The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation dedicated to biological and biomedical data science which federates bioinformatics activities throughout Switzerland.
The institute was established on 30 March 1998 and its mission is to provide core bioinformatics resources to the national and international life sciences research community in fields such as genomics, proteomics and systems biology, as well as to lead and coordinate the field of bioinformatics in Switzerland. It promotes research, develops open databanks and software tools, is involved in teaching and service activities and in the coordination of national and international life science infrastructure projects.
It is partly funded by the Swiss government as a research infrastructure of national importance under the Federal Act on the Promotion of Research and Innovation (RIPA).
The institute was originally created to provide a framework for stable long-term funding for both the Swiss-Prot database and the Swiss EMBnet node. Swiss-Prot in particular went through a major funding crisis in 1996, which led the leaders of the five research groups active in bioinformatics in Geneva and Lausanne, Ron Appel, Amos Bairoch, Philipp Bucher, Victor Jongeneel and Manuel Peitsch to propose the creation of SIB. <br/>
The Swiss government was at the time looking to support transdisciplinary centers of excellence in future economically important scientific fields, and provided the seed funding. Once established as a non-profit Foundation, the Institute could then apply for Federal funding: by law that support could only amount to 50% of expenses, however. The rest had to come from other sources, i.e. competitive grants and matching funds.
The SIB includes about 200 employees distributed across Switzerland (Geneva, Lausanne, Basel, Zurich), along with 700 affiliated members across most of SwitzerlandâÂÂs major academic institutions.
SIBâÂÂs 90 groups are active in fields as varied as environmental bioinformatics, proteomics, transcriptomics, genomics, systems biology, structural bioinformatics, evolutionary bioinformatics, modelling, imaging, biophysics, population genetics and clinical bioinformatics. SIB organizes a biannual international scientific meeting, the [BC]<sup>2</sup> (Basel Computational Biology Conference).
The first director of the institute was Victor Jongeneel followed by Ernest Feytmans. Ron Appel, one of its founding members, then led the institution until 2022.
SIB receives public funding to support the development of open-data databases and the long-term preservation of scientific data, especially from the Swiss State Secretariat for Education, Research and Innovation (SERI), which contributes around CHF 6.5 million per year. The development of several databases hosted by the SIB also benefited from public funding from the United States.
The institute offers a wide range of resources for the life science research community, most being open and accessible through Expasy, the SIB bioinformatics resource portal. They include:
SIB develops and maintains databases of international standing, including UniProtKB/Swiss-Prot (curated protein sequence database providing a high level of annotation), neXtProt (human-centric protein knowledge platform), SWISS-MODEL Repository (three-dimensional protein structure models), STRING (protein interaction networks for Systems Biology), SwissRegulon (genome-wide transcription regulatory networks), Eukaryotic Promoter Database (EPD), SWISS-2DPAGE (2D gel database), WORLD-2DPAGE Repository (2D gel repository), PROSITE (protein families and domains), MyHits (protein sequences and motifs), Bgee (database to retrieve and compare gene expression patterns between animal species), OpenFlu (database for human and animal influenza virus), ViralZone (portal to viral UniProtKB entries), GlycoSuiteDB (glycan database), SugarBindDB (Pathogen Sugar-Binding Database), OrthoDB (the hierarchical catalogue of eukaryotic orthologs), miROrtho (the catalogue of animal microRNA genes), ImmunoDB (insect immune-related genes and gene families) and Cellosaurus (a knowledge resource on cell lines).
SIB develops and supplies software for the global life science research community, such as SWISS-MODEL (protein structure homology modelling), SwissDrugDesign (computer-aided drug design), Melanie (2D gel analysis platform), MSight (LC-MS imaging and analysis software), OMA (Orthology Matrix), V-pipe (viral genomics pipeline), DeepView/Swiss-PdbViewer (protein visualization, modelling and analysis), and Newick utilities (high-throughput phylogenetic tree processing).
SIB manages several bioinformatics core facilities that provide informatics and statistical support, as well as services and advice to life scientists, thus enabling them to conduct their research projects and analyse the resulting data. Core facilities have been set up for genomics, transcriptomics and proteomics research. SIB also maintains the Vital-IT High Performance Computing Centre that provides computational resources, development support and consultancy to the Swiss life science community both in academia and industry. The Vital-IT infrastructure is distributed to three sites: University of Lausanne, EPFL and University of Geneva. Compute resources and bioinformatics expertise are also provided in the Basel area with sciCORE, the Basel Computational Biology Center.
One of SIBâÂÂs priorities is to promote and coordinate education in bioinformatics. SIB members are directly, or indirectly, involved in a number of bioinformatics courses at all educational levels â from high school to undergraduate and graduate degrees â as well as in specialized training for life scientists. SIB also promotes a PhD Training Network in bioinformatics, which is open to graduate students at Swiss schools of higher education. The objectives of this network are two-fold:
The SIB is also involved in bringing bioinformatics to the layman. Understanding the growing importance this relatively recent science has in todayâÂÂs society is becoming fundamental. Indeed, in not too distant a future, patients will be referring to results directly generated by bioinformatics methods. Since the year 2000, in order to heighten public awareness, the SIB has taken part in numerous science fairs, created two online magazines, an outdoor exhibition and, in 2012, a virtual exhibition.