Making sense of the cell using computer power

Interview with Bas van Breukelen

Bas van Breukelen co-founded the Utrecht Bioinformatics Center and the popular Master's programme Bioinformatics and Biocomplexity programme. What explains its success? "Students soon discover that bioinformatics is not such nerdy world where you sit behind a computer all day."

Dr. Bas van Breukelen
Dr. Bas van Breukelen

He is "quite a computer geek", says Bas van Breukelen, the type of guy who already programmed computers when he was a kid. But that does not make him a poster child for the students who participate in Bioinformatics and Biocomplexity, the Master's programme he helped to design.

After years of preparation, he and his colleagues welcomed the first students in 2020, who enrolled in large numbers. The popularity of the master's programme exceeded all their expectations.

What makes the programme such a success?
"For more and more students taking life sciences, bioinformatics is a must. In the course of their studies, they discover that they need computer science to handle the data coming from their own experiments."

"In many areas of life sciences, you are soon confronted with enormous amounts of data. You want to be able to process and understand it yourself. You don’t want to have to take your data to someone like me to ask: ‘Bas, can you please have a look to see if I have discovered something relevant?"

Is bioinformatics the domain of nerds?
"Absolutely not. Students have come to understand that bioinformatics is not at all a nerdy world in which you sit in front of a computer all day. This also partly explains the success of the Master’s programme. Aside from carrying out computer analyses, you can still have one foot in the lab and do your own experiments."

Does working with big data scare potential students off?
"No, on the contrary. Students discover that big data is not solely used by, for example, tech companies or supermarkets, who track your profile and consumer behaviour. Big data is booming. In many fields of science, it now plays a huge role."

In many fields of science, big data now plays a huge role

How did you become fascinated with bioinformatics?
"When I did my PhD research at the UMC Utrecht, round about 1997, I spent four years researching a single protein. Back then, you used a computer only to write your thesis. This changed when the first so-called micro arrays appeared. On these plates you can print an entire genome. That was really cool. Instead of analysing just one protein, this allowed you to analyse the whole genome at once. But to do that, you needed the power of a computer. That is when my two passions suddenly fused: biology and computers. Fascinating!"

Were you fascinated by computers at an early age?
"I have always been quite a computer geek. When I was in primary school, the Commodore 64 computer was a big thing. We got one at home, because my mother worked for a training institute and had to type all kinds of course manuals on the computer. My little brother and I started working on it too. We each did so in our own way: he mainly played games on it, and I programmed it."

You were a co-founder of the Utrecht Bioinformatics Center. How did you establish this network?
"Bioinformatics is a focus area of Utrecht University, and with the funding from that, we set up the Utrecht Bioinformatics Center. It was mainly bottom-up: the inspiration, ideas and drive really came from the researchers themselves."

"The inspiration, ideas and drive really emerge from the researchers themselves”

We started to build a community with all parties on the campus involved in bioinformatics. In other words, not just the Faculty of Science, but also the Faculty of Veterinary Medicine, UMC Utrecht and the Hubrecht Institute. Later, Danone, RIVM and the Princess Máxima Center joined. The community is still growing. We create so many collaborations, which is incredibly valuable. Thanks to the bottom-up approach, it is supported by everyone involved.”

How will the this collaboration develop in the coming years?
"It has been agreed that from 2023 onwards, bioinformatics will no longer be a focus area. We will have to find some way to maintain our central role, keep the community together, organise symposiums, etc. Maintaining a community takes a lot of time and effort. I really hope that we can continue to find ways to make that happen."

How can bioinformatics help us understand all the processes in a cell?
"I think that currently we haven’t yet arrived at a complete understanding of what happens in cells. In the past, you would examine just one part of a cell. You’d study the proteins, or the genes, or the physiology. Now we are putting all those parts together and we can even add evolution to them."

Bioinformatics allows you to construct a helicopter view, and the world that you are able to see then is absolutely amazing

"The result is a world with so many layers of information that you really need a supercomputer to handle it. With bioinformatics, you construct a kind of helicopter view of all that information. The world that you are able to see then is absolutely amazing. In the end, we want to model a complete cell or organism in a computer. That’s the ultimate goal."