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BIODIVERSITY VIRTUAL LABORATORY (BIOVEL) PILOT PROJECT AND OTHER BIODIVERSITY E-SCIENCE PROJECTS
Alex Hardisty Cardiff University
Biodiversity Forum, 4th April 2013, Beijing
Biodiversity monitoring and research networks
• LTER, Genomic Observatories, EMBRC, Natural
History Museums, EU BON, EMBOS, BioSOS
Biodiversity information systems
• ViBRANT, i4Life, PESI, WORMS, OBIS, GBIF,
GeneBank, AquaMaps, agINFRA, pro-iBioSphere,
OpenUp!, BioFresh, etc.
Biodiversity e-science infrastructures
• LifeWatch, BioVeL, iMarine, EUBrazilOpenBio
European e-Science Infrastructures for Biodiversity and Ecosystem Research
Data analysis
Data curation and access
Data generation
AN E-INFRASTRUCTURE AND E-SCIENCE ENVIRONMENT SUPPORTING RESEARCH ON BIODIVERSITY
Alex Hardisty Coordinator, Cardiff University
Biodiversity Forum, 4th April 2013, Beijing
Biodiversity Virtual e-Laboratory
• Aims to foster cooperation in the community by:
– Discussing scientific use cases
– Identifying and deploying important Web Services
– Designing and offering workflows
– Training scientists
• Aims to create a “Service Network”
– Web services for interdisciplinary analysis of biodiversity
• And “workflows” for science
Ecological Niche Modelling Biogeochemical modelling Metagenomics Phylogenetics Population Modelling Taxonomy Geospatial Visualization
An international network of experts connecting 2 scientific communities: biodiversity and ICT,
to create a general purpose Virtual e-Laboratory
The Service Network idea
Users’ workflows and applications
Service and Data Providers (LifeWatch, BioVeL, GBIF, CoL, EBI, etc.)
Resource Providers (EUDAT, EGI.eu, PRACE, commercial cloud, etc.)
www.biodiversitycatalogue.org A fully curated, well-founded catalogue of
Web services for biodiversity science
Part of a workflow to study the
ecological niche of the Horseshoe crab
(Limulus polyphemus)
Products are “workflows” built from “services”
• 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 own research and/or from existing libraries (e.g., GBIF, Catalogue of Life)
• Access a library of workflows Re-use existing workflows
– Improves efficiency by reducing research time and overhead expenses
www.myexperiment.org A repository for sharing workflows
• Niche modelling of interactions between forest insects and their host trees under various climate change scenarios
• Quantifying taxonomic and geographical change over seven decades of anthropogenic pressures in the North East Atlantic
• Deriving quantitative ecosystem service indicators and developing a new IT tool based on terrestrial ecosystem simulations
• Studying microbial communities through metagenomics and a functional trait-based ecology
• Spatial-Temporal Visualisation of Biodiversity Data: an integrative Tool for Ecologists
• Large scale modelling of the distribution and impact of invasive species in the Baltic Sea
• Carbon Sequestration • Ecosystem Functioning and Valuation • Invasive Species Management
6 submissions to INTECOL 2013 (waiting)
Creates powerful data processing tools for biodiversity research
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
14. University of Gothenburg, Sweden 15. University of Manchester, UK
• 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 contribution to 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.
A Data e-Infrastructure and specialised Virtual Laboratory initiative for Fisheries Management and Conservation of Marine Living Resources – based on a managed Ecosystem Approach
www.i-marine.eu
i-Marine
“The creation of the marine knowledge begins with the observation of the sea and oceans. Data from these observations are assembled, then analysed to create information and knowledge. Subsequently, the knowledge can be applied to deliver smart sustainable growth, to assess the health of the marine ecosystem or to protect coastal communities.”
Source: EC Communication on Marine Knowledge 2020
Multiple apps across integrated information
14
FIGIS (reports)
MyOcean (environmental data)
GENESI-DEC (earth observations)
DRIVER (publications)
OBIS (marine species data)
GBIF (occurrence points)
Catalogue of Life (taxonomy)
WoRMS (marine taxonomy)
ITIS (taxonomy)
AO SDMX Registry (stat. data)
AquaMaps (species maps)
FLOD (open linked data)
Geonetwork (georefenced data)
…Everything accessible through TAPIR, DigiR, OAI-PMH, OpenSearch, OGC W*S ,SDMX,….
software system)
Open e-Infrastructure capabilities to enhance Biodiversity community research
CRIA, SP
UFF, RJ CESAR, PE
RNP, RJ
BSC, Spain
CNR-ISTI, Italy
SP2000, UK
Trust-IT, UK
UPVLC, Spain
www.eubrazilopenbio.eu
Combining Biodiversity Science and Open Access to deploy a joint European and Brazilian e-Infrastructure
• Use case 1: Integration between Regional & Global Taxonomies – Cross-map the regional List of Species of Brazilian Flora with the Global
Catalogue of Life
• Use Case II: Data usability and ecological niche modelling – Use of openModeller in a distributed environment to run the models
• Open Access project e-Infrastructure – Research resources (HW, SW, Data) can be shared and exploited on-
demand in collaborative way (in virtual laboratory applications)
– Integration of resources from Brazil and Europe for benefit of both scientific communities
www.scratchpads.eu
The Catalogue of Life
4D4Life
Many information systems have a taxonomic (name) component. Before 1996 no single authoritative index of valid names, synonyms, common names was available. Authorized species names are important for reliable information services in society. The Catalogue of Life was set up to provide that service.
CoL
INDEX
Legislation: Species protection
Import/export Observations
Literature Reference systems
E-publications
Chemical substances: Source species
Medical information: E.g. medicinal plants
Image libraries: Images, videos, sounds
Molecular data: Sequences
Protein data
Identification data: Identification keys
Identification characters
Biological collections: (type) specimen
Historical data
Type strains
Ecological relations: E.g. Food web structures
Host-parasite relations
Taxonomic dbs
Hierarchies, names
What is the Catalogue of Life?
A Resource…
• an electronic synonymic species checklist,
• a tightly integrated taxonomic hierarchy,
• intended for all 1.9 M extant known species.
….constructed through international networking
• both checklist and hierarchy constructed from sectors from
many networked databases around the world
• and integrated using an international review panel of experts
www.catalogueoflife.org
Developments 2009-2013
Two e-infrastructure projects funded by the EC: 4D4Life: improving the internal infrastructure and services i4Life: building a virtual community of users
The 4D4Life Project (2009 – 2012)
builds a state-of-the art e-infrastructure that: • modernized information management tools • partly automated tasks; more efficient CoL production • structured information exchange in the project networks • synthesises a globally significant resource for science • dissemination in an array of web-services and e-products • multi-hub structure for regional deployment
4D4Life: Distributed Dynamic Diversity Databases for Life
4D4Life
The i4Life project (2010 – 2013) Establish a Virtual Research Community to integrate the indexing of biological species between the world’s major biodiversity programmes
• It uses the Catalogue of Life as a yardstick with which to compare and unify what is known
• will for the first time provide a summary of all species known on earth
• It will create a global standard for taxonomic data integration in electronic infrastructures world-wide
i4Life: Indexing for Life
More questions?