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51 events found

Keywords: Genome Assembly  or HDRUK 

  • 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
  • Introduction to R for Biologists (ONLINE LIVE TRAINING)

    28 - 29 October 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to R for Biologists (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/introduction-to-r-for-biologists-online-live-training-a8e95d49-6369-4b4d-9c1e-d92dcab08320 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. 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. R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard. 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=3573906&course-title=Introduction%20to%20R%20for%20Biologists).'' 2020-10-28 09:30:00 UTC 2020-10-29 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR 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
  • The PRIDE database: storing, disseminating and integrating proteomics data in the public domain

    28 October 2020

    Elixir node event
    The PRIDE database: storing, disseminating and integrating proteomics data in the public domain https://tess.elixir-europe.org/events/the-pride-database-storing-disseminating-and-integrating-proteomics-data-in-the-public-domain This webinar will provide an introduction to proteomics approaches and the PRIDE database, followed by examples of PRIDE public data re-use, including “big data” approaches. 2020-10-28 15:30:00 UTC 2020-10-28 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Introducing the new UniProt Disease Portal

    29 October 2020

    Elixir node event
    Introducing the new UniProt Disease Portal https://tess.elixir-europe.org/events/introducing-the-new-uniprot-disease-portal This webinar will provide an interactive introduction to the new UniProt Disease Portal: a single centralized resource of UniProt disease-centric information which has been developed with the help of our users to better serve the needs of the research community and facilitate protein discoverability. 2020-10-29 15:30:00 UTC 2020-10-29 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Introduction to Scientific Figure Design (ONLINE LIVE TRAINING)

    30 October 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Scientific Figure Design (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/introduction-to-scientific-figure-design-online-live-training PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online in conjunction with the presenters. This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Further information and access to the course materials is [here](http://www.bioinformatics.babraham.ac.uk/training.html#figuredesign). 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=3566463&course-title=Introduction%20to%20Scientific%20Figure%20Design).'' 2020-10-30 09:30:00 UTC 2020-10-30 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation 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
  • Bioinformatics & Functional Genomics in Zebrafish

    2 - 5 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Bioinformatics & Functional Genomics in Zebrafish https://tess.elixir-europe.org/events/bioinformatics-functional-genomics-in-zebrafish-ff8f3fea-a89e-4b25-93b1-111191cae4b7 This course has been designed specifically for researchers working within the Zebrafish community, providing an introduction and practical knowledge of tools and resources for working with functional genomics data. 2020-11-02 09:00:00 UTC 2020-11-05 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Metagenomics bioinformatics

    2 - 6 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Metagenomics bioinformatics https://tess.elixir-europe.org/events/metagenomics-bioinformatics-91c48308-c2e6-48eb-b1ea-113f79da1edd This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including marker gene, whole gene shotgun (WGS) and assembly-based approaches. 2020-11-02 09:00:00 UTC 2020-11-06 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] HDRUK
  • Metagenomics bioinformatics (Virtual)

    2 - 6 November 2020

    Hinxton, United Kingdom

    Elixir node event
    Metagenomics bioinformatics (Virtual) https://tess.elixir-europe.org/events/metagenomics-bioinformatics-virtual Gain knowledge on the tools, processes and analysis approaches used in the field of metagenomics. 2020-11-02 09:00:00 UTC 2020-11-06 17:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] HDRUK
  • Europe PMC: Programmatic access

    3 November 2020

    Elixir node event
    Europe PMC: Programmatic access https://tess.elixir-europe.org/events/europe-pmc-programmatic-access This webinar will introduce the Europe PMC Articles RESTful API and show how to programmatically access publications and related information, such as citations, references, data links, or text-mined terms. 2020-11-03 14:00:00 UTC 2020-11-03 15:00:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Variant submission and data access at the European Variation Archive

    4 November 2020

    Elixir node event
    Variant submission and data access at the European Variation Archive https://tess.elixir-europe.org/events/variant-submission-and-data-access-at-the-european-variation-archive This webinar will cover how to access data using the EVA UI/API and the methodology of variant data submission to the EVA, specifically focusing on data transformation and formats. 2020-11-04 15:30:00 UTC 2020-11-04 16:30:00 UTC [] Ajay Mishra [] [] [] [] HDRUK
  • Introduction to Statistical Analysis (Online)

    5 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Statistical Analysis (Online) https://tess.elixir-europe.org/events/introduction-to-statistical-analysis-online 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 provides a refresher on the foundations of statistical analysis. The emphasis is on interpreting the results of a statistical test, and being able to determine the correct test to apply. Practicals are conducted using a series of online apps, and we will not teach a particular statistical analysis package, such as R. For courses that teach R, please see the links under "Related courses" . This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at [CRUK Cambridge Institute](http://www.cruk.cam.ac.uk/). 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 Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3593310&course-title=Introduction%20to%20Statistical%20Analysis).'' 2020-11-05 09:30:00 UTC 2020-11-05 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Ensembl Browser workshop, University of California San Francisco, 9-10 November 2020

    9 - 10 November 2020

    Hinxton, United Kingdom

    Elixir node event
    Ensembl Browser workshop, University of California San Francisco, 9-10 November 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-university-of-california-san-francisco-9-10-november-2020 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2020-11-09 17:00:00 UTC 2020-11-10 21:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Michal Szpak [] [] [] [] HDRUK
  • CABANA Train the Trainer Workshop for XMXP20

    11 November 2020

    Elixir node event
    CABANA Train the Trainer Workshop for XMXP20 https://tess.elixir-europe.org/events/cabana-train-the-trainer-workshop-for-xmxp20 This virtual workshop takes place within the X-meeting eXperience 2020 symposium. It will provide new trainers with knowledge, skills, guidance and tips for developing and delivering training. 2020-11-11 09:00:00 UTC 2020-11-11 17:00:00 UTC Virtual format Virtual format [] Piraveen Gopalasingam [] [] [] [] HDRUK
  • MGnify today: analysing microbiome data

    11 November 2020

    Elixir node event
    MGnify today: analysing microbiome data https://tess.elixir-europe.org/events/mgnify-today-analysing-microbiome-data This webinar will describe how MGnify can assist you in your microbiome research by providing a broad overview of resources available in MGnify. During the webinar, we will cover what types of microbiome data are included, improvements we have made to our analysis pipeline, as well as ways to search for data. 2020-11-11 15:30:00 UTC 2020-11-11 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Biological data analysis using the InterMine User Interface (Online)

    16 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Biological data analysis using the InterMine User Interface (Online) https://tess.elixir-europe.org/events/biological-data-analysis-using-the-intermine-user-interface-online PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. 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. [InterMine](http://intermine.org/) is a freely available open-source data warehouse built specifically for the integration and analysis of complex biological data. InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafishHymenoptera, Planaria, and more recently human. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. InterMine provides sophisticated query and visualisation tools both through a web interface and a powerful web service API, with multiple language bindings including Python and R. This course will focus on the InterMine web interface and will introduce participants to all aspects of the user interface, starting with some simple exercises and building up to more complex analysis encompassing several analysis tools and comparative analysis across organisms. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available (a comprehensive list of InterMine databases is available [here.](http://registry.intermine.org/)) This event is organised alongside a half day course on Biological data analysis using the InterMine API. More information on this event is available [here](https://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-intermineAPI). 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 Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3603729&amp;course-title=Biological%20data%20analysis%20using%20InterMine).'' 2020-11-16 13:00:00 UTC 2020-11-16 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] The course is aimed at <b>bench biologists and bioinformaticians</b> who need to analyse their own data against large biological datasetsor who need to search against several biological datasets to gain knowledge of a gene/gene setbiological process or function.This course is for researchers from a broad biological background as the techniques learned can be applied to any InterMine databasecovering a diverse range of organisms and biological data.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Biological data analysis using the InterMine API (Online)

    17 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Biological data analysis using the InterMine API (Online) https://tess.elixir-europe.org/events/biological-data-analysis-using-the-intermine-api-online PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. 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. [InterMine](http://intermine.org/) is a freely available open-source data warehouse built specifically for the integration and analysis of complex biological data sets. InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafish, Hymenoptera, Planaria, and more recently human. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. InterMine provides sophisticated query and visualisation tools both through a web interface and a powerful web service API, with multiple language bindings including Python and R. This course will focus on programmatic access to InterMine through the API and InterMine searches will be done using Python and R scripts. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available (a comprehensive list of InterMine databases is available [here](http://registry.intermine.org/). This event is organised alongside a half day course on Biological data analysis using the InterMine User Interface. More information on this event are available [ https://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-intermine here]. 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 Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3603743&amp;course-title=Biological%20data%20analysis%20using%20the%20InterMine%20API).'' 2020-11-17 13:00:00 UTC 2020-11-17 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] This course is aimed at <b>bench biologists and bioinformaticians</b> who are interested in large scale and/or automated analysis of their own or existing data against large biological datasetsor who are interested in graphs and other visualisations of data generated through an InterMine search.The course is also suitable for anyone wanting to know what an API is and how the ability to access data programmatically could help them in their research.This course is for researchers from a broad biological background as the techniques learned can be applied to any InterMine databasecovering a diverse range of organisms and biological data.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Basics to advanced genome annotation at Ensembl and REST Application Programming Interfaces (APIs)

    17 - 20 November 2020

    Elixir node event
    Basics to advanced genome annotation at Ensembl and REST Application Programming Interfaces (APIs) https://tess.elixir-europe.org/events/basics-to-advanced-genome-annotation-at-ensembl-and-rest-application-programming-interfaces-apis Introduction to the Ensembl Genome Browser and REST API, in collaboration with NextGenHelper. 2020-11-17 18:00:00 UTC 2020-11-20 20:30:00 UTC Virtual format Virtual format [] Emily Perry [] [] [] [] HDRUK
  • Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING)

    18 - 20 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/analysis-of-bulk-rna-seq-data-online-live-training-018bc625-9d97-4f56-97fa-4a78c1f5e75e 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. The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. 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=3593329&amp;course-title=Analysis%20of%20bulk%20RNA-seq%20data).'' 2020-11-18 09:30:00 UTC 2020-11-20 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR RNA-Seq Data mining Transcriptomics Data visualisation Functional genomics Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • MGnify API: accessing microbiome data computationally

    18 November 2020

    Elixir node event
    MGnify API: accessing microbiome data computationally https://tess.elixir-europe.org/events/mgnify-api-accessing-microbiome-data-computationally This webinar will provide an overview of the MGnify API. It will include how to utilise the API using a browser; where to find documentation; how to use filtering and pagination; available output formats; and scripting examples in Python. 2020-11-18 15:30:00 UTC 2020-11-18 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Structural bioinformatics

    23 - 27 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Structural bioinformatics https://tess.elixir-europe.org/events/structural-bioinformatics-de38d612-6cf9-481f-9a57-3a54511976de This course explores bioinformatics data resources and tools for the interpretation and exploitation of bio-macromolecular structures. 2020-11-23 09:00:00 UTC 2020-11-27 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Structural bioinformatics (Virtual)

    23 - 27 November 2020

    Hinxton, United Kingdom

    Elixir node event
    Structural bioinformatics (Virtual) https://tess.elixir-europe.org/events/structural-bioinformatics-virtual This course explores bioinformatics data resources and tools for the browsing, analysis and interpretation of bio-macromolecular structure information. 2020-11-23 09:00:00 UTC 2020-11-27 17:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • An Introduction to Machine Learning (ONLINE LIVE TRAINING)

    23 - 25 November 2020

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Machine Learning (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/an-introduction-to-machine-learning-online-live-training-ca34af0c-9423-4e3c-bfe3-539c1ed8b05d 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. Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes. 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=3590664&amp;course-title=An%20Introduction%20to%20Machine%20Learning).'' 2020-11-23 09:30:00 UTC 2020-11-25 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Data mining University of Cambridge Bioinformatics Training [] This is aimed at life scientists with little or no experience in machine learning and that are looking at implementing these approaches in their research.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • CABANA: Bioinformatics for plant biology

    30 November - 4 December 2020

    San Jose, Costa Rica

    Elixir node event
    CABANA: Bioinformatics for plant biology https://tess.elixir-europe.org/events/cabana-bioinformatics-for-plant-biology Please note this course will now be held in Costa Rica. It was previously due to run at EMBL-EBI in the UK. 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC University of Costa Rica (UCR), San Jose, Costa Rica University of Costa Rica (UCR) San Jose Costa Rica CB10 1SD [] Marina Pujol [] [] [] [] HDRUK
  • CABANA: Bioinformatics for plant biology (Postponed until 2021)

    30 November - 4 December 2020

    San Jose, Costa Rica

    Elixir node event
    CABANA: Bioinformatics for plant biology (Postponed until 2021) https://tess.elixir-europe.org/events/cabana-bioinformatics-for-plant-biology-postponed-until-2021 This course was postponed from 2020. EMBL-EBI plans to deliver the majority of its 2021 events face-to-face with a small number of virtual events. Please note that some events that are currently listed as ‘on-site’ might need to be delivered virtually, depending on the prevailing status of the pandemic at the time. More courses will be added to this programme as our plans develop further. 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC University of Costa Rica (UCR), San Jose, Costa Rica University of Costa Rica (UCR) San Jose Costa Rica [] Marina Pujol [] [] [] [] HDRUK
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    30 November 2020 - 31 January 2021

    Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-3e9f10a2-bd0a-4af3-bc39-0d11856143e2 # 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 2020-11-30 09:00:00 UTC 2021-01-31 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • CABANA Workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 Pandemic

    1 - 4 December 2020

    Hinxton, United Kingdom

    Elixir node event
    CABANA Workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 Pandemic https://tess.elixir-europe.org/events/cabana-workshop-applied-bioinformatics-molecular-epidemiology-and-the-sars-cov-2-pandemic This workshop will provide training on the use of bioinformatic tools for the design and analysis of SARS-CoV-2 sequences. 2020-12-01 08:45:00 UTC 2020-12-04 12:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Piraveen Gopalasingam [] [] [] [] HDRUK
  • Managing your Research Data (Online)

    1 December 2020

    Cambridge, United Kingdom

    Elixir node event
    Managing your Research Data (Online) https://tess.elixir-europe.org/events/managing-your-research-data-online 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. How much data would you lose if your laptop was stolen? Have you ever emailed your colleague a file named 'final_final_versionEDITED'? Have you ever struggled to import your spreadsheets into R? Would you be able to write a Data Management Plan as part of a grant proposal? As a researcher, you will encounter research data in many forms, ranging from measurements, numbers and images to documents and publications. Whether you create, receive or collect data, you will certainly need to organise it at some stage of your project. This workshop will provide an overview of some basic principles on how we can work with data more effectively. We will discuss the best practices for research data management and organisation so that our research is auditable and reproducible by ourselves, and others, in the future. Course materials are available [here](https://datachampcam.github.io/avoid-data-disaster/) This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at [CRUK Cambridge Institute](http://www.cruk.cam.ac.uk/). 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=3593322&amp;course-title=Managing%20your%20Research%20Data).'' 2020-12-01 10:00:00 UTC 2020-12-01 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • CABANA: Genomic Data for Surveillance of Communicable Disease

    7 - 11 December 2020

    Cambridge, United Kingdom

    Elixir node event
    CABANA: Genomic Data for Surveillance of Communicable Disease https://tess.elixir-europe.org/events/cabana-genomic-data-for-surveillance-of-communicable-disease This course will develop skills in the analysis of field-collected microbial genomes samples and how to use data this genomic in the surveillance of communicable diseases. 2020-12-07 09:00:00 UTC 2020-12-11 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] HDRUK
  • Next Generation Sequencing Bioinformatics

    7 - 11 December 2020

    Cambridge, United Kingdom

    Elixir node event
    Next Generation Sequencing Bioinformatics https://tess.elixir-europe.org/events/next-generation-sequencing-bioinformatics-8bb1d757-0644-44ce-b8f0-29dafc320ce2 This course will provide an introduction to the technology, analysis workflows, tools and resources for next generation sequencing data analysis. 2020-12-07 09:00:00 UTC 2020-12-11 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK

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