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WP5 Overview (Data services)

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  • 1. Identification and Analysis Tools for Scratchpads NEIL CAITHNESS University of Oxford [email_address] Workpackage 5 Interaction and Services Overview Taxon Data ViBRANT Virtual Biodiversity External Computing Services
  • 2. Who we are & what we do 2 of 10 Who we are What we do 4 UOXF Oxford Neil Caithness Milo Thurston e-Science e-Science 2.6 36 3% 41% 6 JKI Berlin Gregor Hagedorn Standards 19 22% 11 VIZZ Madrid Javier de la Torre Visualization 12 14% 13 UPMC Paris Régine Vignes-Lebbe To be appointed Identification Identification 3 12 3% 14% 16 ULR Reunion Noël Conruyt Identification 3 3% 87.6 100%
  • 3. Brief bio 3 of 10
    • South Africa – Zoology (UCT & Wits University)
      • Teaching: evolution and speciation
      • Field work on African Antelope: South Africa, Zimbabwe, Botswana (sometimes on horseback)
      • (Hugh Paterson, Elisabeth Vrba, Robin Crewe)
    • USA – Post-doc (American Museum of Natural History)
      • Ornithology: bioclimatic modelling of African Passerine birds
      • (Joel Cracraft, George Barrowclough, Gary Nelson)
    • UK –
      • NHM (zoology, entomology, botany)
      • Reading – grid pilot project for computational workflows supporting biodiversity science
      • Oxford – research facilitator for general e-Science, now moving more towards biology with collaborations in Oxford Zoology
  • 4. What we will do in ViBRANT
    • Design and implement a mechanism for Scratchpads to send jobs to external computing services and to receive the results …
      • Design and maintain the Tools API
      • Implement and maintain a working system
    4 of 10
  • 5. What we will do in ViBRANT
    • Provide a series of working services …
      • Phylogenetic services
        • GARLI, PAUP, TNT, Mr Bayes …
      • Bioclimatic modelling services
        • GARP, MaxEnt, CSM …
      • Identification services for molecular data
        • NCBI BLAST, Barcode of Life Database (BOLD) …
      • Identification services for morphological descriptions (UPMC)
        • Xper2, Lucid …
    5 of 10
  • 6. What we will do in ViBRANT
    • Work behind the scenes …
      • Computing platforms deployment infrastructure
        • Oxford Supercomputing Centre
        • NGS Campus Grids
        • Volunteer computing (e.g. BOINC)
        • Amazon cloud-like services
      • Job description and metadata repository
        • A complete history of jobs shown to the user via the Enhanced Scratchpad User Interface
      • Enhanced user interface and matrix editor (JKI)
      • Enhanced visualization services (VIZZ)
      • Biodiversity patterns and indices (VIZZ)
    6 of 10
  • 7. … Schematic Summary WP5 WP5 WP5 API (BB) 7 of 10 Visualization Data tools Virtual Biodiversity ViBRANT Scratchpad Scratchpad Scratchpad Scratchpad Scratchpad Scratchpad Scratchpad Scratchpad Scratchpad Scratchpad Service Service Service Service Service Service Service Service Service
  • 8. Linking workpackage activities within ViBRANT
    • WP1. for project management
    • WP2. for dependent engineering of core Drupal systems
    • WP3. for user feedback on desired tools and services
    • WP4. for linkage between data API and tools API
    • WP5. … that’s us
    • WP6. (none planned – consider metatdata to aid markup)
    • WP7. (none planned – consider data mining as a service)
    • WP8. for linkage with biodiversity patterns and indices work
    8 of 10
  • 9. Who are our users & how will they engage?
    • Scratchpad users
    • Service providers anyone providing a new computational service to Scratchpads
    • Admin users providing usage tracking for external services
    9 of 10
  • 10. Risk & Mitigation
    • We may not do what we said we were going to do.
    • We will always do what we say we will do.
    • IN OTHER WORDS
    • Be agile enough to do what is considered best.
    • Communication and mutual agreement are the key.
    10 of 10 RISK MITIGATION
  • 11. Schedule of Talks 12:05 WP5 Overview (Data analysis services) Neil Caithness, WP leader 12:15 Distributed services Milo Thurston 12:20 Identification keys Régine Vignes-Lebbe 12:25 Ontologies for description, classification and identification processes Noël Conruyt 12:30 Descriptive data supporting keys – SDD Gregor Hagedorn 12:35 Mobile phone apps monitoring biodiversity Javier de la Torre 12:40 Biodiversity indices Javier de la Torre 12:45 WP5 general discussion and questions Facilitator: Neil Caithness 12:50 LUNCH Museum Canteen

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