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
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
Virtual Laboratory for e-Science
Aim
To develop and apply a Grid and Virtual Lab technology
based information system and research environment.
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
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
VL- e
e-Science in Applications
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
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)
VL- e
e-Science in Applications
biodiversity
CBPG
Virtual Laboratory for e-Science
Biodiversity
Two main components:
1.
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)
VL- e
e-Science in Applications
biodiversity
EcoGrid
Ecogrid
Objectives
1.
Construct a virtual database that is
connected to geographically distributed databases which
contain information on the distributions of species, on
landscape characteristics and on weather.
Ecogrid
Objectives
1.
2.
Construct a virtual database that is
connected to geographically distributed databases which
contain information on the distributions of species, on
landscape characteristics 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
Objectives
1.
2.
3.
Construct a virtual database that is
connected to geographically distributed databases which
contain information on the distributions of species, on
landscape characteristics 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
- ...
Example: insect diversity and Red-backed Shrikes
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Ecogrid - data acquisition
Initial Situation
Vlinderstichting
FLORON
NMV
RAVON
BLWG
VZZ
ANNEMOON
EIS-NL
Tinea
SOVON
VOFF
Ecogrid - data acquisition
taxonomy
observation
locality
central
VOFF
database
SOVON
NCO databases
central databases
Data shared by all NCO’s
NCO databases
NCO-specific data
RAVON
central databases
WEB
GIS
webpages
maps
etc.
METADATA
PERSONS
TAXONOMY
portal login
NCO databases
GIS
LOCATION
ACTIVE MEMBER
PK
Person ID
SPECIES
PK
Taxon ID
km hok
x, y
route
relevé
OBSERVATOR GROUP
OBSERVATION
PK
Observation ID
Species ID
FK
Person ID
FK
Observation ID
Main Observator
EXTRA INFO
spatial databases
• Spatial functions to
query (SQL) within
and across layers:
• Equals()
• Disjoint()
• Intersects()
• Touches()
• Crosses()
• Within()
• Contains()
• Overlaps()
‘Layers’ build with these data types,
stored as tables in PostgreSQL/PostGIS.
• Special indexing
techniques (GisT)
Ecogrid system - overview
data
acquisition
portal
science
portal
central
databases
VOFF
EcoGrid
virtual
meta
database
landscape
BAMBAS
database
geostatistics
Spotfire
scale conversion
modules
data mining
modules
model
experiments
weather
processed
data
VL-eScience Research Environment
Ecogrid system - prototype
data
acquisition
portal
science
portal
SOVON
EcoGrid
virtual
meta
database
landscape
BAMBAS
database
geostatistics
Spotfire
scale conversion
modules
data mining
modules
model
experiments
weather
processed
data
VL-eScience Research Environment
Ecogrid - portal prototype
Ecogrid - portal prototype
Ecogrid - portal prototype
Ecogrid - portal prototype
Ecogrid - portal prototype
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