AN E-INFRASTRUCTURE AND E-SCIENCE ENVIRONMENT SUPPORTING RESEARCH ON BIODIVERSITY

Alex HardistyCoordinator, Cardiff University

10th e-Concertation, 6-7th March 2013, BrusselsTrack 4: Digital environments for collaboration

Biodiversity Virtual e-Laboratory

Creates powerful data processing tools for biodiversity research

• Carbon Sequestration• Ecosystem Functioning and Valuation• Invasive Species Management

• Aims to foster cooperation in the community by:– Discussing scientific use cases– Identifying and deploying important Web Services– Designing and offering workflows– Training scientists

An international virtual network of experts connecting2 scientific communities: biodiversity and ICT

Ecological Niche ModellingBiogeochemical modellingMetagenomicsPhylogeneticsPopulation ModellingTaxonomyGeospatial Visualization

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

research time and overhead expensesPart of a workflow to study the ecological niche of the horseshoe crab

• 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

Fits into a portfolio of initiatives

Supported by many friends

Important contributionto infrastructure

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.)

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.)

Complete?No!

Maybe 10% of what is necessary

*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

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

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)

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

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.

Questions?

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.