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1 Biodiversity Virtual e-Laboratory Project Overview BioVeL is an e-laboratory that supports research on biodiversity using large amounts of data from.

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Presentation on theme: "1 Biodiversity Virtual e-Laboratory Project Overview BioVeL is an e-laboratory that supports research on biodiversity using large amounts of data from."— Presentation transcript:

1 1 Biodiversity Virtual e-Laboratory Project Overview BioVeL is an e-laboratory that supports research on biodiversity using large amounts of data from cross-disciplinary sources. Alex Hardisty Project Coordinator Cardiff University

2 2 Biodiversity Virtual e-Laboratory An 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

3 3 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

4 4 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

5 5 Biodiversity Virtual e-Laboratory 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 Showcase study 2: re-use a workflow

6 6 What does BioVeL consist of? (1) User Collections Biodiversity Data Spatial (Web) OGC BioVeLData Manager xls, csv Catalogue of Life Observations Annotations Taxonomic data Data Services Catalogues / Repositories Collaboration raster data REST sensor data BioVeL GeoServer BioVeL GeoServer CSW REST OGC nodes GBIF Workflows Genomic data documents GenBank REST

7 7 What does BioVeL consist of? (2) Phylogenetic Taxonomic Biodiversity Services Visualization WebDaV Data Management BLAST,Hmmer, MrBayes, Blast, PAML, EMBOSS,… BLAST,Hmmer, MrBayes, Blast, PAML, EMBOSS,… R R Synonyms Execution environment Catalogues / Repositories Modelling / GeoProcessing BioSTIF Google Refine CSW openModeller WPS / WCPS Authentication / Authorisation Authentication / Authorisation OpenSearch Provenance Taverna Workbench Taverna Workflow Engine Grid, Cloud, etc.

8 8 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 CO 2 sequestration Visualization and geospatial

9 9 Biospheric CO 2 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 Unstable Earth systems SCIENTIFIC CHALLENGES Model improvement Model & data downscaling Model verification >> data-model calibration >> higher processing capacity

10 10 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 CO 2 sequestration (2)

11 11 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 irreve r sible 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 T rade offs between ecosystem functions and management regimes >> quantify ecosystem functioning >> develop ecosystem service indicators >> potential of metagenomics in ES valuation Ecosystem functioning / valuation (1)

12 12 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)

13 13 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)

14 14 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)

15 15 Biodiversity Virtual e-Laboratory BioVeL is a consortium of 15 partners from 9 countries 1.Cardiff University, UK – Coordinator 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 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, Finland  University of Gothenburg, Sweden  University of Manchester, UK

16 16 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

17 17 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

18 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 – Distributed observatories / sensors – Databases, processing and analytical tools – Computational capability and capacity – Collaborative environments – Support, training, partnering, fellowship – Open access, single portal Earlier projectsConceivePreparationsConstruction Operation & Evolution €5m~ €234m

19 Distributed core operations owned by LifeWatch Independent entities contributing to LifeWatch operations LifeWatch as a distributed research infrastructure

20 Core operations BioVeL European Taxonomic Backbone Other ICT Core elements 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 core operations owned by LifeWatch Independent entities contributing to LifeWatch operations

21 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 core operations owned by LifeWatch Independent entities contributing to LifeWatch operations Distributed core operations owned by LifeWatch Independent entities contributing to LifeWatch operations

22 22 Finally White Paper initiative – Our community vision for biodiversity informatics, to inform Horizon 2020 – Now, – Listen, enjoy the presentations – Network and socialise – Express your opinions and influence our work for the next months

23 23 Biodiversity Virtual e-Laboratory BioVeL 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. contact Alex Hardisty:


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