Challenge: Boosting Public Health with Medical Research
Karolinska Institutet is one of the world’s leading medical universities. Its mission is to contribute to the improvement of human health, and generates more than 6,000 peer-reviewed scientific publications per year. The university has a unique position in academia, as the Nobel Assembly at Karolinska Institutet is responsible for selecting Nobel laureates in Physiology or Medicine.
The Centre for Translational Microbiome Research (CTMR) at Karolinska Institutet’s Department of Microbiology, Tumor and Cell Biology is an innovative public-private partnership with Ferring Pharmaceuticals. Ferring Pharmaceuticals is a research-driven, specialty biopharmaceutical company headquartered in Switzerland and with roots in Sweden.
Researchers at the CTMR are working on accelerating research into all aspects of chronic diseases in the gastrointestinal tract and to better understand the impact of the microbiome in reproductive health. The primary goal is to unlock the potential of the human microbiome—the community of microbial organisms found in the body’s digestive systems—to improve treatments and prevent diseases.
Fredrik Boulund, Head of Bioinformatics at the CTMR, explains: “A lot of our work is analyzing lab samples. When we look at DNA sequencing data, the first step is to determine which microbes are in the sample. We analyze the multidimensional microbiome data to understand the community composition. The second step is to look into what the microbes are doing in the sample—what they consume and what they can produce. We need to establish how the capabilities of the microbiome communities in the samples relate to our research questions.”
This research is very compute- and memory-intensive. The CTMR has access to shared high-performance computers (HPC) via the Swedish National Infrastructure for Computing (SNIC). However, it needed access to more flexible compute capacity throughout the year to process large batches of samples that arrive at hard-to-predict timepoints.
“Using external compute resources was a valuable option, but it also limited our productivity,” says Boulund. “The overall workflow provided a slow feedback loop. After planning the analysis, we had to upload the raw data to the shared HPC systems and submit compute jobs to the central queue. Then we had to wait for hours or even days until the jobs had completed—or failed. As we started to outgrow our allocations on the shared HPC systems, we started looking for new options to gain insights faster and more flexibly.”
In 2020, CTMR was also tasked by the Swedish government to move beyond fundamental research and set up a new National Pandemic Centre (NPC). The NPC was launched together with the Science for Life Laboratory (SciLifeLab), an organization supporting molecular biosciences in Sweden. Strengthening Sweden’s COVID-19 response, the NPC analyzed approximately 45,000 PCR-based COVID-19 tests per week. Over the course of the pandemic in Sweden it grew to become one of the largest lab facilities in Sweden for SARS-CoV-2 (COVID-19) analyses. At times the NPC provided up to a fifth of the country’s total testing capacity.
One of the NPC’s key responsibilities is to make advanced technologies and expertise available to researchers working on COVID-19. “When the pandemic work began, we suddenly had to deal with a lot more data,” adds Boulund. “Our team needed to quickly expand our capability to analyze data so that we could help to advance SARS-CoV-2 research.”