4 SWISS BIOINFORMATICS | November 2011 What is bioinformatics? SWISS BIOINFORMATICS Over the past 30 years new biological research techniques, along A newsletter published by SIB Swiss Institute of Bioinformatics November 2011 with developments in information technology, have increased both Bioinformatics Resource Portal the amount and complexity of biological data. That is why scientists Contents must often apply information technology to biological problems – Editorial a science called bioinformatics. Editorial 1 More than 120 bioinformatics With the recent arrival of novel research technologies, such as Life scientists use bioinformatics to store, process and analyse next-generation sequencing, the data produced by researchers News in brief 1 large amounts of data, advancing their knowledge and under- resources for life science have increased dramatically over the past decade, and the trend Research 2 standing of biological processes. This, in turn, can lead to scientific researchers worldwide, such as: is not likely to slow down. Indeed, as sequencing techniques breakthroughs that enhance our quality of life in fields such as de- improve, costs decrease and the amount of data produced in Education and outreach 3 signing better medical treatments or improving crop yields. Translate biological experiments becomes simply daunting. Needless to say, data production by biologists is a prerequisite to progress About Bioinformatics and SIB 4 About SIB www.isb-sib.ch ProtParam in health care, and such a flow is a goldmine of information. Generating data is one thing though; the information also needs The SIB Swiss Institute of Bioinformatics is an academic not- SWISS-MODEL to be stored and interpreted so as to extract knowledge which will be key to a research project and pave the way to for-profit foundation, recognised of public utility and federating new discoveries. It is also crucial to share the available data and knowledge with the research community by way of databases which are bioinformatics activities throughout Switzerland. Its two-fold mission STRING comprehensive and well maintained. Moreover, to ensure that quality prevails over quantity, the data need to be annotated by meticulous is to provide world-class core bioinformatics resources to the life curators. Hence, more than ever, life science researchers need bioinformatics expertise and support. This is why SIB is involved in a sciences research community at both the national and international PROSITE growing number of academic and industrial research projects, and more and more research groups want to join our institute. In November levels in key fields such as genomics, proteomics and systems 2008, SIB counted 24 groups. Currently, SIB totals 31 research and service groups and six new ones have recently expressed their biology, as well as to lead and coordinate the field of bioinformatics neXtProt interest to join the institute. in Switzerland. Naturally, the need for bioinformatics support is not limited to Switzerland. Researchers all over the world need to access and share It has a long-standing tradition of producing state-of-the-art software SwissRegulon quality databases as well as other core resources, whose existence and maintenance must be secured. It is also crucial to train the next for the life sciences research community, as well as carefully- generation of bioinformaticians who will have to handle the data in the coming years. ELIXIR, the pan-European initiative to operate a annotated databases. The SIB includes 31 world-class research UniProtKB/Swiss-Prot sustainable infrastructure for managing and safeguarding biological information in Europe is an illustration of this developing awareness. and service groups that bring together more than 450 researchers The Swiss Confederation officially engaged in this major initiative by signing the Memorandum of Understanding for the construction and in the fields of proteomics, transcriptomics, genomics, systems ViralZone implementation of ELIXIR, and SIB will act as the Swiss node within this major European collaboration. Our institute is proud to share its biology, structural bioinformatics, evolutionary bioinformatics, experience and expertise and is looking forward to the results of this promising venture. modelling, imaging, biophysics and population genetics in Basel, Bern, Fribourg, Geneva, Lausanne and Zurich. SIB expertise Ron Appel, Executive Director is widely appreciated and its infrastructure and bioinformatics resources are used by life science researchers worldwide. Institutional members: News in brief Swiss Federal Institute of Technology Lausanne (EPFL) Swiss Federal Institute of Technology Zurich (ETHZ) HUPO Distinguished Achievement member of ELIXIR’s Steering Committee, sees in this collaborative University of Basel Award for Amos Bairoch international project a genuine opportunity to foster life science University of Bern research: “The successful 10 year-old collaboration between just On September 7 Amos Bairoch received the University of Fribourg two of Europe’s major life science data providers - SIB and EMBL- HUPO Distinguished Achievement Award in University of Geneva EBI - has shown what can be achieved when experts pool their Proteomics Sciences during the 10th World University of Lausanne knowledge and vision. But we need to take this further. With the Congress on Proteomics – HUPO (Human University of Zurich support of European and national funding agencies, ELIXIR will Proteome Organisation) - which was held in Ludwig Institute for Cancer Research (LICR) allow for collaboration on an unprecedented scale, and open the Geneva. This Award honours Amos Bairoch Friedrich Miescher Institute for Biomedical Research (FMI) door to the science of the future.” for his outstanding career in the field of protein Geneva Bioinformatics (GeneBio) S.A. science, particularly for the development of www.elixir-europe.org/ Hewlett Packard diverse worldwide resources such as the protein sequence and Collaborative work between the FAO and SIB to enable the A full list of SIB research projects can be found at: information database Swiss-Prot which has become indispensable www.isb-sib.ch/research/projects. for the life science research community. linking of influenza outbreaks with genomics data The FAO (Food and Agriculture Organization of the United Nations) The Swiss Confederation officially engaged with ELIXIR and SIB have started a collaboration for the development of a On 20 October, Switzerland signed Genetic Virus Module in EMPRES-i, FAO’s global animal health the Memorandum of Understanding information system. The objective of this collaboration is to create to catalyse the implementation and a methodology allowing to link the epidemiological influenza construction of ELIXIR, the pan- data available in EMPRES-i to the genomic data contained in the European initiative to operate a sus- OpenFlu database maintained by SIB. This effort is leading to a tainable infrastructure for managing novel approach for the detection and risk assessment of influenza and safeguarding biological information in Europe. Six other outbreaks through consideration of genomic information. This SIB | Swiss Institute of Bioinformatics countries (Denmark, Finland, the Netherlands, Spain, Sweden tool will support molecular epidemiology and the monitoring Quartier Sorge and the United Kingdom) and the EMBL (European Molecular of viruses with specific markers, for example associated with Bâtiment Génopode Biology Laboratory) also recently signed the memorandum and increased risks to human health. This genetic module has been CH-1015 Lausanne thus officially engaged with ELIXIR. Other countries are planning endorsed by the OIE*/FAO global network of expertise for animal Switzerland to join in the near future. SIB will act as Switzerland’s node and influenza (OFFLU). t +41 21 692 40 50 will share its experience and expertise as one of the leading www.offlu.net f +41 21 692 40 55 Swiss Bioinformatics is written by SIB Communications with bioinformatics institutes on the international scene. Ron Appel, *OIE: World Organisation for Animal Health www.isb-sib.ch contributions from SIB Members. Design and layout D. Meyer Swiss Bioinformatics 11-11 2 SWISS BIOINFORMATICS November 2011 3 Research The study also provides an explanation for the similar levels of mammals are very well reflected in their organs’ gene activities. one of its most recent applications. Neanderthal ancestry in Europe and Asia. It shows that the In other words, the comparison of gene expression levels among In AlEx, models are built using a specially- Why aren’t we all Neanderthals? hybridization range was not limited to Europe and the Near East, species for each organ reflects perfectly the position of each designed programming language that reflects but extended to the Altai mountains, North of the Himalaya. Distinct species in the mammalian evolutionary tree. biological processes. This results in an executable interbreeding events probably took place beyond the Middle East, program able to run on a computer – in this case, a “virtual flu” that The scientists also assessed at what speed each organ evolved after the split between Europeans and Asians. Such a hypothesis proceeds with the first stages of infection. by measuring the rate of gene expression change over time. predicts that further studies should reveal different components of They found that the brain is the most slowly evolving organ. This Using this particular model, the researchers