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Slide 1 - Bioinformatics in Switzerland From BIONET to SIB1984-2000
Slide 2 - Swiss-Prot 20th anniversaryFortaleza, Brazil Obscurantism, Swiss style Biology students are forbidden to take computer science courses (CVJ, circa 1970, Manuel Peitsch, circa 1980) Sequence analysis is not considered to be an acceptable study area for a PhD (Philipp Bucher, circa 1980) A well-known Swiss scientist claims that he can find patterns and restriction sites in a sequence faster by eye than with a computer (circa 1985)
Slide 3 - Swiss-Prot 20th anniversaryFortaleza, Brazil But in the meantime… Amos Bairoch teaches himself computer science, and convinces his boss (Robin Offord) that bioinformatics is a legitimate field of study Philipp Bucher gets trained in sequence analysis with Ed Trifonov (Weizmann Inst) and Sam Karlin (Stanford) CVJ learns basic computer science at UNC Chapel Hill and UC San Francisco Ron Appel gets his education as a computer scientist in Geneva Manuel Peitsch gets trained in molecular modeling with Jacob Maizel (NCI, Frederick)
Slide 4 - Swiss-Prot 20th anniversaryFortaleza, Brazil Beginnings 1982: Amos starts BIONET, a group of hackers, biologists and software pirates in Geneva and Lausanne 1983: Staden package installed for ISREC on a computer at EPFL 1983-4: microcomputers (Sirius/Victor) find their way into some biology labs in Switzerland 1984: first release of the ancestor of PC-Gene 1984: Manuel Peitsch (undergraduate) starts developing software on a microcomputer at ISREC
Slide 5 - Swiss-Prot 20th anniversaryFortaleza, Brazil Problem #1: infrastructure Obscurantism redux: biologists do not need mainframe computers! Real issues: Enough storage for local copies of sequence databases Enough CPU power and memory to search through databases (FASTA, then BLAST) Robust software suite for sequence analysis (GCG, Intelligenetics, Staden, etc) Administrator level access for software maintenance, database updates, etc. 1984-2003: constant battle to have access to sufficient computing resources
Slide 6 - Swiss-Prot 20th anniversaryFortaleza, Brazil Infrastructure – a continuing saga 1984-1998: repeatedly rejected attempts to use the computer center of the U. of Lausanne 1985-1988: access to the computer and software of the Friedrich Miescher Inst. (Basel), but at a cost! 1989-2003: series of agreements and collaborations with a.o. The Swiss EMBnet node in Basel Epidemiologists at the Medical Faculty Pharmacists at the Natural Science Faculty The Swiss National Scientific Computing Centre The Ludwig Institute for Cancer Research 2003: inauguration of the Vital-IT Centre, HPC facility dedicated to life science research
Slide 7 - Swiss-Prot 20th anniversaryFortaleza, Brazil Nucleotide sequence databases Distribution of data was a real issue – had to rely on 9 mm tapes, and later CDs sent by post from Heidelberg Swiss EMBnet node (1988, Reinhard Doelz, Basel) created distribution mechanism (HASSLE, FTP), but international network bandwidth remained a major problem Proper mirroring of databases has become “easy” only thanks to the evolution of the Internet into a well-connected, high-speed network
Slide 8 - Swiss-Prot 20th anniversaryFortaleza, Brazil Personalities and achievements Switzerland has been lucky to be home to a few scientists and politicians with a real vision and commitment to bioinformatics … and apologies to those I may have forgotten
Slide 9 - Swiss-Prot 20th anniversaryFortaleza, Brazil Milestones in Swiss bioinformatics - 1 1986: Swiss-Prot 1.0 !!! 1988: founding of Swiss EMBnet node, run by Reinhard Doelz (Basel) Development of HASSLE protocol, incorporating many features of modern Grid computing 1989: collaboration between Ron Appel and Amos Bairoch creates a bioinformatics center focussed on proteomics
Slide 10 - Swiss-Prot 20th anniversaryFortaleza, Brazil Milestones in Swiss bioinformatics - 2 1990: creation of a bioinformatics group at ISREC Philipp Bucher, with primary interest in the analysis of promoters (EPD) and of sequence motifs Roland Luethy, with primary interest in the analysis of sequence-structure relationships
Slide 11 - Swiss-Prot 20th anniversaryFortaleza, Brazil Milestones in Swiss bioinformatics - 3 1991: first version of Swiss-Model, an automated server for producing 3D models (Manuel Peitsch) 1991: The first Entrez client outside the US is installed in Lausanne (Manuel Peitsch) 1993: ExPASy goes live as the first Web server dedicated to life sciences Among first servers offering database search services Among first applications of “push” technology (Swiss-Shop) Integration and “portal” concept at the core of the server
Slide 12 - Swiss-Prot 20th anniversaryFortaleza, Brazil Milestones in Swiss bioinformatics - 4 1992: Gaston Gonnet and Steven Benner use the “all against all” protein sequence comparison approach to derive novel substitution matrices 1993: Swiss-2DPAGE pioneers the concept of providing a common framework for federating data from multiple sources (Ron Appel) 1996: First version of Swiss.PdbViewer, a public domain 3D viewer and modelling environment (Nicolas Guex) 1997: MOLLUSCS, an early implementation of distributed sequence database searches on a Linux PC cluster (Thomas Junier, Christian Iseli) 1998: 3D-Crunch, an effort to produce genome-scale high-quality protein structure models (Nicolas Guex, Manuel Peitsch)
Slide 13 - Swiss-Prot 20th anniversaryFortaleza, Brazil Switzerland and the EBI Bernhard Hirt was Chairman of the EMBL Council during the period when EBI was conceived and created (1991-1994) Developing the concept Outlining funding model (problems with EC!) Selection of the site: Hinxton, because of superior Internet connectivity! Paolo Zanella (U. of Geneva & CERN) first Director Collaboration with SWISS-PROT at center of EBI database group activities Amos Bairoch and Klaus Müller members of the Advisory Board defining initial EBI activities
Slide 14 - Swiss-Prot 20th anniversaryFortaleza, Brazil The rocky road to SIB A series of funding crises 1991: both EMBnet.ch and Swiss-Prot try to get support for their activities – Swiss-Prot receives some funding from SNF 1996: EMBnet.ch in Basel throws in the towel, Swiss-Prot fails to receive expected EC funding – international outcry 1996-2000: BandAid solutions keep services going, Swiss-Prot goes commercial A series of initiatives Push from Swiss Govt to merge service activities with existing Academies or to create a fundable institution Trying to create a consensus within and between the Universities of Lausanne and Geneva Birth of an institution 30 March 1998: the Geneva Cantonal Govt sponsors the creation of a new non-profit Foundation, the SIB 15 May 1998: first meeting of the SIB Foundation Council 1 Jan 2000: Federal funding starts
Slide 15 - Swiss-Prot 20th anniversaryFortaleza, Brazil Behind the scenes - Geneva Robin Offord (Professor, Biochemistry) Supported Amos and his work through many difficult times Was instrumental in lobbying the Government for resources and support Denis Hochstrasser (Professor, Hospital Labs) Gave the impetus for the development of proteomics Major force in founding SIB, Genebio, Geneprot Guy-Olivier Segond (politician) Realized the importance of bioinformatics for the development of Geneva Forced Universities and political authorities to create SIB
Slide 16 - Swiss-Prot 20th anniversaryFortaleza, Brazil Behind the scenes - Lausanne Bernhard Hirt (Director, ISREC) Supported development of bioinformatics at ISREC and University of Lausanne Provided help for Swiss-Prot during several crises Chairman of EMBL Council, instrumental in creating and siting EBI Lloyd Old (Director, Ludwig Inst. Worldwide) Provided generous support to start the SIB groups in Lausanne Daniel Mange (Professor of Computer Science) Realized importance of biological models for computer science (bio-inspired computing)
Slide 17 - Swiss-Prot 20th anniversaryFortaleza, Brazil Behind the scenes - Basel Thomas Bickle (Professor, Biozentrum) Obtained support and funding for first Swiss EMBnet node Participated in creation of bioinformatics groups Gian-Reto Plattner (Professor of Physics and Senator) Obtained funding and support for bioinformatics at University of Basel Member of the SIB Executive Board Joachim Seelig (Director, Biozentrum) Ensured support from the Swiss National Fund Andreas Engel (Professor, Biozentrum) Oversaw development of bioinformatics at Biozentrum
Slide 18 - Swiss-Prot 20th anniversaryFortaleza, Brazil Behind the scenes - more Charles Kleiber, Secretary of State for Education and Research Jean-Raoul Scherrer (Geneva University Hospital) Christian Pellegrini (U. of Geneva) Paul Herrling (Novartis) Jonathan Knowles (Glaxo, Roche)
Slide 19 - Swiss-Prot 20th anniversaryFortaleza, Brazil Lessons learned from SIB A bottom-up approach often works better than top-down Scientists working together can accomplish more than ministries handing down decisions Funding is important, but cannot replace enthousiasm and commitment Much of the landmark work performed by current SIB group leaders was done “outside of working hours” and not specifically funded A well-funded Institute needs professional management It is not enough to do good science and provide efficient services, you have to produce the documents that prove it
Slide 20 - Swiss-Prot 20th anniversaryFortaleza, Brazil Thanks guys, it has been a fun ride! Ron Appel Amos BairochPhilipp BucherManuel PeitschVictor Jongeneel Nicolas Guex Torsten SchwedeMike Primig Cédric Notredame Mauro DelorenziOlivier Michielin Bastien Chopard Erik van NimwegenMihaela Zavolan Marc Robinson-RechaviSven BergmannEvgeni Zdobnov Bernard MoretJoerg StellingGaston Gonnet Ernest Feytmans