With advocacy activities on various data-driven research infrastructure topics, community gatherings to foster synergies, and high impact projects in Switzerland and abroad, 2024 was a year full rich in exciting accomplishments and new prospects.
The image used to illustrate our holiday card this year represents a map of all enzyme-driven biochemical reactions extracted from the PubMed literature database using LLMs, overlaid with those already documented in SIB’s Rhea reaction knowledge base, to help biocurators identify those to annotate as a priority. Colours denote whether the activity is described in Rhea (red), extracted from PubMed using LLMs (green) or both (pink). Enzymatic activities are grouped based on their similarity in terms of compound structure change. The ability of LLMs to extract this type of knowledge was “fine-tuned” using a newly curated collection of scientific literature about enzymes. This work was performed in collaboration with the PubMed team at NCBI.
Discover more in the SIB Profile 2024.
Link to publication
Advocating for data-driven research infrastructure in the life sciences and the impact of bioinformatics
This year’s highlights include the presentation of SIB at the National Council's Committee for Science, Education and Culture (CSEC-N), and at the Commission for superior education at the Geneva Parliament, to showcase the importance of bioinformatics and our role in the life science ecosystem and for society.
Our sustained involvement to develop the Swiss open research data ecosystem as well as the European Life Science infrastructure – as a Swiss node of ELIXIR and as a new member of the European Open Science Cloud (EOSC) – are illustrations of our deep belief that biological and biomedical data science are essential to solve societal challenges.
Strengthening ties within the national community and with the European network
From the creation of new nationwide focus groups (Core Facilities, Large Language Models for genomics, pathogen bioinformatics – see all) to a record attendance to the SIB days – the Swiss bioinformatics summit in the spring, our lively community keeps growing and bringing the field forward across Switzerland.
On the European level, we have also deepened our ties with ELIXIR. Our scientists now participate in all 5 platforms (Data, Tools, Compute, Interoperability, Training), co-lead 4 communities (3D-Bioinfo, Biodiversity, Food and Nutrition and Human Copy Number Variation) and 2 Focus Groups (FAIR training and Pathogen Data). Switzerland was thus very well represented at the ELIXIR yearly conference in Sweden. On top of this, we secured our involvement into 6 ELIXIR competitive grants, to begin in 2025.
Boosting our involvement into high-stake projects with impact for society and the community
In a nutshell:
- Disease control
With the participation of our partners, we took several important steps to strengthen Switzerland and international disease control this year. For example, the scope of the Swiss Pathogen Surveillance Platform (SPSP) has been expanded to include new pathogens, both for the Federal Office of Public Health (FOPH) and the Federal Food Safety and Veterinary Office (FSVO). Since its launch in September, the Center for Pathogen Bioinformatics offers expertise and services to the Swiss federal authorities and the global research community to contribute to pandemic preparedness in a coordinated and sustainable fashion. Moreover, SIB leads an NIH-funded project to develop a global Pathogen Data Network (PDN) to enhance pandemic preparedness at the global level.
- Human genomic research
We have launched the Swiss Federated European Genome-phenome Archive (Swiss FEGA), with our partners and as part of SPHN. The purpose of the consortium is to enhance human genomic research by providing Swiss researchers with a legally compliant platform for data sharing and collaboration.
- Biodiversity
The European Reference Genome Atlas (ERGA), led by SIB’s Environmental Bioinformatics group, has launched a pilot project to create a collaborative, decentralized model for generating high-quality reference genomes to better understand and protect European biodiversity.
- Securing funding for resources
SIB was invited at the AI-Bioscience Collaborative Summit in Washington, DC—a prestigious gathering co-organized by the US Department of State and Microsoft – where the need for sustainable funding for curated data resources was highlighted. The event emphasized SIB's contributions to essential tools like UniProt, and its influential role in advancing AI-driven bioscience.
Events coming up in the new year
Mark your calendars for the [BC]2 Basel Computational Biology Conference next year! Scheduled for 8 - 10 September 2025, the event will explore the theme: “Bioinformatics meets AI: shaping the future of data-driven biology”.
While you have your calendars open, you may also want to save the date for eccb 2026, which will take place from 31 August to 4 September 2026 in Geneva. We are thrilled and honoured that our proposal to host this prestigious conference has been selected
We wish you a great holiday season and the best for the new year!
