Biodiversity Virtuale-LaboratoryProject OverviewBioVeL is an e-laboratory that supports researchon biodiversity using larg...
Biodiversity Virtual e-LaboratoryAn international network of experts connecting 2scientific communities: ICT and biodivers...
Biodiversity Virtual e-Laboratory BioVeL is a powerful data processing tool • Import data from your own research and/or fr...
Biodiversity Virtual e-LaboratoryShowcase study 1: create a workflow*Study on the ecological niche of the south east Asian...
Biodiversity Virtual e-LaboratoryShowcase study 2: re-use a workflowStudy on the ecological niche of the American horsesho...
What does BioVeL consist of? (1) Biodiversity Data        Data Services        Catalogues /User                           ...
What does BioVeL consist of? (2)                        Catalogues /                      ExecutionBiodiversity Services  ...
Service sets driven by science• Phylogeny and metagenomics services   – Measures of genetic diversity and     adaptation t...
Biospheric CO2 sequestration (1)SCIENCE & POLICY CONTEXT Emission is continuously increasing – 10 GtC in 2010 Sequestratio...
Biospheric CO2 sequestration (2)REVIEW IN PROGRESS Collected papers                         39 Selected and annotated pape...
Ecosystem functioning / valuation (1)SCIENCE & POLICY CONTEXT„Over the past 50 years, humans have changed ecosystems morer...
Ecosystem functioning / valuation (2)REVIEW IN PROGRESS Collected papers                    14 (will be completed) Selecte...
Invasive species management (1)SCIENCE & POLICY CONTEXT   Invasions of alien species are a leading cause of biodiversity l...
Invasive species management (2)REVIEW IN PROGRESS Collected papers                        9 (will be completed) Selected a...
Biodiversity Virtual e-LaboratoryBioVeL is a consortium of 15 partners from 9 countries1.  Cardiff University, UK – Coordi...
Supported by many friends• Become a ‘Friend of BioVeL’  – Deploy robust (Web) services for    biodiversity analysis and wo...
Fits in a portfolio of initiativesNoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.Projects: agINFRA, Aquamaps, Art...
• Exploring patterns of biodiversity and                                processes of biodiversity across time and         ...
LifeWatch as a distributed                     research infrastructure                                    Independent     ...
LifeWatch as a distributed                                  research infrastructure                                  Indep...
Finally ... ...• White Paper initiative  – Our community vision for biodiversity    informatics, to inform Horizon 2020  –...
Biodiversity Virtual e-LaboratoryBioVeL is funded by the European Commission7th Framework Programme (FP7).It is part of it...
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Biodiversity Virtual e-Laboratory (BioVeL)

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BioVeL (Biodiversity Virtual e-Laboratory) is an e-laboratory that supports research on biodiversity using large amounts of data from cross-disciplinary sources.

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  • BioVeLfocusses on:DNA sequence-based phylogeny and metagenomics services that help link knowledge of model organisms to a broad range of species, that provide a measure of genetic diversity used in conservation planning and that help to understand adaptation in relation to climate change;Taxonomy services to provide the underpinning checklist of diversity in Europe, identification aids to native, invasive and economic species; Niche and population modelling for species, to better understand the processes of conservation and invasive species management; and, Ecosystem functionality and valuation services, to improve modelling capabilities to ecosystem services and CO2 sequestration.
  • Terrestrial sequestration is also increasing, but only 26% of the total emission, oceans can eliminate about 24%About 50% of the total emission remains and accumulates in the atmosphere --- In 2010REF: Global Carbon Project 2010; Updated from Le Quéré et al. 2009, Nature Geoscience; Canadell et al. 2007, PNAS
  • Fluxnet –coordinates regional and global analysis of observations from micrometeorological tower sites. The flux tower sites use eddy covariance methods to measure the exchanges of carbon dioxide (CO2), water vapor, and energy between terrestrial ecosystems and the atmosphere. NTSG : Numerical Terradynamic Simulation GroupGHG-Europe : Greenhouse Gas management in European land use systems
  • „Over the past 50 years, humans have changed ecosystemsmore rapidly and extensively than in any comparable period oftime in human history, largely to meet rapidly growing demands forfood, fresh water, timber, fiber, and fuel. This has resulted in a substantialand largely irreversible loss in the diversity of life on Earth.”Millenium Ecosystem Assessment 2005Challenges:Role of biodiversity and community ecology in ecosystem functioning2. "How much are the productivity and other services of the ecosystems in given ecological circumstances and management regimes? - maybe it would be better (provoking) to say "How much (and what measure) are the other ecosystem services than productivity?" - Because we know a lot about productivity of different type of ecosystems (easy to measure in agroecosystems, not so easy to measure/estimate in natural ecosystems), but what about other ecosystem services such as maintaining hydrologic cycles, regulating climate, cleansing air and water, maintaining atmospheric composition, pollination, soil genesis, storing and cycling of nutrients ...3. "What is the trade off among different ecosystem functions and management regimes in various ecosystems at landscape levels?" - mostly if we consider extensive and/or sustainable agriculture and/or various mosaic of landuse patterns, not massive uniform large croplands ...
  • Biodiversity Virtual e-Laboratory (BioVeL)

    1. 1. Biodiversity Virtuale-LaboratoryProject OverviewBioVeL is an e-laboratory that supports researchon biodiversity using large amounts of data fromcross-disciplinary sources.Alex HardistyProject CoordinatorCardiff University 1
    2. 2. Biodiversity Virtual e-LaboratoryAn international network of experts connecting 2scientific communities: ICT and biodiversityOffers access to a variety of data processingservices, linked as ‘workflows’ for assistingstudies in biodiversity science • You will hear about these during this workshop • You will be able to influence their designAims to foster cooperation in the community by: • Discussing use cases • Identifying important Web Services • Training scientists 2
    3. 3. 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 expensesWorkflow for population modelling (stage-based matrix projection models)based on Stubben and Milligan. Journal of Statistical Software, 22(11), Sept 2007 3
    4. 4. Biodiversity Virtual e-LaboratoryShowcase study 1: create a workflow*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 4 * courtesy Matthias Obst, University of Gothenburg, Sweden
    5. 5. Biodiversity Virtual e-LaboratoryShowcase study 2: re-use a workflowStudy 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 crabCompare 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 5
    6. 6. What does BioVeL consist of? (1) Biodiversity Data Data Services Catalogues /User Repositories xls, csv BioVeLData REST Manager documents GenBank RESTCollections Genomic data Catalogue REST Taxonomic data of Life CSW Observations GBIF RESTSpatial (Web) OGC raster sensor nodes data data BioVeL RESTCollaboration GeoServer OGC Annotations Workflows 6
    7. 7. What does BioVeL consist of? (2) Catalogues / ExecutionBiodiversity Services Repositories environmentPhylogenetic BLAST,Hmmer, Provenance WebDaV Data MrBayes, Management Blast, PAML, EMBOSS,… TavernaTaxonomic Workbench OpenSearch SynonymsVisualization BioSTIF Taverna Google Refine CSW Workflow EngineModelling / Authentication / AuthorisationGeoProcessing R Grid, Cloud, etc. openModeller WPS / WCPS 7
    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 CO2 sequestration 8• Visualization and geospatial
    9. 9. 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 changeSCIENTIFIC CHALLENGES Model improvement Model & data downscaling Model verification >> data-model calibration >> higher processing capacity 9
    10. 10. Biospheric CO2 sequestration (2)REVIEW IN PROGRESS Collected papers 39 Selected and annotated papers 35MOST RELEVANT RESEARCH GROUPS/PROJECTS The Global Carbon Project, Fluxnet – eddy covariance tower measurements, GHG Europe, ICOS, NTSG (University Montana) and Biome-BGC users & developers worldwideBiome-BGC is a computer model that estimates fluxes and storage of energy,water, carbon, and nitrogen for the vegetation and soil components ofterrestrial ecosystems.TYPICAL „WORKFLOWS” around Biome-BGC Weather to Biome-BGC; Biome-BGC CARBON; Biome-BGC Sensitivity Analysis; Biome-BGC Data-Model HarmonizationWEB SERVICES no such kind of services operating yet new service sets identified and prioritised to develop: 4 data retrieval services 10 6 Biome-BGC modelling services
    11. 11. Ecosystem functioning / valuation (1)SCIENCE & POLICY CONTEXT„Over the past 50 years, humans have changed ecosystems morerapidly and extensively than … this has resulted in a substantial andlargely irreversible loss in the diversity of life on Earth.”„… degradation of many ecosystem services [causes] increased risksof nonlinear changes …”„… reversing the degradation of ecosystems while meetingincreasing demands for their services can be partially met under somescenarios …, but these involve significant changes in policies, institutions,and practices that are not currently under way.” MEA 2005SCIENTIFIC 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 11 >> potential of metagenomics in ES valuation
    12. 12. Ecosystem functioning / valuation (2)REVIEW IN PROGRESS Collected papers 14 (will be completed) Selected and annotated papers -MOST RELEVANT RESEARCH GROUPS/PROJECTS not evaluated yetTYPICAL „WORKFLOWS” calculating ecosystem service indicators based on model simulation … will be completedWEB 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 12
    13. 13. Invasive species management (1)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) 13
    14. 14. Invasive species management (2)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 yetTYPICAL „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, … 14
    15. 15. Biodiversity Virtual e-LaboratoryBioVeL is a consortium of 15 partners from 9 countries1. Cardiff University, UK – Coordinator2. 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, Italy10. Netherlands Centre for Biodiversity (NCB 13. University of Eastern Finland, Finland Naturalis), The Netherlands 14. University of Gothenburg, Sweden11. Stichting European Grid Initiative, 15. University of Manchester, UK The Netherlands12. University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics, The Netherlands 15
    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 16
    17. 17. Fits in a portfolio of initiativesNoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.Projects: agINFRA, Aquamaps, ArtDataBanken, BioFresh, Envri,EU BON, EUBrazilOpenBio, Fauna Iberica, iMarine, MicroB3,OpenPlantBio, ViBRANTGlobal: Catalogue of Life, COOPEUS, CReATIVE-B, EoL, GBIF, GSCBiodiversity WG, TreeBase, and many moreRecognised as providing animportant contribution ofinfrastructure 17
    18. 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 portal1995 2005 2008 2011 2016 Operation & Earlier projects Conceive Preparations Construction 19 5+2 Evolution €5m ~ €234m
    19. 19. LifeWatch as a distributed research infrastructure Independent entities contributing to LifeWatch operationsDistributed coreoperationsowned byLifeWatch
    20. 20. LifeWatch as a distributed research infrastructure Independent entities contributing to LifeWatch operations National contributions • BelgiumDistributed coreoperations • Hungaryowned byLifeWatch • Italy • Netherlands Core operations • Romania • BioVeL • Spain • European Taxonomic Backbone • Sweden • Other ICT Core elements 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
    21. 21. 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 22
    22. 22. Biodiversity Virtual e-LaboratoryBioVeL is funded by the European Commission7th 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 developmentand 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 theadoption of e-Infrastructures by user communities.BioVeL is free and available via internet.www.biovel.eu, contact Alex Hardisty: HardistyAR@cardiff.ac.uk 23

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