Event: Plant and Animal Genomes Conference 2012
Speaker: Cath Brooksbank
Train online (www.ebi.ac.uk/training/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.
1. Cath Brooksbank
Head of Outreach and Training
EMBL-EBI
Train online
Free online courses from EMBL-EBI
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
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
• www.ebi.ac.uk/training/handson/
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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:
• www.ebi.ac.uk/training/roadshow
/
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6. 30 January 2015
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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
• www.ebi.ac.uk/training/online
7. How to find Train online from EBI home
www.ebi.ac.uk/training/online
Select ‘Train
online’ from the
Training menu
8. The welcome page
Register here if
you want to do
quizzes and
receive updates
Full list of
courses
Courses by
category
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. 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. Course structure
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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. 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
17. Exercises
If you get stuck,
there’s a hints page
Apply your knowledge
with exercises
18. ‘How we did it’ videos
Find out how the experts
completed the task
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
22. Who wrote this course?
Find out who the course
authors are
23. Learning pathways
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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
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. Who develops Train online?
Web
development
I’m
here!
I’m
here!
Come and see us at
booth 302!
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.