Editing Swiss Institute of Bioinformatics

{{COI|date=July 2018}}
{{Use dmy dates|date=August 2020}}
{{Use British English|date=February 2014}}
{{Infobox organization
| name = SIB Swiss Institute of Bioinformatics
| abbreviation = SIB
| logo = SIB logo.jpg
| logo_alt = SIB logo
| formation = {{start date and age|df=yes|1998|03|30}}
| website = {{URL|sib.swiss}}
| headquarters = SIB Swiss Institute of Bioinformatics<br/>Quartier Sorge<br/>Batiment Amphipole<br/>1015 Lausanne<br/>Switzerland
| region = [[Switzerland]]
| type = [[Academia|academic]] [[Nonprofit organization|not-for-profit]] [[Foundation (charity)|foundation]]
| leader_name = [[Christophe Dessimoz]]
| leader_title = Joint Executive Director
}}



The '''SIB Swiss Institute of Bioinformatics''' is an [[Academia|academic]] [[Nonprofit organization|not-for-profit]] [[Foundation (charity)|foundation]] 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 science research community in fields such as [[genomics]], [[proteomics]] and [[systems biology]] as well as to lead and coordinate the field of bioinformatics in Switzerland. In particular, it promotes research, develops [[database|databanks]] and computer technologies, and is involved in teaching and service activities.

[[File:Christophe Dessimoz ISMBECCB19-108 (48722254541).jpg|thumb|Christophe Dessimoz, SIB Director]]

== History ==

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,<ref>[http://expasy.org/sprot/crisis96/crisis96.html SWISS-PROT funding crisis of 1996], on the website of the Swiss-Prot database. Last accessed 15 October 2007.</ref> 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 create SIB.<ref name=Bairoch2000>{{cite journal |author=Bairoch Amos |title=Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times! |journal=Bioinformatics |volume=16 |pages=48–64 |year=2000 |pmid=10812477 |doi=10.1093/bioinformatics/16.1.48 |issue=1 |url=http://bioinformatics.oupjournals.org/cgi/reprint/16/1/48 |url-status=dead |archive-url=https://web.archive.org/web/20050407070942/http://bioinformatics.oupjournals.org/cgi/reprint/16/1/48 |archive-date=7 April 2005|doi-access=free }} — a historical account by Bairoch.</ref> Once created, the institute could then apply for funding under a Swiss law that allows the government to fund up to 50% of expenses of vital research and teaching infrastructures.<ref>{{cite swiss law|sr=420.1|link=420_1|art=16|date=7 October 1983|fr=Loi fédérale sur la recherche|frab=LR|de=Bundesgesetz über die Forschung|deab=FG}}, al. 3b,c.</ref> 

The first director of the institute was Victor Jongeneel followed by [[Ernest Feytmans]] between 2001 and September 2007. From 1 October 2007 until July 2018, the institute was led by [[Ron Appel]], one of its founding members.<ref>[http://www.isb-sib.ch/aboutsib/organisation/management.html Management] {{Webarchive|url=https://web.archive.org/web/20101210193216/http://www.isb-sib.ch/aboutsib/organisation/management.html |date=10 December 2010 }}, on the web site of the institute.</ref><ref>[https://archive.today/20110813071731/http://www3.interscience.wiley.com/cgi-bin/abstract/117859860/ABSTRACT?CRETRY=1&SRETRY=0 "Announcement: Prof. Ron D. Appel is appointed as new Director of the Swiss Institute of Bioinformatics"], [[Proteomics (journal)|Proteomics]], 7, 2007. p. 4413.</ref> Between July 2018 and March 2022, the SIB was led by Christine Durinx and Ron Appel, as Joint Executive Directors. Starting 1st April 2022, [[Christophe Dessimoz]] replaced Christine Durinx as joint executive director.<ref>[https://www.sib.swiss/about-sib/news/10891-christophe-dessimoz-is-appointed-joint-executive-director-succeeding-christine-durinx Christophe Dessimoz is appointed Joint Executive Director, succeeding Christine Durinx], 24 January 2022</ref> Since October 2022 Christophe Dessimoz is sole Executive Director, following the retirement of Ron Appel.<ref>[https://bioalps.org/ron-appel-sibs-president-retires/ Ron Appel, SIB’s president, retires], accessed 27 November 2023</ref>

== Organisation ==

The SIB Swiss Institute of Bioinformatics is a federation of research groups with affiliated bioinformaticians at 21 SIB partner institutions, including the Universities of [[University of Basel|Basel]], [[University of Bern|Bern]], [[University of Fribourg|Fribourg]], [[University of Geneva|Geneva]], [[University of Lausanne|Lausanne]], [[University of Lugano|Lugano]] and [[University of Zurich|Zurich]], the Federal Institutes of Technology in [[École Polytechnique Fédérale de Lausanne|Lausanne]] and [[ETH Zurich|Zurich]], the [[Friedrich Miescher Institute for Biomedical Research]], the Institute of Oncology Research in [[Bellinzona]], and the Geneva School of Business Administration (HEG). Current research groups in SIB are located in [[Basel]], [[Bern]], [[Fribourg]], [[Geneva]], [[Lausanne]], [[Lugano]], [[Zürich|Zurich]], [[Yverdon-les-Bains|Yverdon]], [[Wädenswil]], [[Bellinzona]] and [[Davos]].

SIB federates more than 70 research, service and infrastructure groups, gathering more than 700 scientists in fields as varied as [[proteomics]], [[transcriptomics]], [[genomics]], [[systems biology]], [[structural bioinformatics]], [[evolutionary bioinformatics]], modelling, imaging, [[biophysics]], [[population genetics]] and clinical bioinformatics. The SIB organizes an annual international scientific meeting, the [BC]2 [[Basel Computational Biology Conference]].

== Bioinformatics resources ==

The institute offers a wide range of resources for the life science research community, most being [[Open science|open]] and accessible through [[Expasy]], the SIB bioinformatics resource portal. They include:

=== Databases ===

SIB develops and maintains databases of international standing, including [[Swiss-Prot|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 ([http://epd.vital-it.ch/ 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).

=== Software tools ===

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 software|2D gel analysis platform]]), MSight ([[Mass spectrometry software|LC-MS imaging and analysis software]]), [[Orthologous MAtrix|OMA]] (Orthology Matrix), V-pipe (viral genomics pipeline), DeepView/Swiss-PdbViewer (protein visualization, modelling and analysis), and Newick utilities (high-throughput phylogenetic tree processing).

=== Core facilities ===

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 [https://www.vital-it.ch/ Vital-IT] [[High-performance computing|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]], [[École Polytechnique Fédérale de Lausanne|EPFL]] and [[University of Geneva]]. Compute resources and bioinformatics expertise are also provided in the Basel area with [https://scicore.unibas.ch/ sciCORE], the Basel Computational Biology Center.

== Education and training ==
One of SIB’s 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 – from high school to undergraduate and graduate degrees – 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:
# To offer graduate students in bioinformatics a set of cutting-edge courses that provide both the theoretical and the practical knowledge necessary to work on a successful PhD research project in bioinformatics.
# To foster the development of a network of PhD students and promote the exchange of ideas, as well as the mobility of the students between participating institutions.

== Popular science ==
The SIB is also involved in bringing bioinformatics to the layman. Understanding the growing importance this relatively recent science has in today’s 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,<ref>[http://web.expasy.org/spotlight/ Protein Spotlight], on the Expasy server.</ref><ref>[http://web.expasy.org/prolune/ Prolune], on the Expasy server.</ref> an outdoor exhibition and, in 2012, a virtual exhibition.<ref>[http://www.chromosomewalk.ch/ Chromosome Walk], the SIB virtual exhibition.</ref>

== See also ==
* [[Lausanne campus]]
* [[List of biological databases]]
* [[Science and technology in Switzerland]]

== Notes and references ==
{{Reflist|30em}}

== External links ==
* {{Official website|http://www.sib.swiss/}}
* [https://www.expasy.org/ Swiss Bioinformatics Resource Portal (Expasy)]

{{Bioinformatics}}
{{Research institutes in Switzerland}}

{{authority control}}

{{DEFAULTSORT:Swiss Institute Of Bioinformatics}}
[[Category:Bioinformatics organizations]]
[[Category:Research institutes in Switzerland]]
[[Category:Organizations established in 1998]]