INTERFACE Special | November 2011 1 ≥ NBIC Special Rapidly growing bioinformatics community DEVELOPMENTS IN BIOINFORMATICS ≥ Interview three pioneers At the cradle Special | November 2011 Netherlands Bioinformatics Centre NBIC INTERFACE 2 Content Special | November 2011 Content EDITORIAL Interface Special Issue 3 INTERvieW The three pioneers who connected 4 two worlds NBIC Consortium 7 Toolbox 20 Bioinformatics Network 39 NBIC Research Programme, BioRange 8 Support Programme, BioAssist 14 Education Programme, BioWise 22 Dissemination & Exploitation, NBICommons 32 BIOinFORMATics Life Sciences & Health 11 IN THE FieLD OF Horticulture 17 Food & Nutrition 25 Industrial Biotechnology 35 THeses/ John van Dam 13 PORTRAITS Umesh Nandal 27 Anand Gaval 31 Jules Kerssemakers 37 RSG network 38 INTERNATIONAL Ewan Birney 18 VisiON (Cambridge, UK) Philip Bourne 19 (University of California, San Diego) Burkhard Rost 28 (TU Munich, Germany) Amos Bairoch 29 (University of Geneva, Switzerland) NBIC INTERFACE Editorial Special | November 2011 3 Interface Special Issue Board of directors ioinformatics is driving the convergence of biology B and technology disciplines, skills and infrastructures and is key to current data-intensive life sciences R&D. The broad field is under accelerated international development as biological systems turn out to be more complex than previously realised, and data sources are growing rapidly due to the ongoing flow of new key technologies. Re-use of large and information-rich datasets at an international scale is an emerging challenge. In fact, for any data driven research programme in contemporary From left to right: Jaap Heringa, scientific director of bioinformatics life sciences, bioinformatics has become indispensible. education; Ruben Kok, managing director; Barend Mons, scientific director of support & external relations; Marcel Reinders, scientific director of bioinformatics research. More often than not, the capacity and expertise needed to tackle bioinformatics challenges exceed the scope to comment on the latest developments in bioinformatics of the individual data generating institutes. To avoid within the scope of the data-intensive life sciences. stagnation of discoveries and to seize the innovation potential of its vital life sciences R&D sectors, the A list of theses combined with some portraits of our Netherlands needs a strong bioinformatics knowledge junior researchers has been included to celebrate their infrastructure. It is our mission to create an internationally key role in NBIC. They have contributed greatly to the operating centre of excellence in bioinformatics research scientific productivity of the NBIC groups, and they and education that supports life sciences R&D. have been key to the success of a broad range of our partner’s biology projects. As a growing community of In this special issue of Interface you will discover what our first generation PhD students, many have found the NBIC partners have achieved so far. Read about our one another through the Dutch Regional Student Group activities in research, support, education, dissemination, of the International Society for Computational Biology, and about the examples of where this has led to exploitation a highly active group in the international field. Well of research output by entrepreneurial bioinformaticians. trained within the NBIC faculty, the group of young NBIC All topics are illustrated with facts and figures, example scientists constitute the bioinformaticians of our near projects and comments from our collaborating biology future and will no doubt play an important role in future partners. In addition, as a reference for you to judge how discovery research. Hopefully, they will also bring the far we have come in realising our mission three pioneers lively atmosphere in Dutch bioinformatics with them in the Dutch field of bioinformatics look back on how NBIC to their jobs in academic and industrial research. started. We have invited some international colleagues Ruben Kok COLOPHON TEXT WRITING AND EDITING CONCEPT AND REALISATION Esther Thole Marian van Opstal Interface is published by the Netherlands Marga van Zundert Bèta Communicaties, The Hague Bioinformatics Centre (NBIC). The magazine Bo Blanckenburg aims to be an interface between developers Astrid van de Graaf PRINTING and users of bioinformatics applications. Marian van Opstal Bestenzet, Zoetermeer Netherlands Bioinformatics Centre INFOGRAPHICS DISCLAIMER 260 NBIC Thijs Unger Although this publication has been prepared P.O. Box 9101 with the greatest possible care, NBIC 6500 HB Nijmegen PHOTOGRAPHY cannot accept liability for any errors it t: +31 (0)24 36 19500 (office) Thijs Rooimans may contain. f: +31 (0)24 89 01798 Ivar Pel e: [email protected] iStockphoto To (un)subscribe to ‘Interface’ please send w: http://www.nbic.nl Shutterstock an e-mail with your full name, organisation and address to [email protected] EdITORIAL BOARD NBIC DESIGN AND LAY-OUT Marc van Driel, Femke Francissen Clever Franke, Utrecht Celia van Gelder, Karin van Haren t4design, Delft Rob Hooft Copyright NBIC 2011 NBIC INTERFACE 4 Founders Special | November 2011 The three pioneers who connected two worlds he biologists and computer scientists These three men stood at the cradle of NBIC, the had chosen seats at different tables, Netherlands Bioinformatics Centre, the Dutch network of and they talked in different languages. bioinformatics experts active in research, education and Jacob de Vlieg, one of the three pioneers support. How did they become involved, when and why? Tof the Netherlands Bioinformatics Centre, What were their roles? What did they learn? What have remembers the beginning of Dutch bioinformatics they enjoyed, and what has disappointed? And how do they vividly. “We brought two worlds together.” picture the future of bioinformatics in the Netherlands? THE beginning In 1999, Gert Vriend returned to the The secret of the team has to be that they complement Netherlands from Heidelberg’s EMBL to establish and lead each other so well. Because, apart from being scientists, the Centre for Molecular and Biomolecular Informatics the three pioneers of the successful Netherlands (CMBI) in Nijmegen. Vriend reminisces: “One of my tasks Bioinformatics Centre (NBIC) almost seem to come was to set up a national Dutch bioinformatics centre. It from different planets. The first is Gert Vriend, a highly was kind of spectacular because while we were working creative biochemist and for many the face of Dutch on it the project became bigger and bigger in terms of bioinformatics. His natural habitat is his laboratory, budget. But it also became increasingly troublesome working with sleeves rolled-up on model building and because everyone wanted to get aboard and people began structure determination. Then there is Bob Hertzberger, to pull strings. I saw the best and the worst of my scientific a high-energy physicist by education. The high point of colleagues in those days.” Bob Hertzberger was asked his scientific career was at CERN in the early 1980s, when to assist Vriend in calming the hornets’ nest. He believes he worked with then future Nobel Prize winners Carlo that building an institute like NBIC above all requires a Rubbia and Simon van der Meer on the discovery of W clever architect, because the trick is in structuring the and Z particles. He has been retired since 2006, but his projects in such a way that everyone is at their best place. home is a busy place with scientists walking in and out Hertzberger observes: “People may say that I’m short- for good advice. Jacob de Vlieg, the man with the suit, tempered, but when scientists share my goal, I can be a completes the trio of NBIC pioneers. He adds the business very patient listener and puzzle together all the wishes.” touch, having worked for over twenty years at Unilever Jacob de Vlieg joined NBIC’s pioneering team as the and Organon Research. Today he is the busy CEO of the chairman of the NWO research programme BioMolecular recently established eScience Centre in Amsterdam. Informatics, which was to be merged into the new research Gert Vriend “It was kind of spectacular because NBIC became bigger and bigger” NBIC INTERFACE Founders Special | November 2011 5 Jacob de Vlieg “We have brought two worlds together” centre. “The Dutch industry saw great potential in the NBIC’s structure and to compile NBIC’s applications emerging field of bioinformatics, and I was very eager to for funding. Vriend recalls: “We had fierce, but good join the scientific advisory board. But I broke out in a cold discussions. Writing the proposals took an awful lot of sweat at our first meeting with the field. Biologists and time but in the end we succeeded in shepherding them computer scientists had chosen seats at different tables, through all the procedures.” One notable hurdle to be and real communication was hard to achieve; they talked in taken was to convince the CPB, the Netherlands Bureau different languages.” for Economic Policy Analysis, to assign budgets from the Dutch natural gas revenues (BSIK) to the new field of THE WORK According to De Vlieg it was the ‘wild days’ bioinformatics. Vriend elaborates: “The competition was of bioinformatics; the sheep had still to be separated incredibly diverse; we were, for example, competing with from the goats. “Some biologists wanted the computer a plan to drill under the North Pole ice.” The commission scientists to build websites for them; they really had was also very different from the scientific boards Vriend no clue what bioinformatics was about. Therefore, it had dealt with before. “I was very happy that we had Appie was even more important to formulate our targets and Reuver of IBM in our delegation; he spoke their language.” goals precisely, not only those for the scientific projects, Above all Hertzberger remembers a very interesting time. but also those for the educational programme and the The field of biology was quite new to him but immediately computational services that NBIC would encompass.” For caught his interest. When he was asked to become the some months, Gert Vriend, Bob Hertzberger and others first director of NBIC in 2001, he was easily convinced.