Getting to know us: Arne from Ensembl Infrastructure

In this edition of our Getting to know us blog series, we introduce Arne Becker, member of the Infrastructure team at Ensembl who joined the European Bioinformatics Institute (EMBL-EBI) in March 2022. Arne transitioned from IT security to bioinformatics and his work focuses on enhancing the efficiency of data processing pipelines.

When did you join and what is your job in Ensembl?

I joined EMBL-EBI in March 2022. I work in the Infrastructure team at Ensembl. It may sound like this is about hardware, but that’s not the case. Infrastructure here refers only to software. We maintain and develop software packages and pipelines that process biological data. Frequently this also includes making processing faster or more efficient.

Portrait of Arne Becker.

What do you enjoy about your job?

I always liked to make things run smoothly and efficiently. Currently, the amount of data that we at EMBL-EBI are dealing with is growing fast. I really enjoy being involved in discussions on how to transform our approaches to storage and processing to be able to deal with more data. I also enjoy that my work is useful – we regularly get feedback or questions from scientists around the world. With a bit of indirection, my work enables research that is important and helps us understand the fascinating complexity of biological processes.

What are you currently working on?

I have recently changed the way we build and deploy software on our cluster. I have set up a software environment with Spack and added around 2,000 packages to it. Currently, I’m working on a pipeline that prepares data for our web site. So far, I made it much faster – instead of many hours it now takes from 30 seconds to two minutes to prepare data for one species.

What did you do before joining Ensembl?

I was working for a small company in Germany specialising in building IT security appliances like firewalls and VPN gateways. Surprisingly, my main programming language was Perl back then and it still is Perl now. Although there is a clear shift to other languages like Python and Rust. I already know Python and I’m quite happy to use Rust professionally, so this works well for me.

How did you get into bioinformatics?

I didn’t, in a sense. Until I joined EMBL-EBI, there was no bio in the informatics I was doing.
But biological processes have always fascinated me. DNA being read and copied inside the body all the time, proteins being built, viruses identified and attacked, digestion turning food into fuel and building materials – there is a long list of complex things going on in nature. Another area of interest was machine learning. In 2021, DeepMind used their AlphaFold system to predict protein structure, a huge step forward. I was reading about that when I discovered that DeepMind was giving access to their data in collaboration with EMBL-EBI. It was the first time I heard about EMBL-EBI. Since I was looking for a bit of change in my professional career, I decided to have a look at their open positions – and just a bit later, I switched jobs and moved to the UK!

What advice would you give for those wanting to start a career in bioinformatics?

  • Don’t be afraid to apply for a job, even if you don’t have a biology background. There are plenty of things to do at EMBL-EBI that are strongly informatics-focused. And everyone is happy to teach you what you don’t know.
  • Develop good programming skills and build know-how on how to compute things efficiently.
  • Machine learning works very well for many biology-related analyses. Investing your time to build up skills here is recommended.