Interview: Wearing many hats

Maintaining academic software is just one part of the role Computational Scientist Tom Burnley performs for the electron microscopy community.
Interview
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In crystallography, researchers rely on sophisticated software packages to analyse X-ray diffraction data and determine the structures of proteins. In 2012 Tom Burnley was a postdoc at Utrecht University and the first author on an eLife paper that described an improved method for fitting 3D protein structures to X-ray diffraction data with one of these packages. Burnley now works at the Science and Technology Facilities Council on a project that supports similar software packages – and the community that uses them – for electron microscopy data.

Tom Burnley celebrating the acceptance of his paper in eLife. Image credit: Rebecca Burnley.

What did you enjoy most about postdoc research?

One of the reasons why I did a postdoc was because I asked a friend of mine whether or not I should do one. “Of course you should”, he said, “it’s the only job in the world where you’re paid to think”. That was the best part of the job. I love my job now, but it involves a little bit of lots of different things: when I was doing my postdoc I was able to think about just one thing. Of course, the downside is that it can be a bit dispiriting when the one thing you’re concentrating on doesn’t work. But in the end, when it worked it was great.

Was the work that you described in your eLife paper the major focus of your postdoc?

Yes, it was my main project when I was in Utrecht, and that paper was the main paper that detailed the methodological developments that occurred over a period of three years. It followed up a paper that my boss, Piet Gros, had published in Science in 1990. The validation metrics that we used in the eLife paper weren’t available then, so his paper was interesting but it was difficult to prove that it worked. We extended the method and validated that work to fix the issues with it.

Do you remember what you were doing when the paper was finally published?

I must admit I can’t remember where I was when the paper came out, but I remember vividly where I was when it was accepted. The other authors and I finished off the paper just before I went on holiday with my wife to South Africa for three weeks for her sister’s wedding. It was kind of a trip of a lifetime for us. We were a bit surprised by how fast eLife turned around the paper – the editorial comments came back so quickly that I ended up spending the first part of my holiday writing the corrections. A few days later Piet texted me when I was on a train between Cape Town and Johannesburg to let me know that the paper had been accepted. So I was on this beautiful train travelling through the South African countryside, and best of all they had a dining car on the train. So I went and bought a glass of wine to celebrate!

At that point, did you have a plan for what you were going to do for the next five years?

I had no idea really. About a year later my current job was advertised and I really liked the sound of it because I wanted to go more into software development rather than algorithm development and because I really liked the idea of joining a project at the start. My wife and I also wanted to move back to the UK and so it worked out very nicely.

Were you aware of other academic software projects before starting in your current role?

Crystallography has two exemplar projects – Phenix, which is the project I worked on in Utrecht, and CCP4 (which is short for Collaborative Computational Project 4). They’ve been really successful as judged by the communities they’ve kindled and the science they’ve done. And I think they work because they’ve had long-term funding. It’s really easy to say we’ll give money for a three-year postdoc to come up with a new algorithm, a new cool piece of software, but there are limitations – unless you have some way of sustaining it, the software will just fade away.

How does your work relate to those projects?

The project I am working on now – CCP-EM, where EM is short for electron microscopy – is linked with CCP4, which has been running since 1979 – which is amazing for an academic software project. We get help from them on a scientific and technical level.

So what are the main roles of the CCP-EM project?

We have three roles that are equally important. Firstly, we help to train users. We run three or four workshops a year where we get PhDs, postdocs and PIs, academics or industrial equivalents to spend a day or two here and we teach them software routines for analysing their data. Secondly, we run an annual conference: the CCP-EM Spring Symposium, that has become a national EM conference in the UK. Thirdly, we also help the developers themselves. This can be at a very low level, writing the nuts and bolts of software (technical stuff like File I/O and file standards), and at a higher level where we write the interface to the software (the GUIs that people use). We also help write and test the algorithms that people run, and provide software support. So I feel like a person who wears lots of hats. And actually that’s good fun.

Out of all the many parts of your job, which part do you find the most satisfying?

The symposium gives me the most excitement. Especially when it starts and you see 200 people in the room for the event that you put together (with the support of colleagues and collaborators). We’ve run it for three years now, it’s grown each year, and it seems to be very successful.

And what do you find most challenging?

I’d like an extra day or two in the week! No, just balancing long-term goals and short-term needs. There are longer-term things I’d like to do that are always put on the back burner. And I would like to do some more algorithm development again, but I never quite have time to sit down and do it.

What do you do in your free time?

Mostly cycling. I race, I do a lot of road cycling, and I’m the club secretary for the Thames Velo cycling club. But I’ve got a year and a half old daughter at home now so my time for cycling’s been cut down a little.

What would you like to be doing career-wise in five years time?

I want to carry on doing what I’m doing and grow our project. At the moment it’s fairly small. We have five years of funding from the MRC but I want to build on that – write up some more grants, get a bigger pool of developers and expand what we do. CryoEM is such an exciting field that there are many things we’d like to do.

What career advice would you give to postdocs in a similar situation to the one you were in five years ago?

Don’t be afraid to do something different. My postdoc was very different from my PhD – I went from mainly nuclear magnetic resonance to mainly crystallography – and I learnt a whole new set of things. I know people who felt that because they’d done a PhD in technique X, that meant that they were a crystallographer or electron microscope person and carried on doing that. If you really like that particular method then that’s cool, but I think it’s more fun to learn new things.

Tom Burnley CV

  • 2013 – present: Computational scientist, Science and Technology Facilities Council, UK
  • 2008 – 2013: Postdoctoral researcher, Utrecht University, The Netherlands
  • 2007 – 2008: Postdoctoral researcher, University of Leeds, UK
  • 2003 – 2007: PhD student at the Astbury Centre for Structural and Molecular Biology, University of Leeds, UK
  • 1999 – 2003: MBiochem in Biochemistry, University of Bath, UK