Do you want to learn more about the Ensembl browser? Are you unable to host or attend an in-person Ensembl workshop? Do you still want to learn in real-time with instructors on hand to help you out?

The new Ensembl online training series might be for you.

What is it?

The Ensembl online training series consists of a series of live webinars, once a week over seven weeks. In each webinar you will learn about a specific aspect of Ensembl data or tools – see the online course for details. You will then have access to exercises so that you can practice what you’ve learnt.

You can dip in and out of webinars, taking only those that interest you. If you miss one, we will post the videos to our YouTube channel and embed them in the online course so that you can catch up.

What makes it special is that the course is fully interactive. If you attend the live webinars, you will have an opportunity to ask the instructors questions in real time. Afterwards, while you work on the exercises, you can interact with the instructors and other participants via our dedicated Facebook group. If you prefer not to use Facebook, you can also email us for help. Plus, you’ll be able to re-watch all or part of the videos at your leisure.

When is it?

We start on the 24th March, and will hold seven webinars on Thursday afternoons, up until the 5th May. The live webinars will take place at 4 pm British time (GMT before 27th March, BST after 27th March), but if you are unable to attend live, the videos will be posted shortly afterwards.

After the live course finishes, we will leave the full course of recordings and exercises online, so that you can take it independently whenever you choose.

How do I sign up?

You can visit the course pages to see what’s going on without signing up. If you want to attend the webinars live, you will need to sign up, but there’s no charge for doing so. You may also wish to join the Facebook group.

My recent trip to Malawi as part of a Wellcome Trust Open Door Workshop has really reminded me how privileged I really am. I’m an Outreach Officer, which means that I have the privilege to travel out to institutes around the world to deliver free Ensembl workshops. Most of the time, these workshops are in Europe or the US, at fancy research institutes and universities, and it’s an awesome privilege to facilitate research at these institutes.

An even greater privilege is to be involved in the Open Door Workshops on Working with the Human Genome Sequence, organised by Wellcome Trust Advanced Courses, which head out to more developing countries to teach. They’re called ‘Open Door’ because all the resources we teach in them are free and open on the web, which means anyone, anywhere, with nothing but an internet connection can do it. I teach the Ensembl section of the course, but we also cover other resources from the EBI, Sanger Institute, NCBI and elsewhere.

We hold these courses at Wellcome Trust research centres, for example the Malawi-Liverpool Wellcome Trust I visited recently, which are fantastic investments by the Wellcome Trust in research around the world. Participants travel from all over the continent to attend the course; attendance is free (with selection) and the Wellcome Trust can even fund travel bursaries. It is a great privilege for me to be able to travel to these locations and to teach them all about Ensembl.

Group photograph

The group from the Open Door Workshop at the Malawi-Liverpool Wellcome Trust. Featuring instructors me (seated, second from left), Jane Loveland (Sanger Institute; seated, middle), Rob Finn (EBI; back row, far left), Charlie Steward (Sanger Institute; back row, middle) and Matt Clark (TGAC; back row, second from right). Photo by Heidi Hauser (Wellcome Trust Advanced Courses).

I am proud to present Ensembl to these workshops participants. Partly because I think it’s an amazing resource that can really facilitate research. Partly because we give it away for free, and I know this makes a huge difference to researchers whose labs are not well funded. Even in labs with £1 million grants, money is always tight, but for many of the people who attend our workshops, labs struggle with knackered PCR machines, ghost equipment that they can’t afford to buy the reagents to use and a complete reliance on Open Access publishing as they can’t pay for journal subscriptions, yet they still manage to produce world-class science. If they had to choose between replacing those broken machines and a pay-per-use or subscription-only bioinformatics resource, it would really be a no-brainer. But by giving them a free resource means they don’t have to make that choice. Indeed, it gives them the opportunity to carry out research that doesn’t need any expensive equipment or reagents.

The Wellcome Trust is one of the major funders of Ensembl. We are so grateful to them for allowing us to make our data freely available, so that everybody can make use of it. It really is a privilege.

Do you have an Ensembl account? If not, why not?

Maybe you think you have to pay for it. Maybe you think you’ll be joining up to a mailing list that will spam you relentlessly. Maybe you didn’t know we have accounts, or you don’t know what you get from them.

Quick reassurance: they’re free and there are no emails, annoying or otherwise – we promise. You now know we have them, but what can they do for you?

The two main perks are saving and sharing. Keep reading to learn more.

Saving

The bookmark this page button

Found an interesting page? Bookmark it.

All kinds of data can be saved to your user account, including bookmarks, configurations and your own custom data. Once saved to your account, you can open them from any computer you use, allowing you to access them at work, at home or from a public computer.

Favourite genomes are zebra finch, duck, chicken, turkey and flycatcher.

If you work with birds, why not have avian genomes on your homepage?

You can bookmark any Ensembl page, such as your gene of interest, a variant page or a genomic region. This allows you to jump back to these pages quickly and easily. You can even customise the Ensembl homepage to feature your preferred species.

Many Ensembl pages, such as Region in Detail, can be configured to view your features of interest. These configurations can be saved to your account, so that you can easily change a view to how you want it. This is especially useful if there are a few different ways you like to look at a view and want to switch between them. If there are lots of views you like to look at, you can make sets of these configurations. A set has one configuration for one view in Ensembl, and another configuration for another view. For example you could create a regulation set for a particular cell line, so that for every view with regulation data available, the data for that cell line would be shown.

Region and sequence views configured to show variation data

I’ve configured all these pages to show variation data, and saved it as a configuration set.

There are many ways to upload your own data to Ensembl, whether it’s custom data tracks in the Region in Detail page, BLAST/BLAT searches or variation data using the VEP. All of these data can be saved to your account, allowing you to go back to them at any time.

Table of previous VEP analyses

All of my VEP uploads are saved to my account, so I can go back to them at any time.

Sharing

If you can save it, you can share it.

You can share views by sending your colleagues and collaborators email links, but Ensembl accounts makes this even easier. If other members of your team have Ensembl accounts, you can create a group. Now anything that you’ve saved to your account (bookmarks, configurations and custom data) can be shared with the group, and all members of the group can access it via their accounts. This is great for working collaboratively on projects (especially long-distance collaborations), standardising analysis in a lab and getting new group members started.

How to do it

Get started right now by clicking on the Login/Register link that you’ll see at the top right of any Ensembl page to set up your account and explore the links you’ll find.

The Login/Register link in Ensembl.

The Login/Register link in Ensembl.

If you get stuck on any of this, there’s a help page on using accounts here.

Working as an Outreach Officer for Ensembl means lots of exciting adventures around the world to teach Ensembl to local scientists. Last month I was privileged to be able to travel to South Korea to give an ENCODE workshop with Bob Kuhn from UCSC.

Bob and me, with our Korean hosts

Bob and me, with our Korean hosts

The participants were interested to learn about how Ensembl and UCSC use genome assemblies from projects like the Genome Reference Consortium. It was clear that many people had not realised the extent of the work that goes into producing a genome assembly, by sequencing the genome in contigs then putting them back together (learn more in this video). Or how errors in the human genome are dealt with using patches. I was able to explain to them how Ensembl works together with groups like Havana to produce the genes for the trusted GENCODE gene sets for human and mouse, and how they could find out about these genes in Ensembl.

Even more excitingly, I got to preview some new data. The Ensembl regulation team gave me access to their new regulatory build track hub, which you can learn more about in Daniel Zerbino’s blog post. I was able to show off how Ensembl bring together and process the raw ChIP-seq data from ENCODE and other sources to try to identify where regulatory features might be on a genome-wide scale, and the activities of those features. It was exciting to be able to preview something new for the workshop participants, and their feedback suggests that the new regulatory build is going to be a hit.

Bob showed off the UCSC genome browser in the same workshop, and we worked together well. Though we have competing browsers, we’re really on the same team: the team that believes high quality genomic data and tools should be available to all and works hard to provide that. We can learn from each other to provide the best way of giving our users the data and analyses they need.

My next stop is the Open Door Workshop in Uruguay. Don’t forget, you can host a workshop at your institute to learn the basics of using Ensembl, and to find out about the latest Ensembl functionality and what’s coming with the new human assembly.

We’re pleased to announce the launch of our new online API course.

Take it for free on EBI’s Train Online platform.

This course provides an introduction to the Ensembl API and how to use it to explore Ensembl gene, sequence, variation, regulation and comparative genomics data, and was filmed over a three-day course at the EMBL-EBI. You take the course from start to finish, or you can dip in and out of your favourite module. The course is complete with video lectures and exercises with full solutions, including sample scripts and commentary.

Many thanks to all the instructors who were filmed for this course: Magali Ruffier, Anja Thormann, Nathan Johnson, Matthieu Muffato and Stephen Fitzgerald. The course was compiled together by Ensembl’s Emily Pritchard, working with Mark Adams from EBI’s Outreach and Training who filmed, edited and processed the videos and slides.

If you like the course, you might want to host a real-life course at your institute.

Any questions? Contact Ensembl helpdesk.

ASHG 2013 logoEnsembl will be at the ASHG meeting in Boston this year. Look out for Paul Flicek (head of EBI Vertebrate Genomics, including Ensembl) and Emily Pritchard (Ensembl Outreach Officer) at the conference.

Photo of Paul Flicek

Paul Flicek – Head of EBI Vertebrate Genomics

We’ll be holding a 90 min workshop entitled Ensembl Highlights Interactive Workshop: Intermediate/Advanced Users, taught by Emily. This workshop will look at some of the advanced access features in Ensembl, including BioMart, the Ensembl Perl APIs and custom data upload, as well as some of the new features in Ensembl, the Variant Effect Predictor, the REST API and sharing data. This course will only provide a very brief introduction to Ensembl itself: before the course you may wish to get up-to-date on what Ensembl is and the kind of data it provides using our Quick Tour. If you’re already registered for ASHG, you can register for the course through the ASHG conference website and there is a small charge of US$25.

Photo of Emily Pritchard

Emily Pritchard – Ensembl Outreach Officer

If you would like to meet up and chat informally about Ensembl at ASHG, Emily will be happy to speak to you. Do you have any specific questions about Ensembl, or would like to solve some your Ensembl problems by speaking to us? We can walk through the Ensembl website to see if we can solve your problems. Please bring along any data or information we’d need. Perhaps you’re also interested in hosting an Ensembl workshop at your institute and would like to find out more about it? We can discuss what a workshop would entail, how to organise it and maybe pencil in some dates.

You can book an appointment to meet Emily using our booking system, then we’ll arrange somewhere to meet up. Appointments are free, but please state briefly what you would like to chat about when you book. There may also be a limited number of slots to speak to Paul. There will be lots of people on the Workshop, so don’t assume that you’ll be able to ask your questions then; it may just be too busy. Even if you’re going to the Workshop, you might still want to book an appointment to talk about your specific issue.

I’ve been working for EMBL, the European Molecular Biology Laboratory, for around nine months now, and only last week did I really start to understand the organisation that I’m part of. Like two-thirds of the Ensembl team, I work at the European Bioinformatics Institute on the Genome Campus near Cambridge, a campus we share with the Wellcome Trust Sanger Institute, which hosts the other third of Ensembl.

Logo for EMBL Lab Day, tagline: Drop EverythingLast Friday I attended EMBL Lab Day, a conference/celebration for scientists working at all of the five EMBL sites around Europe, held in EMBL’s fabulous helix-shaped ATC in Heidelberg. I was looking forward to speaking to the EMBL audience about Ensembl and all the exciting new data and tools we’ve been adding recently (see other entries in this blog to see our recent news). In return, I was excited to find out about all the interesting lab work and data that came out of EMBL, and to get talking to some of my EMBL colleagues.

I was not disappointed. There was such a variety of interesting work being presented in the talks, from new methods of identifying protein structures, to studying the development of haematopoietic cells and the factors affecting cancer recurrence. I was fascinated to learn about new methods to manipulate cell activity using light pulses and how platelets, such small and seemingly simple cells, are able to reorganise their structure on activation using their cytoskeleton. The talks were all short, 12 minutes plus questions, giving enough time to get a taster of the work without getting bogged down with details. Most of the presenters were at a relatively early stage of their research careers, making Lab Day an important opportunity for the speakers to get experience speaking to a receptive and varied audience.

The crowd watching the EMBL choir singing at Lab Day

The EMBL choir singing at Lab Day – courtesy of Adam Gristwood, EMBL

There were long breaks in between the talk sessions, so we had plenty of time to network with other EMBLers and look at the posters, which were displayed all the way up each side of the helix, both serious posters detailing the work of the labs, and fun posters introducing the lab members. Congratulations to Matthias Ziehm from Janet Thornton’s group at the EBI who won a poster prize.

Once the talks were over we celebrated the achievements of young EMBL scientists with a PreDoc (that’s EMBL-speak for PhD student) graduation ceremony, followed by a champagne reception. Afterwards, there were performances by the EMBL choir and drum group, then we had a disco. I made lots of new friends and even got invited to a barbeque on the banks of the Necker in Heidelberg the following evening.

emblComing back from Heidelberg, I was struck by two things about EMBL. Firstly, EMBL is a hub of scientific excellence, producing fantastic science and training up young scientists both in and out of the lab to become the scientific leaders of the future. Secondly, it’s just such a nice place to work, promoting scientific and social interaction between its members in so many ways and celebrating the achievements of its members. I’m glad to be part of the EMBL family, and I’m looking forward to Lab Day next year.

If you think you’d like to join EMBL, take a look at the EMBL jobs page to find out more about jobs and fellowships.

As an Ensembl Outreach Officer I get asked a lot of questions. Mostly questions about our data and interfaces but occasionally, just occasionally, something a bit more blue sky.

A couple of weeks ago I was teaching an Ensembl Browser workshop at the Erasmus MC in Rotterdam. I was just explaining that all our data and code was completely free to use, open source and open access, when someone asked me: Why? What’s in it for you?

Why indeed? Why are there forty people dedicated to producing this project? Why do our funders give us all this money to do it? Why do we just give it all away for free?

Why do science at all?

The fundamental answer varies for all of us. Things like improving people’s lives, curiosity, discovery. These are the motivations that got most of us into careers in science at all. Ensembl may not be directly be doing research, but we’re enabling it.

Servers from the Ensembl farm

A tiny portion of the Ensembl farm

The Economic argument

There’s also an economic answer – in terms of time, money and infrastructure. How much does it cost to annotate a genome? To do pairwise sequence comparisons of over a million genes? To annotate variation? To make regulatory data meaningful? How much does it cost to put this into an easily accessible format? How much does it cost to regularly update this with new data? How many terabytes of memory do you need to actually store this stuff?

Even though these are non-trival costs, infrastructure projects in bioinformatics are about saving money overall. Funders and scientists understand that lots of different labs need the data and the analysis that we produce. However, it would be horribly inefficient if each lab who needs the resources we provide had to produce it themselves, repeating work that somebody else has already done, spending money that has already been spent, spending time that they could be spending doing other experiments or doing other analysis. Therefore, we have a system where we do it for them and put it all up where they can find it. Nothing’s repeated. Plus, our experience, expertise and raw computing power means that we can do it more cheaply and quickly than most labs can.

Free to be serendipitous

By giving the data away for free, we allow serendipitous discovery. If we charged people to use Ensembl in some kind of per-use manner, then they’d only use Ensembl to look for things they knew they were looking for. Yet we know that much of scientific discovery occurs when people accidentally stumble across things, like Alexander Fleming’s mouldy Staphylococcus plates. By allowing people to browse Ensembl freely, without worrying about costs, they may stumble across the tool or data that will be exactly what they need.

A relatively big group of people work for the project and they don’t work for free. But overall, we save the research community money by enabling science to be built on our foundation.

So, the answer to “what’s in it for me?”: I work for a project that makes science happen as efficiently as possible.

  • Are you new to Ensembl and want some help on using the browser?
  • Have you used Ensembl before, and want to learn more about it?
  • Do you want to get data quickly using BioMart?

These Online Tutorials are helpful for beginners looking for pointers in browsing their favourite gene, variation or region of interest, or those looking to further develop their skills.

The Quick Tour. A good place for beginners, this gives a brief overview of the kinds of data you can find on Ensembl and where to look for it. There are also links throughout to more detailed tutorials. This is only a thirty minute course so don’t expect to be an Ensembl expert at the end of it!

The Beginner’s Ensembl Course. This is a good place for beginners, or for Ensembl users wanting to expand their knowledge about the browser. In total, this three-hour overview covers Ensembl genes, variation, comparative genomics, and regulation. You’ll learn where the data comes from and how to access it.

 

Video Tutorials. These videos range from 2 minute clips to 20 minute overviews on a particular topic in Ensembl. This is a good place for anyone from beginners to frequent users to increase knowledge and understanding of the wealth of data and resources Ensembl provides. All of our videos are found on our YouTube channel, and our YouKu channel if you’re accessing Ensembl from China.

Looking for more? Have a look at our tutorials page.

Don’t forget, we run customised browser and API workshops if you want an Ensembl expert to take you first-hand through the site.

Can’t find what you’re looking for? Just contact us and let us know!