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Swiss Orchid Foundation Scratchpads and ViBRANT overview

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  • 1. Ed BakerNatural History Museum, London, UK
  • 2. ViBRANT Virtual BiodiversityWhy Scratchpads?
  • 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. 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. 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. ViBRANT Virtual BiodiversityGoal “a scholarly communication system that is intertwined with the pursuit of natural history, rather than an after- thought or annex”
  • 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. 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. ViBRANT Virtual BiodiversityScratchpad Application FormFree to any individual or community
  • 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. ViBRANT Virtual BiodiversityFlexible Template SiteWith easy navigation
  • 12. ViBRANT Virtual Biodiversity
  • 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. 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. ViBRANT Virtual BiodiversityScratchpad Technical Overview
  • 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. ViBRANT Virtual BiodiversityScratchpad Developers Site http://dev.scratchpads.eu/
  • 18. ViBRANT Virtual BiodiversityScratchpadFunctionality Summary
  • 19. ViBRANT Virtual BiodiversityTaxonomy Taxonomy import, management and navigation
  • 20. ViBRANT Virtual BiodiversityBibliographic dataReference manager /Endnote support forbibliographies
  • 21. ViBRANT Virtual BiodiversityImagesImage galleries,image upload &annotation
  • 22. ViBRANT Virtual BiodiversityCharacter Matricies Molecular & morphological character matricies (discrete, morphometric and text characters)
  • 23. ViBRANT Virtual BiodiversityMapping • Point & TDWG region maps • Flexible polygon maps & annotations • GBIF point imports • Edit point location & metadata
  • 24. ViBRANT Virtual BiodiversitySpecimens & locations Specimen & location records (DwC)
  • 25. ViBRANT Virtual BiodiversityPages, Forums, Blogs
  • 26. ViBRANT Virtual BiodiversityMass Import Import from Excel file to any content type
  • 27. ViBRANT Virtual BiodiversityAdministration
  • 28. ViBRANT Virtual Biodiversity Putting it all together- an example site
  • 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. ViBRANT Virtual BiodiversityHome page
  • 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. ViBRANT Virtual BiodiversityScratchpad 2 multimedia gallery • New look • Video support • Faceted search & browse • Embed YouTube & Vimeo
  • 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. 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. ViBRANT Virtual BiodiversityUser Support
  • 36. ViBRANT Virtual BiodiversityGetting help http://scratchpads.eu/help
  • 37. ViBRANT Virtual BiodiversityThe Sandbox
  • 38. ViBRANT Virtual BiodiversityBuilt in help, the FAQ & issues queue