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Biodiversity Virtual e-LaboratoryProject OverviewBioVeL is an e-laboratory that supports research on biodiversity using large amounts of data from cross-disciplinary sources.

Alex HardistyProject CoordinatorCardiff University

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Biodiversity Virtual e-LaboratoryAn international network of experts connecting 2 scientific communities: ICT and biodiversity

Offers access to a variety of data processing services, linked as ‘workflows’ for assisting studies in biodiversity science

• You will hear about these during this workshop

• You will be able to influence their design

Aims to foster cooperation in the community by:• Discussing use cases• Identifying important Web Services• Training scientists

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Biodiversity Virtual e-Laboratory

• 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

BioVeL is a powerful data processing tool

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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Biodiversity Virtual e-Laboratory

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

Showcase study 1: create a workflow*

* courtesy Matthias Obst, University of Gothenburg, Sweden

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Biodiversity Virtual e-LaboratoryStudy 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

Showcase study 2: re-use a workflow

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What does BioVeL consist of? (1)

User

Collections

Biodiversity Data

Spatial (Web)

OGC

BioVeLDataManager

xls, csv

Catalogueof Life

Observations

Annotations

Taxonomic data

Data Services Catalogues /Repositories

Collaboration

raster data

REST

REST

REST

sensor data BioVeL

GeoServer

CSWREST

OGCnodes

GBIF

Workflows

Genomic data

documents

GenBank

REST

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What does BioVeL consist of? (2)

Phylogenetic

Taxonomic

Biodiversity Services

Visualization

WebDaV Data Management

BLAST,Hmmer,MrBayes,

Blast, PAML,EMBOSS,…

R

Synonyms

Execution environment

Catalogues /Repositories

Modelling / GeoProcessing

BioSTIFGoogle Refine CSW

openModeller

WPS / WCPS Auth

entic

ation

/ A

utho

risati

onO

penS

earc

hPr

oven

ance

TavernaWorkbench

TavernaWorkflow Engine

Grid, Cloud, etc.

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Service sets driven by science• Phylogeny and metagenomics services

– Measures of genetic diversity and adaptation to changing conditions

• Taxonomy services– Checklists, identification, data cleaning, ...

• Niche and population modelling services– Processes of conservation and invasive

species management• Ecosystem functionality and valuation

services

– Modelling of ecosystem services and CO2 sequestration

• Visualization and geospatial

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Biospheric CO2 sequestration (1)

SCIENCE & POLICY CONTEXT Emission is continuously increasing – 10 GtC in 2010 Sequestration is the only sustainable process to mitigate Terrestrial Sequestration highly depends on land use & climate change

UnstableEarth systems

SCIENTIFIC CHALLENGES Model improvement Model & data downscaling Model verification

>> data-model calibration >> higher processing capacity

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REVIEW IN PROGRESS Collected papers

39 Selected and annotated papers 35

MOST RELEVANT RESEARCH GROUPS/PROJECTS The Global Carbon Project, Fluxnet – eddy covariance tower measurements, GHG Europe, ICOS, NTSG (University Montana) and Biome-BGC users & developers worldwide

Biome-BGC is a computer model that estimates fluxes and storage of energy, water, carbon, and nitrogen for the vegetation and soil components of terrestrial ecosystems. TYPICAL „WORKFLOWS” around Biome-BGC Weather to Biome-BGC; Biome-BGC CARBON; Biome-BGC

Sensitivity Analysis; Biome-BGC Data-Model Harmonization

WEB SERVICES no such kind of services operating yet new service sets identified and prioritised to develop: 4 data retrieval services 6 Biome-BGC modelling services

Biospheric CO2 sequestration (2)

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SCIENCE & POLICY CONTEXT„Over the past 50 years, humans have changed ecosystems more rapidly and extensively than … this has resulted in a substantial and largely irreversible loss in the diversity of life on Earth.”„… degradation of many ecosystem services [causes] increased risks of nonlinear changes …” „… reversing the degradation of ecosystems while meeting increasing demands for their services can be partially met under some scenarios …, but these involve significant changes in policies, institutions, and practices that are not currently under way.” MEA 2005

SCIENTIFIC CHALLENGES Role of biodiversity and community ecology in ecosystem functioning How productive and effective are various ecosystem services (ES) - maintaining hydrologic cycles, regulating climate, cleansing air/water Trade offs between ecosystem functions and management regimes >> quantify ecosystem functioning >> develop ecosystem service indicators >> potential of metagenomics in ES valuation

Ecosystem functioning / valuation (1)

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REVIEW IN PROGRESS Collected papers 14 (will be completed) Selected and annotated papers -

MOST RELEVANT RESEARCH GROUPS/PROJECTS not evaluated yet TYPICAL „WORKFLOWS” calculating ecosystem service indicators based on model simulation … will be completed

WEB SERVICES no such kind of applicable services operating yet new service sets identified and prioritised to develop: 2 services for Stand level Ecosystems Service Indicators (SESSI) 2 services for Landscape level ES Indicators (LESSI)

TAXO, NICHE, META & POP services also need to be considered

Ecosystem functioning / valuation (2)

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SCIENCE & POLICY CONTEXT Invasions of alien species are a leading cause of biodiversity loss and related economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation ...

SCIENTIFIC CHALLENGES Risk assessment as climate change proceeds and considering the effect of different human activities Simulating pest control or mitigation strategy options

>> ecological niche modelling (ENM)

Invasive species management (1)

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REVIEW IN PROGRESS Collected papers

9 (will be completed) Selected and annotated papers -

MOST RELEVANT RESEARCH GROUPS/PROJECTS GISIN – Global Invasive Species Information Network and … but not evaluated yet TYPICAL „WORKFLOWS” Ecological Niche Modelling of (potential) invasive alien species Ecological Niche Modelling of (forest) pest species …

WEB SERVICES openModeller service with environmental data layers TAXO, NICHE, …

Invasive species management (2)

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Biodiversity Virtual e-LaboratoryBioVeL is a consortium of 15 partners from 9 countries1. Cardiff University, UK – Coordinator 2. Centro de Referência em Informação

Ambiental, Brazil3. Foundation for Research on Biodiversity,

France4. Fraunhofer-Gesellschaft, Institute IAIS,

Germany5. Free University of Berlin – Botanical

Gardens and Botanical Museum, Germany6. Hungarian Academy of Sciences Institute of

Ecology and Botany, Hungary7. Max Planck Society, MPI for Marine

Microbiology, Germany8. National Institute of Nuclear Physics, Italy9. National Research Council: Institute for

Biomedical Technologies and Institute of Biomembrane and Bioenergetics, Italy

10. Netherlands Centre for Biodiversity (NCB Naturalis), The Netherlands

11. Stichting European Grid Initiative, The Netherlands

12. University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics, The Netherlands

13.University of Eastern Finland, Finland14. University of Gothenburg, Sweden15. University of Manchester, UK

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Supported by many friends

• 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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Fits in a portfolio of initiatives

Recognised as providing an important contribution of infrastructure

NoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.

Projects: agINFRA, Aquamaps, ArtDataBanken, BioFresh, Envri, EU BON, EUBrazilOpenBio, Fauna Iberica, iMarine, MicroB3, OpenPlantBio, ViBRANT

Global: Catalogue of Life, COOPEUS, CReATIVE-B, EoL, GBIF, GSC Biodiversity WG, TreeBase, and many more

• Exploring patterns of biodiversity and processes of biodiversity across time and space and scales

Genetic <-> Species <-> Ecosystem<-> LandscapeA Systems approach

• A European Research Infrastructure– Distributed observatories / sensors– Databases, processing and analytical tools– Computational capability and capacity– Collaborative environments– Support, training, partnering, fellowship– Open access, single portal

1995 2005 2008 2011 2016

Earlier projects Conceive Preparations Construction Operation &Evolution

€5m ~ €234m19 5 + 2

Core operations• BioVeL• ICT Core• European Taxonomic Backbone

LifeWatch as a distributed research infrastructure

National contributions• Belgium• Hungary• Italy• Netherlands• Romania• Spain• Sweden

Thematic contributions• Population biology of migrating birds• Understanding the role of marine wetlands on biodiversity migration patterns• Impacts of invading alien species• Assessment of regional biodiversity• Preservation of ecosystem services (curing habitat destruction)• Human observations of biodiversity

Distributed coreoperationsowned by LifeWatch

Independententities contributing to LifeWatch operations

Distributed coreoperationsowned by LifeWatch

Independententities contributing to LifeWatch operations

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Finally ... ...

• White Paper initiative– Our community vision for biodiversity

informatics, to inform Horizon 2020– http://is.gd/WhitePaperChapters

• Now, – Listen, enjoy the presentations– Network and socialise– Express your opinions and influence

our work for the next months

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Biodiversity Virtual e-LaboratoryBioVeL is funded by the European Commission 7th Framework Programme (FP7).It is part of its e-Infrastructures activity.

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.

BioVeL is free and available via internet.

www.biovel.eu, contact Alex Hardisty: HardistyAR@cardiff.ac.uk