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EMBL Programme 2012–2016 EMBL Programme 2012–2016 EMBL Programme 2012–2016 Table of Contents A. Executive summary ..................................................... 8 B. Introduction ...................................................................... 14 C. Research ........................................................................... 30 1. Backward look 2005-2009 ................................................ 30 1.1 Introduction ................................................................... 30 1.2 Selected research highlights 2005-2009 ........................ 30 1.3 Selected technology development highlights 2005-2009 .......................................................... 43 2. Research themes 2012-2016 ............................................ 48 2.1 Bridging dimensions: from molecules to cells to organisms ............................................................. 48 2.1.1 Bridging molecular and cellular resolution: From protein-protein interactions to networks in cells ................... 48 2.1.2 From cells to organisms: dynamic organisation and imaging ........................................................................ 52 2.2 Unravelling biological complexity .............................. 61 2.2.1 Illuminating complexity through experiment ................ 61 2.2.2 Analysing and representing complexity ....................... 64 2.2.3 Physical modelling and simulation .............................. 66 2.3 Exploring biological variation ..................................... 69 2.3.1. Evolution: inter-species variation ................................ 69 2.3.2. Genetic variation: intra-species variation .................... 70 EMBL Programme 2012–2016 2.3.3. Disease models and mechanisms ............................. 72 2.4 The need for and use of bioinformatics ..................... 78 2.4.1 Bioinformatics research is changing fast ..................... 78 2.4.2 Future vision ............................................................... 78 3. Initiatives to foster interdisciplinary collaboration ........... 81 3.1 EMBL Centres ............................................................... 82 3.1.1 New Centres for 2012-2016 ....................................... 83 3.1.2. The mature Centres ................................................... 86 D. Infrastructure and services to the member states .............................................................. 90 1. Bioinformatics services and databases ................................ 90 2. Structural biology facilities ................................................... 103 3. Core Facilities and IT infrastructure ...................................... 111 E. Training ............................................................................... 120 1. EMBL’s training mission and the EMBL International Centre for Advanced Training (EICAT) .................................. 120 2. EMBL International PhD Programme (EIPP) ......................... 121 3. EMBL Postdoctoral Programme .......................................... 123 4. Mentoring of young group leaders ....................................... 124 5. EMBL Visitor and Scholar Programmes ............................... 124 6. Courses, conferences and workshops .................................. 125 7. ELLS, EMBL’s link to schools and school teachers ............... 127 F. EMBL’s impact on the economy and society .. 130 1. Case studies of research driven impact ............................... 131 2. Technology Transfer ............................................................. 134 5 Table of contents 3. EMBL’s support for European bio-industries ........................ 137 4. Communication and Public Relations .................................. 139 5. Science and Society ............................................................ 142 G. Member state relations ............................................. 144 1. EMBL member states and associated member states ......... 145 2. Partnerships with member state institutions ......................... 146 3. Collaborations with institutions in non-member states ......... 150 4. EMBL Alumni ...................................................................... 151 H. European integration .................................................. 154 1. European research infrastructures ....................................... 155 2. Relations with the institutions of the European Union ........... 161 3. EIROforum: past achievements, future plans ....................... 161 4. The Initiative for Science in Europe ...................................... 162 I. Administration ................................................................... 164 1. EMBL Administration ........................................................... 164 2. Resource Development ....................................................... 170 Annexes ................................................................................... 172 Appendix B.1 EMBL’s missions, goals and strategic objectives ....................................................... 172 Appendix C.1 Selected research highlights 2005-2009 ...... 175 Appendix D.1 Research highlights from the external scientific community in structural biology ............................. 184 Appendix D.2 Research projects that have been enabled by Core Facilities 2005-2009 ................................. 187 Appendix E.1 Curriculum of the EMBL EIPP Core Course ....................................................................... 190 6 EMBL Programme 2012–2016 List of boxes C. Research Box C.2.1: Cellular systems biology of a minimal bacterium .................................................. 49 Box C.2.2: Correlative microscopy of viral and cellular budding systems .............................. 52 Box C.2.3: High throughput functional imaging for systems biology ...................................... 54 Box C.2.4: Structure and dynamics of nuclear pore complexes during assembly and transport ........................................................................................................ 56 Box C.2.5: Mapping the patterning of gene expression at single-cell resolution .................... 59 Box C.2.6: The control of developmental timing by biological clock ...................................... 60 Box C.2.7: Building predictive networks in single cells and multicellular systems................... 62 Box C.2.8: Metagenomics .................................................................................................... 65 Box C.2.9: Dissecting the forces behind organogenesis ....................................................... 68 Box C.2.10: Functional imaging in mouse models and in the clinic ....................................... 75 Box C.2.11: Studies of influenza RNA polymerase. ............................................................... 77 D. Infrastructure and services to the member states Box D.1. EBI: Data security and replication ........................................................................... 98 E. Training Box E.1. The EMBL International PhD Programme at a glance ............................................. 122 Box E.2. The EMBL Advanced Training Centre ..................................................................... 126 Box E.3. The EMBL-EBI User Training Programme .............................................................. 128 F. EMBL’s impact on the economy and society Box F.1. EMBLEM technology transfer in numbers ............................................................... 136 Box F.2. Members of the EBI Industry Programme ................................................................ 138 7 A. Executive Summary 1. EMBL’s place in Europe Science is the driving force of progress. Basic research provides the un- derstanding of the world that we need to responsibly interact with it and make sustainable use of its resources. It also lies at the heart of innovation. Throughout the world, countries have realised that their future growth and prosperity relies heavily on innovation arising from key areas of research and development (R&D). The three areas of R&D widely expected to drive prog- ress in the first half of this century are information and communication tech- nology, nanotechnology and the life sciences. In 2000 Europe, in the form of the EU governments, therefore adopted the goal of becoming the world’s leading knowledge economy. In 2002, the EU set itself the Barcelona target of spending 3% of its GDP on R&D by 2010. In actual fact, EU expenditure on R&D only increased from 1.82% of combined GDP in 2002 to 1.9% in 2009 (Science and Engineering Indicators 2010, National Board of Science) and the EU2020 Vision therefore recently renewed the target of 3% of Europe’s GDP, now proposed to be spent on R&D by 2020. In the past decade, the gap in R&D expenditure between the USA and Europe widened consider- ably and the EU countries’ R&D budget, which had been greater than the combined efforts of the Asian countries in 2002, represented only 78% of Asian expenditure in 2007 (Figure A.1.). This trend means that during the first decade of the century there has been a significant reduction in the share of world R&D activity taking place in Europe. EMBL Programme 2012–2016 Figure A.1. R&D expenditures for United States, EU and Asia 1996-2007. Source: Science and Engineering Indicators 2010, National Board of Science. If Europe is to remain competitive in this situation, it is critical that European countries invest their limited resourc- es where they have the greatest impact and obtain
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