101 questions with a bioinformatician #8: Nick Loman

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.

Nick Loman is an Independent Research Fellow in the Institute of Microbiology and Infection at the University of Birmingham, UK. You may know Nick for his involvement in producing the only world map of high-throughput sequencers (at least I'm assuming that this is the only map of its kind…I'm too lazy to check). Maybe you know him for the exclusive interview that he managed to secure with some of Oxford Nanopore's head honchos at the 2012 AGBT meeting (the scene of a certain wowser moment in high-throughput sequencing). Or maybe you just know Nick for his epicurean passions.

I like to think of Nick as the Jack of Clubs in the deck of cards that is the bioinformatics blogging community (this works as a metaphor, right?). Actually, on some days he's more like the Ten of Diamonds, but then he goes and writes great pieces like this (co-authored with fellow 101 alumni Mick Watson):

If you are interested in bioinformatics, and if you want to keep up with the latest developments in high-throughput sequencing technology, then you really should be keeping a close eye on people like Nick (though not too close, give the man some privacy!).

You can find out more about Nick by following him on twitter (@pathogenomenick) or keeping up with his excellent blog (Pathogens: Genes and Genomes). And now, on to the 101 questions...



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

I mainly enjoy the daily battles with crashing servers with cryptic memory errors, incompatible software versions, buggy scripts (mine and others) and full hard drives. 

Hah! That was the famous British sarcasm you will have read about.

The obvious answer is that the projects I get involved in are incredibly diverse, and I get to interact with many interesting people, because sequencing and bioinformatics skills are in such demand.

Another thing I enjoy is that I can reach out, via Twitter and blogging, to discuss with all the great computation biologists in the world struggling with the same problems. I have no idea what it must be like to feel isolated and slog away in a windowless laboratory without that kind of communication.


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

I whinge quite a lot on my Twitter feed, but I wish bioinformaticians (including myself) wouldn't spend so much time reinventing the wheel (Keith: it's bioinformatics sin number 1 on this list), and instead try and muck-in together to solve really important problems.

A model of bioinformatics research a bit more like the Linux kernel might work. Imagine an international network of committed bioinformaticians working together. We would achieve great things quickly. But the academic model of recognition is broken for things like this, where everyone needs their own papers to justify their positions.


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

I guess I would have got into the details of Bayesian statistics and machine learning earlier. These skills are very useful and I am only picking them up properly just now (I am on a Medical Research Council Training Fellowship).

Probably would have slipped myself a copy of Grays Sports Almanac too.

More prosaic: GNU parallel I discovered way too late and is an essential tool. And screen.


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

There's very little you can't get done with BLAST. It has its funny little quirks, but you know where you are with it. 



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

Well, it would be rather British to suggest T. But I prefer coffee.