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Scratchpad training


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2011 Scratchpad training course presentation.

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Scratchpad training

  1. 1. Vince Smith & Ed Baker Natural History Museum, London, UK Training session
  2. 2. Overview of the day <ul><li>Expectations, introductions & goals </li></ul><ul><li>Overview presentation (30-40 minutes) </li></ul><ul><li>Overview of (10 minutes) </li></ul><ul><li>Training course options </li></ul><ul><ul><li>Basic training (2-5 hours) </li></ul></ul><ul><ul><li>Advanced training (3 hours) </li></ul></ul><ul><ul><li>Publication tool (1 hour) </li></ul></ul><ul><li>Final Q&A </li></ul><ul><li>Feedback form </li></ul>
  3. 3. Why Scratchpads?
  4. 4. 21st Century taxonomy <ul><li>Inventory the Earth’s species </li></ul><ul><li>Document their relationships </li></ul><ul><li>“ Publish” & apply these data </li></ul>Goal… The challenge for modern taxonomists <ul><li>1.8 M described spp. (10M names) </li></ul><ul><li>300M pages (over last 250 years) </li></ul><ul><li>1.5-3B specimens </li></ul>Data set… People… <ul><li>4-6,000 scientists </li></ul><ul><li>30-40,000 “pro-amateurs” </li></ul><ul><li>Many more citizen scientists? </li></ul>
  5. 5. Towards a solution The European Distributed Institute of Taxonomy <ul><li>A Network of Excellence (NoE) </li></ul><ul><li>29 leading European, North American, </li></ul><ul><li>& Russian natural history collections-based </li></ul><ul><li>institutions </li></ul><ul><li>Circa 12M €, funded under EU FP6 </li></ul><ul><li>March 2006 - February 2011 </li></ul>Products… <ul><li>Funding </li></ul><ul><li>Training & outreach </li></ul><ul><li>Websites </li></ul><ul><li>Integrated scientific activities </li></ul><ul><li>Inventories </li></ul><ul><li>Computer tools </li></ul>
  6. 6. Fast Intuitive Fit for use What is a Scratchpad? A website for you & your community Your data 1 “ Published” & reviewed on your site 3 Uploaded & tagged 2
  7. 7. Scratchpads Overview <ul><li>Hosted websites for taxonomists </li></ul><ul><li>Research & publication platform </li></ul><ul><li>Modular (Drupal) & flexible </li></ul><ul><li>Supports the taxonomic workflow </li></ul><ul><li>Bottom-up design, agile dev. </li></ul><ul><li>Ecosystem of communities (200) </li></ul><ul><li>2,500+ users (unpaid) from 2007 </li></ul>
  8. 8. Scratchpads A multisite implementation of Drupal
  9. 9. Scratchpad Application Form Free to any individual or community
  10. 10. Flexible Template Site With easy navigation
  11. 11. Sites: 200+ Users: 2500+ Pages: 300k+ Circa 2 new sites/wk. Since Mar. ‘07 10% access per mnth An ecosystem of communities 40% accessed per mnth
  12. 13. 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” <ul><li>A Virtual Research Environment ( Scratchpads ) where users can safely store, share and manage their research information. </li></ul><ul><li>Analytical services for users to build identification keys and phylogenetic trees. </li></ul><ul><li>A publication platform for users to automatically compile taxonomic manuscripts from their research database. </li></ul><ul><li>A portal for users to centrally access publicly accessible biodiversity research information and literature. </li></ul><ul><li>Training, support & sociological study , helping research communities to use these tools and services. </li></ul><ul><li>A standards compliant technical architecture that can be sustained by the biodiversity research community. </li></ul>
  13. 14. ViBRANT logistics <ul><li>Starts December 2010 (36 months) </li></ul><ul><li>Project website ( http: //vbrant . eu ) </li></ul><ul><li>Virtual Research Communities, CP-CSA, EU FP7 </li></ul><ul><li>€ 6.2M Euros (EU Contribution €4.75M) </li></ul><ul><li>17 Partners in 9 countries, 603 person months </li></ul> of 14 Collaboration… <ul><li>ESFRI Projects: LifeWatch, ELIXIR & EMBRC </li></ul><ul><li>GBIF - controlled vocabularies, nodes & observational data recording </li></ul><ul><li>PESI, 4D4Life & related EU projects </li></ul><ul><li>Encyclopedia of Life, Barcode of Life & Biodiversity Heritage Library </li></ul><ul><li>South African National Biodiversity Institute & Atlas of living Australia </li></ul>
  14. 15. ViBRANT Project plan The “chromosome” SERVICE WP5. Data WP6. Publishing WP4. Standards WP8. Mobilisation RESEARCH WP2. Architecture WP7. Literature NETWORKING WP3. Training
  15. 16. Scratchpad Technical Overview
  16. 17. Scratchpad Object Model
  17. 18. Scratchpad management Scalable & sustainable technology One virtual machine, open-source, self-archiving, backed-up, multi-site configuration ( easy to move & upgrade, secure & reliable, screencasts, low admin., low marginal costs ) Hardware, software & user support
  18. 19. Scratchpad Developers Site
  19. 20. Scratchpad SVN
  20. 21. Scratchpad Functionality Summary
  21. 22. Taxonomy Taxonomy import, management and navigation
  22. 23. Bibliographic data Reference manager / Endnote support for bibliographies
  23. 24. Images Image galleries, image upload & annotation
  24. 25. Phylogeny Nexus / Newick import for visualizing phylogenies
  25. 26. Character Matricies Molecular & morphological character matricies (discrete, morphometric and text characters)
  26. 27. Distribution Maps Presence absence country maps
  27. 28. Specimens & locations Specimen & location records (DwC)
  28. 29. Pages, Forums, Blogs, Newsletters Web fora with e-mail integration User blogs Static web pages Newsletters with e-mail integration
  29. 30. Mass Import Import from CSV text file to any content type
  30. 31. Create & switch between content in any language Multilingual Support
  31. 32. Administration Simple & advanced admin. AutoTag content (automatically adds structure) Private Groups Customized user profiles
  32. 33. Putting it all together - an example site
  33. 34. Scratchpad structure Taxonomy biblio Content types image page taxon page view term 1 term 2 term 3 node view list view custom view
  34. 35. Knowledgebase on a family of flies General Information
  35. 36. User Comments Special Information
  36. 37. Taxonomy Taxonomy import, management and navigation Classification
  37. 38. ‘ Content’ menu
  38. 39. Image galleries
  39. 41. Link to image details
  40. 42. Image details Classification and other tags
  41. 43. Species page Nomenclature and taxonomy Images Bibliography Specimen Specimen map Links Pages Authors & Sources BHL Species description Countries map
  42. 44. Glossary Definition of term Explanation Character evolution
  43. 45. character matrix export to SDD and Nexus Milichia online revision
  44. 46. Phylogeny Nexus / Newick import for visualizing phylogenies
  45. 47. Pages, Forums, Blogs, Newsletters Web forums with e-mail integration User blogs Rich text editor Newsletters with e-mail integration
  46. 48. Special functions Multilingual support Private groups – an area on your site that is visible only to selected users Autotagging – automatically add structure to your content
  47. 49. Paper publication
  48. 50. User Support
  49. 51. Getting help
  50. 52. The Sandbox
  51. 53. of Built in help, the FAQ & issues queue
  52. 54. Screencast s, but…
  53. 55. Questions?
  54. 56. Scratchpad Training http://training[X] Username: username Password: password Sites will be available for 2 weeks Scratchpad Log-in Scratchpad Training Files Example Completed Site - Carnidae