Swiss Orchid Foundation Scratchpads and ViBRANT overview

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Swiss Orchid Foundation Scratchpads and ViBRANT overview

  1. 1. Ed BakerNatural History Museum, London, UK
  2. 2. ViBRANT Virtual BiodiversityWhy Scratchpads?
  3. 3. ViBRANT Virtual Biodiversity21st Century taxonomyThe challenge for modern taxonomists Goal… • Inventory the Earth’s species • Document their relationships • “Publish” & apply these data Data set… • 1.8 M described spp. (10M names) • 300M pages (over last 250 years) • 1.5-3B specimens People… • 4-6,000 scientists • 30-40,000 “pro-amateurs” • Many more citizen scientists?
  4. 4. ViBRANT Virtual BiodiversityThe problem Science is global • It needs global standards • Global workflows • Cooperation of global players Science is carried out “locally” • By local scientists • Being part of local infrastructures • Having local funders
  5. 5. ViBRANT Virtual BiodiversityTowards a solutionThe European Distributed Institute of Taxonomy • A Network of Excellence (NoE) • 29 leading European, North American, & Russian natural history collections-based institutions • Circa 12M !, funded under EU FP6 • March 2006 - February 2011 Products… • Funding • Training & outreach • Websites • Integrated scientific activities • Inventories • Computer tools
  6. 6. ViBRANT Virtual BiodiversityGoal “a scholarly communication system that is intertwined with the pursuit of natural history, rather than an after- thought or annex”
  7. 7. ViBRANT Virtual BiodiversityWhat is a Scratchpad? A website for you & your community 1 2 3 Your data Uploaded & “Published” & reviewed tagged on your site Fast Intuitive Fit for use
  8. 8. ViBRANT Virtual BiodiversityScratchpadsOverview • Hosted websites for taxonomists • Research & publication platform • Modular (Drupal) & flexible • Supports the taxonomic workflow • Bottom-up design, agile dev. • Ecosystem of communities (330+) • 7,350+ users (unpaid) from 2007
  9. 9. ViBRANT Virtual BiodiversityScratchpad Application FormFree to any individual or community
  10. 10. ViBRANT Virtual BiodiversityCategories of Scratchpads Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
  11. 11. ViBRANT Virtual BiodiversityFlexible Template SiteWith easy navigation
  12. 12. ViBRANT Virtual Biodiversity
  13. 13. ViBRANT Virtual BiodiversitySustaining ScratchpadsViBRANT: Building on EDIT & the Scratchpads “To set up the means, tools and infrastructure to produce a more rational and a more effective framework for European Biodiversity research” • A Virtual Research Environment (Scratchpads) where users can safely store, share and manage their research information. • Analytical services for users to build identification keys and phylogenetic trees. • A publication platform for users to automatically compile taxonomic manuscripts from their research database. • A portal for users to centrally access publicly accessible biodiversity research information and literature. • Training, support & sociological study, helping research communities to use these tools and services. • A standards compliant technical architecture that can be sustained by the biodiversity research community.
  14. 14. ViBRANT Virtual BiodiversityViBRANT logistics • Starts December 2010 (36 months) • Project website (http://vbrant.eu) • Virtual Research Communities, CP-CSA, EU FP7 • !6.2M Euros (EU Contribution !4.75M) • 17 Partners in 9 countries, 603 person monthsCollaboration… • ESFRI Projects: LifeWatch, ELIXIR & EMBRC • GBIF - controlled vocabularies, nodes & observational data recording • PESI, 4D4Life & related EU projects • Encyclopedia of Life, Barcode of Life & Biodiversity Heritage Library • South African National Biodiversity Institute & Atlas of living Australia
  15. 15. ViBRANT Virtual BiodiversityScratchpad Technical Overview
  16. 16. ViBRANT Virtual BiodiversityScratchpad management Scalable & sustainable technology Hardware, software & user supportOne virtual machine, open-source, self-archiving, backed-up, multi-site configuration (easy to move & upgrade, secure & reliable, low admin., low marginal costs)
  17. 17. ViBRANT Virtual BiodiversityScratchpad Developers Site http://dev.scratchpads.eu/
  18. 18. ViBRANT Virtual BiodiversityScratchpadFunctionality Summary
  19. 19. ViBRANT Virtual BiodiversityTaxonomy Taxonomy import, management and navigation
  20. 20. ViBRANT Virtual BiodiversityBibliographic dataReference manager /Endnote support forbibliographies
  21. 21. ViBRANT Virtual BiodiversityImagesImage galleries,image upload &annotation
  22. 22. ViBRANT Virtual BiodiversityCharacter Matricies Molecular & morphological character matricies (discrete, morphometric and text characters)
  23. 23. ViBRANT Virtual BiodiversityMapping • Point & TDWG region maps • Flexible polygon maps & annotations • GBIF point imports • Edit point location & metadata
  24. 24. ViBRANT Virtual BiodiversitySpecimens & locations Specimen & location records (DwC)
  25. 25. ViBRANT Virtual BiodiversityPages, Forums, Blogs
  26. 26. ViBRANT Virtual BiodiversityMass Import Import from Excel file to any content type
  27. 27. ViBRANT Virtual BiodiversityAdministration
  28. 28. ViBRANT Virtual Biodiversity Putting it all together- an example site
  29. 29. ViBRANT Virtual BiodiversityScratchpad structure list view Content types image biblio page Taxonomy taxon page view term 1 term 2 custom view node view term 3
  30. 30. ViBRANT Virtual BiodiversityHome page
  31. 31. ViBRANT Virtual BiodiversityScratchpad 2 faceted search • Rapid content discovery • Systematic browsing • Content specific facet display (e.g. biblo, media) • Slickgrid filters for other content types
  32. 32. ViBRANT Virtual BiodiversityScratchpad 2 multimedia gallery • New look • Video support • Faceted search & browse • Embed YouTube & Vimeo
  33. 33. ViBRANT Virtual BiodiversityScratchpad 2 taxon pages • Easy publishing to EOL • Better content control • Direct editing • Parent-child data inheritance • Inspired by Natural History Guides
  34. 34. ViBRANT Virtual BiodiversityScratchpad 2 “publication” options Taxon descriptions • Manuscripts from Scratchpads to ZooKeys & PhytoKeys • Produced directly from the database • Three exemplar papers produced via SP1 • Comprehensive new data structure in SP2 1. Define the 2. Enter 3. Select taxa 4. Organise 5. Submit to publication metadata & content manuscript journal
  35. 35. ViBRANT Virtual BiodiversityUser Support
  36. 36. ViBRANT Virtual BiodiversityGetting help http://scratchpads.eu/help
  37. 37. ViBRANT Virtual BiodiversityThe Sandbox
  38. 38. ViBRANT Virtual BiodiversityBuilt in help, the FAQ & issues queue

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