European Marine Biological Research Centre EMBRC 4 th

European Marine Biological Research Centre EMBRC 4 th meeting of the expert group on Marine Research Infrastructure Brussels – 9 -10 December 2010 Prof Roberto Di Lauro Coordinator Dr Wiebe H. C. F. Kooistra Acting Project Manager Stazione Zoologica Anton Dohrn Villa Comunale 80121 Naples, Italy +390815833271 Info@embrc. eu www. embrc. eu 01 of 29

A distributed research infrastructure 12 Marine institutes and EMBL 8 Countries 300 Scientists Associated partners Spain, Ireland, Israel, Lithuania, Turkey 02 of 29

EMBL Germany 12 Marine institutes and EMBL SZN, Italy SAMS, UK AWI, Germany CCMAR, Portugal MBA, UK HMRC, Greece SOI, UK SBR, France Lovén, Sweden SARS, Norway OOV, France OOB, France 03 of 29

Our Vision Marine biodiversity constitutes the richest and most diverse source of organisms on earth. Exploration of marine biodiversity, enabled by the knowledge of marine genomes and by novel molecular and imaging technologies, can be pursued with integrated molecular, cellular and organismal approaches. Marine organisms will provide novel knowledge on basic biological mechanisms and on complex disciplines such as neuroscience and developmental biology. An in depth knowledge of marine organisms will shed light on the role of these organisms in sustaining global climate equilibrium. 04 of 29

Our Mission What does EMBRC wish to achieve? Create a distributed research infrastructure of coastal marine laboratories with a single entry point; Establish existing and emergent marine model organisms; Enable scientists, SMEs and industry to study the composition, functioning and diversity of marine organisms using up-to-date techniques and omics information; Build prototype equipment to maintain marine organisms in a marine-free environment; Foster integration of marine biology with the life-sciences as a whole, e. g. , biomedicine. 05 of 29

Timeline and estimated costs Preparatory phase: 3 years 2011 -2014 € 3. 900. 000 from EC Construction phase: years 3 -8 2014 -2019 € 100. 000 Operation phase: year 5 -25…. € 60. 000 / year 06 of 29

Where are we now with EMBRC? • SZN Naples coordinating partner • Start date: 01 Feb 2011, • Kickoff General Assembly Meeting: 24 -25 Feb 2011, 07 of 29

Preparatory Phase WPs Management of the preparatory phase of EMBRC: • WP 1: Coordination of the prep phase Logistical work; planning of research services and facilities: • WP 2: Strategic work: • WP 3: E-infrastructure - proof of concept: • WP 4: Construction plans: Support actions: • WP 5: Legal work. • WP 6: Financial work. • WP 7: Risk management and quality assurance. • WP 8: Logistical planning of human resources/ personnel Outreach: • WP 9: Consolidation of EMBRC, embedding with stakeholders and the wider community. • WP 10: End-user community • WP 11: Information serving and outreach: 08 of 29

Maturation process Framework/forum Marine Genomics, Mar. BEF, Euroceans Networks of Excellence (No. E) 2004 -2008 ASSEMBLE-Marine Infrastructure initiative 2009 -13 EMBRC Research Infrastructure 2011 -2025 09 of 29

ASSEMBLE-Marine, www. assemblemarine. org proof of concept for EMBRC Infrastructure initiative 2009 -2013 (2013 -2017) within 7 th Framework Program. Partner marine stations: Loven-Sweden, SBR-France, OOB-France, SAMS-UK, SZN-Italy, CCMAR-Portugal, IUI-Israel, MPI-Germany, ECIM-Chili Provide researchers across the life sciences with trans-national access to partner marine stations to utilize their marine scientific and technological infrastructure. Use locally available organisms and ecosystems in a sustainable way Cover (part of) travel and hotel costs of guests, provide hosing laboratories and services with bench fees and overheads. Include basic laboratory disposables. Make access competitive, calls for proposals every half year. On-site committees screen for do -ability of proposed projects, international selection committee selects among proposals. Preference for new users. 1 st half year call for access 100 applications, second call >150 Value of approx € 500, 000 60% new users. 10 of 29

Biological and Medical Sciences (BMS) Infrastructures BBMRI Biobanking and Biomolecular Resources Research Infrastructure EATRIS European Advanced Translational Research Infrastructure in Medicine ECRIN European Clinical Research Infrastructures Network ELIXIR European Life Science Infrastructure for Biological Information EMBRC European Marine Biological Resource Centre EU-OPENSCREEN European Infrastructure of Open Screening Platforms for Chemical Biology Euro-Bio. Imaging European Biomedical Imaging Infrastructure ERINHA European Research Infrastructure on Highly Pathogenic Agents Infrafrontier European Infrastructure for Phenotyping and Archiving of Model Mammalian Genomes INSTRUCT Integrated Structural Biology Infrastructure for Europe 11 of 29

Biological and Medical Sciences (BMS) Infrastructures European Parliament hearing BMS group 25 -26 Oct 2010. Presentation of Position Paper 12 of 29

Environmental Sciences Infrastructures LIFEWATCH EMSO: the European Multidisciplinary Seafloor Observatory EMECO: European Marine Ecosystem Observatory SIAEOS: Svalbard Integrated Arctic Earth Observing System WP 9: Consolidation of EMBRC, embedding with stakeholders and the wider community 13 of 29

One of the mission components was: Establish existing and emergent marine model organisms A non-human species, widely studied to understand biological phenomena, with the expectation that discoveries made in the model provides insight into the workings of other organisms. Lots of information available, interdisciplinary; Example: explore potential causes and treatments for human disease when human experimentation is unfeasible or unethical. The strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution. 14 of 29

Why marine animals as models? 34 fundamental animal taxa: 17 have terrestrial representatives 32 have marine representatives 13 are exclusively marine 15 of 29

Example of application Aequorea victoria is a jellyfish from which the luminescent protein aequorin and the fluorescent molecule GFP (green fluorescent protein) have been extracted, purified and cloned. These two products are now widely used in biomedical research as a fluorescent marker-protein. 2008 Nobel Prize Osamu Shimomura, Woods Hole; Martin Chalfie, Columbia U. , New York Roger Tsien, U. California San Diego 16 of 29

Why marine unicells as models? Coccolithophore Calcium carbonate Diatom Silica Dinoflagellate Organic Radiolarian Silica Examples of model organisms for RTD: electronics and nanotech industry can make intricate structures on this scale, but not under ambient pressure, temperature and p. H. 17 of 29

Why marine unicells as models? Plants Alveolates Cercozoa Stramenopiles Amoebozoa Discicristates Excavates Opisthokonts Baldauf, et al. , in Assembling the Tree of Life, 2004 18 of 29

Needs of EMBRC Issues and gaps in EMBRC development towards serving the end-user community: Marine biodiversity is global, not only European, whereas EMBRC focuses on European coastal biodiversity Establish existing and emergent marine model organisms Build prototype equipment to maintain marine organisms in a marine-free environment. Enable end-users to study marine organisms using up-to-date techniques and -omics information Calls: coordination and support actions, implementation of common solutions across infrastructures. 19 of 29

GEMBIOL link EMBRC within global network of marine institutes to give European researchers access to marine systems world-wide INFRA-2011 -3. 2: Coordination actions, conferences and studies supporting policy development, including international cooperation, for research infrastructures in all fields of Science and Technology. EMBRC HMS MBL JAMBIO Hawaii Australia NZ 20 of 29

Establish existing and emergent marine model organisms Build prototype equipment to maintain marine organisms in a marine-free environment This was part of our WP 3 in the original proposal but it has been taken out by the Commission because and Infrastructure is not doing the research, it lets the end users do the research. Develop new model organisms: Find out what are the needs of the End User Communities Determine the organisms that fit the demands Bring them into culture Develop resources Joint Research Activities focused on the needs of the external end users community. Proof of concept: ASSEMBLE 21 of 29

Enable end-users to study marine organisms using up-todate techniques and -omics information Exploration of marine biodiversity, enabled by the knowledge of marine genomes and by novel molecular and imaging technologies, can be pursued with integrated molecular, cellular and organismal approaches. Extract information from different kinds of databases that overlay and interface with genomic databases. Problem: rapid technological progress and the flood of information generated, especially in genomics approaches challenges traditional academic ways of synthesizing information across fields. DISRUPTIVE TECHNOLOGY. 22 of 29

A problem with up-to-date techniques and -omics information Disruptive technology “A technology becomes disruptive when the rate at which it improves exceed the rate at which users can adapt to the new performance. ” The Innovator's Dilemma. Clayton M. Christensen. Harvard Press. 1997 Slide by Andrew Lyall, ELIXIR Project Manager 23 of 29

Towards solutions Transferring all the data into biological knowledge across scientific disciplines requires to: - Standardize - Store - Analyze - Compare - Integrate - Visualize - Interpret The data an make them accessible for the scientists and other end-users Slides by Rolf Apweiler, EBI 24 of 29

Towards solutions Collaboration EMBRC Data Collaboration In between Facilities Diversity analysis Genomics Metagenomics Proteomics Transcriptomics Model organisms Contextual data Training Specialised databases Data processing Quality management Standardization Data curation Ontologies Data integration Visualization Data deposition Training Data Acquisition Data Management Data ELIXIR Data repositories IT technology Public access Data exchange Interoperability Standards Link to industry Training Interoperability 25 of 29

Bio. Med. Bridges Building data bridges and services between biological and medical infrastructures in Europe INFRA-2011 -2. 3. 2: Implementation of common solutions for a cluster of ESFRI infrastructures in the field of "Life sciences". “Bio. Med. Bridges will construct the e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains. ” Tasks: • Develop and harmonise standards and ontologies across the domains represented in the BMS RIs. • Implement a federated access system to the diverse data sources in the BMS RIs. • Develop and implement protocols to ensure secure and appropriate access to heterogeneous data types across the BMS RIs. Associated use cases will provide input and test-beds for each task. 26 of 29

Towards solutions of data management between EMBRC and the Environmental Sciences Infrastructures EMSO EMECO Collaboration EMBRC Data LIFEWATCH SIAEOS Facilities Diversity analysis Genomics Metagenomics Proteomics Transcriptomics Model organisms Contextual data Training Data Acquisition Specialised databases Data processing Quality management Standardization Data curation Ontologies Data integration Visualization Data deposition Training Data Management Data repositories IT technology Public access Data exchange Interoperability Standards Link to industry Training Interoperability 27 of 29

Wrap-up Support of EMBRC assessment of marine biodiversity: Link information from environmental genomics approaches with indepth information (genomics, imaging, …), of a series of reference model species. Standardize and integrate procedures of data handling across infrastructures. Enable JRA to develop emergent model organisms from across newly discovered diversity, to make them available to the end-user community. Export the Infrastructure idea globally to enable European End Users to access biodiversity elsewhere. 28 of 29

Thanks to expert group on Marine Research Infrastructure for inviting EMBRC Prof Roberto Di Lauro Coordinator Dr Wiebe H. C. F. Kooistra Acting Project Manager Stazione Zoologica Anton Dohrn Villa Comunale 80121 Naples, Italy +390815833271 Info@embrc. eu www. embrc. eu 29 of 29