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WP5 Overview (Data services)


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WP5 Overview (Data services)

  1. 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. 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. 3. Brief bio 3 of 10 <ul><li>South Africa – Zoology (UCT & Wits University) </li></ul><ul><ul><li>Teaching: evolution and speciation </li></ul></ul><ul><ul><li>Field work on African Antelope: South Africa, Zimbabwe, Botswana (sometimes on horseback) </li></ul></ul><ul><ul><li>(Hugh Paterson, Elisabeth Vrba, Robin Crewe) </li></ul></ul><ul><li>USA – Post-doc (American Museum of Natural History) </li></ul><ul><ul><li>Ornithology: bioclimatic modelling of African Passerine birds </li></ul></ul><ul><ul><li>(Joel Cracraft, George Barrowclough, Gary Nelson) </li></ul></ul><ul><li>UK – </li></ul><ul><ul><li>NHM (zoology, entomology, botany) </li></ul></ul><ul><ul><li>Reading – grid pilot project for computational workflows supporting biodiversity science </li></ul></ul><ul><ul><li>Oxford – research facilitator for general e-Science, now moving more towards biology with collaborations in Oxford Zoology </li></ul></ul>
  4. 4. What we will do in ViBRANT <ul><li>Design and implement a mechanism for Scratchpads to send jobs to external computing services and to receive the results … </li></ul><ul><ul><li>Design and maintain the Tools API </li></ul></ul><ul><ul><li>Implement and maintain a working system </li></ul></ul>4 of 10
  5. 5. What we will do in ViBRANT <ul><li>Provide a series of working services … </li></ul><ul><ul><li>Phylogenetic services </li></ul></ul><ul><ul><ul><li>GARLI, PAUP, TNT, Mr Bayes … </li></ul></ul></ul><ul><ul><li>Bioclimatic modelling services </li></ul></ul><ul><ul><ul><li>GARP, MaxEnt, CSM … </li></ul></ul></ul><ul><ul><li>Identification services for molecular data </li></ul></ul><ul><ul><ul><li>NCBI BLAST, Barcode of Life Database (BOLD) … </li></ul></ul></ul><ul><ul><li>Identification services for morphological descriptions (UPMC) </li></ul></ul><ul><ul><ul><li>Xper2, Lucid … </li></ul></ul></ul>5 of 10
  6. 6. What we will do in ViBRANT <ul><li>Work behind the scenes … </li></ul><ul><ul><li>Computing platforms deployment infrastructure </li></ul></ul><ul><ul><ul><li>Oxford Supercomputing Centre </li></ul></ul></ul><ul><ul><ul><li>NGS Campus Grids </li></ul></ul></ul><ul><ul><ul><li>Volunteer computing (e.g. BOINC) </li></ul></ul></ul><ul><ul><ul><li>Amazon cloud-like services </li></ul></ul></ul><ul><ul><li>Job description and metadata repository </li></ul></ul><ul><ul><ul><li>A complete history of jobs shown to the user via the Enhanced Scratchpad User Interface </li></ul></ul></ul><ul><ul><li>Enhanced user interface and matrix editor (JKI) </li></ul></ul><ul><ul><li>Enhanced visualization services (VIZZ) </li></ul></ul><ul><ul><li>Biodiversity patterns and indices (VIZZ) </li></ul></ul>6 of 10
  7. 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. 8. Linking workpackage activities within ViBRANT <ul><li>WP1. for project management </li></ul><ul><li>WP2. for dependent engineering of core Drupal systems </li></ul><ul><li>WP3. for user feedback on desired tools and services </li></ul><ul><li>WP4. for linkage between data API and tools API </li></ul><ul><li>WP5. … that’s us </li></ul><ul><li>WP6. (none planned – consider metatdata to aid markup) </li></ul><ul><li>WP7. (none planned – consider data mining as a service) </li></ul><ul><li>WP8. for linkage with biodiversity patterns and indices work </li></ul>8 of 10
  9. 9. Who are our users & how will they engage? <ul><li>Scratchpad users </li></ul><ul><li>Service providers anyone providing a new computational service to Scratchpads </li></ul><ul><li>Admin users providing usage tracking for external services </li></ul>9 of 10
  10. 10. Risk & Mitigation <ul><li>We may not do what we said we were going to do. </li></ul><ul><li>We will always do what we say we will do. </li></ul><ul><li>IN OTHER WORDS </li></ul><ul><li>Be agile enough to do what is considered best. </li></ul><ul><li>Communication and mutual agreement are the key. </li></ul>10 of 10 RISK MITIGATION
  11. 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