101 questions with a bioinformatician #1: Mick Watson

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.


This week's interviewee is well suited for a career in biology and bioinformatics. After all, his name is only one substitution, insertion, and translocation away from reading as 'Watson Crick'. Welcome to 101 questions...Mick Watson.

Mick is Head of Bioinformatics at Edinburgh Genomics and a research group leader at The Roslin Institute. He also professes to be Titus Brown’s code-tester, and Nick Loman’s conscience.

His Opiniomics blog should be required reading for anyone interested in bioinformatics and you can also learn a lot if you follow him on twitter (@biomickwatson). The most important thing that you should know about Mick is that he doesn't really have strong views on anything...especially about what's wrong with the current state of bioinformatics research.


001. What's something that you enjoy about current bioinformatics research?

I just love biology, and bioinformatics is part of biology. Being a bioinformatician means you come into contact with lots of biologists and every single one of them has an interesting story to tell, a fascinating challenge and a problem that needs to be solved. I love solving those problems. Bioinformatics is now the key skill required in so many areas of biology, and it is bioinformaticians who now make the discovery, it is bioinformaticians who now have the eureka moment. It’s all very exciting!


010. What's something that you *don't* enjoy about current  bioinformatics research?

How long have you got? I hate the language wars – I hate how every single bioinformatics algorithm has to be implemented and re-implemented in 7 different languages; I hate “the 2% club” who publish something because it’s 2% better than an existing tool on a very specific dataset dreamt up by the authors; I hate the fact that we have several hundred “short-read aligners”. I hate the waste of time and resource that that represents. I hate the way that many bioinformaticians have stopped being biologists, and I hate the way our science has been enslaved; I hate that we have allowed it to happen that bioinformaticians are employed in lab groups just to process their data, and no more. I hate that people see us as “support”, not researchers. I hate that, after 15 years in the field, the same problems come around again and again, and I hate that we haven’t learned from our mistakes.

And I despise anonymous peer review. Stand proud next to your words, it’s the only way.


011. If you could go back in time and visit yourself as a 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

Be confident. YES. YOU. CAN. I know this is cheesy, but the simple fact is that most bioinformaticians have the ability to be amazing; we have biological knowledge and we are not scared of computers. So much of bioinformatics is about setting yourself a goal and just doing it. If there is one thing you don’t think you can do, that’s the thing I’d recommend you go out and do right now. Be confident. You can do it. Nothing is impossible.


100. What's your all-time favorite piece of bioinformatics software, and why?

The first one I used – I remember telnet-ing into a server somewhere in about 1997 and using The Wisconsin Package. Wonderful. I also like Clustal and it’s weird menu system. I’m constantly amazed that people assembled a 3 Gbp genome using Staden. And I love the fact you can run EMBOSS’s revseq and choose not to reverse or complement the sequence.

In terms of impact, I’d say it is BLAST. However, I also think Ensembl is amazing – it is a complete genome annotation and management package, and it is completely free and open-source. I think it’s the biggest and best open-source bioinformatics project out there.


101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality? 

I’d be N, because as a bioinformatician, you have to be everything: software engineer, mathematician, bioinformatician, database designer, biologist, statistician etc. etc.