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  • Omics Integration and Systems Biology

    20 - 24 April 2020

    Lund University

    Elixir node event
    Omics Integration and Systems Biology https://tess.elixir-europe.org/events/omics-integration-and-systems-biology-08d3c603-6e36-4bda-a298-9bf93d371030 #training #url: https://www.scilifelab.se/events/omics-integration-and-systems-biology-2/ Important dates Application now open! Apply here: https://forms.gle/x3DCxb8dPW6ZjGFT6 Application closes: 19 March Confirmation to accepted students: 23 March For questions about the course, please contact Rui Benfeitas (rui.benfeitas@scilifelab.se), Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se), or Ashfaq Ali (ashfaq.ali@nbis.se) 2020-04-20 09:00:00 UTC 2020-04-24 00:00:00 UTC Lund University Lund University [] jessica.lindvall@scilifelab.se [] [] workshops_and_courses [] #trainingtraining
  • Tools for reproducible research (NBIS course)

    27 - 30 April 2020

    Solna, Sweden

    Elixir node event
    Tools for reproducible research (NBIS course) https://tess.elixir-europe.org/events/tools-for-reproducible-research-nbis-course #training url: https://www.scilifelab.se/events/tools-for-reproducible-research-4/   Important dates Application open: February 17 Application deadline: March 27 Confirmation to accepted participants: April 6 Apply here: https://forms.gle/12g7vvVH6cqAJ1QG9  Course homepage <https://nbis-reproducible-research.readthedocs.io> 2020-04-27 09:00:00 UTC 2020-04-30 00:00:00 UTC Solna, Sweden Solna Sweden [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
  • RNA-seq data analysis

    27 - 29 April 2020

    Uppsala, Sweden

    Elixir node event
    RNA-seq data analysis https://tess.elixir-europe.org/events/rna-seq-data-analysis-1603975c-443a-409a-b6ab-c9a75b40e292 #training #url: https://www.scilifelab.se/events/rna-seq-data-analysis-3/ Important dates Application open: January 16, 2020 Application deadline: March 13, 2020 How to apply https://forms.gle/huf6rcf2fyADLCKJ6 2020-04-27 09:00:00 UTC 2020-04-29 00:00:00 UTC Uppsala, Sweden Uppsala Sweden [] jessica.lindvall@scilifelab.se [] [] workshops_and_courses [] #trainingtraining
  • 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
  • Genome assembly using Galaxy

    14 July 2020

    Saint Lucia, Australia

    Genome assembly using Galaxy https://tess.elixir-europe.org/events/genome-assembly-using-galaxy-bfd44b56-d4a3-4863-a62b-e7656374a9a9 2020-07-14 09:00:00 UTC 2020-07-14 17:00:00 UTC QCIF The University of Queensland, Saint Lucia, Australia The University of Queensland Saint Lucia Queensland Australia 4072 University of Queensland Mark Crowe - mark.crowe@qcif.edu.au [] Postgraduate studentsPostdoctoral researchers [] [] Genome AssemblyDe novo genome assemblyGalaxyBioinformatics
  • NBIS Course Uppsala: Python programming with applications to bioinformatics

    19 - 24 October 2020

    Uppsala, Sweden

    Elixir node event
    NBIS Course Uppsala: Python programming with applications to bioinformatics https://tess.elixir-europe.org/events/nbis-course-uppsala-python-programming-with-applications-to-bioinformatics #training TBA edu.intro-python@nbis.se or education@nbis.se Course leaders: Nina Norgren and Malin Klang 2020-10-19 09:00:00 UTC 2020-10-24 00:00:00 UTC Uppsala, Sweden Uppsala Sweden [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
  • NBIS Course Umeå: Python programming with applications to bioinformatics, Umeå

    19 - 24 October 2020

    Glasburen

    Elixir node event
    NBIS Course Umeå: Python programming with applications to bioinformatics, Umeå https://tess.elixir-europe.org/events/nbis-course-umea-python-programming-with-applications-to-bioinformatics-umea-2dee9df0-cf81-4e7d-b14e-1dd65909a0fa #training TBA edu.intro-python@nbis.se or education@nbis.se Course leaders: Nina Norgren and Malin Klang 2020-10-19 09:00:00 UTC 2020-10-24 00:00:00 UTC Glasburen Glasburen [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
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