Software Engineer Fedde Schaeffer

Software Engineer Fedde Schaeffer (33) joined The Hyve in October 2015 after finishing his studies in Bioinformatics. He worked on cBioPortal for a few years, then switched to Open Targets. Both in his studies and in his current job, Fedde values the mix of programming, language, and biochemistry. In his spare time, he enjoys playing all kinds of board and card games with colleagues and friends.

Can you tell me a bit about your background?

After secondary school, I considered a study in laboratory research. However, I couldn’t choose between biology and chemistry. When I visited an information day at the University of Applied Sciences in Leiden and learned about Bioinformatics, I realized this was the perfect fit for me since it combined my interests in molecular biology, informatics, and programming. There is even a link with my interest in languages and linguistics. After all, computer programming is about language, expressing ideas, communication. It’s just a very specific way of writing. Very different from, say, writing a novel.

After completing my bachelor’s degree in Leiden, I continued my studies with a Master in Bioinformatics and Systems Biology − a joint programme of the University of Amsterdam and the Free University − in Amsterdam. Interestingly, quite a number of students from that Master programme ended up working at The Hyve.

How did you get to know The Hyve?

I attended an open day at The Hyve. The company visit was organized by the student organization for bioinformatics students RSG NL/Young CB. By the end of the day, I left my CV and that has led to a job at The Hyve.

What attracted me to the company, was the idea of developing software that would be used more than once. In academia, you often write a computer program to answer a specific research question. Once that question is answered, the program or code is hardly ever reused.

I was also intrigued by The Hyve’s vision to encourage the use of open-source software in biomedical and pharmaceutical research and to stimulate collaboration between research groups.

When did you join the company and what team or products are you involved with?

I started working at The Hyve in October 2015, so I’ve been here almost seven years. First, I was involved with cBioPortal, a platform for visualizing and analyzing large-scale cancer genomics datasets. Over the years, I’ve seen that turn into a true open-source community.

A few years ago, the company decided to extend its services and expertise to Open Targets and I joined that team. Open Targets, a drug target validation platform and genetics portal, has only recently become an open-source platform. That makes for a different dynamic and a different relationship to the people who first developed it at the European Bioinformatics Institute (EBI) in Cambridge (UK) than I was used to with cBioPortal. The open-source community is still very much in development.

At The Hyve, both cBioPortal and Open Target are part of the Cancer Genomics and Target Discovery team. So I’m definitely still in touch with the colleagues working on cBioPortal.

What do you do at The Hyve?

My main focus as a Software Engineer is on programming for the Open Targets stack: adding features to the frond-end of the web application, building extensions for clients, finding ways to automate installation, et cetera.

When The Hyve develops a feature and we think it’s useful to a wider range of users, I get in touch with the people at EBI, who are in charge of maintaining Open Targets, and file a review request to get it accepted for use within the open-source community. When they find our work useful, it will be tested by more people and they might even build on top of it. Also, when EBI and other partners appreciate how we extended the software, further additions they make are less likely to accidentally clash with it. This makes maintenance work less complicated for all of us.

What do you like about working at The Hyve?

I like the challenge of writing maintainable code that is nice and clean and remains readable. When it comes to review requests, I always find it a challenge to demonstrate the usefulness of a feature we developed. To communicate what makes it useful not just for us or for our client but for the wider Open Targets community. That’s what attracted me to The Hyve in the first place: developing something that’s usable and useful for others.

What do you like to do when you're 'off-duty'?

I like board games and card games. I have a collection of about a hundred games, I think. I like to take games to work, so we can play them during drinks (borrels) after work. The corona pandemic made me give more single-player games a try. While I do still enjoy those occasionally, I’m very glad that I’ve been able to play board and card games with colleagues and friends again in recent months.