1. Biodiversity Virtual e-Laboratory
AN E-INFRASTRUCTURE AND E-SCIENCE
ENVIRONMENT SUPPORTING RESEARCH
ON BIODIVERSITY
Alex Hardisty
Coordinator, Cardiff University
10th e-Concertation, 6-7th March 2013, Brussels
Track 4: Digital environments for collaboration
2. Creates powerful data processing tools Ecological Niche Modelling
Biogeochemical modelling
for biodiversity research Metagenomics
• Carbon Sequestration Phylogenetics
Population Modelling
• Ecosystem Functioning and Valuation Taxonomy
Geospatial Visualization
• Invasive Species Management
An international virtual network of experts connecting
2 scientific communities: biodiversity and ICT
• Aims to foster cooperation in the community by:
– Discussing scientific use cases
– Identifying and deploying important Web Services
– Designing and offering workflows
– Training scientists
3. Products are “services” and “workflows”
• Workflows allow to process vast
amounts of data, repeatedly
– Build your own workflow: select and
apply successive “services” (data
analysis and processing steps)
– Import data from one’s own research
and/or from existing libraries (i.e.
GBIF, Catalogue of Life)
• Access a library of workflows and
re-use existing workflows.
– Improves efficiency by reducing Part of a workflow to study the
ecological niche of the horseshoe crab
research time and overhead expenses
4. Supported by
many friends
Fits into a portfolio
of initiatives
• NoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.
• Projects: 4D4Life, agINFRA, Aquamaps, ArtDataBanken,
BioFresh, Envri, EU BON, EUBrazilOpenBio, Fauna Iberica,
i4Life, iMarine, Micro B3, OpenPlantBio, ViBRANT
• Global: CAMERA, Catalogue of Life, COOPEUS, CReATIVE-B,
EoL, GBIF, GSC Biodiversity WG, TreeBase, and many more
Important contribution
to infrastructure
5. Where are we, the community in this process?
We have users’ workflows and
applications
We have Service and Data Providers
(LifeWatch, BioVeL, GBIF, CoL,
EBI, etc.)
We have Resource Providers
(EUDAT, EGI.eu, PRACE,
commercial cloud, etc.)
6. Where are we, the community in this process?
Complete?
We have users’ workflows and
applications
No!
Maybe 10% of
We have Service and Data Providers
what is necessary
(LifeWatch, BioVeL, GBIF, CoL,
EBI, etc.)
We have Resource Providers
(EUDAT, EGI.eu, PRACE,
commercial cloud, etc.)
7. *A Decadal view of biodiversity informatics:
Challenges and priorities
• The Grand Challenge for Biodiversity Informatics
– An infrastructure to allow the available data to be brought
into a coordinated coupled modelling
environment, capable of addressing questions relating to
our use of the natural environment, that captures the
variety, distinctiveness and complexity of all life on Earth
• To achieve it we need:
– To build user confidence
– Integrative flexible e-Science environments
– Predictive models across multiple scales, coupled
* Alex Hardisty, Dave Roberts, and the biodiversity informatics community
- 80 people took part in the open debate that led to this whitepaper. To be published in BMC Ecology
8. To build user confidence
• Thus far, all projects share a common problem of
keeping services running after project funding ended
• New models are needed
• To create translational pipelines to industry adoption
• To encourage institutional adoption for care and
maintenance
• For recognition of contribution other than through
publication of academic papers
– Stronger marketing and outreach
• Invest more in up-skilling and hand-holding
9. Integrative flexible e-Science environments
• Using standardised building blocks and workflows
– Interoperable components
– With access to data from multiple sources
• Recognise different kinds of VRE
– General-purpose / specialised / single scientific objective
• cf. chemistry laboratory vs forensics lab vs HIV vaccine lab
• BioVeL / AquaMaps and iMarine / CarbonWaterCloud
• Must generate immediate benefit for users
– Science driven with scientists as active participants in creation
of infrastructure
– Functions people find useful; Simple and intuitive
– Technology invisible (disappears into background)
10. Predictive models across multiple scales
• A new framework of methods, techniques, standards to
bring about interoperability of data and models across
different biological scales
– From Genetic through species and ecosystem to landscape
– Learn from Virtual Physiological Human and from Numerical
weather prediction and climatology Edwards (2010). A Vast Machine
– “General Ecological Models” Purves et al. (2013). doi:10.1038/493295a
• Evolvable to incorporate new scientific insights
– Re-analysis models
• Making data we already have into global datasets
– Implies ‘inversion’ of existing infrastructure
11. Questions?
BioVeL is funded by the
European Commission
7th Framework Programme (FP7).
It is part of its e-Infrastructures activity.
BioVeL contributes to LifeWatch and GEO BON.
BioVeL products are free to access.
Under FP7, the e-Infrastructures activity is part of the Research Infrastructures
programme, funded under the FP7 'Capacities' Specific Programme. It focuses on the further
development and evolution of the high-capacity and high-performance communication network
(GÉANT), distributed computing infrastructures (grids and clouds), supercomputer
infrastructures, simulation software, scientific data infrastructures, e-Science services as well as
on the adoption of e-Infrastructures by user communities.
Hinweis der Redaktion
CarbonWaterCloud focusses on predictive modelling of carbon sink, primary production (including crop production) and hydrology of natural and transformed terrestrial ecosystems.
CarbonWaterCloud focusses on predictive modelling of carbon sink, primary production (including crop production) and hydrology of natural and transformed terrestrial ecosystems.The emphasize on access in this context is from the productivity standpoint of view. Open access policy on data makes infrastructure needs much more lean.
‘inversion’ of existing infrastructure is about re-examining every element of data we have to re-construct the past biodiversity, as a guide and calibrator of models that can predict the future