Closing  16:30   End of fourth day https://events.prace-ri.eu/event/1028/ 2020-06-09 07:00:00 UTC 2020-06-12 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • First steps in Python, and more!

    9 - 11 June 2020

    Basel, Switzerland

    Elixir node event
    First steps in Python, and more! https://tess.elixir-europe.org/events/first-steps-in-python-and-more Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-06-09 09:00:00 UTC 2020-06-11 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • [ONLINE] Working effectively with HPC systems @ SNIC

    10 June 2020

    [ONLINE] Working effectively with HPC systems @ SNIC https://tess.elixir-europe.org/events/online-working-effectively-with-hpc-systems In brief The seminar will present useful tools and best practices for working effectively on HPC systems. It is expected to be of interest for a general HPC system user, both at a more familiar (intermediate) or starting (beginner) level. To participate, register down below. Introduction Working efficiently with HPC starts with the tools you use to interact with the HPC system. It is also helpful to understand the general anatomy of HPC systems and storage. Following on from these fundamentals, we will give some recommendations for data organization on the system and examples of various types of file systems (e.g. parallel vs. local) and their individual strengths and weaknesses. We will then discuss the concepts of parallelism, scalability, scheduling and what types of OS and software you can expect of HPC systems. We will go through some important things to consider when building and installing software. Finally, we will look at different ways of running software on HPC systems and ways to monitor your software as it is running, with the aim of ensuring that your jobs are not poorly configured or wasting resources. While the content and the practices are useful for HPC systems in general, we will show examples and tools more specific for the NSC clusters, e.g. Tetralith and Sigma. Schedule The schedule for the day is divided into two main parts, before and after lunch break. The parts include several blocks of 20-40 minutes with breaks in between. Each block will include opportunities for questions. 10:00 -12:00 Part I 12:00 -13:00 L u n c h 13:00 -15:00 Part II Topics/blocks (preliminary) Welcome, introductions and practicalities Tools at your end (e.g. terminal, ssh config., file transfer tools, VNC) HPC system anatomy (login and compute nodes, interconnect, storage) Properties and features of storage areas (e.g. quotas, performance, locality, backups, snapshots, scratch) Concept of parallelism (Amdahl’s law), scalability, scheduling and practical advice for good performance Software on an HPC system (OS, modules, python envs., concept of build envs., containers with Singularity) Ideas and strategies for organizing your workflow (data and file management, traceability and reproducibility) Interacting with the Slurm queueing system (requesting resources interactively or in batch) Practical examples (preparing, submitting, monitoring and evaluating job efficiency) Presenters Peter Kjellström, Weine Olovsson, Torben Rasmussen, Hamish Struthers, all at NSC, LiU, Sweden.   https://events.prace-ri.eu/event/1026/ 2020-06-10 08:00:00 UTC 2020-06-10 13:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to new accelerated partition of Marconi, for users and developers@CINECA

    15 - 17 June 2020

    Introduction to new accelerated partition of Marconi, for users and developers@CINECA https://tess.elixir-europe.org/events/introduction-to-new-accelerated-partition-of-marconi-for-users-and-developers-cineca Description: The present course intends to support the scientific community to efficiently exploit the architecture of the new accelerated partition of Marconi system. More precisely, the course aims at providing a full description of its  configuration, with special emphasis on main crucial aspects for users and application developers. For instance, details about compilation, debugging and optimization procedures will be provided, together with an overview of the libraries, tools and applications available on the system. Examples of submission jobs will be discussed, together with scheduler commands and queue definitions. Skills: By the end of the course each student should be able to: •    compile a code on this architecture in a performing way •    run a code taking advantage of accelerated resources •    move easily in the configured hpc environment Target Audience: Researchers and programmers who want to use this new accelerated partition of Marconi  Pre-requisites: No pre-requisites Grant: A grant of 200 EUR (for foreign students) and 100 EUR (for Italian students) will be available for participants not funded by their institution and not working in the Bologna area. Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lessons and about 1 month after the ending of the course. For further information about how to submit for the grant, please wait the confirmation email that you are accepted to the course about 3 weeks before the date of the beginning of the lessons.  The lunch for the 2 days will be provided by Cineca. Coordinating Teacher: Dr. S.Giuliani https://events.prace-ri.eu/event/975/ 2020-06-15 07:00:00 UTC 2020-06-17 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • [POSTPONED] High-performance scientific computing in C++ @ JSC

    15 - 17 June 2020

    [POSTPONED] High-performance scientific computing in C++ @ JSC https://tess.elixir-europe.org/events/high-performance-scientific-computing-in-c-jsc-7577a0b2-ea9c-4d4d-831c-b75adb7ec714 This course has been postponed to autumn 2020. Modern C++, with its support for procedural, objected oriented, generic and functional programming styles, offers many powerful abstraction mechanisms to express complexity at a high level while remaining very efficient. It is therefore the language of choice for many scientific projects. However, achieving high performance by today's standards requires understanding and exploiting multiple levels of parallelism, and understanding C++ code from a performance centric viewpoint. In this course, the participants will learn how to write C++ programs which better utilize typical HPC hardware resources of the present day. The course is geared towards scientists and engineers already familiar with C++17 (at the very least C++14), who wish to develop maintainable and fast applications. They will learn techniques to better utilize CPU caches, instruction pipelines, SIMD functionality and multi-threading. Shared memory parallel programming on multiple CPU cores will be introduced using parallel STL of C++17 and Intel (R) Threading Building Blocks. The participants will also learn basic GPGPU programming in C++ using NVidia CUDA and Thrust. Prerequisites: Good working knowledge of C++, especially the C++14 standard. Please check with these questions whether your C++ knowlegde fulfills the requirements. Application Registrations are only considered until 15 May 2020 due to available space, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructor: Dr. Sandipan Mohanty, JSC Contact For any questions concerning the course please send an e-mail to s.mohanty@fz-juelich.de https://events.prace-ri.eu/event/984/ 2020-06-15 07:00:00 UTC 2020-06-17 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Advanced topics in scientific visualization with Blender: geometry, scripts, animation, action! @ SURFsara

    15 - 26 June 2020

    [ONLINE] Advanced topics in scientific visualization with Blender: geometry, scripts, animation, action! @ SURFsara https://tess.elixir-europe.org/events/online-advanced-topics-in-scientific-visualization-with-blender-geometry-scripts-animation-action-surfsara Overview In this course you will learn the basics of the Python API in Blender. You will learn how the API is structured and eventually start making some simple geometry with code. Another important part of the course is that you will work on a visualisation based on your own research or other endeavours. The course is set up to run over two weeks, beginning with an introductory webinar. During the course period you work on the assignments in your own time. We provide a communication channel with the course teachers that you can use for questions and feedback during the course. There are also severak webinars were we discuss your projects and make sure you are able to make progress. Part of the course material, like our YouTube videos and tutorials, is available outside the course timetable. Your own project and data To get the most out of the course we would like you to take a dataset from your work that you want to use for visualisation with Blender. This course will give you the skills to start on your own project. During the interactive moments (webinars and chat channel) our visualisation team will help you further with your specific project and challenges. So please collect some data you think would be great to make a 3D visualisation of. During the webinars we will expect input from you also. We would like you to present your visualisation goals, your data and your first try at making a visualisation with Blender. This course is a pilot Due to the Covid-19 situation we have decided to start an online course, as alternative to our regular on-site courses. This course module is intentionally small because we want to test how and see if we can effectively use online tools for our training programs, especially for a hands-on topic like using Blender. We hope that you are open to giving us feedback on the setup and execution of this course. The next parts of the course will be improved based on your input. All the contents and more detailed information Please visit the main web page of this course in the GitHub page of SURFsara: https://surfsara-visualization.github.io/blendercourses/ https://events.prace-ri.eu/event/1032/ 2020-06-15 08:00:00 UTC 2020-06-26 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Deep Learning and GPU programming workshop

    15 - 18 June 2020

    [ONLINE] Deep Learning and GPU programming workshop https://tess.elixir-europe.org/events/deep-learning-and-gpu-programming-workshop-lrz-ba641b1b-54b7-4b0e-82d4-770259954fd0 This course will be delivered as an ONLINE COURSE for remote participation because of the COVID-19 measures enforced by most European governments. REGISTRATION is strictly NECESSARY since the details to access the online course will be provided to the registered and accepted attendees only. The workshop will take place online 10:00-12:00 and 13:00-16:00 CEST each day. If you want to be set on the waiting list, please contact weinberg@lrz.de. Overview Learn how to train and deploy a neural network to solve real-world problems, how to generate effective descriptions of content within images and video clips, how to effectively parallelize training of deep neural networks on Multi-GPUs and how to accelerate your applications with CUDA C/C++ and OpenACC. This 4-days workshop  combines lectures about fundamentals of Deep Learning for Multiple Data Types and Multi-GPUs with lectures about Accelerated Computing with CUDA C/C++ and OpenACC. The lectures are interleaved with many hands-on sessions using Jupyter Notebooks. The exercises will be done on a fully configured GPU-accelerated workstation in the cloud. The workshop is co-organized by LRZ, IT4Innovations and NVIDIA Deep Learning Institute (DLI) for the Partnership for Advanced Computing in Europe (PRACE). LRZ as part of GCS and IT4Innovations are both PRACE Training Centres which serve as European hubs and key drivers of advanced high-quality training for researchers working in the computational sciences. NVIDIA DLI offers hands-on training for developers, data scientists, and researchers looking to solve challenging problems with deep learning.  All instructors are NVIDIA certified University Ambassadors. Agenda 1st day: Fundamentals of Deep Learning for Multiple Data Types This day explores how convolutional and recurrent neural networks can be combined to generate effective descriptions of content within images and video clips. Learn how to train a network using TensorFlow and the Microsoft Common Objects in Context (COCO) dataset to generate captions from images and video by: Implementing deep learning workflows like image segmentation and text generation Comparing and contrasting data types, workflows, and frameworks Combining computer vision and natural language processing Upon completion, you’ll be able to solve deep learning problems that require multiple types of data inputs. 2nd day: Fundamentals of Accelerated Computing with OpenACC On the last day you learn the basics of OpenACC, a high-level programming language for programming on GPUs. Discover how to accelerate the performance of your applications beyond the limits of CPU-only programming with simple pragmas. You’ll learn: How to profile and optimize your CPU-only applications to identify hot spots for acceleration How to use OpenACC directives to GPU accelerate your codebase How to optimize data movement between the CPU and GPU accelerator Upon completion, you'll be ready to use OpenACC to GPU accelerate CPU-only applications. 3rd day: Fundamentals of Accelerated Computing with CUDA C/C++ The CUDA computing platform enables the acceleration of CPU-only applications to run on the world’s fastest massively parallel GPUs. On the 3rd day you experience C/C++ application acceleration by: Accelerating CPU-only applications to run their latent parallelism on GPUs Utilizing essential CUDA memory management techniques to optimize accelerated applications Exposing accelerated application potential for concurrency and exploiting it with CUDA streams Leveraging command line and visual profiling to guide and check your work Upon completion, you’ll be able to accelerate and optimize existing C/C++ CPU-only applications using the most essential CUDA tools and techniques. You’ll understand an iterative style of CUDA development that will allow you to ship accelerated applications fast. 4th day: Fundamentals of Deep Learning for Multi-GPUs The computational requirements of deep neural networks used to enable AI applications like self-driving cars are enormous. A single training cycle can take weeks on a single GPU or even years for larger datasets like those used in self-driving car research. Using multiple GPUs for deep learning can significantly shorten the time required to train lots of data, making solving complex problems with deep learning feasible. On the 2nd day we will teach you how to use multiple GPUs to train neural networks. You'll learn: Approaches to multi-GPUs training Algorithmic and engineering challenges to large-scale training Key techniques used to overcome the challenges mentioned above Upon completion, you'll be able to effectively parallelize training of deep neural networks using TensorFlow. Important information After you are accepted, please create an account under courses.nvidia.com/join . Ensure your laptop / PC will run smoothly by going to http://websocketstest.com/ Make sure that WebSockets work for you by seeing under Environment, WebSockets is supported and Data Receive, Send and Echo Test all check Yes under WebSockets (Port 80).If there are issues with WebSockets, try updating your browser. If you have any questions, please contact Marjut Dieringer at mdieringer"at"nvidia.com.  PRACE Training and Education The mission of PRACE (Partnership for Advanced Computing in Europe) is to enable high-impact scientific discovery and engineering research and development across all disciplines to enhance European competitiveness for the benefit of society.  PRACE has an extensive education and training effort through seasonal schools, workshops and scientific and industrial seminars throughout Europe. Seasonal Schools target broad HPC audiences, whereas workshops are focused on particular technologies, tools or disciplines or research areas. NVIDIA Deep Learning Institute The NVIDIA Deep Learning Institute delivers hands-on training for developers, data scientists, and engineers. The program is designed to help you get started with training, optimizing, and deploying neural networks to solve real-world problems across diverse industries such as self-driving cars, healthcare, online services, and robotics. https://events.prace-ri.eu/event/1007/ 2020-06-15 08:00:00 UTC 2020-06-18 14:00:00 UTC [] [] [] workshops_and_courses [] []

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