SpecialSpecial iissuessue EMBnetEMBnet CConferenceonference 22008008 – 2200thth AnniversaryAnniversary CCelebration:elebration: ProgrammeProgramme aandnd AAbstractbstract BBookook 2 EMBnet Volume 14 Nr. 3 Editorial Contents The present volume is a special number for Editorial .............................................................. 2 several reasons. Our 20th aniversary may be Nils-Einar Eriksson: “EMBnet, a brief history and a the most important one. But, for our readers it current picture” .................................................. 3 represents a chance of getting the abstracts, the program and the list of participants in the Pedro Fernandes: “The spirit of EMBnet and its 2008 EMBnet conference, on top of our usual human dimension” ............................................ 6 set of articles. In this issue we tried to obtain Laurent Falquet : “The fabulous destiny of texts about EMBnet's early steps and its role EMBnet.news ”.................................................... 8 for so many Bioinformatics users and profes- sionals, with its presence, its spirit as a support José R. Valverde: “The EMBnet e-learning server”. 9 provider, and its outreach, mainly obtained Conference Programme ................................. 15 with EMBnet.news. An article on EMBnet's - Committees..................................................... 16 e-learning portal brings you up to date with Welcome letter ................................................ 17 what our community is doing in this area. As- usual feel free to comment on EMBnet.news Tutorial & Conference Speakers....................... 18 via the portal and send us your contributions. Conference Programme ................................. 19 You may like to know that EMBnet.news is very Keynote Lectures ............................................. 25 widely spread as an electronic newsletter. The number of downloads is huge and incre- Oral Presentations ............................................ 32 asing. We hope that you enjoy the reading. Posters.............................................................. 63 Authors Index ................................................. 112 The editorial board: Erik Bongcam-Rudloff, Domenica D’Elia, Pedro Fernandes, Kimmo National & Specialist Nodes........................... 117 Mattila and Lubos Klucar. Conference Sponsors .................................... 119 Editorial Board: Erik Bongcam-Rudloff, The Linnaeus Lubos Klucar, Institute of Molecular Biology, Centre for Bioinformatics, SLU/UU. SE SAS Bratislava, SK Email: [email protected] Email: [email protected] Tel: +46-18-4716696 Tel: +421-2-59307413 Fax: +46-18-4714525 Fax: +421-2-59307416 Domenica D’Elia, Institute for Biomedical Kimmo Mattila, CSC, Espoo, FI Technologies - CNR, Bari, IT Email: [email protected] Email: [email protected] Tel: +358-9-4572708 Tel: +39-80-5929674 Fax: +358-9-4572302 Fax: +39-80-5929690 Pedro Fernandes, Instituto Gulbenkian. PT Email: [email protected] Tel: +315-214407912 Cover picture: Trulli, Martina Franca (Puglia), Fax: +315-214407970 Italy, 2008 [© Domenica D’Elia] Volume 14 Nr. 3 EMBnet 3 Nils-Einar Eriksson Domenica D'Elia Erik Bongcam-Rudloff Chairman EMBnet technical manager Node manager, Italian national node; Chairman EMBnet, Swedish national programme committee (TMPC), Institute for Biomedical Technologies, EMBnet node, Department of Animal Swedish national EMBnet node, Bari, Italy Breeding and Genetics, SLU, Uppsala Biomedical Centre (BMC), Computing Department, Uppsala time, considered an enor- EMBnet, a brief history and a current mous amount of data requiring tens of gigabytes of picture data storage. The 20th anniversary of the function resulted in huge Organizing, annotating and European Molecular Biology amounts of data. storing the data were tasks network, EMBnet, will be that the Data Library could celebrated at its Annual The new data had to be manage. But when facing the General Meeting in Martina maintained, organised and problem of making the data Franca, Italy in Sept 18-20, made accessible to the available for analysis to 2008. biomedical research com- biological scientists in all of During these years a new munity for analysis. In Europe, Europe, aspects not under science, bioinformatics, has this was taken care of by the control of the biologists had to evolved and EMBnet has Data Library group (Graham be considered. played an important role as a Cameron, Peter Stoehr and provider of bioinformatics coworkers) of the European At that time, high-speed data services for a large Molecular Biology Laboratory communication across community of researchers. (EMBL) at Heidelberg in Europe was in its infancy. Germany. EMBL, (www.embl.- Scientists wanted to use client The 20th century brought us an org), the flagship of European workstations with graphical enormous growth of know- molecular biology, was user interfaces that de- ledge in the field of life established in 1974 and is manded interaction without sciences. Research on na- supported by at present 20 delays with the server that ture's methods to code, store member states and one was providing the data or and translate genetic associate member. performing the analysis. information into biological Accessing a remote com- During the 1980-ies it was puter using an ordinary com- clear that an almost mand-line oriented terminal exponential growth of DNA- wasn't enough. Obviously, the sequence data could be solution to eliminate com- anticipated. Plans were munication delays would be evolving for the Human to use local computers with Genome Project (HUGO), i.e. local copies of the data. The the complete sequencing of sheer amount of compute the human genome. This resources needed for Euro- project alone, was expected pean research in this field also Figure 1. 1993, EMBnet AGM in Basel (CH) to produce what was, at that pointed to a distributed solu- 4 EMBnet Volume 14 Nr. 3 meetings were divided into two parts, an ordinary scientific workshop and a more formal administrative part, the Annual General Meeting (AGM). In 1991, EMBnet received a grant from the European Community within its frame- work BRIDGE (Biotechnology Research for Innovation, Development and Growth in Europe 1990-1994). The major objective of the project was Figure 2. 1997, EMBnet AGM in Bari (IT) essentially the promotion of EMBnet as a European tion. Computer cluster tech- In November 1988 a letter was computer network for bio- nology got widespread acce- sent from the EMBL Director informatics. The main topics ptance much later. General to all EMBL Council for the development of the members asking them to network were essentially three: Thus, an organized way of stimulate processes in their the setting up of a bulletin distributing the data from EMBL regions to identify regional board, the study and to all its member states had to EMBnet nodes. development of the techno- be established. The first logical tools for data distri- practical steps were taken by In May 1989 the second bution and planning of EMBL in the spring of 1988 to EMBnet Workshop was orga- specialised courses and get feedback from scientists nized at EMBL with repre- workshop. A Steering Com- around Europe. The concept sentation for all 14 EMBL mittee (SC) was nominated of a network of national nodes member states. Established during the business meeting serving each country with up- national nodes now included held in Nijmegen (NL) in July to-date biological databases France, Sweden, the UK, the 1992 whose role was to and also providing compute Netherlands, Spain, Israel, promote new projects and to resources for data analysis was Norway, Italy and Denmark. stimulate inter-node coope- formulated. It was given the Switzerland, West Germany, ration. name The European Molecular Austria, Greece and Finland This and subsequent grants Biology network, EMBnet. were gearing up. have been important for the In July 1990 the third EMBnet success of EMBnet. The initially Some highlights: workshop, the first to be intended purpose of EMBnet In July 1988 the first EMBnet organized outside Heidelberg, was fulfilled. During its first 6-8 Workshop was organized at was held at Uppsala years, the national nodes EMBL involving participants Biomedical Centre (BMC), were the centres where from EMBL, Daresbury (UK), Sweden. Since then almost all researchers in each European CITI2 (France), CAOS/CAMM European countries have country could access bio- Centre (the Netherlands) and hosted these annual EMBnet informatics data that were Hoffmann-La Roche. workshops. Quite early the kept in perfect synchrony with An early focus was on network protocols for the distribution of data from the EMBL Data Library. At first DECNET was intended as the data carrier but it was soon to be replaced by TCP/IP. A set of client-server data transfer programs, xNDT, was later developed at the Swedish node. Another important issue on the agenda was the preparation of an approach to the European Community to apply for a grant for a pilot EMBnet project. Figure 3. 1999, EMBnet AGM in Brugge (BE) Volume 14 Nr. 3 EMBnet 5 system (http://edu.embnet.- org). The new system is based on the Moodle (http://moo- dle.org) software with a few plugin extensions and provides facilities to support on-site training as well as a rich remote training facility for on line learning. The e-Learning server is offered as a com- munity service providing trai- ning material and experience for end-users, such as bioinfor- maticians, teachers and life science researchers in