1. European Marine Biological Research Centre
EMBRC
4th 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
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2. A distributed research infrastructure
12 Marine institutes and EMBL
8 Countries
300 Scientists
Associated partners
Spain, Ireland, Israel,
Lithuania, Turkey
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3. 12 Marine institutes and EMBL
EMBL Germany
12 Marine institutes and EMBL
SZN, Italy
CCMAR, Portugal
HMRC, Greece
Lovén, Sweden
SAMS, UK
MBA, UK
SOI, UK
SARS, Norway
AWI, Germany
SBR, France
OOV, France
OOB, France
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4. 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.
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5. What does EMBRC wish to achieve?
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.
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6. Timeline and estimated costs
Preparatory phase: 3 years € from EC
Construction phase: years 3-8 €
Operation phase: year 5-25…. € / year
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7. Where are we now with EMBRC?
SZN Naples coordinating partner
Start date: 01 Feb 2011,
Kickoff General Assembly Meeting: Feb 2011,
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8. Preparatory Phase WPs Management of the preparatory phase of EMBRC:
WP1: 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:
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9. Maturation process Framework/forum Marine Genomics, MarBEF, Euroceans
Networks of Excellence (NoE)
ASSEMBLE-Marine
Infrastructure initiative
EMBRC
Research Infrastructure
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10. ASSEMBLE-Marine, www.assemblemarine.org proof of concept for EMBRC
Infrastructure initiative ( ) within 7th 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.
1st half year call for access 100 applications, second call >150
Value of approx €500,000
60% new users.
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11. 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-BioImaging
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
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12. Biological and Medical Sciences (BMS) Infrastructures
European Parliament hearing
BMS group Oct Presentation of Position Paper
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13. Environmental Sciences Infrastructures
LIFEWATCH
EMSO: the European Multidisciplinary Seafloor Observatory
EMECO: European Marine Ecosystem Observatory
SIAEOS: Svalbard Integrated Arctic Earth Observing System
WP9: Consolidation of EMBRC, embedding with stakeholders and the wider community
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14. 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.
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15. Why marine animals as models?
34 fundamental animal taxa:
17 have terrestrial representatives
32 have marine representatives
13 are exclusively marine
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16. 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
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17. 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 pH.
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18. Why marine unicells as models?
Plants
Alveolates
Cercozoa
Stramenopiles
Amoebozoa
Discicristates
Excavates
Opisthokonts
Baldauf, et al., in Assembling the Tree of Life, 2004
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19. 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.
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20. GEMBIOL link EMBRC within global network of marine institutes to give European researchers access to marine systems world-wide INFRA : 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
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21. Establish existing and emergent marine model organisms
Build prototype equipment to maintain marine organisms in a marine-free environment
This was part of our WP3 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
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22. Enable end-users to study marine organisms using up-to-date 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.
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23. The Innovator's Dilemma. Clayton M. Christensen. Harvard Press. 1997
A problem with up-to-date techniques and -omics information
Disruptive technology
“A technology becomes disruptive when the rate at which it improves exceeds 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
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24. 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
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25. Specialised databases
Towards solutions
EMBRC
ELIXIR
In between
Collaboration
Collaboration
Data
Data
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 repositories
IT technology
Public access
Data exchange
Interoperability
Standards
Link to industry
Training
Data Acquisition
Data Management
Interoperability
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26. BioMedBridges Building data bridges and services between biological and medical infrastructures in Europe INFRA : Implementation of common solutions for a cluster of ESFRI infrastructures in the field of "Life sciences" .
“BioMedBridges 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.
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27. Specialised databases
Towards solutions of data management between EMBRC and the Environmental Sciences Infrastructures
EMSO
EMECO
EMBRC
LIFEWATCH
Collaboration
Data
SIAEOS
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 repositories
IT technology
Public access
Data exchange
Interoperability
Standards
Link to industry
Training
Data Acquisition
Data Management
Interoperability
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28. Wrap-up Support of EMBRC assessment of marine biodiversity:
Link information from environmental genomics approaches with in-depth 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.
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29. expert group on Marine Research Infrastructure for inviting EMBRC
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
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