Council of Governor meeting, 4th October 2005, Berlin, De

1
Welcome to the Council of Governors Marine
Genomics Europe NoE 4th of October 2005 -
Berlin Max Planck Institute for Molecular Genetics
Council of Governor meeting, 4th October 2005,
Berlin, De
General presentation of the project
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EU-FP6- Network of Excellence
EU-funded networks of excellence (NoE) are
intended to tackle the fragmentation of European
research by helping to structure and shape the
way research is conducted in a particular field.
Council of Governor meeting, 4th October 2005,
Berlin, De
Key words Defragmentation Long term
integration Sharing platforms, technologies
Knowledge portfolio Spreading activities Gender
issues
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Marine Genomics Europe EU-FP6- Network of
Excellence
Coordinated by Catherine Boyen, SBR-CNRS, Fr
"Marine Genomics Europe" is a crossroads between
Life Sciences, Ecology, Environment,
Bioinformatics and High Technologies within a
multicultural European network. MGE is a Network
of excellence devoted to the development,
utilization and spreading of high-throughput
approaches for the investigation of the biology
of marine organisms.
3 Main objectives
Council of Governor meeting, 4th October 2005,
Berlin, De

• Integration
• Make use of bioinformatics tools for everyone
• Share Technology Platforms
• Share enabling technologies
• Gender Action Plan
• Common Management Platform

• Spreading
• Educate early stage researchers in the field
• Educate marine biologist to bioinformatics and
  genomics tools
• Educate scientists to Intellectual property
• Educate the Society about marine genomics and
  sciences

• Jointly Executed Research programme
• Join traditional marine biology with
  genomics
• Implement high-throughput technologies

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Statistics of Marine Genomics Europe
45 institutions (2 SMEs)
Integration
16 countries
450 members
10 M
2004 -2008
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Time table
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JOINT PROGRAMME of Activity 1
Integration
Science Community
Council of Governor meeting, 4th October 2005,
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Companies
Policy Makers
Society
Knowledge Management System
Virtual Laboratory
13 WP
8 WP
4 WP
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Management Marine Genomics Europe
EU Cathy Eccles Executive Officer
Council of Governors 16 members
Scientific project management Catherine
Boyen CNRS-SBR, 2
Financial Administrative Coordination, Legal
IP affairs FIST, 1
Scientific Steering Committee (23) Consortiums
decision JPA Scientific and Technological
Coordinators National representatives
Scientific council (consultatory, 5 mb)
Council of Governor meeting, 4th October 2005,
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IPUD committee
Bioinformatic committee
Node project Committees -Microbial -Algal -EDD
-Fish Shellfish
Technological Platform committee
Advisory and implementation bodies (6 members)
Training and Education Council
Research
Integration
Spreading
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The Council of Governors
The Council of Governors (Paragraph 4.1.1. p12,
Consortium agreement for the network of
excellence Marine Genomics Europe under the
sixth framework Programme (European contract N
505403). Composition The Council of Governors
is composed of high level representatives from
the participating countries. Contractors from
each country appoint a single representative from
their organisations Thus, each country should be
represented i.e. 16 members have to be
nominated. In the case of several institutions
within one country, only one representative would
be nominated. Role The Council of Governors is
an advisory body and shall provide the network
with a discussion forum that will help to
coordinate the networks policy with that of the
national research agencies. The Council of
Governors shall nevertheless have decision-making
responsibilities and decide by unanimous vote and
when appropriate minus that of the country
representative concerned upon inclusion,
withdrawal and exclusion of a Contractor.
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The Council of Governors
To understand what is a Network of Excellence and
what is going on in this ambitious project
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To help us in reaching a long term integration
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• Integrating Activities

• Jointly Executed Research

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• Spreading Activities

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Integrating Activities

• Technological Platform Project

• Bioinformatic Project

• Jointly Develop Enabling Technologies

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• Gender Action Plan

• Exploratory Workshops

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Technology Platforms Project (1)
Gaining Collectively acess to major Genomics
Centres

• Objective get support from European Genomics
  Centres
• Offer a competitive price for sequencing
• Provide us with expertise for sequencing and
  annotation of genomes
• Fund a few projects (call for applications)

Marine cytophagalesBacteriea specialized for
polymer-degradation MPI-MM, CNRS and University
of Alicante
Council of Governor meeting, 4th October 2005,
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Alvinella pompejanaA thermotolerant polychete
annelid
Phaeodactylum tricornutumPhotosynthetic Marine
Diatom
Ectocarpus siliculosusA large scale genome
project for the brown algae
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Technology Platforms Project (2)
WP 22
Platform sharing
9 platforms currently active

• High throughput Facilities
• BAC libraries construction
• Sequencing
• Microarrays
• Genotyping
• Imaging

• MPI MG, Berlin
• MPI MM, Bremen
• AWI, Bremerhaven
• Univ. Bielfeld
• CRIBI Biotech Centre, Padova
• SZN, Naples
• BAS, Cambridge
• Univ. Of Birmingham
• SBR-CNRS, Roscoff

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Access scheme
Technology Platform Project (3)

• Three Schemes are available for Access to
  Technology Platforms
• Bursary scheme for short visits to the Technology
  Platforms.
• Technology platform visiting fellowships. Longer
  visits for up to 1 month
• - Technology platform consumables grant.
  consumables towards a research project.

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• Evaluation by Access Scheme committee
• Final validation by the SSC

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Integrating Activities

• Technological Platform Project

• Jointly Develop Enabling Technologies

• Bioinformatic Project

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• Gender Action Plan

• Exploratory Workshops

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Jointly Develop Enabling Technologies (1)
Flagship projects Promote integration and
support scientific excellence through the funding
of a few ambitious projects which are
inter-nodal and focus on cross-conceptual
barriers of organism, discipline or research
groups. Projects should also aim to develop
enabling technologies (i.e. common tools,
collections, protocols etc..)
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• First Call in April 2004 (funds 611,000 over 3
  years)

• Second Call in July 2005 (funds available
  400,000 over 3 years)

External evaluation
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Jointly Develop Enabling Technologies (2)
Synchips WP 27-a Combined microarray
hybridisation and transposon mutagenesis to study
the impact of environmental stresses on marine
Synechococcus. Partners 45, 2, 8, 17 Hebrew
University, Eilat 340,000
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Ficell WP 27-b Develop molecular tools towards
the identification of gene function in Fish.
Microinjection of RNAi, large scale in situ
hybridizations, cell cultures/lines. Partners
21, 34, 25, 35 271, 450
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Integrating Activities

• Technological Platform Project

• Jointly Develop Enabling Technologies

• Bioinformatic Project

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• Gender Action Plan

• Exploratory Workshops

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BioInformatics Centre (1)
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CEBITECH, Bielefeld University, Germany
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BioInformatics Centre (5)

• view all MGE data
• organized as separate projects
• manage access
• delegated authority

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https//www.cebitec.uni-bielefeld.de/groups/brf/so
ftware/mge-portal/
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Integrating Activities

• Technological Platform Project

• Jointly Develop Enabling Technologies

• Bioinformatic Project

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• Gender Action Plan

• Exploratory Workshops

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Gender Action Plan
Numbers MGE Consortium 30 women -49 PhD
students -81 post-doc and senior
researchers -19 research group leaders,
directors professors
WP 24
The under-representation of women in the natural
sciences is also true within MGE
Every MGE participant is a member of the GAP
Workpackage
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• Day care fellowships
• Mentoring Programme (Web site modules)
• The main objectives are to strengthen
  understanding, extend networking, and develop
  effective strategies for the advancement of women
  
• One-month fellowships for young women
• Short fellowships each year for outstanding
  women scientists (1,800 for 1 month). The main
  objective is to ensure that gifted young women
  scientists are actively promoted. 7 funded
  projects, 14,400

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Integrating Activities

• Technological Platform Project

• Bioinformatic Project

• Jointly Develop Enabling Technologies

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• Gender Action Plan

• Exploratory Workshops

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Exploratory Workshops
Aim Foster integration within scientists from
the different nodes. These Workshops are expected
to demonstrate the potential to open up new
directions in Marine Genomics research and
should also show potential for developing future
collaborative actions.
 Stress responses to environmental
variations  Cambridge UK September 25-27th
Alex Rogers 12
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 Genomics approaches to the study of
evolution  Roscoff, F, February 2006 2-3 rd
Pedro Martinez 35
  Annotating Genomes problems Strategies with
special reference to the Sea Urchin
Genome  Villefranche, F Mike Thorndyke, 38
Late October publish a call for new Exploratory
workshops
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• Integrating Activities

• Jointly Executed Research

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• Spreading Activities

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Jointly Executed Research 1
Jointly Executed Research 2
Comparative Genomics W. Hess 45
Functional Genomics C. Bowler 2
Environmental Genomics J. Olsen 28
Area
Project
Microbial Node R. Amann 4
WP-1 C. Pedros-Alios 33
WP-2 W. Hess 45
WP-3 R. Amann 4
WP4 H. Moreau 2
WP 5 M. Cock 2
WP-6 G. Pearson 21
Algal Node H. Moreau 2
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WP-10 F. Patti 22
WP-9 A. Rogers 12
WP-9 C. Cook 12
Evolution, Development Biodiversity Node M.
Thorndyke 38
WP7 P. Martinez 35
WP8 M-I Armone 22
WP-11 F. Viard, 2 22
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• Jointly Executed Research

• The Microbial Node

• The Algal Node

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• The Evolution Development and Diversity Node

• The Fish and Shell Fish Node Node

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Microbial Node (1)

• Comparative Genomics
• Sequencing of the marine bacterium Gramella
  forsetii
• a snow bacterium (MPI Berlin 65 000 readings,
  genome characteristics 3.7 M bp, 3500 genes)
• involved in polymer-degradation

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Microbial Node (2)

• Functional Genomics
• Construction and optimization of a micro-arrays
  for heterotrophic (Rhodopirellula baltica) and
  photoautotrophic bacteria (Synechococcus)
• Identification and characterization of the
  expression of their stress-specific genes.
• Microarray study accompanied by a parallel
  quantification of transcript levels by
  alternative methods

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Microbial Node (3) Plans for JER 2
Improved European integration by joint
annotation jamborees using common bioinformatic
platforms (GenDB) and accepted standards
cross-disciplinary training of marine biologists
in bioinformatics.
Syn-Chips will reveal niche-adaptation of the
globally important cyanobacterium Synechococcus
a strong European consortium will enter a phase
of international collaboration with US/Japanese
partners.
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Spreading of metagenomics on both planktonic and
benthic sites to various European labs sharing
of expertise and libraries discovery of novel
genes in extreme environments.
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• Jointly Executed Research

• The Microbial Node

• The Algal Node

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• The Evolution Development and Diversity Node

• The Fish and Shell Fish Node Node

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Algal node (1)
European phycologists study a very wide range of
species and the resulting fragmentation of
resources strongly impairs the development of
algal genomics in Europe The first general
objective of the algal node is to promote a
genomic approach applied to a limited number of
models selected for their suitability for
comparative, functional and environmental studies
Council of Governor meeting, 4th October 2005,
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Scientific projects of the algal node One large
scale project sequencing of a multicellular
brown alga (Ectocarpus siliculosus) Comparative
genomics both between phylogenetically closely
related and distant species Functional genomics
Development of new molecular tools on a limited
number of models Environmental genomics gene-to
genome- level studies in the area of biodiversity
and ecosystems
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Algal node (2)
Toward more integration
Three main model organisms Phaeodactylum,
Ostreococcus and Ectocarpus for comparative and
functional genomics
Sequencing
Micro-array
Council of Governor meeting, 4th October 2005,
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Bioinformatics
Gene function in different environmental
conditions
Molecular tools (transformation, RNAi)
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• Jointly Executed Research

• The Microbial Node

• The Algal Node

Council of Governor meeting, 4th October 2005,
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• The Evolution Development and Diversity Node

• The Fish and Shell Fish Node Node

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EDD Node (1)
Functional Genomics
Generation of EST libraries from 4 key embryonic
stages of the sea urchin Paracentrotus lividus
complete. Sequencing in progress
Micro-array slides for Ciona intestinalis 1980
genes selected 2000 oligos and 500 chips due in
February 2006
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Octopus and Brittlestar cDNA Libraries. Trial
libaries made. Full libraries ready end 2005.
Small scale sequencing in progress
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EDD Node (2)
Environmental Genomics Molecular Identification
of species richness
Planktonic Copepod bar coding project
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EDD Node (3)
Environmental Genomics Natural and
anthropogenic effects on genetic diversity
Project 1 Biogeography and phylogeography .
Focus on Mediterranean.
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Project 2 Invasive and patrimonial species
Focus on invasive species in European
Atlantic-English Channel coasts
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EDD Node (4)
Future cross node integrative programmes

• Evolution of regulatory networks in bilaterians
• Larval dispersal and adult transition
• Genomic identity of species
• Comparative genomics of stress

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• Jointly Executed Research

• The Microbial Node

• The Algal Node

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• The Evolution Development and Diversity Node

• The Fish and Shell Fish Node Node

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Fish and Shellfish NodeObjectives

• To implement an integrative genomics programme
  aimed at the evaluation of ecosystem functioning,
  global change, selective fishing and sustainable
  aquaculture
• Integration
• Common Tool Development and Platform Sharing
  (technical / bioinformatic)
• Crossing of Approaches and Methodologies
  (workshops, PhD student and Post-doctoral
  exchanges)

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Understanding of population structure as a means
of evaluating ecosystem functioning, climate
change and selective fishing
Biodiversity
Populations
Integrated toolbox
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FS Next 18 Months Tool / Resource Development

• Further EST development (double output)
• Microarrays to determine gene expression profiles
  in different environmental conditions for sea
  bream, sea bass and oyster
• High throughput identification of genetic markers
  (microsatellites, SNPs) in sea bass, sea bream,
  mussels and oysters
• Database assembly of gene functions in fish and
  shellfish

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• Integrating Activities

• Jointly Executed Research

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• Spreading Activities

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• Spreading Activities

• Training and Education programme

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• Web site and Management tool

• Science and Society

• Intellectual properties

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Spreading activities
The Training Education Programme

• OBJECTIVES
• Integrating the MGE members through the
  implementation of short, training courses as well
  as summer courses.
• Raising the level of genomic knowledge to a
  common level across the MGE Network.
• The T E Council
• Mike Thorndyke, KMRS (chair)
• Euan Brown, Naples
• Akira Peters, Roscoff
• Alex Rogers, BAS
• Filip Volckaert, Leuven
• Johanna Wesnigk, Bremen
• Ulrika Hjelm, KMRS (manager)

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Spreading activities
The Training Education Programme

• FIRST YEAR
• Short courses
• Bioinformatics I Bremen, October 18-22, 2004
• Bioinformatics II Bielefeld, February 21-25,
  2005
• Microarrays I, II III Bremerhaven
  Bielefeld,
• March 4-11, 2005
• Proteomics Rennes, April 25-29, 2005
• Summer course
• Marine Evolutionary Ecological Genomics
• Naples, Italy, June 6-17, 2005
• Participants
• 76 PhD students post docs from
• 30 of the 44 network partners

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Spreading activities
The Training Education Programme
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Spreading activities
The Training Education Programme

• FUTURE COURSES
• Short courses
• The first set of short, training course will be
  repeated as they were over subscribed and got
  very good evaluations from the participants
• Summer courses
• Marine Evolutionary Ecological Genomics to be
  repeated 2006
• Developmental Marine Genomics I KMRS 2006
• Developmental Marine Genomics II Naples 2007
• Study Bloom Development using Genomic tools -
  Blanes 2007

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Spreading activities
The Training Education Programme
MGE PHD STUDENTS POST DOCS 13 students and 14
post docs with MGE funded positions At the
Berlin workshop (Oct 2-3) 18 of the students
and post docs met in order to get to know each
other, to learn about each others project and
also to learn more about Marine Genomics Europe.
This will continue as an annual event.
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• Spreading Activities

• Training and Education programme

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• Web site and Management tool

• Science and Society

• Intellectual properties

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Spreading activities
External Communication Companies, Scientists,
policy makers
Web site
Internal communication
All Information !!
Council of Governor meeting, 4th October 2005,
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Management Platform RexTool
http//www.marine-genomics-europe.org
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• Spreading Activities

• Training and Education programme

Council of Governor meeting, 4th October 2005,
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• Web site and Management tool

• Science and Society

• Intellectual properties

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Science and Society Committee Michèle Barbier,
Fr (coordinator), Eva Boon, NL, Jomuna
Choudhuri, De, leonor Cancela, Pt Ricardo Leite,
Pt, Shai Shafir, Is
ImaGene Photo contest
MGE meeting, 1st October 2005, Berlin, De
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• Spreading Activities

• Training and Education programme

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• Web site and Management tool

• Science and Society

• Intellectual properties

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Intellectual Property Use and Dissemination WP21

• Consortium Agreement

• IPUD Committee FIST S.A (F. Legros)

IPUDC advises contractors about Knowledge that
might be protected, assist in the negotiation of
Access rights between Contractors and propose
solutions to any intellectual property issues
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• Data policy release
• Survey on Intellectual properties (questionnaire
  to scientists)
• Database on companies of interest
• Web site, brochures
• Improve IP management and dissemination toward
  MGE community

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2004-2005
MGE outcomes
23 new collaborative projects 16 new scientific
porjects funded Europe, national,
regional (Ectocarpus project 4M) 11
publications MGE 44 conferences attendance
Science
14 posters (non scientific) 4 400 Brochures 1
web site 20,000 different visitors 1
newsletter (460 p.)
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Stakeholders
25 conferences for general public 1 partnership
school-lab 1 book  Once upon the timeThe marine
Sciences  (e.) 1 travelling photos
exhibition 25 press releases (journal, radio, web
site..)
Citizens
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Major event
International Marine Genomics Conference IMGC So
rrento Italy October 2006 500
participants Co-Sponsored by MGE- SZN- SARS
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People
- All Scientific Steering Committee members
- Four women have an essential role in the
management, coordination and integration of MGE
activities
Ulrika Hjelm Trainign and eductaion programme
Manager
Jomuna Choudhuri Bioinformatic project Manager
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Michèle Barbier Project Manager Spreading
activities
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