Three new biodata resources recognized as crucially important for the global life science community will benefit from SIB’s unique support for their further development. Their designation as SIB Resources follows a stringent evaluation by an external Scientific Advisory Board, and is a tribute to the respective groups and their partners. The SIB portfolio now numbers 17 leading resources, which together consist of 40 open databases and software tools for managing, analysing and interpreting biological and biomedical data.
Enabling evolutionary studies from pathogens to penguins
BEAST2 performs phylogenetic analysis of molecular sequences using Bayesian methodologies, with applications including evolutionary and developmental biology, epidemiology, cancer evolution – and even language evolution. For example, the resource:
- improved estimations of influenza evolution, with the CoalRe package (recognized as a SIB Remarkable Output in 2019);
- quantified epidemiological dynamics of SARS-CoV-2 in real time during the pandemic, based on viral genomes and confirmed case data;
- provides easy simulation of species trees and populations over time using the ReMASTER package;
- allows species divergence times to be estimated using data from both extinct species (fossil morphology) and present-day species (genetic sequences), using packages first developed for studying penguin evolution.
BEAST2 is co-developed by our Computational Evolution group at ETH Zurich and researchers at the University of Auckland, in collaboration with other scientists around the world.
Profiling microbe communities
mOTUs quantifies the relative abundance and activity of microorganisms in biological samples, from wastewater to animals to human body sites. It uses so-called ‘universal marker genes’ to identify species from their DNA – a new approach that is more efficient than previous methods and allows analysis of microbes that lack a representative genome sequence.
Applications include:
- profiling the composition of the global ocean microbiome (recognized as a SIB Remarkable Output in 2022);
- identifying microbial signatures in clinical phenotypes, such as those specific for colorectal cancer.
An accompanying online database enables interactive searching and browsing of the underlying genome resource, and is itself one of the largest prokaryotic genome resources to date. The tool is developed by our Microbiome Research group at ETH Zurich, the Swiss National Centre of Competence in Research (NCCR) Microbiomes, EMBL, Keio University and Leiden University.
Joining a portfolio of essential bioinformatics resources
SIB Resources are used by over 10 million users each year for applications ranging from designing cancer vaccines to developing new crops to predicting species extinction – and demand is ever growing. As one example SwissDrugDesign, developed by our Molecular Modelling group at the University of Lausanne to support computer-aided drug discovery, saw its usage increase by over 40% in 2024 to 5 million annual user requests.
These resources form a carefully selected subset of all 160 software platforms and databases developed by the SIB community, all of which are openly available on Expasy, the Swiss Bioinformatics Resource Portal.
Keeping track of the enemy
The Swiss Pathogen Surveillance Platform (SPSP) supports molecular monitoring of microorganisms occurring in humans, animals and the environment, enabling a One Health approach at a national level.
Joining a portfolio of essential bioinformatics resources
SIB Resources are used by over 10 million users each year for applications ranging from designing cancer vaccines to developing new crops to predicting species extinction – and demand is ever growing. As one example SwissDrugDesign, developed by our Molecular Modelling group at the University of Lausanne to support computer-aided drug discovery, saw its usage increase by over 40% in 2024 to 5 million annual user requests.
These resources form a carefully selected subset of all 160 software platforms and databases developed by the SIB community, all of which are openly available on Expasy, the Swiss Bioinformatics Resource Portal.
This online platform – which provides near real-time sharing of whole genome sequences and associated public metadata – played a major role during the COVID-19 pandemic. Its scope is now extending to several pathogens impacting human health, animal health and food safety. The resource informs the Federal Office of Public Health's infectious disease dashboard, starting with SARS-CoV-2 variants. SPSP also contributes to the recently inaugurated Centre for Pathogen Bioinformatics.
The platform is developed by our Clinical Bioinformatics group in collaboration with the University Hospitals of Basel, Geneva and Lausanne; VetSuisse Bern and Zurich; and the Universities of Bern and Zurich.
