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  • Executive Masters in Management of Research Infrastructures

    13 November 2018 - 26 June 2020

    Milan, Italy

    Elixir node event
    Executive Masters in Management of Research Infrastructures https://tess.elixir-europe.org/events/executive-masters-in-management-of-research-infrastructures-12abb26e-f3b7-45ac-92c6-24008017292d This Masters development programme is aimed at current Research Infrastructures managers and leaders who wish to develop the competencies required to meet the needs of Research Infrastructures in the planning, construction and operation phases. 2018-11-13 12:00:00 UTC 2020-06-26 12:00:00 UTC University of Milano-Bicocca, Milan, Italy University of Milano-Bicocca Milan Italy 20126 [] Claire Johnson [] [] [] [] HDRUK
  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    16 September - 30 December 2019

    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 2019-09-16 09:00:00 UTC 2019-12-30 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK
  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    4 November - 16 December 2019

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-562964f7-002f-4d58-8d54-da81b6d29cc8 # 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 2019-11-04 09:00:00 UTC 2019-12-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    11 November - 23 December 2019

    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 2019-11-11 09:00:00 UTC 2019-12-23 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • Analysis of single cell RNA-seq data

    16 - 17 December 2019

    Cambridge, United Kingdom

    Elixir node event
    Analysis of single cell RNA-seq data https://tess.elixir-europe.org/events/analysis-of-single-cell-rna-seq-data-1cd0c9cc-dbb1-416f-8738-5bd702af8877 Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging. In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq. The course website providing links to the course materials can be found [here](http://hemberg-lab.github.io/scRNA.seq.course/index.html). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3097806&&course-title=Analysis%20of%20single%20cell%20RNA-seq%20data).'' 2019-12-16 09:30:00 UTC 2019-12-17 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Transcriptomics Functional genomics Data visualisation Data mining 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
  • Snakemake workshop

    6 - 7 January 2020

    Cambridge, United Kingdom

    Elixir node event
    Snakemake workshop https://tess.elixir-europe.org/events/snakemake-workshop Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. The [Snakemake](https://snakemake.readthedocs.io/en/stable/) workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. With over 100k downloads on Bioconda, Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications. This 2-day workshop with, at the first day, teach how to use Snakemake for reproducible data analysis. On the second day, we will further discuss advanced topics and everybody is welcome to apply the obtained knowledge for his or her own analysis project while getting help from the organizers. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3108957&course-title=Snakemake%20workshop).'' 2020-01-06 09:30:00 UTC 2020-01-07 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
  • Introduction to R for Biologists

    15 - 16 January 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to R for Biologists https://tess.elixir-europe.org/events/introduction-to-r-for-biologists-5984ebec-9d4f-45d1-b258-b43555de5a1d 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. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3097826&course-title=Introduction%20to%20R%20for%20Biologists).'' 2020-01-15 09:30:00 UTC 2020-01-16 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
  • Ensembl Browser Workshop, UC San Diego, 16 January 2019

    16 January 2020

    San Diego, United States of America

    Elixir node event
    Ensembl Browser Workshop, UC San Diego, 16 January 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-uc-san-diego-16-january-2019 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. 2020-01-16 09:00:00 UTC 2020-01-16 17:00:00 UTC University of California, San Diego, San Diego, United States of America University of California, San Diego San Diego United States of America 92161 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl Browser Workshop- American University in Cairo, 21st January 2020

    21 January 2020

    Cairo, Egypt

    Elixir node event
    Ensembl Browser Workshop- American University in Cairo, 21st January 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-american-university-in-cairo-21st-january-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. 2020-01-21 09:00:00 UTC 2020-01-21 09:00:00 UTC American University in Cairo, Cairo, Egypt American University in Cairo Cairo Egypt 11835 [] Benjamin Moore [] [] [] [] HDRUK
  • Introduction to RNA-Seq and Functional Interpretation

    21 - 24 January 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to RNA-Seq and Functional Interpretation https://tess.elixir-europe.org/events/introduction-to-rna-seq-and-functional-interpretation-e2471a7b-692d-419f-8746-a251893793f3 This course is aimed at life science researchers wanting to learn more about processing RNA-Seq data and later downstream analysis. 2020-01-21 09:00:00 UTC 2020-01-24 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
  • Ensembl Browser Workshop, Stanford University, 21 January 2019

    21 January 2020

    Stanford, United States of America

    Elixir node event
    Ensembl Browser Workshop, Stanford University, 21 January 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-stanford-university-21-january-2019 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. 2020-01-21 09:00:00 UTC 2020-01-21 17:00:00 UTC Stanford University, Stanford, United States of America Stanford University Stanford United States of America 94305 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl REST API workshop, American University in Cairo, 22nd January 2020

    22 January 2020

    Cairo, Egypt

    Elixir node event
    Ensembl REST API workshop, American University in Cairo, 22nd January 2020 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-american-university-in-cairo-22nd-january-2020 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2020-01-22 09:30:00 UTC 2020-01-22 09:30:00 UTC American University in Cairo, Cairo, Egypt American University in Cairo Cairo Egypt 11835 [] Benjamin Moore [] [] [] [] HDRUK
  • Ensembl Train the Trainer Workshop, American University in Cairo, 23rd January 2020

    23 January 2020

    Cairo, Egypt

    Elixir node event
    Ensembl Train the Trainer Workshop, American University in Cairo, 23rd January 2020 https://tess.elixir-europe.org/events/ensembl-train-the-trainer-workshop-american-university-in-cairo-23rd-january-2020 Work with the Ensembl outreach team to develop teaching skills and practice delivering Ensembl Browser workshops. 2020-01-23 09:00:00 UTC 2020-01-23 09:00:00 UTC American University in Cairo, Cairo, Egypt American University in Cairo Cairo Egypt 11835 [] Benjamin Moore [] [] [] [] HDRUK
  • Extracting biological information from gene lists

    23 January 2020

    Cambridge, United Kingdom

    Elixir node event
    Extracting biological information from gene lists https://tess.elixir-europe.org/events/extracting-biological-information-from-gene-lists-06e84be3-c3c2-40da-b84a-1465e1a5571a Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists. This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication. Course materials are available [here](https://www.bioinformatics.babraham.ac.uk/training.html#fagl). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3097799&course-title=Extracting%20biological%20information%20from%20gene%20lists).'' 2020-01-23 09:30:00 UTC 2020-01-23 17:30:00 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
  • Ensembl Browser Workshop, UC Davis, 23 January 2019

    23 January 2020

    Davis, United States of America

    Elixir node event
    Ensembl Browser Workshop, UC Davis, 23 January 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-uc-davis-23-january-2019 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. 2020-01-23 09:30:00 UTC 2020-01-23 17:00:00 UTC University of California, Davis, Davis, United States of America University of California, Davis Davis United States of America 95616 [] Astrid Gall [] [] [] [] HDRUK
  • What is Genetic Counselling?

    27 January - 19 April 2020

    What is Genetic Counselling? https://tess.elixir-europe.org/events/what-is-genetic-counselling-de9049ee-4df5-4c8c-a099-9f91c2696d3b # Overview * **Duration:** 6 weeks live, 2 hours per week * **Free** * **Certificate of achievement** available on satisfactory completion * **Start Date:** The course is run ‘live’ for 6 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? Who are genetic counsellors? Who has genetic counselling and what does a genetic counsellor do? On this course, you will find the answers to these questions whilst learning about the role of genetic counselling in healthcare and the genomic era. You will discover why people seek genetic counselling and how it compares in different contexts and countries. You will explore the main skills and knowledge needed of a genetic counsellor, as well as their key responsibilities to patients. You will also discuss the ethical issues of genetic counselling, and its varied opportunities and challenges for the future. ### Who is the course for? This course is designed for healthcare professionals, clinicians, biomedical research scientists, and anyone curious about genetic counselling. Although not required, a basic knowledge of genetics, genetic testing technologies, and inheritance patterns would help support your learning on this course. # Programme ### What topics will you cover? * Why people would see a genetic counsellor * Some of a genetic counsellor’s key tasks * A genetic counsellor’s key skills and knowledge: counselling skills, medical and scientific knowledge * Ethical issues in genetic counselling * What the future might hold for genetic counsellors ### What will you achieve? By the end of the course, you'll be able to... * Identify why people have genetic counselling and the different contexts in which people receive genetic counselling * Describe the different skills and knowledges needed by genetic counsellors * Compare genetic counselling in different contexts and different countries * Reflect on some ethical issues that arise in genetic counselling * Discuss the role of genetic counselling in healthcare as we enter the ‘genomic era'. ### What software or tools do you need? No specific software, hardware or other resources are required to complete the course. # Educators ## Lead Educators ### Anna Middleton I am the Chair of the Association of Genetic Nurses and Counsellors in the UK and ROI (2018/19) and Head of Society and Ethics Research at the Wellcome Genome Campus, Connecting Science, Cambridge, UK ### Jonathan Roberts I am a pre-registration genetic counsellor at Addenbrooke’s Hospital, Cambridge. I am also a Staff Scientists at the Wellcome Genome Campus. I conduct my research within the Society and Ethics Research group. # 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 2020-01-27 09:00:00 UTC 2020-04-19 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] geneticcounsellingHDRUK
  • Health-RI Conference 2020

    30 January 2020

    Utrecht, Netherlands

    Health-RI Conference 2020 https://tess.elixir-europe.org/events/health-ri-conference-2020 At this year's Health-RI conference, leading experts will highlight how data is helping us to remain healthy, and how it can drive us towards a healthy future. We all want to stay healthy for as long as possible. How do we keep people healthy? When we do get ill, we look for the best treatment - the right treatment at the right time, tailor made. How can we learn from today's patients so that tomorrow's patients get better treatment? It's a matter of continuous learning and improvement - evidence based with the help of enormous amounts of data in different formats and from various sources. We're already learning how to combine that data in clever ways, tailoring it to specific situations and applying it to our everyday health choices. 2020-01-30 09:00:00 UTC 2020-01-30 17:00:00 UTC Health-RI Jaarbeurs Supernova, Utrecht, Utrecht, Netherlands Jaarbeurs Supernova, Utrecht Utrecht Utrecht Netherlands [] [] [] meetings_and_conferences [] FAIRHealthcarepersonalized medicinepersonal health trainArtificial Intelligence
  • Bioinformatics for Discovery

    4 February 2020

    Cambridge, United Kingdom

    Elixir node event
    Bioinformatics for Discovery https://tess.elixir-europe.org/events/bioinformatics-for-discovery-b8d92a0c-662f-4bcf-9e23-e005357edfa2 We are sorry to announce that this course has been cancelled and will not be running in 2020. 2020-02-04 09:00:00 UTC 2020-02-04 09:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Ensembl Browser Workshop, Erasmus MC Rotterdam, 5/6 February 2020

    5 - 6 February 2020

    Rotterdam, Netherlands

    Elixir node event
    Ensembl Browser Workshop, Erasmus MC Rotterdam, 5/6 February 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-erasmus-mc-rotterdam-5-6-february-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. 2020-02-05 09:30:00 UTC 2020-02-06 17:00:00 UTC Erasmus MC Rotterdam, Rotterdam, Netherlands Erasmus MC Rotterdam Rotterdam Netherlands 3015 CE [] Astrid Gall [] [] [] [] HDRUK
  • Introduction to working with UNIX and bash

    6 February 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to working with UNIX and bash https://tess.elixir-europe.org/events/introduction-to-working-with-unix-and-bash-4a140b91-7694-4b99-9eb4-4ea22b5f1a1c Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands. Building on this foundation, the course will use a bioinformatics example to demonstrate how the skills learnt can be applied to connecting to external resources/servers, installing specialist tools and ultimately combining commands into scripts for automation and reproducibility. This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3271167&course-title=Introduction%20to%20working%20with%20Unix%20and%20bash).'' 2020-02-06 09:30:00 UTC 2020-02-06 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
  • Exploring Human Genetic Variation

    11 - 12 February 2020

    Cambridge, United Kingdom

    Elixir node event
    Exploring Human Genetic Variation https://tess.elixir-europe.org/events/exploring-human-genetic-variation-13efb0bd-ea44-48b8-8e1e-7d6fd7ee8c95 Do you want to understand more about genetic variation? Are you aware of the resources available for finding, viewing and exploring variant data? Are you trying to link variant data to phenotypes? This two-day workshop will demonstrate resources and bioinformatics tools available at EMBL-EBI and the Sanger Institute that will aid understanding of human genetic variation. 2020-02-11 09:00:00 UTC 2020-02-12 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Rebecca Nicholl [] [] [] [] HDRUK
  • Data Science in Python

    11 - 12 February 2020

    Cambridge, United Kingdom

    Elixir node event
    Data Science in Python https://tess.elixir-europe.org/events/data-science-in-python-6eb99e4e-46e9-4333-8857-192f9123f631 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. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3166602&course-title=Data%20Science%20in%20Python).'' 2020-02-11 09:30:00 UTC 2020-02-12 16:30:00 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
  • An introduction to long-read sequencing

    13 - 14 February 2020

    Cambridge, United Kingdom

    Elixir node event
    An introduction to long-read sequencing https://tess.elixir-europe.org/events/an-introduction-to-long-read-sequencing Analysis of whole genome data sets unearths a multitude of variants of different classes, which need to be filtered, annotated and validated to arrive at a causative variant for the disease. The current short length sequences, whilst being excellent at identifying single nucleotide variants and short insertions/deletions, struggle to correctly map structural variants (SVs). Long-read sequencing technologies offer improvements in the characterization of genetic variation and regions that are difficult to assess with short-read sequences. The aim of this course is to familiarise participants with long read sequencing technologies, their applications and the bioinformatics tools used to assemble this kind of data. Lectures will introduce this technology and provide insight into methods for the analysis of genomic data, while the hands-on sessions will allow participants to run analysis pipelines, focusing on data generated by the Oxford Nanopore Technologies (ONT) platform. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3327123&course-title=An%20Introduction%20to%20long-read%20sequencing).'' 2020-02-13 09:30:00 UTC 2020-02-14 17:00:00 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 [] This is aimed for life scientists with little or no experience in long-read sequencing 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
  • Reproducible Research with R

    18 February 2020

    Cambridge, United Kingdom

    Elixir node event
    Reproducible Research with R https://tess.elixir-europe.org/events/reproducible-research-with-r-343119a7-ebad-409f-9957-c968fe5f6d1c This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3239509&course-title=Reproducible%20Research%20with%20R).'' 2020-02-18 09:30:00 UTC 2020-02-18 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
  • Mining PDBe and PDBe-KB using a graph database

    18 - 20 February 2020

    Cambridge, United Kingdom

    Elixir node event
    Mining PDBe and PDBe-KB using a graph database https://tess.elixir-europe.org/events/mining-pdbe-and-pdbe-kb-using-a-graph-database This workshop covers the use of the PDBe graph database to extract data for solving complex structural biology queries. 2020-02-18 12:00:00 UTC 2020-02-20 14:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • An Introduction to Machine Learning

    19 - 21 February 2020

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Machine Learning https://tess.elixir-europe.org/events/an-introduction-to-machine-learning-4a589171-221a-4bc7-b5f7-f0172c7ab980 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. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3241183&course-title=An%20Introduction%20to%20Machine%20Learning).'' 2020-02-19 09:30:00 UTC 2020-02-21 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 Bioinformatics 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
  • Statistics bootcamp using R

    25 - 28 February 2020

    Cambridge, United Kingdom

    Elixir node event
    Statistics bootcamp using R https://tess.elixir-europe.org/events/statistics-bootcamp-using-r This 4-days bootcamp provides an in depth look at statistical analyses using R. Day 1 aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. As well as introducing core R language concepts, this course also provides the basics of using the Tidyverse for data maniupulation, and ggplot for plotting. It will focus on entering and manipulating data in R and producing simple graphs. Day 2-4 will focus on the statistical possibilities of R, covering from experimental design to analysis of quantitative and qualitative data. Ample time will be given to participants to practice different type of analysis and interact with the trainers to discuss their statistical problems. This event is organized in collaboration with the [Babraham Institutes's Bioinformatics Group](https://www.bioinformatics.babraham.ac.uk/index.html) and it is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3246150&course-title=Statistics%20bootcamp%20using%20R).'' 2020-02-25 11:30:00 UTC 2020-02-28 15:00:00 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 Workshop: NGS analysis applied to virome sequencing in agricultural systems

    2 - 4 March 2020

    San Jose, Costa Rica

    Elixir node event
    CABANA Workshop: NGS analysis applied to virome sequencing in agricultural systems https://tess.elixir-europe.org/events/cabana-workshop-ngs-analysis-applied-to-virome-sequencing-in-agricultural-systems This workshop will provide training around the experimental design and detailed computational analysis of virome data from agricultural systems. 2020-03-02 08:30:00 UTC 2020-03-04 17:00:00 UTC University of Costa Rica (UCR), San Jose, Costa Rica University of Costa Rica (UCR) San Jose Costa Rica [] CABANA UCR Costa Rica [] [] [] [] HDRUK
  • Introduction to Multiomics Data Integration

    2 - 5 March 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Multiomics Data Integration https://tess.elixir-europe.org/events/introduction-to-multiomics-data-integration-beba48af-1cd5-40f2-b174-16fd200be7d5 We are currently developing the course programme for 2020, and as further information about the course becomes available we will update this page. 2020-03-02 09:00:00 UTC 2020-03-05 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] EMBL-EBI Training Team [] [] [] [] HDRUK
  • Introduction to Multiomics Data Integration and Visualisation

    2 - 6 March 2020

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Multiomics Data Integration and Visualisation https://tess.elixir-europe.org/events/introduction-to-multiomics-data-integration-and-visualisation This introductory course will highlight the challenges that researchers face in integrating multiomics data sets using biological examples. 2020-03-02 09:00:00 UTC 2020-03-06 13:30:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
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