integration and reshaping of the infrastructure basis work package 3 wouter los & wp3...

Integration and Reshaping of the Infrastructure Basis

Work Package 3

Wouter Los& WP3 collaborators

28/06/06 Kickoff Meeting

Scheme of WP relations

Expert basis

Infrastructure basis

Coordinating research

Internet platform for cybertaxonomy

Web-basedtaxonomy

Application inconservation

Training and public awareness

Tools & ProductsResourcesCoordinationand integration

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Managing EDIT



Expert basis




Web-basedtaxonomy



Tools & ProductsResourcesCoordinationand integration

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Managing EDIT

WP3


Considerations

• The Commission wants us to address fragmentation: What is an unified vision for the infrastructural basis at the European level?

• Can we adapt to collaborate in undertaking large-scale challenges as a European taxonomic infrastructure?

• How to bring together the separate components in a next generation infrastructure?

• This would imply different work processes, and reduction of the number of links in the decision-making chain.


WP3 components

3.1 Physical infrastructures3.2 Information infrastructure3.3 Sustaining the cybertaxonomy process3.4 Large-scale instrumental facilities3.5 Liaison with international infrastructures


WP3 in the first 18 months

3.1 Physical infrastructuresa. Integrationb. Concept of Biological Resource Centres

3.2 Information infrastructurea. Information backboneb. European Taxonomic Information Servicesc. Bioinformatics Toolbox

3.3 (Sustaining the cybertaxonomy process)3.4 Large-scale instrumental facilities

a. DNA barcoding in Europe

3.5 Liaison with international infrastructures


3.1 Physical infrastructures

• Integration.Identify impediments for collaborative united action.Discuss mechanisms for change

(started with OECD-GSF initiative)Consortium development (alternative models for national, regional and European consortia; implications of “virtual organisations” model).

• Biological Resources Centres.Consider BRC concept for our natural history collections.Appropriate performance indicators?.How to enter into negotiations with funding bodies?


3.2a Information backbone

• Architecture of an information backbone of taxonomic information (names), specimen data, and molecular markers (DNA). -> Landscape of the alternative views.

• Identification of the components, and definition of functionalities for a new generation infrastructure.(contribution to the LIFE WATCH plan development).

• Preparation (also with other partners) of funding plans (for example: liaison with ZooBank initiative).


3.2b European Taxonomic Information Services

• Common management approach for the continuation, maintenance and integration of the Pan-European species checklists.

– (Together with WP2) securing the expert basis of the checklist services (as partly organised in SMEBD).

– Organisation (and keeping alive) the relevant institutional networks. (Such as Fauna Europaea Focal Points Network).

• Promotion of checklist updates and validation.

• Preparation of plans (and funding proposals) to expand the checklist services (in data and in geographical scope).


3.2c Bioinformatics toolbox

• Design of a user-friendly bioinformatics toolbox for interpolating and processing phylogenetic trees, matrices, DNA barcodes, and other relevant biodiversity data to facilitate research and conservation outcomes.

• Analyse components for the www prototype (and already available tools).

• Use selected taxonomic groups (also used in other EDIT parts) to demonstrate in case studies.


3.4a DNA barcoding

• Coordination of DNA-barcoding in Europe for all organism groups (also in support of CBOL).

• Coordination.– Strategy to set up a DNA barcoding consortium in Europe (ECBOL)– Coordination and quality issues (genes to use, networks, standards and

reporting, results and problems, international cooperation).– Website for ECBOL with introductory info, coordination info, technicical info,

membership list + who is doing what, reprints, links.

• Models for DNA banks and testing of new storage system.

• Starting plans for macro/micro arrays and bio-sensors.


Major partners

Phys. infrastruct.

Information infrastruct.

Cyber-taxonomy

DNA-barcoding

Paris X X

Copenhagen X

Amsterdam X X X

Leiden X

CBS Utrecht X

BGBM Berlin X X

Kew Gardens X

CU Bratislava X

SMEBD X

INRA X



Expert basis




Web-basedtaxonomy



ProductsResourcesCoordinationand integration

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Managing EDIT

Bringing integrationinto reality (BoD)

Tools / Testing

Raise a new generation

Thank you

integration and reshaping of the infrastructure basis work package 3 wouter los & wp3...

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