The Latvian Biomedical Research and Study Centre has been extensively using the resources of the RTU HPC Centre’s supercomputer in recent years. Projects such as the European "1+ Million Genomes" initiative and the establishment of the Latvian State Genome Bank would not be possible without the use of supercomputers or high-performance computing (HPC) resources.
It Wasn't a One-Day Decision
The first introduction to the potential of supercomputers and how they could assist in scientific research took place at a presentation held at the University of Latvia’s Biomedical Research and Study Centre, led by RTU expert Lauris Cikovskis.
“How much time passed between the presentation and the decision to use the HPC cluster, it’s hard to measure from today’s perspective. I remember one day when a group of our researchers came into my office and said – if we were to process genomic data on our own resources, we’d be talking about results only after three months. It would take that long for our computers to analyze the genomic data. Meanwhile, the HPC cluster could handle the same task in just a few hours,” recalls Jānis Kloviņš, Head of the Precision Medicine Group at the Biomedical Research and Study Centre. "We looked at both commercial offers and the RTU HPC Centre’s resources and concluded that the best fit for our research was precisely the offer from the RTU HPC Centre. Our experts can easily access the HPC resources, and we only pay for what we use.”
Kloviņš believes the collaboration with RTU HPC Centre is a great example of how Latvia’s scientific community can benefit from university-based research resources.
Was It Easy to Start Using HPC Resources?
“Yes, as far as I remember, it was relatively straightforward. Our staff followed the instructions and gained additional knowledge. Currently, we use the supercomputer’s resources quite extensively,” says Kloviņš. Comparing statistical data over time, since 2018, data processing has seen significant growth, and this trend will continue in the future.
3 Main Areas of Supercomputer Use:
- 1+MG
The European-level project *"1+ Million Genomes"*. The Latvian Biomedical Research and Study Centre is studying Latvian human genomes. The project plans to collect genomes from 3,500 individuals, which will be available for use by scientists and doctors worldwide. Latvian residents who wanted to participate could become part of this study, and participants will be able to receive an analysis of their genomic data next year. This means that theoretically, they could learn about potential risks for future diseases and adjust their healthy lifestyle habits now to avoid these conditions later.
The main goal of this project is to create a reference genome for the Latvian population, which will be used for disease prognosis, screening planning, treatment optimization, and scientific development. The Latvian genome reference created within the project will be included in the European genome database as part of the *1+ Million Genomes* initiative. The goal of the *1+MG* initiative is to ensure secure access to genetic and associated clinical data across Europe to improve research, develop personalized healthcare, and aid decision-making in health policy.
In the implementation of this project, the Biomedical Research and Study Centre is working closely with RTU Associate Professor Jānis Kampars.
- Latvian Genome Bank
A national genome database is being developed as part of a Latvian state program. The aim of this project is to create a national-level research platform for biomedicine.
Could this mean that in the future, people will give blood samples, and from the results, they could find out potential health risks? "Yes, you could say that this is the direction in which medicine is currently developing. We are building a large data bank. Usually, data needs to be collected for at least 20 years. Latvia is currently at the very beginning of this journey," explains Kloviņš, outlining the future of medicine that science is currently helping to develop. A doctor, when working with a specific patient, may realize that it’s necessary to further explore the individual’s genome. They create a task, defining which data to find in the genome bank based on specific selection criteria. By pressing a button, the task is completed across Europe (or, in the most idealistic future scenario, globally). As a result, the doctor obtains a vast amount of data that could assist in the ongoing treatment of the specific patient.
- Covid-19 Research Continues
“During the pandemic, supercomputer resources were used to track the spread of the Covid-19 virus and identify the leading strain in society at a given moment. In cooperation with BIOR, wastewater was monitored, and data was gathered,” Kloviņš explains. During the pandemic, a significant amount of unique virus data was accumulated, which would no longer be possible to obtain, as people have now been vaccinated, and some, sadly, have died. Research related to Covid-19 is still ongoing. Although virus data is relatively small compared to human genome data, HPC resources still significantly accelerate the research process.
The Covid-19 pandemic was a challenging and difficult time for many, but it also brought about new innovations. One such innovation was the creation of a data network by the Latvian Biomedical Research and Study Centre in cooperation with SIA *Mikrotīkls* and LMT, which is still in use today. This network ensures fast transmission of large data sets.
Advice for Those Just Starting to Use Supercomputing Resources
“The key is not to be afraid to explore the possibilities of supercomputers. There are plenty of instructions available to follow. HPC resource providers usually offer consultations and support, which was also helpful to our specialists,” Kloviņš encourages those looking to explore new possibilities.
He agrees that there are still relatively few HPC experts in Latvia, and their lack is felt, so it would be useful if all those working in the field would stick together and support each other. “A coaching and mentoring program would be a great idea. We have implemented something similar in our institute. All bioinformaticians sit in one room. Experienced colleagues train newcomers. New experts find it easy to master HPC systems. If they can do it, I can conclude that it’s not that hard to learn how to start using a supercomputer,” Kloviņš concludes the conversation. If an initiative were to be created in Latvia where existing HPC experts collaborate and share knowledge and experience, the Latvian Biomedical Research and Study Centre would be willing to participate in such an initiative.
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