We are EMBL: Thomas Weber on his journey beyond EMBL’s labs
While in Sweden, ARISE Fellow Thomas Weber gained practical experience in cloud orchestration and production-grade software development, advancing the ‘Depictio’ project
Thomas Weber, ARISE Fellow, in Gamla Stan, Stockholm. Credit: Cécile Boistelle
Tell us a little about your scientific background.
I started my curriculum with a bachelor’s in environmental engineering, but towards the end, I found my true calling in bioinformatics. I’d always loved computers and biology, and this field perfectly blended those passions. I then went straight into a Master’s and PhD in bioinformatics at the ICube laboratory in Strasbourg. Under Olivier Poch, my research involved creating models and metrics to help pinpoint mutations linked to rare human genetic diseases. After my PhD, I became an ARISE fellow at EMBL Heidelberg, based in the Data Science Centre (DSC).
What drew you to the ARISE Programme, and why did you decide to do your secondment at SciLifeLab?
As my PhD was wrapping up, Olivier told me about the ARISE programme. Its focus on training activities, secondments within and outside EMBL, opportunities for collaboration, as well as its strong focus on research infrastructures and technology development really appealed to my interest in creating practical tools that help researchers.
I got in touch with Jan Korbel, Head of EMBL’s DSC, to discuss an ARISE project. We decided on a proposal for scientific workflow results analysis and visualisation, which is now called ‘Depictio.’ The tool 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 data analysis of large datasets.
After a joint Data Science workshop with SciLifeLab in 2023, we realised their Data Centre (DC) would be perfect for a long secondment that would allow me to gain hands-on experience in cloud orchestration and production-grade software development, skills that were required to drive the Depictio project forward. During my secondment at the SciLifeLab, I collaborated with experienced engineers and received constructive feedback on various technical implementations, enhancing my understanding of best practices in testing, continuous integration, and cloud orchestration. A key achievement was integrating Depictio into the SciLifeLab’s ‘Serve’ platform, offering Swedish researchers seamless and scalable access to the platform – and promoting synergies between Data Science Centre of the EMBL and SciLifeLab’s programme in the Data Sciences.
What are you bringing back to EMBL from this experience?
Seeing how production-grade systems are built and managed at SciLifeLab expanded my technical skills needed for my project. I also picked up practical insights into agile methodologies like Scrum, which has broadened my understanding of team collaboration.
What are your thoughts on SciLifeLab as a secondment option for ARISE?
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?
My time in Sweden was fantastic! I loved Uppsala, a charming city much like Heidelberg or Strasbourg, with its cathedral, cobbled streets, and bike-friendly vibe. Being just a 35-minute train ride from Stockholm meant easy access to the Data Centre office in Solna, plus plenty of chances to explore the capital’s museums and events.
I really appreciated Sweden’s citizen-focused services, which made daily life so convenient. As a sports fan, I enjoyed local football and even saw a Sweden-France ice hockey World Cup match. Swedish spring is incredibly vibrant, with events like Kulturnatt, Valborg, and Midsummer – I’d highly recommend it to visitors for the long days, beautiful blooming gardens, and festive atmosphere.
About SciLifeLab
SciLifeLab, a Swedish national infrastructure for the advancement of molecular biosciences, is a collaboration initiated by the Karolinska Institutet, the KTH Royal Institute of Technology, Stockholm University, and Uppsala University, but engages the whole country. SciLifeLab offers access to cutting-edge life science infrastructure and provides expertise in areas such as biomedicine, cell and molecular biology, ecology, and evolution.
In 2021, SciLifeLab and EMBL signed a memorandum of understanding. As a partner in the ARISE Programme, SciLifeLab cooperates with EMBL towards training of the Fellows.
This article has been adapted from a news article by SciLifeLab. Find the original story at the SciLifeLab websitehere.
