Katarzyna Sikora

Retaining the command line magic from childhood

Join Katarzyna Sikora, a bioinformatician at MPI-IE, as she tells her journey from biology to bioinformatics, fueled by curiosity and guided by mentorship. Learn how she deals with stress on the job and discover her advice for aspiring girls and young female to start a career as bioinformatician, encouraging them to embrace programming and pursue their passions fearlessly in any environment.

Tell us who you are and what you're working on.

I work as a bioinformatician for the Max Planck Institute in Freiburg, specifically in the bioinformatics unit. My work is divided between maintaining and developing core services such as workflows and pipelines, including snakepipes, for example. All the projects I support are collaborative, originating from a biological lab by a PhD student or a postdoc who needs extensive computational support for their analysis, bridging the gap from the wet lab data that is generated very carefully to the analysis part, which I provide.

The analysis is always designed to meet the project's requirements. Typically, there's a predefined biological question that the user wants to address, and I provide computational means to tackle this question.

Regarding your current position, is it more of a regular 9-5 job, or do you sometimes have an extensive workload that requires overtime and adds stress?

I work part-time, about 70%, which provides a good balance between my private and family life and work. I adhere to my working hours since they align with my child's kindergarten schedule, including some personal time twice a week for mental balance. Currently, I don't work overtime. If there's a need to expedite work for a paper, I can shift priorities and dedicate more time to a specific task, possibly working a small amount of overtime on short notice. From experience, working overtime doesn't always mean faster progress. At some point, you just make more mistakes, and you come in the next day having to correct errors from the previous day, which doesn't save time but actually may lose some. I believe working at a pace that minimizes mistakes is the most efficient way to work.

Can you describe your personal journey to becoming a bioinformatician and what inspired you?

I studied biology and gradually shifted from biology to bioinformatics, significantly influenced by protein interaction screens during my master's and PhD projects. I was fascinated by the vast information within the cell and the co-regulation of biological processes. This led me to pursue an internship in bioinformatics after my PhD in biology at the Swiss Institute of Bioinformatics, where I had great colleagues and projects that immersed me in the field, greatly benefiting my learning. This experience led me to a postdoc in bioinformatics before coming to Max Planck. It wasn't a long-standing plan to become a bioinformatician from my biology studies but rather a result of pursuing research questions that intrigued me, leading me to bioinformatics.

Interestingly, I first encountered programming as a child in school, with extra classes for interested students using "Logo" to program a turtle to draw on the screen. This initial exposure and subsequent personal explorations laid a foundation that was useful later. During my internship at the Swiss Institute of Bioinformatics, I further developed my skills, learning the R programming language and shell scripting, benefiting from a positive learning environment and experienced supervision, which was crucial for my development in bioinformatics.

But you kept a little bit of this from the childhood?

Yes, indeed, I've retained a bit of that magic from childhood—the command line magic. It happened then and stayed with me.

You are in a pretty male-dominated area and many biologists are a bit scared of programming and bioinformatics. And this might also be true for many female biologists. How would you encourage, a girl or young female to work with computers?

I would definitely advise girls to follow their curiosity and intuition. If they like interacting with computers and have an analytic kind of mind, like spending time analyzing things and answering questions in an analytic way, and if they are fascinated by biological questions and pushing the limits of knowledge further to new horizons, they should go for it. They have all they need to flourish in any environment, even in a working group comprising only male fellow programmers. They should see themselves as an enrichment for any working environment and follow their intuition. Everything else can be learned along the way, as long as they feel it's right. They should not give up.

Another piece of advice is that I've definitely benefitted from mentorship and supervision at all stages of my professional career, and I would advise any girl who is perhaps uncertain or doesn't have a role model in the family to seek out a mentor. This can help a lot through any difficult situations and doubts. And also to feel connected, especially if you're the only woman in the room. Apart from this, keep your eyes open for working environments that are inclusive and caring for all kinds of genders and cultures. That's also enough to feel well in a working environment, also at the Max Planck, I would say.