Bioinformatics in Switzerland From BIONET to SIB 1984-2000

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  • Bioinformatics in SwitzerlandFrom BIONET to SIB 1984-2000

  • Obscurantism, Swiss styleBiology 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)

  • But in the meantimeAmos Bairoch teaches himself computer science, and convinces his boss (Robin Offord) that bioinformatics is a legitimate field of studyPhilipp 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 FranciscoRon Appel gets his education as a computer scientist in GenevaManuel Peitsch gets trained in molecular modeling with Jacob Maizel (NCI, Frederick)

  • Beginnings1982: Amos starts BIONET, a group of hackers, biologists and software pirates in Geneva and Lausanne1983: Staden package installed for ISREC on a computer at EPFL1983-4: microcomputers (Sirius/Victor) find their way into some biology labs in Switzerland1984: first release of the ancestor of PC-Gene1984: Manuel Peitsch (undergraduate) starts developing software on a microcomputer at ISREC

  • Problem #1: infrastructureObscurantism redux: biologists do not need mainframe computers!Real issues:Enough storage for local copies of sequence databasesEnough 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

  • Infrastructure a continuing saga1984-1998: 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 BaselEpidemiologists at the Medical FacultyPharmacists at the Natural Science FacultyThe Swiss National Scientific Computing CentreThe Ludwig Institute for Cancer Research2003: inauguration of the Vital-IT Centre, HPC facility dedicated to life science research

  • Nucleotide sequence databasesDistribution of data was a real issue had to rely on 9 mm tapes, and later CDs sent by post from HeidelbergSwiss EMBnet node (1988, Reinhard Doelz, Basel) created distribution mechanism (HASSLE, FTP), but international network bandwidth remained a major problemProper mirroring of databases has become easy only thanks to the evolution of the Internet into a well-connected, high-speed network

  • Personalities and achievementsSwitzerland 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

  • Milestones in Swiss bioinformatics - 11986: 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 computing1989: collaboration between Ron Appel and Amos Bairoch creates a bioinformatics center focussed on proteomics

  • Milestones in Swiss bioinformatics - 21990: creation of a bioinformatics group at ISRECPhilipp Bucher, with primary interest in the analysis of promoters (EPD) and of sequence motifsRoland Luethy, with primary interest in the analysis of sequence-structure relationships

  • Milestones in Swiss bioinformatics - 31991: 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 sciencesAmong first servers offering database search servicesAmong first applications of push technology (Swiss-Shop)Integration and portal concept at the core of the server

  • Milestones in Swiss bioinformatics - 41992: Gaston Gonnet and Steven Benner use the all against all protein sequence comparison approach to derive novel substitution matrices1993: 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)

  • Switzerland and the EBIBernhard Hirt was Chairman of the EMBL Council during the period when EBI was conceived and created (1991-1994)Developing the conceptOutlining funding model (problems with EC!)Selection of the site: Hinxton, because of superior Internet connectivity!Paolo Zanella (U. of Geneva & CERN) first DirectorCollaboration with SWISS-PROT at center of EBI database group activitiesAmos Bairoch and Klaus Mller members of the Advisory Board defining initial EBI activities

  • The rocky road to SIBA series of funding crises1991: both and Swiss-Prot try to get support for their activities Swiss-Prot receives some funding from SNF1996: in Basel throws in the towel, Swiss-Prot fails to receive expected EC funding international outcry1996-2000: BandAid solutions keep services going, Swiss-Prot goes commercialA series of initiativesPush from Swiss Govt to merge service activities with existing Academies or to create a fundable institutionTrying to create a consensus within and between the Universities of Lausanne and GenevaBirth of an institution30 March 1998: the Geneva Cantonal Govt sponsors the creation of a new non-profit Foundation, the SIB15 May 1998: first meeting of the SIB Foundation Council1 Jan 2000: Federal funding starts

  • Behind the scenes - GenevaRobin Offord (Professor, Biochemistry)Supported Amos and his work through many difficult timesWas instrumental in lobbying the Government for resources and supportDenis Hochstrasser (Professor, Hospital Labs)Gave the impetus for the development of proteomicsMajor force in founding SIB, Genebio, GeneprotGuy-Olivier Segond (politician)Realized the importance of bioinformatics for the development of GenevaForced Universities and political authorities to create SIB

  • Behind the scenes - LausanneBernhard Hirt (Director, ISREC)Supported development of bioinformatics at ISREC and University of LausanneProvided help for Swiss-Prot during several crisesChairman of EMBL Council, instrumental in creating and siting EBILloyd Old (Director, Ludwig Inst. Worldwide)Provided generous support to start the SIB groups in LausanneDaniel Mange (Professor of Computer Science)Realized importance of biological models for computer science (bio-inspired computing)

  • Behind the scenes - BaselThomas Bickle (Professor, Biozentrum)Obtained support and funding for first Swiss EMBnet nodeParticipated in creation of bioinformatics groupsGian-Reto Plattner (Professor of Physics and Senator)Obtained funding and support for bioinformatics at University of BaselMember of the SIB Executive BoardJoachim Seelig (Director, Biozentrum)Ensured support from the Swiss National FundAndreas Engel (Professor, Biozentrum)Oversaw development of bioinformatics at Biozentrum

  • Behind the scenes - moreCharles Kleiber, Secretary of State for Education and ResearchJean-Raoul Scherrer (Geneva University Hospital)Christian Pellegrini (U. of Geneva)Paul Herrling (Novartis)Jonathan Knowles (Glaxo, Roche)

  • Lessons learned from SIBA bottom-up approach often works better than top-downScientists working together can accomplish more than ministries handing down decisionsFunding is important, but cannot replace enthousiasm and commitmentMuch of the landmark work performed by current SIB group leaders was done outside of working hours and not specifically fundedA well-funded Institute needs professional managementIt is not enough to do good science and provide efficient services, you have to produce the documents that prove it

  • Ron AppelAmos Bairoch Philipp Bucher Manuel Peitsch Victor JongeneelNicolas GuexTorsten Schwede Mike PrimigCdric NotredameMauro Delorenzi Olivier MichielinBastien ChopardErik van Nimwegen Mihaela ZavolanMarc Robinson-Rechavi Sven Bergmann Evgeni ZdobnovBernard Moret Joerg Stelling Gaston GonnetErnest Feytmans