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Ecogrid & Virtual Laboratory for e-Science PowerPoint PPT Presentation


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Ecogrid & Virtual Laboratory for e-Science. from field observation to spatial knowledge. Willem Bouten, project leader Floris Sluiter, design & implementation Guido van Reenen, data analysis Victor Mensing, Vlinderstichting Dirk Zoetebier, Sovon

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Ecogrid & Virtual Laboratory for e-Science

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Ecogrid virtual laboratory for e science

Ecogrid

&

Virtual Laboratory for e-Science

from field observation to spatial knowledge

Willem Bouten, project leader

Floris Sluiter, design & implementation

Guido van Reenen, data analysis

Victor Mensing, Vlinderstichting

Dirk Zoetebier, Sovon

Aart Jan van der Linden, Talmon Comm.

CBPG


Ecogrid virtual laboratory for e science

Virtual Laboratory for e-Science

Mission

To boost e-Science by creating an e-Science environment and carrying out research on methodologies.

Essential components

-e-Science development areas

-a Virtual Laboratory development area

-a Large-Scale Distributed computing development area, consisting of high performance networking and grid parts


Ecogrid virtual laboratory for e science

Virtual Laboratory for e-Science

Aim

To develop and apply a Grid and Virtual Lab technology based information system and research environment.


Ecogrid virtual laboratory for e science

Virtual Laboratory for e-Science

The VL-e project has four programme lines, most of them containing more than one subprogramme.

P1 – e-Science in Applications

P2 – generic Virtual Laboratory methodology

P3 – large-scale distributes systems

P4 – scaling up & validating in ‘real-time’ applications

VL- e


Ecogrid virtual laboratory for e science

VL- e

e-Science in Applications

Virtual Laboratory for e-Science

Research of the P1 line is carried out within the following subprogrammes:

P1 – e-Science in Applications

SP1 – Data Intensive Science

SP2 – Food Informatics

SP3 – Medical Diagnosis & Imaging

SP4 – Biodiversity

SP5 – Bioinformatics ASP

SP6 – The Dutch Telescience Laboratory


Ecogrid virtual laboratory for e science

VL- e

e-Science in Applications

biodiversity

Virtual Laboratory for e-Science

Biodiversity

Aim

To develop and apply a Grid and Virtual Lab technology based information system and research environment

for identification, distribution, integration and analyses of observations and model results of the dynamics of flora and fauna


Ecogrid virtual laboratory for e science

VL- e

e-Science in Applications

biodiversity

Virtual Laboratory for e-Science

Biodiversity

Partners:

CBPG –Computational Bio- and Physical Geography(IBED – Institute for Biodiversity and Ecosystem Dynamics)

(UvA – Universiteit van Amsterdam)

RNLAF –Royal Netherlands Airforce

VOFF –Association for Research of Flora & Fauna

And co-operation with other programme lines, especially subprogrammes of P2 (generic Virtual Laboratory methodology)

CBPG


Ecogrid virtual laboratory for e science

VL- e

e-Science in Applications

biodiversity

EcoGrid

Virtual Laboratory for e-Science

Biodiversity

Two main components:

a national database for biodiversity information

 this talk (Ecogrid)

2.a PSE for integrated analysis of observations and model results

 topic of Judy Shamoun-Baranes (BAMBAS)


Ecogrid virtual laboratory for e science

Ecogrid

Objectives

  • Construct a virtualdatabase that is connected to geographically distributed databases which contain information on the distributions of species, on landscapecharacteristics and on weather.


Ecogrid virtual laboratory for e science

Ecogrid

Objectives

  • Construct a virtualdatabase that is connected to geographically distributed databases which contain information on the distributions of species, on landscapecharacteristics and on weather.

  • Develop generic methodologies and tools for scale conversions, to be able to integrate and interpret data that are observed at different spatial scales.


Ecogrid virtual laboratory for e science

Ecogrid

Objectives

  • Construct a virtualdatabase that is connected to geographically distributed databases which contain information on the distributions of species, on landscapecharacteristics and on weather.

  • Develop generic methodologies and tools for scale conversions, to be able to integrate and interpret data that are observed at different spatial scales.

  • Use this infrastructure across the boundaries of organisations to indentify:

  • - spatial wood web structures

  • - biodiversity hotspots

  • - effects of changed land-use

  • - ...


Ecogrid virtual laboratory for e science

Example: insect diversity and Red-backed Shrikes


Ecogrid virtual laboratory for e science

}

Nitrogen dep.


Ecogrid virtual laboratory for e science

Ecogrid - data acquisition

Initial Situation

{

VlinderstichtingFLORONNMVRAVONBLWGVZZ ANNEMOON

EIS-NLTinea

SOVON

VOFF


Ecogrid virtual laboratory for e science

Ecogrid - data acquisition

taxonomy

observation

locality

}

central

VOFF

database

SOVON

NCO databases


Ecogrid virtual laboratory for e science

central databases

Data shared by all NCO’s

NCO databases

NCO-specific data

RAVON


Ecogrid virtual laboratory for e science

central databases

WEB

webpages

GIS

maps

etc.

METADATA

PERSONS

portal login

TAXONOMY

NCO databases


Ecogrid virtual laboratory for e science

spatial databases

  • Spatial functions to query (SQL) within and across layers:

    • Equals()

    • Disjoint()

    • Intersects()

    • Touches()

    • Crosses()

    • Within()

    • Contains()

    • Overlaps()

  • Special indexing techniques (GisT)

  • ‘Layers’ build with these data types, stored as tables in PostgreSQL/PostGIS.


    Ecogrid virtual laboratory for e science

    Ecogrid system - overview

    Spotfire

    geostatistics

    data mining

    modules

    scale conversion

    modules

    science

    portal

    data

    acquisition

    portal

    EcoGrid

    virtual

    meta

    database

    BAMBAS

    database

    central

    databases

    VOFF

    landscape

    model

    experiments

    weather

    processed

    data

    VL-eScience Research Environment


    Ecogrid virtual laboratory for e science

    Ecogrid system - prototype

    Spotfire

    geostatistics

    data mining

    modules

    scale conversion

    modules

    science

    portal

    data

    acquisition

    portal

    EcoGrid

    virtual

    meta

    database

    BAMBAS

    database

    SOVON

    landscape

    model

    experiments

    weather

    processed

    data

    VL-eScience Research Environment


    Ecogrid virtual laboratory for e science

    Ecogrid - portal prototype


    Ecogrid virtual laboratory for e science

    Ecogrid - portal prototype


    Ecogrid virtual laboratory for e science

    Ecogrid - portal prototype


    Ecogrid virtual laboratory for e science

    Ecogrid - portal prototype


    Ecogrid virtual laboratory for e science

    Ecogrid - portal prototype


    Ecogrid virtual laboratory for e science

    Concluding remarks

    • PostgreSQL (and Postgis) are especially suited for large scientific databases

    • By the end of this year all the databases will be populated and we will have online data acquisition.

    • Then we will shift our focus on using the data and concentrate on Analysis and Datamining


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