Train online


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Event: Plant and Animal Genomes Conference 2012
Speaker: Cath Brooksbank

Train online ( is a free, web-based learning resource for life scientists. Train online helps you make the most of the huge amount of biological data that EMBL-EBI makes publicly available for the research community. Using a combination of tutorials, guided examples, exercises and quizzes, Train online guides you towards becoming a confident user of open-access data resources. This training portal is there for you to learn in your own time and at your own pace, anywhere in the world. You do not need previous experience in bioinformatics to benefit from our courses.

This presentation will provide a short introduction to the courses currently available in Train online, which will include a demonstration of the resource. After the demonstration, the speaker will welcome questions about Train online and any suggestions that you may have for future courses.

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  • First of all I’d like to thank Sandra and the conference organisers for the opportunity to speak today. I’m going to tell you a little bit about a new initiative at the EBI, called Train online, which provides free access to online courses for end users of the EBI’s data resources. You can also try it out for yourselves at the EBI stand in booth 302.
  • So as my colleagues have already described, the EBI is a highly service-oriented organisation offering access to a comprehensive collection of public databases for life scientists. Hand in hand with its service mission is its training mission. Like any organisation we provide training to our PhD students, postdocs, staff and visitors, but the thing that sets us apart from many others is that one of our core goals is to train users of our data resources.
  • To this aim, we have a three-pronged approach to user training: we have a full programme of courses that we run at the EBI and we travel all over the world training users at their own institutes. Both of these programmes are oversubscribed and we really wanted to be able to offer user training to everyone who needs it, so in September we launched the beta release of Train online – our free online user-training resource.
  • I’m not going to say any more about our hands-on training except to say that if you’d like a full schedule of our 2012 courses we have some beautiful yearplanners at the booth, so come and pick one up.
  • Similarly I’m not going to say any more about our roadshow programme except to say that if you think your organisation may be interested in hosting a roadshow, come and talk to us later or visit us at the booth and we can tell you more.
  • But what I am going to tell you more about is Train online…
  • You can access Train online from the EBI home page…
  • When you get to the welcome page, you can access the courses straight away, either by going to the list of courses organised by category or by browsing the full list of courses. You don’t have to do anything else first, but if you want to be able to do the quizzes or receive news about new courses, you can register. If you register we promise that we’ll only send you information about Train online, and at the moment we’re doing that on approximately a quarterly basis, so we’re not going to spam you! If you register to receive updates at this conference you can take away a love data T-shirt. So, let’s imagine for a moment that I’m a new PhD student and I’m about to start a project to identify differences in gene expression between potatoes that are resistant and susceptible to blight. I want to see whether there are any previous experiments in the public domain that have tried to tackle the same question…
  • If I go to the gene expression topic, I see that there’s a course on investigating gene expression patterns using a data resource called the Gene Expression Atlas. If you want to know more about this, Ibrahim Emam, one of our resident Gene Expression Atlas experts, will be available at our stand throughout the meeting and will be able to give you a demo. For now, all we need to know is that there’s a course that looks relevant to my research goals. I can also see that it’s going to take me a couple of hours.
  • When I click on the course, the first thing I get is a summary page. The course description reassures me that I’m not going to waste those two precious hours, and I can see that in an ideal world I should first complete another course on functional genomics resources at the EBI. Let’s assume that I’ve already completed this course, and make a start…
  • This is a good point for me to describe in general terms the structure and philosophy behind the courses in Train online. Each of our courses starts with a defined set of learning objectives, then shows you how to use the resource in question. You get a chance to review what you’ve learned on the summary page and then you reinforce your learning – first by seeing how what you’ve learned can be applied to a set of example use cases, and then by practicing with a set of use cases. Finally, if you’ve registered with train online you can do a short quiz to check your learning, and then we give you some pointers towards learning more on this topic. This structure is very similar for all of our courses and is designed to cater for people with different learning preferences. You don’t have to do it all. You can dip in and out and do things in any order.
  • I’m the type of person who likes to be shown before I try it for myself, so I’m going to start at the beginning and work my way through.
  • The first part of each course comprises short tutorials with navigation buttons. I can just read the content, or open another window and follow along.
  • If I hover over them the definition pops up. If I click on it I’m taken to the relevant glossary entry in a new tab. Train online uses Wiktionary definitions where possible. New definitions are contributed to Wiktionary.
  • Once I’ve completed all the tutorials, I’m presented with a summary page that reminds me what I’ve just learned.
  • Guided examples present me with research problems and guide me through how to solve them using the relevant data resource. I can open up the resource in a separate window and follow along if I want to.
  • Exercises present me with research problems and ask me to solve them myself using the relevant data resource..
  • EMBL-EBI’s solutions to some of the exercises are presented as short videos
  • Some courses have reference lists, with publications linked to the relevant record in CitExplore, EMBL-EBI’s literature
  • At the end of each course there’s a ‘Learn more’ section pointing me to other useful resources. This section also contains a list of related online and classroom-based courses run by the EMBL-EBI
  • Finally, I can see who wrote the course.
  • I just want to spend a couple of minutes going through our longer-term plans for Train online. For each of the databases we’re aiming to provide a choice of learning pathways where we start out with an introduction to a field, provide a quick tour of each database, then a more comprehensive course that provides the basics. Finally, we plan to provide more advanced courses that will help you to become an expert user of the database in question.
  • So far, we’ve focused on populating train online with courses on our genomics and functional genomics resources. Since we launched, we’ve added introductions and quick tours on a wide range of other databases, and over the next year we’ll be adding full-length courses on these other topics. We’ve also been adding videos and training materials from some of our face-to-face courses. If you have any specific requests, please do send them to us or, even better, come and talk to us at the booth.
  • Finally, all that remains is for me to thank all the people – at EBI and beyond – who have contributed to the development of Train online. I’m here until Tuesday and Katrina’s here throughout the conference, so please do come and have a chat if you’d like to learn more; we’d be delighted to learn more about what you want to do with the EBI’s data and we’re keen to develop exercises and examples that address the needs of the agri-food research community. Don’t forget that if you register with us at this conference you’ll also get a really funky T-shirt.
  • Thank you for listening; I’d be happy to answer any questions.
  • Train online

    1. 1. Cath Brooksbank Head of Outreach and Training EMBL-EBI Train online Free online courses from EMBL-EBI
    2. 2. 2 EMBL-EBI’s Mission • To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • To contribute to the advancement of biology through basic investigator-driven research in bioinformatics • To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • To help disseminate cutting-edge technologies to industry • To coordinate biological data provision across Europe
    3. 3. 3
    4. 4. Training at EMBL-EBI • Hands-on courses for experimental researchers • Selection of applicants to address escalating demand • Immersive philosophy in which networking among trainers and delegates is strongly encouraged • Programme reflects the breadth of our services and is an integral part of EMBL’s course and conference programme • We welcome external experts as trainers and guest lecturers • 30/01/15 4
    5. 5. Training on tour: the roadshow • Mobile training programme offering hands-on training worldwide • Especially suitable for new users • Some roadshows funded by external grants, others by the host • Apply to host a roadshow: • / 30/01/15 5
    6. 6. 30 January 2015 6 Training on demand: Train online • Free, flexible online courses on the EMBL-EBI's most widely used data resources, created for life scientists by experts in our service teams • No previous experience of bioinformatics necessary to benefit from the courses • We want to help you to be highly competent users of our data resources; we are not trying to train you to become bioinformaticians! • You can repeat the courses as many times as you like, or just complete part of a course to brush up on how to perform a specific task •
    7. 7. How to find Train online from EBI home Select ‘Train online’ from the Training menu
    8. 8. The welcome page Register here if you want to do quizzes and receive updates Full list of courses Courses by category
    9. 9. Choosing a course from ‘gene expression’ Let’s take a look at a course on the Gene Expression Atlas This course will take ~2 hours if you complete it in one session
    10. 10. Course description page Let’s assume that you’ve already done the intro course Check that the course will meet your needs Right, let’s start…
    11. 11. Course structure 30/01/15 11 Show and tell Learning objectives What have I learned? Apply learning to real use cases Practice by myself Have I understood the key concepts? Learn more
    12. 12. Learning objectives Work your way through the course from here The first page tells you what you should be able to do once you’ve completed the course …or jump straight to the section that you need from the navigation bar
    13. 13. Tutorials The steps box tells you what to do next
    14. 14. Glossary terms Glossary terms are highlighted with a grey box I can browse the entire glossary from here
    15. 15. The summary page Review your learning on the summary page
    16. 16. Guided examples Revise your knowledge using guided examples
    17. 17. Exercises If you get stuck, there’s a hints page Apply your knowledge with exercises
    18. 18. ‘How we did it’ videos Find out how the experts completed the task
    19. 19. Check your learning If you’re logged in you can do short quizzes to check your learning When you’ve completed a quiz, you get feedback on your answers Your quiz results are stored in your account page, so you can keep a record of progress
    20. 20. References References are linked to journal articles through CiteXplore, the EBI’s resource for the scientific literature
    21. 21. Learn more Find out where you can expand your knowledge further
    22. 22. Who wrote this course? Find out who the course authors are
    23. 23. Learning pathways 30/01/15 23 Introduction to a field Quick tour of db1 Quick tour of db2 Db1 essentials Db1 advancedDb1 advanced Introduction to genomics resources at the EBI Quick tour of Ensembl Quick tour of Ensembl Genomes Ensembl essentials Variation with Ensembl Comparative genomics with Ensembl
    24. 24. 24 Courses as of Jan 2012 Genomes Ensembl (Ensembl Genomes EGA) Genomes Ensembl (Ensembl Genomes EGA) Nucleotide sequence ENA Nucleotide sequence ENA Functional genomics ArrayExpress Expression Atlas Functional genomics ArrayExpress Expression Atlas Protein Sequences UniProt Protein Sequences UniProt Protein families, motifs and domains InterPro Protein families, motifs and domains InterPro Macromolecular structures PDBe Macromolecular structures PDBe Protein activity IntAct , PRIDE Protein activity IntAct , PRIDE Chemical entities ChEBI Chemical entities ChEBI Pathways Reactome Pathways Reactome Systems BioModels BioSamples Systems BioModels BioSamples Literature and ontologies (CiteXplore,) GO Literature and ontologies (CiteXplore,) GO Chemogenomics ChEMBL Chemogenomics ChEMBL Intro or quick tour Full-length ‘essentials’ course
    25. 25. Who develops Train online? Web development I’m here! I’m here! Come and see us at booth 302!
    26. 26. Thank you for listening! ?? ? ? ? ? ? ? ? ? ?