Swiss Orchid Foundation Scratchpads and ViBRANT overview
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This document discusses the challenges of modern taxonomy and proposes Scratchpads as a solution. Scratchpads are customizable, modular websites that allow taxonomists to store, share, and publish their research online. They provide taxonomy tools, multimedia galleries, mapping, and more. The ViBRANT project aims to develop and support Scratchpads further to help taxonomists collaborate globally on biodiversity research.
Swiss Orchid Foundation Scratchpads and ViBRANT overview
- 1. Ed Baker Natural History Museum, London, UK
- 2. ViBRANT Virtual Biodiversity Why Scratchpads?
- 3. ViBRANT Virtual Biodiversity 21st Century taxonomy The 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 Biodiversity The 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 Biodiversity Towards a solution The 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 Biodiversity Goal “a scholarly communication system that is intertwined with the pursuit of natural history, rather than an after- thought or annex”
- 7. ViBRANT Virtual Biodiversity What 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 Biodiversity Scratchpads Overview • 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 Biodiversity Scratchpad Application Form Free to any individual or community
- 10. ViBRANT Virtual Biodiversity Categories of Scratchpads Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
- 11. ViBRANT Virtual Biodiversity Flexible Template Site With easy navigation
- 13. ViBRANT Virtual Biodiversity Sustaining Scratchpads ViBRANT: 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 Biodiversity ViBRANT 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 months Collaboration… • 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 Biodiversity Scratchpad Technical Overview
- 16. ViBRANT Virtual Biodiversity Scratchpad management Scalable & sustainable technology Hardware, software & user support One 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 Biodiversity Scratchpad Developers Site http://dev.scratchpads.eu/
- 18. ViBRANT Virtual Biodiversity Scratchpad Functionality Summary
- 19. ViBRANT Virtual Biodiversity Taxonomy Taxonomy import, management and navigation
- 20. ViBRANT Virtual Biodiversity Bibliographic data Reference manager / Endnote support for bibliographies
- 21. ViBRANT Virtual Biodiversity Images Image galleries, image upload & annotation
- 22. ViBRANT Virtual Biodiversity Character Matricies Molecular & morphological character matricies (discrete, morphometric and text characters)
- 23. ViBRANT Virtual Biodiversity Mapping • Point & TDWG region maps • Flexible polygon maps & annotations • GBIF point imports • Edit point location & metadata
- 24. ViBRANT Virtual Biodiversity Specimens & locations Specimen & location records (DwC)
- 25. ViBRANT Virtual Biodiversity Pages, Forums, Blogs
- 26. ViBRANT Virtual Biodiversity Mass Import Import from Excel file to any content type
- 27. ViBRANT Virtual Biodiversity Administration
- 28. ViBRANT Virtual Biodiversity Putting it all together - an example site
- 29. ViBRANT Virtual Biodiversity Scratchpad 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 Biodiversity Home page
- 31. ViBRANT Virtual Biodiversity Scratchpad 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 Biodiversity Scratchpad 2 multimedia gallery • New look • Video support • Faceted search & browse • Embed YouTube & Vimeo
- 33. ViBRANT Virtual Biodiversity Scratchpad 2 taxon pages • Easy publishing to EOL • Better content control • Direct editing • Parent-child data inheritance • Inspired by Natural History Guides
- 34. ViBRANT Virtual Biodiversity Scratchpad 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 Biodiversity User Support
- 36. ViBRANT Virtual Biodiversity Getting help http://scratchpads.eu/help
- 37. ViBRANT Virtual Biodiversity The Sandbox
- 38. ViBRANT Virtual Biodiversity Built in help, the FAQ & issues queue