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Biodiversity Virtual e-Laboratory

        Alex Hardisty, Coordinator
Who Am I?
 Alex Hardisty
    Director of Informatics Projects
    Cardiff School of Computer Science and Informatics
 My roles (as well as BioVeL Coordinator)
   LifeWatch Strategic Management (Tech. Architect)
   ENVRI Common operations of ESFRI Environmental
    Infrastructures (Workpackage leader)
   CReATIVE-B Coordination of Research e-Infrastructures
    Activities Toward an International Virtual Environment
    for Biodiversity (Workpackage leader)
Vision
 A seamlessly connected environment ...
    Service Oriented Architecture and e-Infrastructure
 that makes it easier for biodiversity scientists to
  carry out in-silico analysis of relevant biodiversity
  data and to pursue in-silico experimentation ...
    Virtual laboratory
 based on composing / executing sequences of
  data manipulations and modelling tasks
    Workflows composed from services
    Taxonomy, Phylogenetics, Metagenomics, Niche
     Modelling, Population modelling, Mapping, etc.
Value added
 Lowering barriers to entry for biodiversity
  e-Scientists
    Range of robust biodiversity services deployed
    Useful packs of workflows for biodiversity research
    Easier user interfaces for creating & using workflows
    Specific Support Centre for help and training
 Supporting science supporting EU biodiversity
  policy objectives
    CO2 sequestration, Invasive species, Ecosystem services
 Steps to integration of biodiversity research assets
Fits in a portfolio of
   Euro-biodiversity informatics
 Reputed NoEs
    ALTER-Net, EDIT, LTER-Europe, PESI, SCAR-MarBIN, etc.
 Funded projects
    4D4Life, Aquamaps, ArtDataBanken, BioDiversityWorld,
     BioFresh, EuroMarine, Fauna Iberica, iMarine, i4Life,
     OpenBio, OpenPlantBio, ViBRANT, etc.
 Important contribution to ESFRI LifeWatch

 Global context
    GBIF, GSC Biodiversity WG, CReATIVE-B
    pending EU-US cooperation
The consortium
                                                       (partners)
Partner                                                                 Scientific   Technical   e-Inf. access
Cardiff University (CU) - Coordinator                                                   X             X
Fraunhofer-Gesellschaft, Institute IAIS (FhG IAIS)                                      X
Hungarian Academy of Sciences Institute of Ecology and Botany (IEB)         X                         X
University of Amsterdam (UvA) Institute of Biodiversity and Ecosystem
                                                                            X                         X
Dynamics
National Research Council (CNR) Institute for Biomedical Technologies       X
University of Gothenburg (UGOT)                                             X                         X
Max Planck Society, MPI for Marine Microbiology (MPG)                       X           X
Centro de Referência em Informação Ambiental (CRIA)                         X           X
Netherlands Centre for Biodiversity (NCB Naturalis) (replaces
                                                                            X
Society for the Management of Electronic Biodiversity Data (SMEBD))
University of Manchester (UNIMAN)                                                       X             X
Foundation for Biodiversity Research (FRB)                                  X           X
University of Eastern Finland (UEF)                                         X                         X
Free University of Berlin – Botanical Gardens and Botanical Museum
                                                                            X           X
(FUB-BGBM)
National Institute of Nuclear Physics (INFN)                                            X             X
Stichting European Grid Initiative (EGI.eu)                                             X             X
Technology - myGrid
 myExperiment
   Workflows
    repository
   Social network
 BioCatalogue
    Services catalogue
 Taverna
    Workflow
     environment
 e-Infrastructures
What we need from
            e-Infrastructures
 Execution of workflow on e-Infrastructure
    Tools as services so environments like Taverna can
     access them
    Foundational services. We don’t want to do generic
     stuff. Clear, open, industry standard interfaces. No
     dependencies on particular provider
 Service scaling
    Capacity on-demand to support large scale analyses
 Strong channels of communication to providers
    e.g., to get technical know-how for packaging
     community services to be “e-Inf ready”
On fundamental model
            for e-Science
 Our project depends on it. Two areas need
  greater attention:
1. Better engagement with industry, leading to
   wide availability and use of sustained standard
   products - is necessary to reach critical mass
2. Closing the gap between what this community is
   doing and what the computing services
   organisations in the HEIs and Research Institutes
   are doing for general research, teaching and
   learning support
Questions?

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E cconcertation lyon-22-sep2011-v3

  • 1. Biodiversity Virtual e-Laboratory Alex Hardisty, Coordinator
  • 2. Who Am I?  Alex Hardisty  Director of Informatics Projects  Cardiff School of Computer Science and Informatics  My roles (as well as BioVeL Coordinator)  LifeWatch Strategic Management (Tech. Architect)  ENVRI Common operations of ESFRI Environmental Infrastructures (Workpackage leader)  CReATIVE-B Coordination of Research e-Infrastructures Activities Toward an International Virtual Environment for Biodiversity (Workpackage leader)
  • 3. Vision  A seamlessly connected environment ...  Service Oriented Architecture and e-Infrastructure  that makes it easier for biodiversity scientists to carry out in-silico analysis of relevant biodiversity data and to pursue in-silico experimentation ...  Virtual laboratory  based on composing / executing sequences of data manipulations and modelling tasks  Workflows composed from services  Taxonomy, Phylogenetics, Metagenomics, Niche Modelling, Population modelling, Mapping, etc.
  • 4. Value added  Lowering barriers to entry for biodiversity e-Scientists  Range of robust biodiversity services deployed  Useful packs of workflows for biodiversity research  Easier user interfaces for creating & using workflows  Specific Support Centre for help and training  Supporting science supporting EU biodiversity policy objectives  CO2 sequestration, Invasive species, Ecosystem services  Steps to integration of biodiversity research assets
  • 5. Fits in a portfolio of Euro-biodiversity informatics  Reputed NoEs  ALTER-Net, EDIT, LTER-Europe, PESI, SCAR-MarBIN, etc.  Funded projects  4D4Life, Aquamaps, ArtDataBanken, BioDiversityWorld, BioFresh, EuroMarine, Fauna Iberica, iMarine, i4Life, OpenBio, OpenPlantBio, ViBRANT, etc.  Important contribution to ESFRI LifeWatch  Global context  GBIF, GSC Biodiversity WG, CReATIVE-B  pending EU-US cooperation
  • 6. The consortium (partners) Partner Scientific Technical e-Inf. access Cardiff University (CU) - Coordinator X X Fraunhofer-Gesellschaft, Institute IAIS (FhG IAIS) X Hungarian Academy of Sciences Institute of Ecology and Botany (IEB) X X University of Amsterdam (UvA) Institute of Biodiversity and Ecosystem X X Dynamics National Research Council (CNR) Institute for Biomedical Technologies X University of Gothenburg (UGOT) X X Max Planck Society, MPI for Marine Microbiology (MPG) X X Centro de Referência em Informação Ambiental (CRIA) X X Netherlands Centre for Biodiversity (NCB Naturalis) (replaces X Society for the Management of Electronic Biodiversity Data (SMEBD)) University of Manchester (UNIMAN) X X Foundation for Biodiversity Research (FRB) X X University of Eastern Finland (UEF) X X Free University of Berlin – Botanical Gardens and Botanical Museum X X (FUB-BGBM) National Institute of Nuclear Physics (INFN) X X Stichting European Grid Initiative (EGI.eu) X X
  • 7. Technology - myGrid  myExperiment  Workflows repository  Social network  BioCatalogue  Services catalogue  Taverna  Workflow environment  e-Infrastructures
  • 8. What we need from e-Infrastructures  Execution of workflow on e-Infrastructure  Tools as services so environments like Taverna can access them  Foundational services. We don’t want to do generic stuff. Clear, open, industry standard interfaces. No dependencies on particular provider  Service scaling  Capacity on-demand to support large scale analyses  Strong channels of communication to providers  e.g., to get technical know-how for packaging community services to be “e-Inf ready”
  • 9. On fundamental model for e-Science  Our project depends on it. Two areas need greater attention: 1. Better engagement with industry, leading to wide availability and use of sustained standard products - is necessary to reach critical mass 2. Closing the gap between what this community is doing and what the computing services organisations in the HEIs and Research Institutes are doing for general research, teaching and learning support