15 years, still growing and many projects for the future

A driving force in the medical field Clinical BioinformaticsThere is little research in the life sciences today without the support of bioinformatics. The same goes for the medical community with the emergence of high-throughput data-generating equipment that covers many different areas: from imaging to genomics. It is very likely that clinicians will soon be confronted with a patient’s whole genome sequence data, for example, as part of their routine. Doctors will also be increasingly faced with data provided by their patients, as technology intended for private use – not to mention the Internet – develops. All this information will have to be accessed, but also understood... which poses new analytic, technological, educational and ethical challenges – both for clinicians and scientists.

Professor Jacques Beckmann, a Belgian national and medical geneticist, joined SIB in December 2012, to develop a novel concept and lead a new initiative: Clinical Bioinformatics. Prof. Beckmann brought with him extensive experience in research and teaching.

The domain of health care is about to experience a revolution. The diversity and volume of available data regarding a person’s health will have to be integrated one way or another. Centralizing individual health data will prove to be not only inevitable, but necessary – both for the individual and the medical community. And this is where clinical bioinformatics comes in.

Health and SIBSIB is involved in two large initiatives in the field of health: the Swiss Integrative Center for Human Health (SICHH) in Fribourg and the Aging Systems Biology project (AgedBrainSYSBIO), as well as in a number of other health-oriented research projects.

SICHHSICHH, planned to start in late spring 2013 is designed to provide academics and clinicians with the latest equipment and highly specialized expert knowledge in the health sciences. The Center hopes to offer innovative small and medium enterprises, start-up companies as well as larger firms the opportunity to outsource part of their research and development activities at attractive prices and in optimum conditions. SIB will be part of this venture through Vital-IT, its high performance computing centre.

AgedBrainSYSBIOAgedBrainSYSBIO is a European collaborative research project. Fourteen academic and industrial partners will cooperate to understand human brain ageing, and the most common type of de-mentia: Alzheimer’s disease. Interactions and pathways involved in normal and disease conditions will be studied by using integrative systems biology and comparative genomics and proteomics. SIB will collaborate by offering its expertise in biocuration, computational system modelling and data integration approaches.

Training SIB’s next generation SIB Fellowship programmeIn 2012, SIB launched its first Fellowship programme to train a selection of outstanding bioinformatics students and promote bioinformatics research for the life sciences.

Thanks to the generous support and trust of its partners, the SIB Fellowship programme offers some of the best students in the world the opportunity to carry out their PhD research in one of the SIB groups located in Switzerland’s schools of higher education. The laureates of the programme receive a financial grant for three years (conditionally extendible for one year) and their research projects span bioinformatics topics that are covered by the SIB groups associated with the programme.

At the end of the first call, 103 candidates had sent in applications; 18 were short-listed and invited for interviews, which took place in late January 2013. SIB is happy to name the six young researchers who started their PhDs in 2013:

Christos Dimitrakopoulos from Greece, directed by Niko Beerenwinkel, Franziska Gruhl from Germany, directed by Henrik Kaessmann, Malgorzata Nowicka from Poland, directed by Mark Robinson, Prisni Rath from India, directed by Michael Baudis and Ioannis Xenarios, Gabriel Studer from Switzerland, directed by Torsten Schwede, Jannik Vollmer from Germany, directed by Dagmar Iber.

We thank our generous partners who made this possible, namely the Leenaards Foundation, the Swiss Foundation for Excellence and Talent in Biomedical Research, SystemsX.ch and the Universities of Geneva, Lausanne and Zurich.

SWISS BIOINFORMATICS A newsletter published by SIB Swiss Institute of Bioinformatics

ContentsEditorial 1

Latest news 1

Internal celebration 1

SIB and popular Science 1

The making of SIB 2-3

Happy Birthday wishes 4

15 years, still growing and many projects for the future 4

EditorialThe SIB Swiss Institute of Bioinformatics was founded 15 years ago. It has grown steadily ever since and foresees an exciting future. With the continuous development of efficient and cost-effective technology, the accumulation of life science data is intimidating. Bioinformatics has become essential not only in storing data, but also in accessing it and analysing it, thus paving the way to novel biological insights. Ultimately, bioinformatics will help to address some of the world’s biggest challenges: food and energy production, sustainability and environmental protection, and of course health issues. However, data and understanding data is not enough. There can be no global progress unless there is an exchange of knowledge and expertise among institutions, research groups and scien-

tists. In this respect, SIB has been – and remains – at the forefront of intercantonal and interinstitutional collaboration, which is illustrated by its continuous growth. By the end of 2013, 46 groups will have joined the Institute without whose expertise and dedica-tion, Swiss bioinformatics would not be where it is today. There is no research without funding. Thanks to the invaluable help of the Swiss government, the Federal Assembly, the State Secretariat for Education, Research and Innovation (SERI), the Swiss National Science Foundation, all those in funding roles and the unwavering support of our partner institutions, SIB currently occupies a leading position in the world of bioinformatics. In this light, and to mark the Institute’s 15th anniversary, we are publishing this special Newsletter – special both in format and content – to allow readers to discover how SIB came to be and to familiarize them with a number of key supported projects, the new SIB Fellowship programme, the latest news and a few “Happy Birthday wishes” from personalities in the government, Swiss universities and the Swiss Federal Institutes of Technology, the scientific community and the media.Ron Appel, Executive Director

“SIB is an exemplary model of intercan­tonal and interinstitutional collaboration.

By developing and maintaining the bio­informatics infrastructure, which is vital to life sciences, SIB positioned itself as a major driver of Swiss research and as an interna tional ambassador of Swiss

innovation and quality. We are proud to support SIB and wish it a Happy Birthday!”

Mauro Dell’Ambrogio, State Secretary for Education, Research and Innovation

Latest news The social life of a fire ant In January, biologist Laurent Keller (University of Lausanne) and SIB offered an answer to a question that has always intrigued scientists: “Why is it that insects which belong to the same species are able to have different social behaviours?”. The scientists studied two types of fire ant (Selenopsis invita) colonies – those that shelter only one queen, and those that shelter several queens. They discovered a “social chromosome”, i.e. a chromosomal rearrangement of no less than 600 genes. This “supergene” has a direct influence not only on the colony’s acceptance of more than one queen but also on the queens’ and the workers’ physiology, scent and behaviour. The study involved the analysis of over 100 billion nucleotides; a colossal job that was entrusted to bioinformatics experts and Vital-IT’s powerful computers.

Swiss-Israel SymposiumAt the end of January, SIB organized the second Swiss-Israel Symposium. Following a first gath-ering with our Israeli colleagues in Rehovot in January 2011, our Institute had the pleasure of welcoming guests from the Weizmann Institute of Science, the Hebrew University of Jerusalem and Tel Aviv University. A full-day session gave rise to interesting exchanges on respective current research projects. The symposium was organized in Biel/Bienne just after the SIB Days so that our guests also had the opportunity to participate and interact with a majority of SIB members.

Leenaards Award In March, Zoltán Kutalik of SIB and the University of Lausanne shared the Leenaards Foundation Award for translational biomedical research with three other researchers from the University Hospitals of Lausanne and Geneva. They will combine their expertise to find new approaches in the diagnosis and treatment of fungal infections. These infections are frequent and life threatening in hospital settings; Candida infection is the most prominent. It is important to develop novel, rapid, sensitive and specific tools to protect individuals at risk but also those who have been infected and require immediate treatment. The genomes of 300 patients suffering from Candida infection will be compared with a view to identifying regions associated with candidemia susceptibility. Such studies are expected to yield clinical applications for prevention, early diagnosis and treatment.

e-learning module for FAO and IAEA In March, SIB was commissioned by the Food and Agriculture Organization of the United Nations and the International Atomic Energy Agency to develop an e-learning module on the phylogenetics of viral pathogens of domestic animals to train veterinarians and biologists. The project was initiated following numerous requests by animal health diagnostic laboratories in developing countries, where animal pathogen sequencing has developed rapidly and data analysis has become necessary. SIB developed an e-learning module based on a decade’s experience in training and educating biologists, as well as earlier experience in e-learning. The module is accessible via a dedicated website; in areas where the internet connection is unstable, the module can be distributed on physical media such as a CD-ROM or a USB-key.

SIB Annual Report 2012The SIB Annual Report 2012 was published in May. Unlike its predecessors, it also acts as the institutional brochure. Due to SIB’s continuous growth, it was becoming difficult to keep the brochure up to date and limit its volume. So, henceforth, the annual report will not only describe the activities of each group but will also include more information on bioinformatics and the Institute.

The PDF version is available on our institutional website. A printed version of the annual report can be requested by contacting Irène Perovsek (irene.perovsek@isb­sib.ch) at SIB’s Communication department.

SIB in ShanghaiWith a view to discussing possible collaborations, an SIB delegation went to Shanghai to meet scientists from different life science and bioin-form atics organizations, including the Shanghai Institutes for Biological Sciences, the Center for Bioinformation Technology, the Chinese Novartis Institute of Biomedical Research and the Chinese Academy of Medical Sciences.

SIB turns 15!June 2013

Happy Birthday wishes

“Science is made of facts, just like a house is made out of stones. However, the accumula­tion of facts is not sufficient to make science, just like a pile of stones is not yet a house”, said Henri Poincaré, mathematician and philoso­pher in 1902. Within Swiss universities, SIB has been supporting scientists with its expertise for the last 15 years to help them turn facts into science and make of their research activities a success. This anniversary is the opportunity for universities to express all their thanks to SIB”.

Dominique Arlettaz, Rector of the University of Lausanne

“The digital simulation of complex biological processes will be the cornerstone of tomorrow’s life sciences. The “Human Brain Project” is itself an example of such a potential. The quality of SIB’s resources and its collaborators’ competencies offer our researchers cutting edge tools and solid bases on which they can found their progress”.

Patrick Aebischer, President of the Federal Institute of Technology in Lausanne (EPFL)

“It is so wonderful that the Swiss Institute of Bioinformatics celebrates its 15th anniversary. I have been in close touch with this excellent establishment ever since its inception. I regard SIB as unique in the world arena, a flagship of hard-core bioinformatics and exemplary in terms of cross­country and international collaborations. Happy birthday!”.

Doron Lancet, Head, Crown Human Genome Center, Dept. of Molecular Genetics, Weizmann Institute of Science, Israel

“Dear SIB, I wish you continuing world class leadership in bioinformatics for at least the next 15 years. Your mission to provide computa­tional and bioinformatics scientific excellence, to coordinate bioinformatics groups in Switzerland and training scientists is and will remain at the core of life science. There are amazing challenges in front of us, I can only wish you to be able to overcome... some at least! All the best and Happy Anniversary”.

Laurent Essioux, Global Head of Translational Technologies and Bioinformatics (TTB),

F. Hoffmann-La Roche Ltd.

“I’m delighted on behalf of EMBL­EBI to wish SIB

a very Happy 15th Anniversary. Over the last 15

years, EBI staff have enjoyed working very closely

with our SIB colleagues on many projects, but

especially UniProt ­ the gold standard database

for protein sequences, which empowers protein

research everywhere. SIB is a shining example

of how to coordinate life science research in

bioinformatics across the country and for the

benefit of life scientists in academia and industry

worldwide. Congratulations!”.

Janet Thornton, Director of the European

Bioinformatics Institute (EBI)

“Oracle and the Swiss Institute of Bioinformatics have been working together for many years now. It has been a fruitful journey that helped both organizations in increasing their technology excellence in the Life Sciences and in supporting the Research community to address its scientific challenges. Life Sciences is a fast­evolving domain and exciting times are ahead of us. We look forward to supporting the SIB scien­tific endeavour and contributing to its success in the years to come: Happy 15th Birthday SIB!”. Monica Marinucci, Director for Research, Oracle

SIB and popular Science: Bringing Bioinformatics to the publicSIB has always sought to explain the necessity of bioinformatics in life science research today, and its growing importance in our society. It has designed several recreational workshops for schools and science fairs, published two online popular science magazines – Protein Spotlight and Protéines à la Une – and created an outdoor exhibition, Chromosome Walk. In 2012, a virtual version of the exhibition was launched – www.chromosomewalk.ch – in English and French; the German version will appear in July 2013. SIB plans to design an itinerant exhibition which will travel to Switzerland’s schools of higher education.

SIB’s virtual exhibition: chromosomewalk.chchromosomewalk.ch is an educational site and presents the world of genes, proteins and bioinformatics. Visitors enter the exhibition at the level of a human cell’s nucleus and its 23 chromosomes. Each chromosome becomes an interactive adventure where visitors discover what the human genome is, why boys are boys, who our ancestors are, how to design a new drug, why we need vitamin C, and how bioinformatics helps in answering all these questions. Videos, links to authentic experimental lab data, scientific publications, numerous popular science articles, quizzes and a glossary enrich the visit.

“The University of Basel is proud of its long­standing partnership with SIB. Over the past years, your Institute has become a key player for the development of bioinformatics in Swiss universities, by coordinating education, fostering research, and providing essential infrastructure and resources for this booming scientific field. The Institute’s continuous success proves that we can reach very ambitious goals if we are able to coordinate our strengths and our competences”.

Antonio Loprieno, Rector of the University of Basel and President of the Rectors’

Conference of the Swiss Universities (CRUS)

“Since its inception SIB has delivered innova­tive and well­curated Bioinformatics services with the precision of Swiss clockwork. As genomic sequencing and other data­intensive technologies are reshaping the analysis of biological systems, bioinformatics will become embedded not only in research but also in our health systems. The need for robust, high­quality resources in Bioinformatics has never been greater”.Niklas Blomberg , Director of ELIXIR

“From my perspective, SIB provides an invalu­able service to the research community. ExPASy is one of the most comprehensive bioinformatics web portals available. Whenever my colleagues and I need a bioinformatics service that we’ve not used before, we turn to ExPASy and a solution is found within minutes. We are deeply grateful to SIB for this invaluable service. Best of luck for the next 15 years and beyond!”.David J. Lipman, Director of the National Center

for Biotechnology Information (NCBI), USA

“The University of Geneva is proud to have played a major part, fifteen years ago, in setting up the Swiss Institute of Bioinformatics. The renowned SwissProt / UniProt database and the first WEB server ever in the life sciences, ExPASy, were developed in large part in our faculty of medicine, thanks to the excellent work of several visionary scientists. We are thus particularly happy to acknowledge the remarkable achievements of the Swiss Institute of Bioinformatics, and we are convinced that it will continue to be highly successful”.Jean-Dominique Vassalli, Rector of the University of Geneva“Biomedical informatics is a major challenge to universities worldwide. SIB provides Swiss institutions with structures and advice to sur­mount problems”.

Daniel Wyler, Vice-rector of the University of Zurich“It is my pleasure to extend my warmest congratulations to SIB on the occasion of its 15th anniversary. Bioinformatics is a relatively new and rapidly evol ving field; however it has already esta blished itself as a key component of new biology. SIB has been a splendid success in inspiring and nurturing talent and promoting excellence in the field of bioinformatics in Switzerland. I offer my best wishes for its continued success”.

Mauro Pezzè, Dean, Faculty of Informatics, Università

della Svizzera Italiana

“Through rapid exchange of data and ideas, information tech­nology has brought scientific research and collaborations to an incredible vibrant level. SIB has taken the leading role in using and pushing these developments to accelerate scientific discovery and the exchange of ideas in life science beyond university and many other boundaries. Thanks to SIB, our research groups and students in bioinformatics are actively involved in a scientific environment that one single university could not offer, neither materially nor in making knowledge available and promoting intellectual exchange in the field”.

Guido Vergauwen, Rector of the University of Fribourg

“A couple of years ago, the University of Bern identified an urgent need to build up expertise in bioinformatics. We turned to SIB and found highly competent partners who helped us in an uncomplicated and productive way. Today, our bioinformatics group is up and running and continues to benefit from close collaborations with SIB. We are looking forward to many years of continued partnership”.

Martin Täuber, Rector of the University of Bern

“Biological sciences produce a vast amount of data. The challenge is to extract meaningful information, where an expertise of both biology and computer science is needed. SIB has established itself in the last 15 years as a worldwide valuable partner for private and university groups, providing expertise and support also in projects within the SystemsX.ch consortium”.Ralph Eichler, President of the Federal Institute of Technology in Zurich (ETH Zurich) and Chairman of the Board of Directors of SystemsX.ch

“Bioinformatics is a complex domain to explain to the layman. However, it is crucial for journalists to try to explain it when the opportunity arises, especially when it is to show that important and practical progress – particularly in the biomedical field – can arise from fundamental research which is not always accessible”.

Olivier Dessibourg, Head Science and Environment

Section at Le Temps

“SIB is an organization to be admired

since it is a true Swiss network with

international reach, of outstanding

competencies, and not only in Bio­

informatics. The future of Medicine

relies increasingly on data mana ge ment

capacity and human skills. SIB is at the

forefront of this technology paradigm

shift”.

Domenico (Nic) Alexakis, CEO Swiss

Biotech Association

SIB | Swiss Institute of BioinformaticsQuartier SorgeBâtiment GénopodeCH-1015 LausanneSwitzerlandt +41 21 692 40 50f +41 21 692 40 55www.isb-sib.ch

Swiss Bioinformatics is written by SIB Communications with contributions from SIB Members. Design and layout: Design-Meyer

Internal celebrationAlmost 400 members, as well as 40 guests, celebrated SIB’s anniversary during our SIB Days in Biel/Bienne, which were held from 28 to 29 January. SIB members were able to present their activities and participate in workshops on diverse bioinforma tics topics. Dr Gregor Haefliger, Head of National Research and Innovation, State Secretariat for Education, Research and Innovation (SERI), gave a talk about the importance of SIB within Swiss research, which was an important

and encouraging message for all SIB members. An acknowledgement of everyone’s efforts was highlighted by a party and a birthday cake, which was sliced by five of SIB’s founding members: Phillip Bucher, Joel Sussman, Amos Bairoch, Ernest Feytmans and Ron Appel. An Israeli delegation as well as 10 young scientists who had been selected to attend the first “SIB Open House” were also invited.

The SIB Days programme always includes a social activity during which our members can test their talents in a non-scientific field. This year, they were requested to express their artistic skills by representing SIB and bioinformatics on a puzzle piece. The 40 pieces were then assembled and the final SIB puzzle turned out to be a masterpiece.

From left to right: Phillip Bucher, Joel Sussman, Amos Bairoch, Ernest Feytmans, Ron Appel

4 1

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A few milestones

YEAR

“In 1962, there were three proteins whose complete sequences had been published and many of us in Sanger’s lab memorized them. In 1965, the first database began... as a printed booklet! Almost 20 years later, in Geneva, my new mass-spectrometer would not work. I can finally explain: the installing technician’s tobacco smoke was causing this. At the time though, Amos Bairoch, then a PhD student in my laboratory, was unable to carry out experiments so he turned to a more tobacco-resistant device: the computer. This was the birth of what is now the world-wide known knowledgebase UniProt/Swiss-Prot, which has over 500,000 entries.

There were always visionary people to help Swiss-Prot overcome bankruptcy, threats of legal action and attempts to eject the project from our department. I hope Amos Bairoch won’t mind my thanking them, on his behalf and mine; the outcome led to the creation of SIB”.Robin Offord

Robin Offord founded the Département de Biologie Structurale et Bioinformatique in 2005 at the Centre Médical Universitaire (Geneva). Amos Bairoch developed the protein sequence database

Swiss­Prot, and is one of the founders of SIB. Frederick Sanger was awarded a Nobel prize in chemistry

for his work on the structure of proteins in 1958.

Databases and the Internet: Swiss-Prot 1986: First release of Swiss-Prot, a protein sequence database. Stored on floppy disks.1989: Advent of CD-ROMs. Swiss-Prot is distri b uted on CDs. The process is time-consuming and expensive, and not everyone had a CD drive!1993: The Internet begins to enter the academic world. ExPASy, the first website in life sciences is created around Swiss-Prot with open access to the life science community, and links to many other bio-molecular databases across the internet.

The very beginnings of bioinformatics

and SIB

1982 YEAR

“The SNSF funding we had obtained for a two-year period came to an end. Its renewal was subject to the obtention of European funding, which was refused. We had only two months to find a solution. We called for support via ExPASy, the server that was hosting Swiss-Prot. In the following days we received thousands of emails and letters as well as the support of the national and international media. At the end of 1996, after short-term help from the Geneva Government, the SNSF granted us two years of financial support to bring Swiss-Prot through and give us some time to find a long-term solution. And this solution was the creation of the SIB Swiss Institute of Bioinformatics in 1998, which was financed by the Swiss government” Amos Bairoch, Director of SIB group CALIPHO and founding member of SIB

Funding crisis for Swiss-Prot and the beginning of SIB

1996 YEAR

5 research groups kick off SIBThe Universities of Geneva and Lausanne, The Ludwig Institute for Cancer Research, The Swiss Institute for Experimental Cancer

Research (ISREC) and Glaxo Wellcome Experimental Research

Creation of Geneva Bioinformatics (GeneBio) SA, commercial arm of SIB

First SIB logo created in few hours using ribbon diagrams.

Creation of SIB

1998 YEAR

On the occasion of its 10th anniversary, the Institute launched the SIB Young Bioinformatician Award. With a grow-ing concern to train and encourage the next generation of bioinformaticians, SIB created this award to recognize talented young scientists. The 2008 winner was post-doc Zoltán Kutalik for his work “A modular approach for integrative ana lysis of large-scale gene-expression and drug-response data”, published in May 2008 in the journal Nature Biotechnology. This tradition has been continued ever since. SIB even introduced a second Award for the Best Graduate Paper.

SIB also created an outdoor exhibition, Chromosome Walk, which was shown to the public for the first time in Geneva’s Botanical Gardens. This successful ex-hibition showcased the minuscule world of chromosomes, genes and proteins.

10 years of SIB

The making of SIB

YEAR

“Swiss-Prot was in jeopardy because of the funding crisis, and Glaxo Wellcome Experimental Research in Geneva was about to close down with many job losses. Ron Appel, Amos Bairoch, Robin Offord and myself sat together in my office thinking about the sad news and perspectives; a solution had to be found! We

then came to the conclusion that the only way out was to create a bioinformatics institute. I then contacted Guy-Olivier Segond, President of the Department of Social and Health Services of the canton of Geneva. And within 24 hours, we ob-tained 500,000 CHF to start the institute.

Problems mean solutions and solutions can thus often be found thanks to motivation and human contacts. And at that time our success was double: we had saved both the employees of Glaxo Wellcome, whom we could re-employ, and the Swiss-Prot database!

Remembering the beginnings of SIB makes me think about Merck Serono in Geneva, whose build-ings will be taken over to create a great biotech campus with the Wyss Institute. Amazing how history sometimes repeats itself!”.

Denis Hochstrasser , Vice Rector, University of Geneva, Head of the Genetic and Laboratory Medicine Department, Hôpitaux Universitaires de Genève and Member of the SIB Foundation Council

Issues often turn out to be opportunities

1997

Strong links with the international Bioinformatics Community

A key role in the construction of ELIXIRELIXIR, the European Life Science Infrastructure for Biological Informa tion, is an initiative launched by the European Union that aims to guarantee the future of biological data. Its objective is to secure funding commitments from government agencies, charities, industry and intergovernmental organizations throughout Europe, as well as to strengthen and sustain a world-class infrastructure for managing and integrating information in the life sciences. This goal can be reached by concentrating on two major factors: coord-ination and the guarantee of sustained funding.

Serving as the Swiss life science infrastructure for biological infor-mation, SIB is already at the national level what ELIXIR intends to become at the European level. To date and thanks to the support of the Swiss government, Switzerland is the only European coun-try to have such a solid bioinformatics infrastructure. SIB will act as the Swiss node in this initiative and our Institute, as a provider of various renowned resources to the international life sciences com-munity, will play an important role in the ELIXIR project.

YEAR

Other anniversaries: 10 years of Vital-IT 15 years of ExPASy 15 years of SWISS-MODEL 20 years of SWISS-2DPAGE 25 years of Prosite 30 years of MELANIEand

10 years of [BC]2 Basel Computational Biology Conference 15 years of Geneva

Bioinformatics (GeneBio) SA

15th anniversary

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2008

YEAR

SIB adopted a new visual identity by creating a new logo, launching a new institutional website and publishing its first newsletter, Swiss Bioinformatics, and its first Annual Report.

New institutional look

2009

YEAR

Researchers from the University of Lausanne and SIB applied sophisticated research methods to sequence and assemble the whole genome of Solenopsis invicta, the particularly destructive red fire ant. The species is responsible for huge damages every year across the United States. Existing methods of fire ant control have failed to halt its spread; the sequencing of its genome and the identification of 15,000 genes should help to develop new pesticides to eradicate colonies without affecting other species or the environment.

Fire Ant: the biggest ever genome sequenced

in Switzerland

2011

YEAR

SIB launched the new generation of ExPASy, a web portal that offers a point of entry to more than 130 SIB bioinformatics resources. ExPASy was first created in 1993 and rapidly became a proteomics-dedicated website used by life science researchers worldwide. Its transformation into a bioinformatics resource portal that allows for data search in various interconnected fields such as proteomics, genomics, phylogeny, systems biology, evolution, drug design and imaging allows life science researchers to optimize their research activities through access to an enriched set of high-quality data. www.expasy.org.

Launch of new generation ExPASy

Bioinformatics Resource Portal

2011

The 11th European Conference on Computational Biology took place in Basel. Organized by SIB and the Biozentrum in Basel, the conference was a tremendous success in terms of programme and attendance. Over one thou-sand participants – twice the expected attendance – from around the world came to listen to keynote speakers such as Aaron Ciechanover, Nobel Laureate in Chemistry (2004), Gene Myers, Søren Brunak and Barry Honig.

YEAR 2012

ECCB’12

SIB has many years of collaboration with the main bioinformatics institutes, such as the European Bioinformatics Institute (EBI) and the Netherlands Bioinformatics Centre (NBIC). Moreover, SIB’s expertise is renowned the world over and the Institute is invited to share its experience with many international institutes and organizations:

2008: Indonesia’s health minister, Dr Siti Fadilah Supari visited SIB. An SIB delegation visited the Scottish Bioinformatics Forum in Edinburgh. An SIB delegation visited the Netherlands Bioinformatics Centre (NBIC)

in Amsterdam.

2010: Joint symposium by SIB and IIT (Indian Institute of Technology) in New Delhi.

2011: Visit of an SIB delegation to the Weizmann Institute of Science in Rehovot, Israel. SIB signed a collaboration agreement with the King Abdullah International Medical Research

Center (KAIMRC) in Riyadh, Kingdom of Saudi Arabia with the objective to assist KAIMRC in the development of their bioinformatics section.

2013: Visit of an SIB delegation to Shanghai. SIB welcomed a delegation from Israel for the second Swiss-Israel Symposium.

Server for modelling three-dimensional protein structures

Biochemists and molecular biologists worldwide have been using this tool increasingly, appreciating its free access and easy utilization. Users simply enter an amino-acid sequence or the UniProt accession code of a protein to build the corresponding 3D model. Initiated in 1993, SWISS-MODEL has undergone constant improvement and, since 2001, its work has been overseen by Prof. Torsten Schwede’s Structural Bioinformatics Group at the Biozentrum (University of Basel) and SIB. Every year, more than 200,000 users from all around the world access the server, requesting about half a million models for protein structures.

Protein structure models find widespread applications in biomedical research, such as structure-based drug design, rational planning of functional studies, or protein engineering. swissmodel.expasy.org

YEAR 2013

20 years of SWISS-MODEL

Inaugurated on the 22nd of April 2003 and headed by Victor Jongeneel, the Lausanne-based Vital-IT centre was equipped with two high-performance clusters of 32 production servers, and eight development servers, based on Intel’s Itanium 2 processor. Life scientists were now able to run complicated software 10 to 50 times faster than before, thereby opening new research avenues. Ioannis Xenarios became director in 2007.

In less than a decade, Vital-IT has become an innovative life science informatics initiative, weaving collaborations among SIB, the Universities of Bern, Fribourg, Lausanne and Geneva, the Ludwig Institute for Cancer Research (LICR), the Swiss Federal Institute of Technology, Lausanne (EPFL), Hewlett Packard Company, Intel Corporation and Oracle. Using their complementary competencies, these partners provide fundamental science and leading edge technology for the construction of a world-class high-performance computing platform, as well as the expertise required

for solving both scientific and commercial issues.

With regard to Vital-IT in particular, the centre provides infrastructure and computational expertise to support research conducted primarily by its partners, and develops hardware and software solutions to allow research

results to be turned into marketable products.

Over the years Vital-IT has been involved in an increasing number of collaborations and scientific projects. This meets real researcher needs and confirms the central role of such a centre in life science research today. So much so that, in Northwest Switzerland, a similar centre – the Basel Computational Biology Center [BC]2 – was created and is a collaborative effort of the Biozentrum of the University of Basel, SIB and other academic biomedical research institutes in Basel.

Supporting and reinforcing the development of such centres all around Switzerland is demonstrated by SIB’s latest collaborative efforts: the

AgedBrainSysBio project and the Health Science Competence Center (see page 4).

Key dates:• April 2003 Vital-IT was officially launched by the SIB Swiss Institute of

Bioinformatics, the Universities of Lausanne and Geneva, and EPFL in cooper-ation with Hewlett-Packard, Intel Corporation and Oracle.

• 2003-2007: Victor Jongeneel was director of the Vital-IT group.• October 2007: Ioannis Xenarios became new director of Vital-IT.• Spring 2011: The Vital-IT infrastructure encompassed two new computing and

storage sites, and was distributed to three sites: UNIL, EPFL and UNIGE.• 2011: Universities of Bern and Fribourg joined Vital-IT.

YEAR

10 years of Vital-IT: SIB’s centre for high-

performance computing

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A few milestones

YEAR

“In 1962, there were three proteins whose complete sequences had been published and many of us in Sanger’s lab memorized them. In 1965, the first database began... as a printed booklet! Almost 20 years later, in Geneva, my new mass-spectrometer would not work. I can finally explain: the installing technician’s tobacco smoke was causing this. At the time though, Amos Bairoch, then a PhD student in my laboratory, was unable to carry out experiments so he turned to a more tobacco-resistant device: the computer. This was the birth of what is now the world-wide known knowledgebase UniProt/Swiss-Prot, which has over 500,000 entries.

There were always visionary people to help Swiss-Prot overcome bankruptcy, threats of legal action and attempts to eject the project from our department. I hope Amos Bairoch won’t mind my thanking them, on his behalf and mine; the outcome led to the creation of SIB”.Robin Offord

Robin Offord founded the Département de Biologie Structurale et Bioinformatique in 2005 at the Centre Médical Universitaire (Geneva). Amos Bairoch developed the protein sequence database

Swiss-Prot, and is one of the founders of SIB. Frederick Sanger was awarded a Nobel prize in chemistry

for his work on the structure of proteins in 1958.

Databases and the Internet: Swiss-Prot 1986: First release of Swiss-Prot, a protein sequence database. Stored on floppy disks.1989: Advent of CD-ROMs. Swiss-Prot is distri b uted on CDs. The process is time-consuming and expensive, and not everyone had a CD drive!1993: The Internet begins to enter the academic world. ExPASy, the first website in life sciences is created around Swiss-Prot with open access to the life science community, and links to many other bio-molecular databases across the internet.

The very beginnings of bioinformatics

and SIB

1982 YEAR

“The SNSF funding we had obtained for a two-year period came to an end. Its renewal was subject to the obtention of European funding, which was refused. We had only two months to find a solution. We called for support via ExPASy, the server that was hosting Swiss-Prot. In the following days we received thousands of emails and letters as well as the support of the national and international media. At the end of 1996, after short-term help from the Geneva Government, the SNSF granted us two years of financial support to bring Swiss-Prot through and give us some time to find a long-term solution. And this solution was the creation of the SIB Swiss Institute of Bioinformatics in 1998, which was financed by the Swiss government” Amos Bairoch, Director of SIB group CALIPHO and founding member of SIB

Funding crisis for Swiss-Prot and the beginning of SIB

1996 YEAR

5 research groups kick off SIBThe Universities of Geneva and Lausanne, The Ludwig Institute for Cancer Research, The Swiss Institute for Experimental Cancer

Research (ISREC) and Glaxo Wellcome Experimental Research

Creation of Geneva Bioinformatics (GeneBio) SA, commercial arm of SIB

First SIB logo created in few hours using ribbon diagrams.

Creation of SIB

1998 YEAR

On the occasion of its 10th anniversary, the Institute launched the SIB Young Bioinformatician Award. With a grow-ing concern to train and encourage the next generation of bioinformaticians, SIB created this award to recognize talented young scientists. The 2008 winner was post-doc Zoltan Kutalik for his work “A modular approach for integrative ana lysis of large-scale gene-expression and drug-response data”, published in May 2008 in the journal Nature Biotechnology. This tradition has been continued ever since. SIB even introduced a second Award for the Best Graduate Paper.

SIB also created an outdoor exhibition, Chromosome Walk, which was shown to the public for the first time in Geneva’s Botanical Gardens. This successful ex-hibition showcased the minuscule world of chromosomes, genes and proteins.

10 years of SIB

The making of SIB

YEAR

“Swiss-Prot was in jeopardy because of the funding crisis, and Glaxo Wellcome Experimental Research in Geneva was about to close down with many job losses. Ron Appel, Amos Bairoch, Robin Offord and myself sat together in my office thinking about the sad news and perspectives; a solution had to be found! We

then came to the conclusion that the only way out was to create a bioinformatics institute. I then contacted Guy-Olivier Segond, President of the Department of Social and Health Services of the canton of Geneva. And within 24 hours, we ob-tained 500,000 CHF to start the institute.

Problems mean solutions and solutions can thus often be found thanks to motivation and human contacts. And at that time our success was double: we had saved both the employees of Glaxo Wellcome, whom we could re-employ, and the Swiss-Prot database!

Remembering the beginnings of SIB makes me think about Merck Serono in Geneva, whose build-ings will be taken over to create a great biotech campus with the Wyss Institute. Amazing how history sometimes repeats itself!”.

Denis Hochstrasser , Vice Rector, University of Geneva, Head of the Genetic and Laboratory Medicine Department, Hôpitaux Universitaires de Genève and Member of the SIB Foundation Council

Issues often turn out to be opportunities

1997

Strong links with the international Bioinformatics Community

A key role in the construction of ELIXIRELIXIR, the European Life Science Infrastructure for Biological Informa tion, is an initiative launched by the European Union that aims to guarantee the future of biological data. Its objective is to secure funding commitments from government agencies, charities, industry and intergovernmental organizations throughout Europe, as well as to strengthen and sustain a world-class infrastructure for managing and integrating information in the life sciences. This goal can be reached by concentrating on two major factors: coord-ination and the guarantee of sustained funding.

Serving as the Swiss life science infrastructure for biological infor-mation, SIB is already at the national level what ELIXIR intends to become at the European level. To date and thanks to the support of the Swiss government, Switzerland is the only European coun-try to have such a solid bioinformatics infrastructure. SIB will act as the Swiss node in this initiative and our Institute, as a provider of various renowned resources to the international life sciences com-munity, will play an important role in the ELIXIR project.

YEAR

Other anniversaries: 10 years of Vital-IT 20 years of ExPASy 20 years of SWISS-MODEL 20 years of SWISS-2DPAGE 25 years of Prosite 30 years of MELANIEand

10 years of [BC]2 Basel Computational Biology Conference 15 years of Geneva

Bioinformatics (GeneBio) SA

15th anniversary

2013

2001

The

Bio

zent

rum

, Uni

vers

ity o

f B

asel

join

s S

IB

2008

YEAR

SIB adopted a new visual identity by creating a new logo, launching a new institutional website and publishing its first newsletter, Swiss Bioinformatics, and its first Annual Report.

New institutional look

2009

YEAR

Researchers from the University of Lausanne and SIB applied sophisticated research methods to sequence and assemble the whole genome of Solenopsis invicta, the particularly destructive red fire ant. The species is responsible for huge damages every year across the United States. Existing methods of fire ant control have failed to halt its spread; the sequencing of its genome and the identification of 15,000 genes should help to develop new pesticides to eradicate colonies without affecting other species or the environment.

Fire Ant: the biggest ever genome sequenced

in Switzerland

2011

YEAR

SIB launched the new generation of ExPASy, a web portal that offers a point of entry to more than 130 SIB bioinformatics resources. ExPASy was first created in 1993 and rapidly became a proteomics-dedicated website used by life science researchers worldwide. Its transformation into a bioinformatics resource portal that allows for data search in various interconnected fields such as proteomics, genomics, phylogeny, systems biology, evolution, drug design and imaging allows life science researchers to optimize their research activities through access to an enriched set of high-quality data. www.expasy.org.

Launch of new generation ExPASy

Bioinformatics Resource Portal

2011

The 11th European Conference on Computational Biology took place in Basel. Organized by SIB and the Biozentrum in Basel, the conference was a tremendous success in terms of programme and attendance. Over one thou-sand participants – twice the expected attendance – from around the world came to listen to keynote speakers such as Aaron Ciechanover, Nobel Laureate in Chemistry (2004), Gene Myers, Søren Brunak and Barry Honig.

YEAR 2012

ECCB’12

SIB has many years of collaboration with the main bioinformatics institutes, such as the European Bioinformatics Institute (EBI) and the Netherlands Bioinformatics Centre (NBIC). Moreover, SIB’s expertise is renowned the world over and the Institute is invited to share its experience with many international institutes and organizations:

2008: Indonesia’s health minister, Dr Siti Fadilah Supari visited SIB. An SIB delegation visited the Scottish Bioinformatics Forum in Edinburgh. An SIB delegation visited the Netherlands Bioinformatics Centre (NBIC)

in Amsterdam.

2010: Joint symposium by SIB and IIT (Indian Institute of Technology) in New Delhi.

2011: Visit of an SIB delegation to the Weizmann Institute of Science in Rehovot, Israel. SIB signed a collaboration agreement with the King Abdullah International Medical Research

Center (KAIMRC) in Riyadh, Kingdom of Saudi Arabia with the objective to assist KAIMRC in the development of their bioinformatics section.

2013: Visit of an SIB delegation to Shanghai. SIB welcomed a delegation from Israel for the second Swiss-Israel Symposium.

Server for modelling three-dimensional protein structures

Biochemists and molecular biologists worldwide have been using this tool increasingly, appreciating its free access and easy utilization. Users simply enter an amino-acid sequence or the UniProt accession code of a protein to build the corresponding 3D model. Initiated in 1993, SWISS-MODEL has undergone con-stant improvement and, since 2001, its work has been overseen by Prof. Torsten Schwede’s Computational Structural Biology Group at the Biozentrum (University of Basel) and SIB. Every year, more than 200,000 users from all around the world access the server, requesting about half a million models for protein structures.

Protein structure models find widespread applications in biomedical research, such as structure-based drug design, rational planning of functional studies, or protein engineering. swissmodel.expasy.org

YEAR 2013

20 years of SWISS-MODEL

Inaugurated on the 22nd of April 2003 and headed by Victor Jongeneel, the Lausanne-based Vital-IT centre was equipped with two high-performance clusters of 32 production servers, and eight development servers, based on Intel’s Itanium 2 processor. Life scientists were now able to run complicated software 10 to 50 times faster than before, thereby opening new research avenues. Ioannis Xenarios became director in 2007.

In less than a decade, Vital-IT has become an innovative life science informatics initiative, weaving collaborations among SIB, the Universities of Bern, Fribourg, Lausanne and Geneva, the Ludwig Institute for Cancer Research (LICR), the Swiss Federal Institute of Technology, Lausanne (EPFL), Hewlett Packard Company, Intel Corporation and Oracle. Using their complementary competencies, these partners provide fundamental science and leading edge technology for the construction of a world-class high-performance computing platform, as well as the expertise required

for solving both scientific and commercial issues.

With regard to Vital-IT in particular, the centre provides infrastructure and computational expertise to support research conducted primarily by its partners, and develops hardware and software solutions to allow research

results to be turned into marketable products.

Over the years Vital-IT has been involved in an increasing number of collaborations and scientific projects. This meets real researcher needs and confirms the central role of such a centre in life science research today. So much so that, in Northwest Switzerland, a similar centre – the Basel Computational Biology Center [BC]2 – was created and is a collaborative effort of the Biozentrum of the University of Basel, SIB and other academic biomedical research institutes in Basel.

Supporting and reinforcing the development of such centres all around Switzerland is demonstrated by SIB’s latest collaborative efforts: the

AgedBrainSysBio project and the Health Science Competence Center (see page 4).

Key dates:• April 2003 Vital-IT was officially launched by the SIB Swiss Institute of

Bioinformatics, the Universities of Lausanne and Geneva, and EPFL in cooper-ation with Hewlett-Packard, Intel Corporation and Oracle.

• 2003-2007: Victor Jongeneel was director of the Vital-IT group.• October 2007: Ioannis Xenarios became new director of Vital-IT.• Spring 2011: The Vital-IT infrastructure encompassed two new computing and

storage sites, and was distributed to three sites: UNIL, EPFL and UNIGE.• 2011: Universities of Bern and Fribourg joined Vital-IT.

YEAR

10 years of Vital-IT: SIB’s centre for high-

performance computing

2013

2 3

2006

21 S

IB g

roup

s T

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sche

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titut

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B

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(FM

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SIB

.

15 years, still growing and many projects for the future

A driving force in the medical field Clinical BioinformaticsThere is little research in the life sciences today without the support of bioinformatics. The same goes for the medical community with the emergence of high-throughput data-generating equipment that covers many different areas: from imaging to genomics. It is very likely that clinicians will soon be confronted with a patient’s whole genome sequence data, for example, as part of their routine. Doctors will also be increasingly faced with data provided by their patients, as technology intended for private use – not to mention the Internet – develops. All this information will have to be accessed, but also understood... which poses new analytic, technological, educational and ethical challenges – both for clinicians and scientists.

Professor Jacques Beckmann, a Belgian national and medical geneticist, joined SIB in December 2012, to develop a novel concept and lead a new initiative: Clinical Bioinformatics. Prof. Beckmann brought with him extensive experience in research and teaching.

The domain of health care is about to experience a revolution. The diversity and volume of available data regarding a person’s health will have to be integrated one way or another. Centralizing individual health data will prove to be not only inevitable, but necessary – both for the individual and the medical community. And this is where clinical bioinformatics comes in.

Health and SIBSIB is involved in two large initiatives in the field of health: the Swiss Integrative Center for Human Health (SICHH) in Fribourg and the Aging Systems Biology project (AgedBrainSYSBIO), as well as in a number of other health-oriented research projects.

SICHHSICHH, planned to start in late spring 2013 is designed to provide academics and clinicians with the latest equipment and highly specialized expert knowledge in the health sciences. The Center hopes to offer innovative small and medium enterprises, start-up companies as well as larger firms the opportunity to outsource part of their research and development activities at attractive prices and in optimum conditions. SIB will be part of this venture through Vital-IT, its high performance computing centre.

AgedBrainSYSBIOAgedBrainSYSBIO is a European collaborative research project. Fourteen academic and industrial partners will cooperate to understand human brain ageing, and the most common type of de-mentia: Alzheimer’s disease. Interactions and pathways involved in normal and disease conditions will be studied by using integrative systems biology and comparative genomics and proteomics. SIB will collaborate by offering its expertise in biocuration, computational system modelling and data integration approaches.

Training SIB’s next generation SIB Fellowship programmeIn 2012, SIB launched its first Fellowship programme to train a selection of outstanding bioinformatics students and promote bioinformatics research for the life sciences.

Thanks to the generous support and trust of its partners, the SIB Fellowship programme offers some of the best students in the world the opportunity to carry out their PhD research in one of the SIB groups located in Switzerland’s schools of higher education. The laureates of the programme receive a financial grant for three years (conditionally extendible for one year) and their research projects span bioinformatics topics that are covered by the SIB groups associated with the programme.

At the end of the first call, 103 candidates had sent in applications; 18 were short-listed and invited for interviews, which took place in late January 2013. SIB is happy to name the six young researchers who started their PhDs in 2013:

Christos Dimitrakopoulos from Greece, directed by Niko Beerenwinkel, Franziska Gruhl from Germany, directed by Henrik Kaessmann, Malgorzata Nowicka from Poland, directed by Mark Robinson, Prisni Rath from India, directed by Michael Baudis and Ioannis Xenarios, Gabriel Studer from Switzerland, directed by Torsten Schwede, Jannik Vollmer from Germany, directed by Dagmar Iber.

We thank our generous partners who made this possible, namely the Leenaards Foundation, the Swiss Foundation for Excellence and Talent in Biomedical Research, SystemsX.ch and the Universities of Geneva, Lausanne and Zurich.

SWISS BIOINFORMATICS A newsletter published by SIB Swiss Institute of Bioinformatics

ContentsEditorial 1

Latest news 1

Internal celebration 1

SIB and popular Science 1

The making of SIB 2-3

Happy Birthday wishes 4

15 years, still growing and many projects for the future 4

EditorialThe SIB Swiss Institute of Bioinformatics was founded 15 years ago. It has grown steadily ever since and foresees an exciting future. With the continuous development of efficient and cost-effective technology, the accumulation of life science data is intimidating. Bioinformatics has become essential not only in storing data, but also in accessing it and analysing it, thus paving the way to novel biological insights. Ultimately, bioinformatics will help to address some of the world’s biggest challenges: food and energy production, sustainability and environmental protection, and of course health issues. However, data and understanding data is not enough. There can be no global progress unless there is an exchange of knowledge and expertise among institutions, research groups and scien-

tists. In this respect, SIB has been – and remains – at the forefront of intercantonal and interinstitutional collaboration, which is illustrated by its continuous growth. By the end of 2013, 46 groups will have joined the Institute without whose expertise and dedica-tion, Swiss bioinformatics would not be where it is today. There is no research without funding. Thanks to the invaluable help of the Swiss government, the Federal Assembly, the State Secretariat for Education, Research and Innovation (SERI), the Swiss National Science Foundation, all those in funding roles and the unwavering support of our partner institutions, SIB currently occupies a leading position in the world of bioinformatics. In this light, and to mark the Institute’s 15th anniversary, we are publishing this special Newsletter – special both in format and content – to allow readers to discover how SIB came to be and to familiarize them with a number of key supported projects, the new SIB Fellowship programme, the latest news and a few “Happy Birthday wishes” from personalities in the government, Swiss universities and the Swiss Federal Institutes of Technology, the scientific community and the media.Ron Appel, Executive Director

“SIB is an exemplary model of intercan­tonal and interinstitutional collaboration.

By developing and maintaining the bio­informatics infrastructure, which is vital to life sciences, SIB positioned itself as a major driver of Swiss research and as an interna tional ambassador of Swiss

innovation and quality. We are proud to support SIB and wish it a Happy Birthday!”

Mauro Dell’Ambrogio, State Secretary for Education, Research and Innovation

Latest news The social life of a fire ant In January, the biologist Laurent Keller (University of Lausanne) and SIB offered an answer to a question that has always intrigued scientists: “Why is it that insects which belong to the same species are able to have different social behaviours?”. The scientists studied two types of fire ant (Selenopsis invita) colonies – those that shelter only one queen, and those that shelter several queens. They discovered a “social chromosome”, i.e. a chromosomal rearrangement of no less than 600 genes. This “supergene” has a direct influence not only on the colony’s acceptance of more than one queen but also on the queens’ and the workers’ physiology, scent and behaviour. The study involved the analysis of over 100 billion nucleotides; a colossal job that was entrusted to bioinformatics experts and Vital-IT’s powerful computers.

Swiss-Israel SymposiumAt the end of January, SIB organized the second Swiss-Israel Symposium. Following a first gath-ering with our Israeli colleagues in Rehovot in January 2011, our Institute had the pleasure of welcoming guests from the Weizmann Institute of Science, the Hebrew University of Jerusalem and Tel Aviv University. A full-day session gave rise to interesting exchanges on respective current research projects. The symposium was organized in Biel/Bienne just after the SIB Days so that our guests also had the opportunity to participate and interact with a majority of SIB members.

Leenaards Award In March, Zoltán Kutalik of SIB and the University of Lausanne shared the Leenaards Foundation Award for translational biomedical research with three other researchers from the University Hospitals of Lausanne and Geneva. They will combine their expertise to find new approaches in the diagnosis and treatment of fungal infections. These infections are frequent and life threatening in hospital settings; Candida infection is the most prominent. It is important to develop novel, rapid, sensitive and specific tools to protect individuals at risk but also those who have been infected and require immediate treatment. The genomes of 300 patients suffering from Candida infection will be compared with a view to identifying regions associated with candidemia susceptibility. Such studies are expected to yield clinical applications for prevention, early diagnosis and treatment.

e-learning module for FAO and IAEA In March, SIB was commissioned by the Food and Agriculture Organization of the United Nations and the International Atomic Energy Agency to develop an e-learning module on the phylogenetics of viral pathogens of domestic animals to train veterinarians and biologists. The project was initiated following numerous requests by animal health diagnostic laboratories in developing countries, where animal pathogen sequencing has developed rapidly and data analysis has become necessary. SIB developed an e-learning module based on a decade’s experience in training and educating biologists, as well as earlier experience in e-learning. The module is accessible via a dedicated website; in areas where the internet connection is unstable, the module can be distributed on physical media such as a CD-ROM or a USB-key.

SIB Annual Report 2012The SIB Annual Report 2012 was published in May. Unlike its predecessors, it also acts as the institutional brochure. Due to SIB’s continuous growth, it was becoming difficult to keep the brochure up to date and limit its volume. So, henceforth, the annual report will not only describe the activities of each group but will also include more information on bioinformatics and the Institute.

The PDF version is available on our institutional website. A printed version of the annual report can be requested by contacting Irène Perovsek (irene.perovsek@isb­sib.ch) at SIB’s Communication department.

SIB in ShanghaiWith a view to discussing possible collaborations, an SIB delegation went to Shanghai to meet scientists from different life science and bioin-form atics organizations, including the Shanghai Institutes for Biological Sciences, the Center for Bioinformation Technology, the Chinese Novartis Institute of Biomedical Research and the Chinese Academy of Medical Sciences.

SIB turns 15!June 2013

Happy Birthday wishes

“Science is made of facts, just like a house is made out of stones. However, the accumula­tion of facts is not sufficient to make science, just like a pile of stones is not yet a house”, said Henri Poincaré, mathematician and philoso­pher in 1902. Within Swiss universities, SIB has been supporting scientists with its expertise for the last 15 years to help them turn facts into science and make of their research activities a success. This anniversary is the opportunity for universities to express all their thanks to SIB”.

Dominique Arlettaz, Rector of the University of Lausanne

“The digital simulation of complex biological processes will be the cornerstone of tomorrow’s life sciences. The “Human Brain Project” is itself an example of such a potential. The quality of SIB’s resources and its collaborators’ competencies offer our researchers cutting edge tools and solid bases on which they can found their progress”.

Patrick Aebischer, President of the Federal Institute of Technology in Lausanne (EPFL)

“It is so wonderful that the Swiss Institute of Bioinformatics celebrates its 15th anniversary. I have been in close touch with this excellent establishment ever since its inception. I regard SIB as unique in the world arena, a flagship of hard-core bioinformatics and exemplary in terms of cross­country and international collaborations. Happy birthday!”.

Doron Lancet, Head, Crown Human Genome Center, Dept. of Molecular Genetics, Weizmann Institute of Science, Israel

“Dear SIB, I wish you continuing world class leadership in bioinformatics for at least the next 15 years. Your mission to provide computa­tional and bioinformatics scientific excellence, to coordinate bioinformatics groups in Switzerland and training scientists is and will remain at the core of life science. There are amazing challenges in front of us, I can only wish you to be able to overcome... some at least! All the best and Happy Anniversary”.

Laurent Essioux, Global Head of Translational Technologies and Bioinformatics (TTB),

F. Hoffmann-La Roche Ltd.

“I’m delighted on behalf of EMBL­EBI to wish SIB

a very Happy 15th Anniversary. Over the last 15

years, EBI staff have enjoyed working very closely

with our SIB colleagues on many projects, but

especially UniProt ­ the gold standard database

for protein sequences, which empowers protein

research everywhere. SIB is a shining example

of how to coordinate life science research in

bioinformatics across the country and for the

benefit of life scientists in academia and industry

worldwide. Congratulations!”.

Janet Thornton, Director of the European

Bioinformatics Institute (EBI)

“Oracle and the Swiss Institute of Bioinformatics have been working together for many years now. It has been a fruitful journey that helped both organizations in increasing their technology excellence in the Life Sciences and in supporting the Research community to address its scientific challenges. Life Sciences is a fast­evolving domain and exciting times are ahead of us. We look forward to supporting the SIB scien­tific endeavour and contributing to its success in the years to come: Happy 15th Birthday SIB!”. Monica Marinucci, Director for Research, Oracle

SIB and popular Science: Bringing Bioinformatics to the publicSIB has always sought to explain the necessity of bioinformatics in life science research today, and its growing importance in our society. It has designed several recreational workshops for schools and science fairs, published two online popular science magazines – Protein Spotlight and Protéines à la Une – and created an outdoor exhibition, Chromosome Walk. In 2012, a virtual version of the exhibition was launched – www.chromosomewalk.ch – in English and French; the German version will appear in July 2013. SIB plans to design an itinerant exhibition which will travel to Switzerland’s schools of higher education.

SIB’s virtual exhibition: chromosomewalk.chchromosomewalk.ch is an educational site and presents the world of genes, proteins and bioinformatics. Visitors enter the exhibition at the level of a human cell’s nucleus and its 23 chromosomes. Each chromosome becomes an interactive adventure where visitors discover what the human genome is, why boys are boys, who our ancestors are, how to design a new drug, why we need vitamin C, and how bioinformatics helps in answering all these questions. Videos, links to authentic experimental lab data, scientific publications, numerous popular science articles, quizzes and a glossary enrich the visit.

“The University of Basel is proud of its long­standing partnership with SIB. Over the past years, your Institute has become a key player for the development of bioinformatics in Swiss universities, by coordinating education, fostering research, and providing essential infrastructure and resources for this booming scientific field. The Institute’s continuous success proves that we can reach very ambitious goals if we are able to coordinate our strengths and our competences”.

Antonio Loprieno, Rector of the University of Basel and President of the Rectors’

Conference of the Swiss Universities (CRUS)

“Since its inception SIB has delivered innova­tive and well­curated Bioinformatics services with the precision of Swiss clockwork. As genomic sequencing and other data­intensive technologies are reshaping the analysis of biological systems, bioinformatics will become embedded not only in research but also in our health systems. The need for robust, high­quality resources in Bioinformatics has never been greater”.Niklas Blomberg , Director of ELIXIR

“From my perspective, SIB provides an invalu­able service to the research community. ExPASy is one of the most comprehensive bioinformatics web portals available. Whenever my colleagues and I need a bioinformatics service that we’ve not used before, we turn to ExPASy and a solution is found within minutes. We are deeply grateful to SIB for this invaluable service. Best of luck for the next 15 years and beyond!”.David J. Lipman, Director of the National Center

for Biotechnology Information (NCBI), USA

“The University of Geneva is proud to have played a major part, fifteen years ago, in setting up the Swiss Institute of Bioinformatics. The renowned SwissProt / UniProt database and the first WEB server ever in the life sciences, ExPASy, were developed in large part in our faculty of medicine, thanks to the excellent work of several visionary scientists. We are thus particularly happy to acknowledge the remarkable achievements of the Swiss Institute of Bioinformatics, and we are convinced that it will continue to be highly successful”.Jean-Dominique Vassalli, Rector of the University of Geneva“Biomedical informatics is a major challenge to universities worldwide. SIB provides Swiss institutions with structures and advice to sur­mount problems”.

Daniel Wyler, Vice-rector of the University of Zurich“It is my pleasure to extend my warmest congratulations to SIB on the occasion of its 15th anniversary. Bioinformatics is a relatively new and rapidly evol ving field; however it has already esta blished itself as a key component of new biology. SIB has been a splendid success in inspiring and nurturing talent and promoting excellence in the field of bioinformatics in Switzerland. I offer my best wishes for its continued success”.

Mauro Pezzè, Dean, Faculty of Informatics, Università

della Svizzera Italiana

“Through rapid exchange of data and ideas, information tech­nology has brought scientific research and collaborations to an incredible vibrant level. SIB has taken the leading role in using and pushing these developments to accelerate scientific discovery and the exchange of ideas in life science beyond university and many other boundaries. Thanks to SIB, our research groups and students in bioinformatics are actively involved in a scientific environment that one single university could not offer, neither materially nor in making knowledge available and promoting intellectual exchange in the field”.

Guido Vergauwen, Rector of the University of Fribourg

“A couple of years ago, the University of Bern identified an urgent need to build up expertise in bioinformatics. We turned to SIB and found highly competent partners who helped us in an uncomplicated and productive way. Today, our bioinformatics group is up and running and continues to benefit from close collaborations with SIB. We are looking forward to many years of continued partnership”.

Martin Täuber, Rector of the University of Bern

“Biological sciences produce a vast amount of data. The challenge is to extract meaningful information, where an expertise of both biology and computer science is needed. SIB has established itself in the last 15 years as a worldwide valuable partner for private and university groups, providing expertise and support also in projects within the SystemsX.ch consortium”.Ralph Eichler, President of the Federal Institute of Technology in Zurich (ETH Zurich) and Chairman of the Board of Directors of SystemsX.ch

“Bioinformatics is a complex domain to explain to the layman. However, it is crucial for journalists to try to explain it when the opportunity arises, especially when it is to show that important and practical progress – particularly in the biomedical field – can arise from fundamental research which is not always accessible”.

Olivier Dessibourg, Head Science and Environment

Section at Le Temps

“SIB is an organization to be admired

since it is a true Swiss network with

international reach, of outstanding

competencies, and not only in Bio­

informatics. The future of Medicine

relies increasingly on data mana ge ment

capacity and human skills. SIB is at the

forefront of this technology paradigm

shift”.

Domenico (Nic) Alexakis, CEO Swiss

Biotech Association

SIB | Swiss Institute of BioinformaticsQuartier SorgeBâtiment GénopodeCH-1015 LausanneSwitzerlandt +41 21 692 40 50f +41 21 692 40 55www.isb-sib.ch

Swiss Bioinformatics is written by SIB Communications with contributions from SIB Members. Design and layout: Design-Meyer

Internal celebrationAlmost 400 members, as well as 40 guests, celebrated SIB’s anniversary during our SIB Days in Biel/Bienne, which were held from 28 to 29 January. SIB members were able to present their activities and participate in workshops on diverse bioinforma tics topics. Dr Gregor Haefliger, Head of National Research and Innovation, State Secretariat for Education, Research and Innovation (SERI), gave a talk about the importance of SIB within Swiss research, which was an important

and encouraging message for all SIB members. An acknowledgement of everyone’s efforts was highlighted by a party and a birthday cake, which was sliced by five of SIB’s founding members: Phillip Bucher, Joel Sussman, Amos Bairoch, Ernest Feytmans and Ron Appel. An Israeli delegation as well as 10 young scientists who had been selected to attend the first “SIB Open House” were also invited.

The SIB Days programme always includes a social activity during which our members can test their talents in a non-scientific field. This year, they were requested to express their artistic skills by representing SIB and bioinformatics on a puzzle piece. The 40 pieces were then assembled and the final SIB puzzle turned out to be a masterpiece.

From left to right: Phillip Bucher, Joel Sussman, Amos Bairoch, Ernest Feytmans, Ron Appel

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