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Author: Emily (Outreach)
Our latest introduction to the Ensembl Team post comes from Sophie Janacek, who takes care of all our money.
Ensembl 90 is now live and it’s absolutely massive! Read on to find out why:
This month we’re meeting Bronwen Aken who heads up our Vertebrate Annotation team.
Ensembl 90 is scheduled for August 2017 and it’s set to be our biggest release ever in terms of new genome annotation. Here’s what you can look forward to:
New assemblies, gene sets and annotations
- Annotation of 15 rodent genomes, including three updates to old genomes:
- Brazilian guinea pig
- Chinese hamster
- Damara mole rat
- Golden Hamster
- Guinea Pig (update)
- Kangaroo rat (update)
- Lesser Egyptian jerboa
- Long-tailed chinchilla
- Naked mole-rat – we have two different assemblies for naked mole-rat so you can keep working with your preferred genome
- Northern American deer mouse
- Prairie vole
- Squirrel (update)
- Upper Galilee mountains blind mole rat
- Bringing in annotation of the well-used rodent cell-line, Chinese Hamster Ovary, and two mouse species, Ryukyu mouse and Shrew mouse.
- Annotation on the latest Pig genome assembly, Sscrofa11.1
- Updating the Human gene set to GENCODE 27.
- Updating the Mouse gene set to GENCODE M15.
- Adding transcript models from RNA-seq to the gene database and pri-miRNAs to the otherfeatures database in Zebrafish.
Other updates and highlights
- Updating our human variation database with:
- COSMIC 81 somatic variants
- HGMD 2016.4
- dbSNP 150
- DGVa structural variants
- TopMed in GRCh37
- Phenotypes from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Cosmic Gene Census, DDG2P, MIM Morbid and Orphanet
- In other species we also have variation updates as follows:
- DGVa in Cow, Dog and Mouse
- Phenotype updates from relevant databases in Cat, Chicken, Chimpanzee, Cow, Dog, Horse, Macaque, Mouse, Pig, Rat, Sheep, Turkey and Zebrafish
- Updating our microarray probe mappings in:
- Caenorhabditis elegans
- Mouse 129S1/SvImJ
- Mouse A/J
- Mouse AKR/J
- Mouse BALB/cJ
- Mouse C3H/HeJ
- Mouse C57BL/6NJ
- Mouse CAST/EiJ
- Mouse CBA/J
- Mouse DBA/2J
- Mouse FVB/NJ
- Mouse LP/J
- Mouse NOD/ShiLtJ
- Mouse NZO/HlLtJ
- Mouse PWK/PhJ
- Mouse SPRET/EiJ
- Mouse WSB/EiJ
- Saccharomyces cerevisiae
For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.
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.
This course allows you to learn about Ensembl for free from the comfort of your own office (or bed, no-one’s judging you), with the ability to interact live with the instructors. Perfect for those who can’t attend or host one of our live courses.
What is it?
The Ensembl online training series comprises a series of live webinars, once a week over seven weeks. Each webinar explores a specific aspect of Ensembl data or tools with a presentation and a demonstration – see the online course for details. You can then practice what you’ve learnt over the following week with online exercises.
Not all of the topics will be useful to you, so you can dip in and out of the webinars. If life gets in the way and you miss one you are keen on, we will post the videos to our YouTube channel and YouKu for those of you in China 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 6th April, and will hold seven webinars on Thursday mornings, up until the 18th May. The live webinars will take place at 9 am BST (GMT+1), but if you are unable to attend live, the videos will be posted shortly afterwards. Since last year’s course was held in the afternoons, good for our American friends, we’re hoping that this morning course will be easier to access for anyone in Asia or Oceania.
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.
Is it any good?
We think so, but don’t take our word for it. Here’s what the attendees from last year had to say:
“Thank you. I really appreciate having access to this course. I’ve learned a lot.”
“Thank you so much for organising this. I really enjoyed!”
“Thank you; the course is very useful. I´m very happy”
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 (or sign up here from China), but there’s no charge for doing so. You may also wish to join the Facebook group.
We think the Ensembl workshops that we offer are a brilliant way to familiarise yourself, and other people in your research institute, with Ensembl data and tools. Don’t take our word for it, over 99% of the people who attended our workshops in the first six months of 2016 would recommend them to a colleague.
So if you (and your colleagues) want to get training on Ensembl, the best option is to join the over 50 institutes a year who benefit from hosting an Ensembl browser workshop, training over 1000 people. Send us an email to find out more.
We appreciate, however, that that’s not an option for everybody. Although we do not charge fees for workshops, we ask our hosts to pick up the tab for all expenses incurred, such as travel, accommodation and subsistence. While we do our best to alleviate these costs, such as tagging together overseas workshops in a series, you may still not have the spare budget for this or may want to host workshop to a different timetable than we can support.
In this case, if you are an experienced Ensembl-user, you may consider teaching an Ensembl workshop of your own. We’d like to help. We want everybody learning about Ensembl to receive the most extensive and up-to-date training possible, and we believe that the second best way to do this (after having us do it) is with our support.
How can I teach a workshop?
All our workshops are hands-on, usually in a computer teaching room, although we can work with people bringing laptops (provided suitable WiFi and somewhere to charge them through the course). We recommend a similar set-up.
Our general style for a workshop is that we split it into modules. The modules we usually offer are:
- Introduction to Ensembl and the Region view
- Genes and transcripts in Ensembl
- Data export with BioMart
- Genetic variation data in Ensembl, including annotating your own variants with the VEP.
- Comparative genomics: homologues and whole genome alignments.
- The Ensembl Regulatory Build: finding features that regulate genes.
- Advanced access to Ensembl data and viewing custom data in Ensembl
Within each module, there are three elements:
- Presentation, where we introduce what the data or tool is and where it comes from.
- Demonstration, where we have a hands-on walkthrough of finding that data or using that tool. We give out printed booklets containing screenshots that take participants through these walkthroughs. This provides a suitable place to make extra notes, and gives participants something to take away and use later. Some participants choose to join in with the walkthroughs, while others just make notes while we go through it on the screen.
- Exercises, where participants can practice using Ensembl to find information. These exercises build on what we do in the demonstration. During the exercises, we circulate the room, ready to answer any question that might come up. We also provide answer sheets (usually electronic only) that guide the participants on how to get the answers and what they are.
We find that combining these three elements gives the participants all the information they need, and provides a holistic learning experience that appeals to different kinds of learning style. We think this is why we consistently get such excellent feedback from our course participants.
You can see an example of a course that follows this structure, with the full set of modules, each with three elements, in our webinar course that we held in Spring 2016. You’re free to harvest the presentations (embedded as pdfs), demonstrations and exercises from that course for your own teaching, although under our Creative Commons BY licence, you need to credit us with their creation.
While we would usually have the workshop as one intensive day of learning, the flexibility of being in your home institute might mean that you prefer to have a module a day over a number of days or or one a week.
Where do I get the materials from?
We like to tailor our courses to match our participants’ interests, so will try to use exercises and walkthroughs that feature the species they’re working with. This is why our exercise page has many similar exercises and walkthroughs with different species. We recommend finding suitable exercises and demos to match your group’s interests and skills. You can also copy the process and style of an existing walkthrough or exercise for an example in a new species of interest.
Because we only update these exercises and walkthroughs when we use them, they can get out-of-date. The “Updated” column on the tables shows you for which Ensembl or Ensembl Genomes release they were last updated. If the exercise or walkthrough you’re looking at is not from the current release (check the release news section of this blog to see what’s current – note the different release numbers for Ensembl and Ensembl Genomes), then you might want to check the content to see if it needs editing at all.
If you do any updates, or make any new exercises, we’d love to hear about it. Email us your new material and we’ll add it to the page for other people to use (and maybe steal it for ourselves too).
For presentations (in pdf) and to see how a whole workshop might fit together, all of the Outreach team post their course materials online for use during and after the courses. You can see the materials from on our training pages.
Remember, if you use any of our materials, do credit us with their creation, as they are distributed under a CC BY licence.
What about website downtime?
Website downtime can be a disaster for a workshop, leaving you floundering with no way to teach. However, downtime is also an occasional necessity when we are running such a huge website and database. If you are planning on running a workshop, we recommend you get in touch to ask if there is any planned downtime. You can usually get around downtime by using one of our mirror sites, but we can advise you on this.
Similarly, if we put out a new release in the days between your preparation and workshop delivery, it can make some of your materials out-of-date. This can be a valuable lesson for your participants in how bioinformatic databases can change, or you can run the workshop from the previous archive site instead.
A release on the day of your workshop means both downtime and changes in the data. If we know you’re having a workshop, we’ll make sure that the archive site from the previous release is up and working before we take the main site down, so that you have something to work with, and you can keep using that even once the new site is up.
Need more help?
The Outreach team are here to support you. Just send us an email if you want practical support on how best to run a workshop, if you have any background questions on our data or tools, or indeed with any other questions or problems you might have with Ensembl.