Tech, teamwork, and growth: Thomas Weber shares his ARISE secondment experience at SciLifeLab

Thomas Weber is an ARISE fellow with Jan Korbel at EMBL Heidelberg, and has been working at SciLifeLab Data Center DC since March. Before his return to Heidelberg we got the chance to ask a few question about the experience at SciLifeLab and in Sweden.

Tell us a little about your scientific background

My academic journey began with a bachelor’s degree in environmental engineering. Towards the end of the program, I discovered bioinformatics, a field that immediately resonated. I had always been fascinated by computers since childhood, and I was searching for a discipline that would allow me to combine this passion with my interest in science, which bioinformatics perfectly provided. I immediately applied to continue both a Master’s and a PhD in bioinformatics at the ICube laboratory in Strasbourg. Under the mentorship of Olivier Poch, my research focused on developing models and metrics to help identify candidate mutations associated with rare human genetic diseases. Following the completion of my PhD, I secured a position as an ARISE fellow at EMBL Heidelberg, where I am hosted within the Data Science Centre (DSC).

What drew you to the ARISE program, and why did you decide to do your secondment at SciLifeLab?

As I was finishing my PhD, Olivier shared an email about the ARISE programme. The programme’s format, including various training activities, secondments within and outside EMBL, opportunities for collaboration, as well as its strong focus on research infrastructures and technology development, were aligned closely with my core interest in developing practical tools that directly support and enhance the research of collaborators.

In planning my ARISE project, I contacted Jan Korbel, Head of the EMBL DSC, and we agreed to submit a proposal around workflow downstream analysis and visualisation. The project is today entitled “Depictio” and is a modern web platform, cloud-compatible, designed to aggregate data from frequently used workflows to further generate interactive dashboards, in order to facilitate quality control issue detection and improve large datasets data analysis. 

Following a joint Data Science workshop in 2023 between SciLifeLab & EMBL Centres, we identified SciLifeLab Data Centre (DC) as an ideal choice for the secondment, which would allow me to gain hands-on experience in cloud orchestration and production-grade software development, transversal skills highly useful for the project.

What have you focused on during your time with SciLifeLab Data Centre?

During my secondment, I aimed to improve my knowledge in cloud orchestration, particularly with Kubernetes, as well as in continuous integration and software testing. I was integrated into the team developing ‘Serve‘, a SciLifeLab platform facilitating machine learning model serving and data science application hosting. This onboarding helped me better understand how a team working on production-grade service used at the national level is leveraging frameworks like Scrum and sprints. By collaborating closely with experienced software engineers, I received constructive feedback on various technical implementations, enhancing my understanding of best practices in testing, continuous integration, and cloud orchestration.

A significant milestone was the integration of Depictio as a new application type on the ‘Serve’ platform. This development will enable Swedish researchers and their collaborators to access Depictio seamlessly within a scalable and robust cloud-compatible environment, moving beyond the constraints of local installations or complex setups.

What are you bringing back to EMBL?

This secondment has provided me  practical exposure to cloud orchestration technologies, particularly Kubernetes. Working alongside experienced engineers has given me insights into how these systems are implemented and managed at the scale of a production-grade service, expanding my technical toolkit in ways that will complement my existing background and support my project. I also gained practical knowledge of agile methodologies, specifically Scrum practices and sprint planning. This has broadened my understanding of collaborative development practices and how these frameworks facilitate team coordination for project management within a developers team. I am looking forward to applying what I have learned while continuing to develop these skills further within my fellowship.

Based on your experience, what are the key similarities and main differences between EMBL and SciLifeLab?

Both EMBL and SciLifeLab are committed to advancing life sciences by supporting data-driven research through robust infrastructure. They have a strong focus with regards to collaboration and training and operate as multi-site organisations. Both organizations demonstrate a systematic coordination between research teams and infrastructure support units, including core facilities and IT services. Their respective Data Science Centres operate as centralised hubs that operate across multiple sites while facilitating connections between developed services and the diverse thematic research areas.

I’d say that the main differences between the two organisations lie in their geographic scope and organisational structure. While EMBL operates at an international level, SciLifeLab functions as an umbrella organisation that coordinates and supports scientists at the Swedish national level. This distinction extends to their operational models, where EMBL research groups are directly hosted within the institution, while at SciLifeLab, research is carried out by groups embedded in Swedish universities. Lastly, EMBL has a more research-centric focused mission, whereas SciLifeLab places greater emphasis on providing and developing a national research infrastructure supporting researchers.

What advice would you give to someone considering an ARISE secondment?

To anyone looking for an ARISE secondment, I would highly recommend SciLifeLab and its Data Centre as an excellent opportunity for professional growth and expanding technical expertise. The SciLifeLab DC is a dynamic, rapidly expanding unit playing a pivotal role within Sweden’s national life science landscape. During my time here, I had the privilege of meeting and collaborating with incredibly knowledgeable and supportive individuals who were always willing to assist and provide feedback. It’s definitely an environment fostering both skill development and networking.

During your time in Sweden, what have you experienced outside of SciLifeLab?

Living in Sweden was a fantastic experience that allowed me to discover a really beautiful and welcoming country. I was based in Uppsala, a charming city with similarities with places like Heidelberg or my hometown of Strasbourg, with its old cathedral, cobblestone pedestrian streets, excellent bike-friendly infrastructure, and numerous parks and gardens. The proximity to Stockholm, just a 35-minute train ride away, allowed me to visit the Data Centre office in Solna regularly, facilitating in-person meetings and project presentations, while also providing opportunities to explore the city, its museums, events such as Kulturnatt, and sightseeing throughout the historic city center.

I really appreciated Sweden’s emphasis on citizen-centered services, making everyday activities like commuting and shopping more convenient. As a sports enthusiast, I enjoyed attending local football games and had the chance to watch a Sweden-France match during the Ice Hockey World Championships in Stockholm. The spring season in Sweden is particularly vibrant and full of cultural events, including Stockholm Kulturnatt, Valborg in Uppsala, the Stockholm Marathon, Sweden’s National Day, and culminating in Midsummer celebrations. I would strongly recommend this period for foreign visitors, as the combination of extended daylight hours, flourishing gardens, and festive atmosphere creates an ideal environment for cultural integration.