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!