After a very successful Ensembl US West Coast Tour last month, the Ensembl Outreach team is presently looking into the possibility of organising a similar tour on the US East Coast in the second half of 2008. At the moment we are mainly thinking of 1-day browser workshops, but if there is interest in an API workshop we can of course also consider this.
The participating institutions would only have to pay the instructor’s expenses and would share the travel costs, but we would not otherwise charge for the workshops. People that are potentially interested in hosting a workshop can contact me for more details.


We are looking forward to Ensembl release 49, which has been delayed to 13 March, 2008. This is a result of some downtime planned at the Wellcome Trust Sanger Institute. Users, beware! Ensembl will not be available from: Friday 7 March – Sunday 9 March

On the 13th March Ensembl version 49 will be available. Keep an eye out for:
Drosophila melanogaster (assembly BDGP 5.4)
Horse (first gene build)

Viral genes have been removed in multiple species. ncRNA updates will be ready for Pika and Mouse Lemur, and new variations from dbSNP 128 (mouse, chicken, cow, and zebrafish) and dbSNP 126 (rat) will be available. Have a look at the new pairwise alignments between human and horse genomes.

Upcoming Workshops – March

A series of talks and workshops are happening in March.

Browser Workshop (2-day course at the EBI) 5-7 March
Browser Workshop (part of a 2 day course, MRC London: EBI Roadshow) 11-12 March
Presentation at the Genomes to Systems 2008 conference in Manchester, 17-19 March

Interested in organising a course in Ensembl and BioMart? Contact our helpdesk.

-The Ensembl Outreach team


(you wouldn’t expect orangutans out of the trees, would you?)

Ensembl 49 will contain good news on the comparative genomics side. Apart from the new whole-genome multiple alignments for which we can now handle segmental duplications and infer ancestral sequences (see Ewan’s post on the 20th of January), two new species will be available, namely horse and orangutan.

We are especially excited about the new orangutan genome as it is a key species in the primate lineage, in between the human, chimp and gorilla group and the Old World monkeys. Its inclusion in our gene trees will result in a better resolution of the phylogeny of the primate genes.

We’re pleased to announce that Ensembl now has a mirror at the Beijing Genomics Institute, Shenzhen (BGI-SZ). The mirror can be found at http://ensembl.genomics.org.cn/


Most of the functionality of the main Ensembl site is mirrored, however we’re still working with our colleagues at the BGI to provide the rest, for example BioMart.


Due to a combination of the volume of data comprising a single Ensembl release (the MySQL data and index files for release 48 take up apround 600Gb, and that’s without counting all f the flat-file dumps) and the very slow Internet connection between the UK and China, the we’re using a “sneakernet” solution – i.e. dumping the data onto a hard drive and shipping it to China. This has proved to be an interesting challenge but it’s working out pretty well so far.

We hope that this mirror will make life easier for our users in and around China. We’re actively trying to set up mirrors elsewhere around the world to reduce network delays and improve peoples’ Ensembl experience; we’ll post here as soon as any new mirrors come online.

I would like to thank our colleagues at the BGI-SZ, particularly Lin Fang, for setting this mirror up.

You might think that only our group and team leaders are traveling the globe, but also the members of the Ensembl outreach team (Xose Fernandez, Giulietta Spudich and myself) spend a fair amount of their time on the road (or in the air ….) to spread the word about Ensembl.

I myself, for example, just returned back in the UK from a 3-week “Ensembl US West Coast tour”. That means no more Margaritas, motels with ocean view or trendy LA restaurants for me for a while, but also no more lost luggage or cancelled or delayed flights (it’s not all glitz and glamour …. ).

My tour started with a visit to the Plant and Animal Genome XVI Conference in San Diego, where I gave a presentation on Ensembl and spent, together with other EBI colleagues, time in the EBI booth to promote our institute. After that I gave Ensembl browser workshops at City of Hope (see picture), the University of Oregon , UCSF, UCSC (where the audience mainly consisted of genome browser folks!), and UCLA. Numbers of participants ranged from around 15 till over 50 and in all places the workshop was very enthousiastically received. In fact, several of my hosts were already asking when we could repeat this ….

The principle aim of our workshops is of course to teach people how to get the most out of Ensembl, but apart from that it also is a really good way for us to stay in contact with our users. We can see what people exactly use Ensembl for, how they use it and what they like and dislike about it, so we always return back home with lots of new ideas and suggestions. One thing that, for instance, often strikes me is that most people are not aware of the existence of our data mining tool BioMart. However, after a short explanation and some hands-on exercises they find it almost without exception very useful! So, we still have some work to do to promote this very handy tool.

By the way, we not only offer browser workshops, but also workshops on the use of the various Ensembl Perl API’s. Keep an eye on this blog to see where and when the next workshops will be. Or, even better, host one at your own university or institute! For more information with regard to our workshops you can contact our helpdesk.

I’ve just been visiting CNIO in madrid – a great, fancy new(ish) institute in Madrid focusing on cancer – it was a great visit if you ignore the 2 hour delay (thanks Iberia) coming out and currently 1 hour delay (thanks BA…) coming back. They are doing all the things one expects from a high-end molecular biology institute. There are a chip-chip guys, moving to chip-seq. There are some classic cell biologists moving into more genome wide assays (in this case, replication). They have a great prospective sample collection in two cancers, and are about to get into a Genome Wide Association Study (GWAS).

David – the head of bioinformatics service – already is leveraging Ensembl alot. They script against our databases (Perl API mainly) and have a local mirror set up. They ran courses, bringing over Ensembl people for both an API course and a Browser course (contact helpdesk if you’d like this to happen at your institute…). But even then, discussions with David made us realise that they could use us even more – for the functional genomics schema and the variation schema in particular.

This is what Ensembl is all about. We make it easier for people who want to work genomically to do the sometimes painful data manipulation and plumbing. In particular, Ensembl provides public domain information in a large scale, well organised and ready to be browsed on the web, scripting against in Perl and accessible to clients like bioconductor. And more than any other group, we help group’s like David’s do more for his institute and have to worry less about the infrastructure. David was very interested in the “geek for a week” program when someone comes to work at Ensembl to help accelerate a project.

Returning to the airline theme, some of the biologists admitted using the UCSC browser in a little embarrassed way. I responded that it was fine – UCSC is a great browser, with some great tools. Like airlines, we know people have a choice browsers, and we hope people come “fly ensembl” and enjoy it, but we know the competition is good (and really friendly as well – we like working with those crazy californians, and have a number of joint projects). If you are a biologist, you should use the best tool for the job at hand. Of course, we know where we’re lacking, in particular in comparison to UCSC, and we are working on getting better. Keep an eye open on changes in Ensembl this year – and do come fly with us even if your “regular browser” is US based.

Finally my plane I think is ready to depart.

(Madrid airport is so big I think I’m half way to the UK already)

Today the 1000 Genomes projects was announced. By any measure this is a big deal.
The goal is simple: to create the most comprehensive and medically useful collection of human variation ever assembled by producing approximately 6 terabases of sequence. To put this amount of data in prospective, 6 terabases is more than 60 times the amount of data that is currently available in the DDBJ/GenBank/EMBL Archive and that took more than 25 years to collect. At the peak production of the 1000 Genomes project more that 8 billion basepairs per day will be sequenced. It’s data output of the the entire human genome project every week. All made publicly available.
The data generation rate and the short read length mean that the bioinformatics requires for the project are equally ambitious (or terrifying depending on your point of view). The EBI and NCBI, working together, are creating a joint DCC (data coordination centre) to collect, organise and provide the data to the world. Steve Sherry at the NCBI and I are eager to take this on.
At Ensembl we’ve been expecting this development and built support for re-sequencing data into our variation database a couple of years ago. So far, we have data for about 6 humans, 5 mouse strains, and a smattering of rat data. Small stuff compared to six months from now, but large enough that we have both experience and confidence dealing with the large-scale resequencing data. We are probably going to need both.
Check out more at http://www.1000genomes.org

Ensembl Workshops in January took us to the West Coast (USA) and the Netherlands. Workshops in February:

Browser workshop (Institute for Animal Health) Compton, UK 12 Feb

Browser workshop (EURATools, University of Edinburgh) Edinburgh, UK 12 Feb

Browser workshop (Cambridge University, Dept of Genetics) Cambridge, UK 28-29 Feb


Picture: Nijmegen, the Netherlands. The NBIC was the site of an Ensembl Browser workshop on 16 Jan, 2008

Interested in hosting a workshop? Contact us!

Richard posted the next release intentions here:

ensembl-dev archive

Lots of good stuff – orangutan, horse being released, the usual tweaks about contamination (viral genes) into the gene sets being removed, little details.

But one thing is quite a change. It is from Javier’s Compara team, and it is simply stated as

“Generate the 7-way alignments using the new enredo-pecan-ortheus pipline”

Unpacking this statement, it is a big change in how we’re thinking about comparative genomics alignments. Enredo is a method to produce a set of co-linear regions, sometimes called a “synteny map” though this term is a dreadful term. The key thing is that it handles duplications in the genome, allowing (say) two regions of human to be co-linear with one region of mouse. This is hard to handle on a genome-wide scale in a scaleable manner. Pecan is the multiple aligner written by the brilliant Ben Paten (used to be my student, and wrote Pecan whilst at the EBI; he is now at UCSC with Jim and David and co). Pecan is the best aligner – by both simulation testing and testing via ancient repeat alignability criteria – it has the highest sensitivity of alignment with the same specificity as the next best aligner. Finally Ortheus, also from Ben, provides (potentially) realignment whilst simultaneously sampling correctly from a probabilistic model of sequence evolution, critically including insertion and deletions, and thus as a side effect, producing likely ancestral sequences. This also has been stringently tested using a hold-one-out criteria, basically can we “predict” the marmoset sequence only using other extant species (answer – not completely correctly, but better than any other method, eg taking the nearest sequence).

So – what does this all mean. Basically there are two key things:

  1. Handling lineage specific duplications. This is a headache, and we have a good solution, providing the alignment of therefore the paralogous and orthologous regions (the paralogy is limited to relatively recent paralogy, ie, within mammals) simultaneously
  2. We can reliably predict ancestoral sequences

One headache is that some of the things we display, in particular the GERP continuous conservation score, needs to be adapted to work on the basis now of regions with paralogy. There is a fascinating piece of theory to work through here – what is the concept of the “neutral tree” when there has been a lineage specific duplication? How should one treat paralogs? Currently this is ignored by virtue of the fact that the alignments don’t allow this. Now the alignments do allow this, and we need to do something sensible, as well as stimulate evolution theory people to look at the data and work out new methods.

The next headache is what do we do with the ancestral sequences? Dump them? Display them? Gene predict on them? If so, how?

The end result is that release 49, even the comparative genomics, wont look very different, but it will have these new alignments, and over 2008 we will be working out how to present, analyse and leverage them more – so if you are interested, please do take them for a spin!

(Release 49 is due to be out sometime in mid-Feb)

The beginning of this week myself and Paul Flicek were in lovely Rotterdam at the Gen2Phen kick off meeting, an EU project lead by Tony Brookes from Leicester. Like all large European projects, the kick off meeting is a get-to-know everyone, have beers (very good ones in Holland) and get a feel for the project.

For me, the exciting thing was getting closer to the locus specific databases – in the project is Johan den Dunnen (from just down the road in Leiden, Holland) and Andy Devereau (from Manchester) who run locus specific databases and diagnostic databases respectively. Getting this valuable data coordinated with genome data (and the fiddly bit is about sequence coordinates, at least at first) is going to be great thing to do.

There’s lots to do in this area – certainly this is something that effects all the big browsers (UCSC, NCBI, ourselves) and has a had a long history of complex systems and sociological tensions in getting things sorted. But my sense in this small room hidden away in the Erasmus medical centre was that we had good people in the room, committed to finding a good solution whilst understanding the complexity of problem. Next up will be more technical meetings, but it was an excellent start. Don’t expect anything tomorrow, but I think we can expect something end of 2008/2009.

And did I mention the beer was good as well?