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  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    31 August 2020 - 3 January 2021

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-2aa0df3a-e74c-4f5c-acc3-8c2ee0847f71 # 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 2020-08-31 09:00:00 UTC 2021-01-03 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK
  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    12 October 2020 - 7 February 2021

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-e18aa62a-65f6-478d-ad25-61b757305166 # 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 2020-10-12 09:00:00 UTC 2021-02-07 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK
  • Epigenomics Data Analysis workshop ONLINE

    23 - 28 November 2020

    Solna, Sweden

    Elixir node event
    Epigenomics Data Analysis workshop ONLINE https://tess.elixir-europe.org/events/epigenomics-data-analysis-workshop-online #training #url: https://www.scilifelab.se/event/epigenomics-data-analysis-from-bulk-to-single-cell-2020  edu.epigenomics@nbis.se 2020-11-23 09:00:00 UTC 2020-11-28 00:00:00 UTC Solna, Sweden Solna Sweden [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
  • RNA-seq data analysis ONLINE

    30 November - 5 December 2020

    Elixir node event
    RNA-seq data analysis ONLINE https://tess.elixir-europe.org/events/rna-seq-data-analysis-online #training #url: https://www.scilifelab.se/event/rna-seq-data-analysis-online Email: edu.rnaseq@nbis.se 2020-11-30 09:00:00 UTC 2020-12-05 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
  • ONLINE (14h00 - 17h30) ELIXIR Train the Trainer (TtT) event

    1 - 5 December 2020

    Elixir node event
    ONLINE (14h00 - 17h30) ELIXIR Train the Trainer (TtT) event https://tess.elixir-europe.org/events/online-14h00-17h30-elixir-train-the-trainer-ttt-event #training #url: https://elixir-iib-training.github.io/website/2020/12/01/train-the-trainer-italy-online.html IMPORTANT DATES Course date: 01-04 December, 2020 - 14:00 - 17:30 CET We will accept a maximum of 20 participants. Priority will be given to candidates from Elixir Italy institutes and other ELIXIR Nodes. Notifications of acceptance will be sent shortly after the application, which will remain open until we reach 20 participants. COURSE DESCRIPTION: The ELIXIR Training Platform, in collaboration with ELIXIR-IT and the National Research Council of Italy, is pleased to announce an ELIXIR Train the Trainer (TtT) event online.   The course is organized around four sessions, covering: * Learning principles and how they apply to training and teaching * Lesson, course, and materials design * Teaching techniques that can be used to enhance learner engagement and participation * Assessment and feedback in training and teaching Examples and discussions will also focus on the challenges presented by academic teaching. Who may be interested in this course? Whoever wants to become a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you. * How learning works? * How can I use learning principles to improve my teaching? * How can I make my teaching more engaging and effective? * How should I adjust my teaching to different types of learners? * How can I help slow learners? * How can I assess whether my students are actually understanding my lessons? Are they actually learning? * What is the best balance between theory and practice? * How can I best assess whether learning is occurring and/or has occurred? * What works in a classroom and what doesn't? * Etc. Should you have any questions, do not hesitate to contact us at elixir.ita.training@gmail.com. Trainers: Allegra Via (ELIXIR-IT) Loredana Le Pera (ELIXIR-IT) Patricia Palagi (ELIXIR-CH) Jessica Lindvall (ELIXIR-SE)   2020-12-01 09:00:00 UTC 2020-12-05 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
  • Single cell RNAseq analysis ONLINE

    25 - 30 January 2021

    Elixir node event
    Single cell RNAseq analysis ONLINE https://tess.elixir-europe.org/events/single-cell-rnaseq-analysis-online #training #url https://nbisweden.github.io/workshop-scRNAseq/ Single cell RNA sequencing analysis course Course leaders: Åsa Björklund, Paulo Czarnewski (edu.sc@nbis.se) Course webpage: https://nbisweden.github.io/workshop-scRNAseq/ Venue: online The course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include: An overview of the current scRNAseq technologies Basic overview of pipelines for processing raw reads into expression values Quality control of scRNAseq data Dimensionality reduction and clustering techniques Data normalization Differential gene expression for scRNAseq data Trajectory analysis Comparison of different analysis pipelines such as Seurat, Scran and Scanpy Application deadline -- December 16 Acceptance notification — December 22 contact: edu.sc@nbis.se 2021-01-25 09:00:00 UTC 2021-01-30 00:00:00 UTC [] Åsa Björklund - asa.bjorklund@scilifelab.se [] [] [] [] #trainingtraining
  • Introduction to Data Management Practices

    13 - 16 April 2021

    Uppsala University

    Elixir node event
    Introduction to Data Management Practices https://tess.elixir-europe.org/events/introduction-to-data-management-practices-3e7da179-219f-4d89-b659-1566d1c02db4 #training #url:https://nbisweden.github.io/workshop-dm-practices/ Introduction to Data Management Practices National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. The course is geared towards life scientists wanting to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. 2021-04-13 09:00:00 UTC 2021-04-16 00:00:00 UTC Uppsala University Uppsala University [] Niclas Jareborg - niclas.jareborg@scilifelab.se [] [] [] [] #trainingtraining

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