Projects

Over 160 tools and databases are developed by the SIB community and openly available on Expasy, the Swiss Bioinformatics Resource Portal. Among them, 17 are designated as SIB Resources, and SPSP just became one of them for the period 2025-2028.

In this project, SPSP works towards implementing FAIRification of its public data for machine-discoverability as well. A documented public API was released and a SPARQL endpoint is under development.

Since the Summer 2024, SPSP centralises, curates, analyses, annotates and shares the SARS-CoV-2, Influenza and RSV genomic data from the national surveillance program on respiratory viruses, funded by the Federal Office of Public Health and led by the CRIVE.

This project supports expanding the SPSP platform to include key bacterial pathogens, enabling genomic data sharing and sequencing-based surveillance in a One Health context. It aims to strengthen public health in Switzerland and Europe by standardizing data exchange and supporting risk analysis.

In this project, SIB, ANRESIS and the clinical microbiology laboratories associated to Swiss University Hospitals have received funding to promote and pilot automated data exchanges with SPSP.

SPSP centralises and annotates the bacterial genomic and MALDI-TOF data generated within the IICU project.

With this project, SPSP enabled large-scale data sharing and validation for SARS-CoV-2, processing over 100,000 samples in 2021. Tools for batch uploads, metadata checks, and ENA export were developed. With 90,000+ open sequences published, SPSP became a European model for open genomic data sharing and standardization.

During the pandemic (Spring 2021 - Summer 2024), SPSP was mandated by the Federal Office of Public Health (FOPH) to centralise, curate, annotate and share to international repositories (GISAID and the European Covid-19 Data Portal) all the SARS-CoV-2 genomic data generated within the national surveillance program.

With this funding, the SPSP prototype was minimally expanded to cover SARS-CoV-2 analyses.

This project kickstarted SPSP and led to a functional prototype platform for near real-time surveillance of multidrug-resistant pathogens. Using MRSA as a proof of concept, it aimed to connect human and veterinary labs, integrate genomic and metadata, and served as a cornerstone for enabling outbreak tracking and research in a One Health context