We’re really excited to be a part of the ESHG conference again, this time in Copenhagen from the 27th-30th May. We can’t wait to see all the great science that’s going to be presented, but here’s a guide to the talks, workshops and posters from Ensembl and some of our close friends:

W18 – Ensembl & GENCODE Workshop

Monday 29th May 3pm-4:30pm Ancona Room 

This joint workshop is organised and will be presented by Ben Moore and Amonida Zadissa from Ensembl and Adam Frankish from HAVANA. It is aimed at attendees familiar with Ensembl, including wet-lab biologists, clinicians and the bioinformatics community.
The workshop will start with a brief introduction to the Ensembl project and genome browser along with a talk about the gene annotation process carried out by the Ensembl and HAVANA teams to produce the GENCODE gene set.

After the introduction to the Ensembl genome browser, there will be hands-on demonstrations to teach you how to:

  • annotate SNPs and CNVs with functional consequences using the Variant Effect Predictor
  • investigate quick alternatives to the browser (BioMart and the REST API)

You can find more information about the workshop location and timings on the ESHG programme. If you have any questions or want to talk about Ensembl and GENCODE you can e-mail the Ensembl Helpdesk to arrange a time to meet, tweet us or simply come by and meet us after the workshop.

Poster Sessions

As well as the Ensembl and GENCODE workshop, Amonida will also be presenting an electronic poster (E-P16.08) that describes genome annotation and assembly assessment in Ensembl. Electronic Posters will be on display in the Poster Area and can be accessed during exhibition opening hours from 09:30 on Saturday 27th May to 17:45 on Monday 29th May by all participants.

Our friends Jackie, Joannella and Maria from the GWAS catalog will be presenting their work at ESHG.

  • Maria will be presenting an electronic poster (E-P16.12) with new ideas they have for increasing the speed that GWAS data is incorporated into the GWAS Catalog. Electronic Posters will be on display in the Poster Area and can be accessed during exhibition opening hours from 09:30 on Saturday 27th May to 17:45 on Monday 29th May by all participants.
  • Jackie will be presenting a poster about the steps they are taking to ‘Increase the utility of the NHGRI-EBI genome-wide association study (GWAS) Catalog for users’. Jackie’s poster number is P16.36D and you can come and talk to her between 16:45 and 17:45 on Monday 29th May.

Jackie and Maria would love to hear feedback from GWAS Catalog users during the conference, particularly on the new and proposed functionality presented in our posters. They will also be able to answer any questions on the GWAS Catalog. Any users who would like to talk to us should e-mail the GWAS Catalog team at gwas-info@ebi.ac.uk, and they can arrange a time to meet, or simply come by and meet them at their posters.

And last, but not least, Giselle Kerry will be representing The European Genome-Phenome Archive (EGA) with a poster about their future plans. Giselle’s poster number is P19.44D and you can come and talk to her between 10:15 and 11:15 on Monday 29th May.

Looking forward to seeing you all there!

This is the second instalment of our monthly posts introducing a member of the Ensembl team, and what they do in Ensembl. This time, it’s Will McLaren who works in the Variation team.

What is your job in Ensembl?

I’m the principal developer in the Ensembl Variation team. Our team produces, maintains and supports all of Ensembl’s variation resources. This includes a number of databases as well as the APIs and tools that use them, including the Variant Effect Predictor (VEP).

What do you enjoy about your job?

I love hacking around with code, making new things, taking things apart and fixing them again. Knowing that we’re contributing to advancing science and medicine by doing that is a huge bonus, and the satisfaction I get from that is what I enjoy the most.

I also enjoy interacting with our users, either helping them out over email or face to face at our workshops. Our users really are the inspiration for what we do, so I think it’s really important that we engage with them as much and as productively as we can.

What are you currently working on?

I usually have a number of projects on the go. A lot of my development time is spent working on and supporting VEP, and I’m currently working on improving how we handle RefSeq genes, as well as managing our recent transition to a major VEP update. I’m also spending some time working on a collaborative project with OpenTargets, the aim of which is to help identify links between genomic variation, genes and disease.

What is your typical day?

A typical day for me usually consists of continuing progress on whatever development project or projects I need to prioritise that day, and for me that usually means a terminal, a text editor and a web browser are my best friends. This will be punctuated by various things. I have a daily standup meeting with my team, saying what we’ve done, what we’re going to do, and discussing any issues that come up from that – it might be a colleague has become stuck on something that someone else has already figured out, so sharing in this way is great for all of us. We also communicate a lot via instant messaging if we can’t in person, and this extends across the whole of Ensembl. There’s usually a couple of help requests from users, and occasionally this will also involve finding and squashing a bug in our code (something we try to prioritise where we can). If the bug turns up in code someone else is responsible for, we might discuss with them before working out how to fix it. There may be a pipeline I need to kick off or check on that generates data as part of Ensembl’s ongoing release cycle. I might also have a conference call or a meeting with collaborators; typically this might be to discuss a manuscript in progress or a shared project.

How did you end up here?

I started my academic life doing Biochemistry and Genetics. I pretty quickly realised I didn’t have the manual skills or the patience for lab work, but I loved the discovery aspect of the science. I’d always had a hobby messing with computers, and was delighted to discover that I could combine my hobby and academic interests in this thing we call bioinformatics.

After a year studying bioinformatics, I got my first job working in informatics for pet health. Not the most glamorous, but it started me down the path of working in variation data, and a change of city led me to working at the Sanger Institute (who share a campus with us here at EMBL-EBI) doing statistical genetics for genome-wide association studies (GWAS).

I’d dabbled with Ensembl before, and when I saw a job advertised in Ensembl in a new-ish team that fit my experience and interests and was looking to expand, I jumped at the chance and haven’t looked back!

What surprised you most about Ensembl when you started working here?

What surprised me most was the diversity in the Ensembl team. We really are an international team with representatives from nearly every continent, which is great on both a personal and professional level. As well as this, we have a surprising diversity in people’s educational and career backgrounds. The combination of these means we have a huge breadth and depth of knowledge across the Ensembl team, which allows us to deliver what I consider a staggering array of data and functionality to our users.

What is the coolest tool or data type in Ensembl that you think everybody should know about?

We have a cool web view called the transcript haplotype view. This shows you whole transcript and protein sequences as they would appear in each individual from the 1000 Genomes project, by considering all of the genomic variation across a gene together. We also have a related tool that you can use on your own data called Haplosaurus, and I think this is going to be a really important step towards seeing the real biological picture in sequenced genomes.

This is the first of our monthly posts introducing a member of the Ensembl team, and what they do in Ensembl. We’ll start with Emily Perry, who runs our Outreach team.

What is your job in Ensembl?

I’m in charge of the Outreach team. There are four of us, including me, and we’re essentially the contact point between all the scientists who use Ensembl and the developers who produce it. We work on things like online help and documentation, delivering training courses, social media, user-testing our new tools and displays, and answering questions via our email helpdesk. We’re always busy, and often have a half-empty office as someone is off delivering a training course somewhere around the world.

What do you enjoy about your job?

I’m one of those strange people who thrive when they have an audience, so I really love the teaching and presenting side of what I do. I’m also fascinated by the data that we have and love learning more about it and what people are using it for. I’m a biologist by trade, not a bioinformatician, but I’ve picked up a bit of coding as part of this job and one of the things I find most satisfying is fixing bugs in people’s code for them, without asking for help from our developers. I’ve also travelled to some amazing places to deliver workshops that I would never otherwise have gone to, such as Malawi, Colombia and South Korea, where I can really feel that I’m benefitting scientific progress.

What are you currently working on?

In Outreach we’re always dipping out of lots of projects, as well as all the reactive jobs we need to do like answering help emails or social media. A few of the things I have ongoing at the moment are looking into the documentation on the site, running a seven-week webinar course and preparing a conceptual course on genetic variation for the EBI’s Train Online platform.

What is your typical day?

Ha, there isn’t one. That’s one of the things I love about this job.

How did you end up here?

As I said, I’m a biologist. I studied genetics at undergrad, then went on to do a PhD in molecular biology. I knew about halfway through that I wanted out of the lab, so pursued a lot of science communication opportunities, both in person and written, as I went on, which led me to working for a year delivering science roadshows in secondary schools. This combination of communication skills and scientific expertise qualified me to start working as an Outreach Officer in Ensembl in 2012, then in 2015 I was promoted to lead the team.

What surprised you most about Ensembl when you started working here?

I had used Ensembl during my PhD, and I remember thinking that I knew what it was all about. Within a few days I was overwhelmed with just how much data and how many different types of data are in Ensembl. Turns out that my PhD work had barely scratched the surface of what was there. I hear the same thing all the time when I teach workshops: people who think they know all Ensembl has to offer (often the host of the course who was planning to just hide at the back and do other work during the course) tell me how surprised they are at all the useful things that are available.

What is the coolest tool or data type in Ensembl that you think everybody should know about?

I worked on chromatin for my PhD so my favourite data type is the regulatory build. I would have killed for those data back when I was a researcher. It’s just so useful having all the promoters, enhancers, CTCF binding sites (I love a bit of CTCF) and everything mapped onto the genome with its activity in different cell types. And I find the way that they just trained a computer to recognise patterns and assign functions from ChIP-seq data just amazing.

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.

If you’re at the Biocuration conference currently happening in Washington DC, feel free to swing by the poster of Amonida Zadissa to learn about the Ensembl gene set (poster number P.87).

Ensembl Genebuild members will also be attending:

5th International Conference on Primate Genomics Bronwen Aken
17-19 April 2012
Houston, Texas, USA

Recomb 2012  Thibaut Hourlier, Poster 276
First session, 21st April, 18:30-20:00
Conference on Research in Computational Molecular Biology
21-24 April 2012
Barcelona, Spain

 

 

Greetings from San Diego!

If you are at the Plant and Animal Genome (PAG) conference, please come and visit the posters by Susan Fairley (P0941: Genome Annotation in Ensembl), Paul Kersey (P0942: Ensembl Plants: An Integrating Resource for Plant Genomics and Variation) and our friends from the Havana group (P0620: Production of a reference gene set for the porcine sex chromosomes). For any questions regarding Ensembl and Ensembl Genomes you can also visit the EBI booth (302).  Just ask!

ICHG 2011The Ensembl team will be delivering a couple of workshops in the 12th International Congress of Human Genetics today and tomorrow. Please come along if you were interested to know about the latest improvements to our browser.

  • Today (Friday 14th October) our workshop will take place at the Palais des Congrès de Montréal (Convention Center, room 524 level 5 from 18.15 to 20.00. We will be exploring Ensembl beyond the browser, highlighting some new features to those more experienced with Ensembl. We will distribute a DVD to those interested to have a virtual machine with the latest APIs installed.
  • Tomorrow 12.30 to 13.30 (room 524, level 5) we will provide a more basic workshop for newcomers or people interested in catching up with genome browsers.

If you want to learn how Ensembl can help you on your research, or perhaps you have some questions, please come along. You are welcome to come with your laptop and join us today and/or tomorrow.

À bientôt!

We are looking for projects that use aspects of the Ensembl code (for example, the webcode, the genebuild pipeline, or comparative analyses).  If you want to be added to our list, please reply to this blog post, or email our helpdesk with your project name, url, and what aspect of the code you are using.

In addition to the projects on our powered by Ensembl page, we have heard from:

Let us know about your project!

 

This year the Human Genome Meeting has brought us to Dubai (in the United Arab Emirates) for a very interesting conference focusing on the genomics of human genetics. Ensembl is featured in one of the satellite events organised, The Open Door Workshop, offering us a unique opportunity to present the latest develoments in the project to participants from 12 countries (Australia, Brazil, India, Indonesia, Iran, Pakistan, Saudi Arabia, Slovenia, Spain, Sri Lanka, Sudan and obviously our host country UAE) with a broad range of interests ranging from clinical genomics to database management.

We have received very positive feedback on some of the latest goodies hidden in our favourite genome browser, such as the possibility of streaming BAM files to display NGS data alongside the Ensembl annotation (undoubtely we should be posting some tips on this very soon).