Bioinformatics in Switzerland
From BIONET to SIB
1984-2000
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)
Swiss-Prot 20th anniversary
Fortaleza, 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)
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, 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 (SwissShop)
Integration and “portal” concept at the core of the server
Swiss-Prot 20th anniversary
Fortaleza, 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 highquality protein structure models (Nicolas Guex, Manuel
Peitsch)
Swiss-Prot 20th anniversary
Fortaleza, 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
Swiss-Prot 20th anniversary
Fortaleza, Brazil
The rocky road to SIB

A series of funding crises




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



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
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
Swiss-Prot 20th anniversary
Fortaleza, Brazil
Behind the scenes - Geneva

Robin Offord (Professor, Biochemistry)



Denis Hochstrasser (Professor, Hospital Labs)



Supported Amos and his work through many difficult times
Was instrumental in lobbying the Government for
resources and support
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
Swiss-Prot 20th anniversary
Fortaleza, Brazil
Behind the scenes - Lausanne

Bernhard Hirt (Director, ISREC)




Lloyd Old (Director, Ludwig Inst. Worldwide)


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
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)
Swiss-Prot 20th anniversary
Fortaleza, Brazil
Behind the scenes - Basel

Thomas Bickle (Professor, Biozentrum)



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)


Obtained support and funding for first Swiss EMBnet node
Participated in creation of bioinformatics groups
Ensured support from the Swiss National Fund
Andreas Engel (Professor, Biozentrum)

Oversaw development of bioinformatics at Biozentrum
Swiss-Prot 20th anniversary
Fortaleza, 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)
Swiss-Prot 20th anniversary
Fortaleza, Brazil
Lessons learned from SIB

A bottom-up approach often works better than topdown


Funding is important, but cannot replace
enthousiasm and commitment


Scientists working together can accomplish more than
ministries handing down decisions
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
Swiss-Prot 20th anniversary
Fortaleza, Brazil
Mauro Delorenzi
Olivier Michielin
Bastien Chopard
Erik van Nimwegen
Mihaela Zavolan
Ron Appel
Amos Bairoch
Philipp Bucher
Manuel Peitsch
Victor Jongeneel
Ernest Feytmans
Nicolas Guex
Torsten Schwede
Mike Primig
Cédric Notredame
Marc Robinson-Rechavi
Sven Bergmann
Evgeni Zdobnov
Bernard Moret
Joerg Stelling
Gaston Gonnet
Swiss-Prot 20th anniversary
Fortaleza, Brazil