Ensembl: making other people’s lives easier

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)

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