Biodiversity Virtual
e-Laboratory (BioVeL) as user
of earth observation products
BioVeL is an e-laboratory that supports research on
biodiversity using large amounts of data from crossdisciplinary sources.
Hannu Saarenmaa
University of Eastern Finland
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Biodiversity Virtual e-Laboratory
BioVeL Partners:
Cardiff University, UK
– Coordinator Alex Hardisty
2. Centro de Referência em Informação
Ambiental, Brazil
3. Foundation for Research on Biodiversity,
France
4. Fraunhofer-Gesellschaft, Institute IAIS,
Germany
5. Free University of Berlin – Botanical
Gardens and Botanical Museum, Germany
6. Hungarian Academy of Sciences Institute of
Ecology and Botany, Hungary
7. Max Planck Society, MPI for Marine
Microbiology, Germany
8. National Institute of Nuclear Physics, Italy
9. National Research Council: Institute for
Biomedical Technologies and Institute of
Biomembrane and Bioenergetics, Italy
11 Netherlands Centre for Biodiversity (NCB
Naturalis), The NetherlandsStichting
European Grid Initiative,
The Netherlands
12 University of Amsterdam, Institute of
Biodiversity and Ecosystem Dynamics,
The Netherlands
BioVeL started 1 Sept 2011.
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13 University of Eastern Finland, Finland
14 University of Gothenburg, Sweden
15 University of Manchester, UK
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Biodiversity Virtual e-Laboratory
BioVeL promotes e-science
• Connects two scientific communities: ICT and biodiversity.
• Shares expertise in workflow studies among BioVeL’s users.
• Fosters an international community of researchers and partners
working on biodiversity issues:
• Invasive species
• CO2 sequestration
• Ecosystem functioning and valuation
•BioVeL builds on myGrid family of e-science technology.
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Biodiversity Virtual e-Laboratory
BioVeL is a powerful data processing tool
• Import data from your own research and/or from existing libraries
• Use workflows (series of data analysis steps) for data processing
• Build your own workflow by selecting and applying successive
web services (data processing techniques)
• Access a library of workflows and re-use existing workflows
• Cut down research time and overhead expenses
Workflow for population modelling (stage-based matrix projection models)
based on Stubben and Milligan. Journal of Statistical Software, 22(11), Sept 2007
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A key methodology: Ecological niche
modelling of species distributions
in different climate and habitat change scenarios
Where do species occur now?
Image from http://www.lifemapper.org
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Where will they occur in the future? http://www.globalamphibians.org/
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Use cases of ecological niche modelling
require data integration
GBIF
Known
Species Locations
Environmental
Characteristics
from gridded
GIS layers
Temperature layer
Develop
Model
Many other layers
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Environmental
Characteristics
Of Surrounding
Geographic Area
Native
Distribution
Prediction
Environmental
Characteristics
Of Different
Geographic Area
Invasion
Area
Prediction
Multidimensional
Ecological Space
D2
Dn
D1 = Temperature
Future Scenarios
Of Environmental
Characteristics
Environmental
Change
Prediction
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Processing service at CRIA, Brazil
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Biodiversity Virtual e-Laboratory
Showcase study 1: create a workflow*
* courtesy Matthias Obst, University of Gothenburg, Sweden
Study on the ecological niche of the south-east Asian horseshoe crab,
an endangered species:
• Import south east Asian data from external library
• Apply succession of “services” = workflow
• Result: ecological niche map
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Biodiversity Virtual e-Laboratory
Showcase study 2: re-use a workflow
* courtesy Matthias Obst, University of Gothenburg, Sweden
Study on the ecological niche of the American horseshoe crab
• Import American data
• Re-use south east Asia crab study workflow
• Result: ecological niche map for American horseshoe crab
Compare the ecological niches of the south east Asian and American crabs.
Potential study of the ecological niche of an African animal
• Import African data
• Re-use horseshoe crab study workflow
• Result: ecological niche map for African animal
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We need to link the BioVeL
Community Catalogues with the GCI
Data and Services
Climate data
WorldClim
IPCC
others
Ecosystems data
Land use
Habitat loss
Catalogues /
Repositories
Execution
environment
Taverna
Workbench
Biodiversity data
GEO BON
LifeWatch
GBIF
Catalogue of Life
Modelling /
GeoProcessing
Taverna
Workflow
Engine
BioVeL
Web
Portal/
Portlets
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User needs from BioVeL for
GEOSS
• Need access to data across SBAs
– Discovery of metadata is not enough, we need
seamless access to data
– We need to speed up installing web service (machineto-machine) access mechanisms to (both historical
data and future scenarios):
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climate data layers
ecosystems data, land use, and habitat loss
biodiversity observations
digitised of historical biodiversity data
• Many/most data and services have been
designed from standpoint of local access
– Orchestration of them is still a tedious patchwork.
– Streamlining and hardening the services needed.
– Challenge: Big datasets/layers.
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BioVeL contribution to
GEO BON (Task BI-01)
• Targets:
– Implementation of a mechanism that enables users
to interact with the development of biodiversity
observations systems and request services.
– GEO BON Detailed Implementation Plan prescribes
use of workflows for integrated analyses
• Actions:
– Integration of in-situ and remote-sensing data.
– Characterize, monitor and predict changes in the
distribution of invasive species.
– Develop a full global analysis of stability of
ecosystem carbon services.
• Resources:
– Work together with LifeWatch, EU BON, …
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BioVeL contribution to ESFRI
research infrastructure
BioVeL
• Exploring patterns of biodiversity and
processes of biodiversity across time and
space and scales
Genetic <-> Species <-> Ecosystem<-> Landscape
A Systems approach
• A European Research Infrastructure
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1995
Earlier projects
2005
Conceive
Distributed observatories / sensors
Databases, processing and analytical tools
Computational capability and capacity
Collaborative environments
Support, training, partnering, fellowship
Open access, single portal
2008
2011
Preparations
€5m
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Construction
~ €234m
2016
Operation &
5 + 2 Evolution
Biodiversity Virtual e-Laboratory
www.biovel.eu
• Become a ‘Friend of BioVeL’
– Deploy robust (Web) services for
biodiversity analysis and workflow
– Encourage adoption of the workflow
approach towards processing and
analysis of biodiversity data
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