introduction to scratchpads & vibrant
TRANSCRIPT
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Ed BakerNatural History Museum, London, UK
Training session
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Virtual BiodiversityViBRANT
Why Scratchpads?
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Virtual BiodiversityViBRANT
21st Century taxonomy
• Inventory the Earth’s species• Document their relationships• “Publish” & apply these data
Goal…
• 1.8 M described spp. (10M names)• 300M pages (over last 250 years)• 1.5-3B specimens
Data set…
People…• 4-6,000 scientists• 30-40,000 “pro-amateurs”• Many more citizen scientists?
The challenge for modern taxonomists
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Virtual BiodiversityViBRANT
Towards 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
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Virtual BiodiversityViBRANT
Your data1
“Published” & reviewedon your site
3Uploaded &
tagged
2
Fast Intuitive Fit for use
What is a Scratchpad?A website for you & your community
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Virtual BiodiversityViBRANT
ScratchpadsOverview
• Hosted websites for taxonomists• Research & publication platform• Modular (Drupal) & flexible• Supports the taxonomic workflow• Bottom-up design, agile dev.• Ecosystem of communities (200)• 2,500+ users (unpaid) from 2007
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Virtual BiodiversityViBRANT
http://scratchpads.eu
ScratchpadsA multisite implementation of Drupal
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Virtual BiodiversityViBRANT
Scratchpad Application FormFree to any individual or community
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Virtual BiodiversityViBRANT
Flexible Template SiteWith easy navigation
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Virtual BiodiversityViBRANT
Sites: 200+
Users: 2500+
Pages: 300k+
Circa 2 newsites/wk.
Since Mar. ‘07
10% access per mnth
An ecosystem of communities
40% accessed per mnth
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Virtual BiodiversityViBRANT
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Virtual BiodiversityViBRANT
Sustaining ScratchpadsViBRANT: Building on EDIT & the Scratchpads
“To set up the means, tools and infrastructure to produce a more rationaland a more effective framework for European Biodiversity research”
• A Virtual Research Environment (Scratchpads) where users can safelystore, share and manage their research information.
• Analytical services for users to build identification keys andphylogenetic trees.
• A publication platform for users to automatically compile taxonomicmanuscripts from their research database.
• A portal for users to centrally access publicly accessible biodiversityresearch information and literature.
• Training, support & sociological study, helping research communities touse these tools and services.
• A standards compliant technical architecture that can be sustained bythe biodiversity research community.
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Virtual BiodiversityViBRANT
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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
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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
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Virtual BiodiversityViBRANT
SERVICEWP5. Data
WP6. Publishing
WP4. StandardsWP8. Mobilisation
RESEARCHWP2. Architecture
WP7. Literature
NETWORKINGWP3. Training
ViBRANT Project planThe “chromosome”
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Virtual BiodiversityViBRANT
ScratchpadTechnicalOverview
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Virtual BiodiversityViBRANT
Scratchpad managementScalable & sustainable technology
One virtual machine, open-source, self-archiving, backed-up, multi-site configuration(easy to move & upgrade, secure & reliable, low admin., low marginal costs)
Hardware, software & user support
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Virtual BiodiversityViBRANT
Scratchpad Developers Site
http://dev.scratchpads.eu/
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Virtual BiodiversityViBRANT
ScratchpadFunctionality
Summary
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Virtual BiodiversityViBRANT
TaxonomyTaxonomy import,management and
navigation
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Virtual BiodiversityViBRANT
Bibliographic data
Reference manager /Endnote support forbibliographies
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Virtual BiodiversityViBRANT
Images
Image galleries,image upload &annotation
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Virtual BiodiversityViBRANT
Phylogeny
Nexus / Newick import forvisualizing phylogenies
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Virtual BiodiversityViBRANT
Character Matricies
Molecular & morphological character matricies(discrete, morphometric and text characters)
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Virtual BiodiversityViBRANT
Distribution Maps
Presence absencecountry maps
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Virtual BiodiversityViBRANT
Specimens & locations
Specimen & locationrecords (DwC)
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Virtual BiodiversityViBRANT
Pages, Forums, Blogs, Newsletters
Web fora with e-mail integration
User blogs
Static web pages
Newsletters withe-mail integration
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Virtual BiodiversityViBRANT
Mass Import
Import from CSV text file to any content type
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Virtual BiodiversityViBRANT
Create & switch between content in any language
Multilingual Support
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Virtual BiodiversityViBRANT
Administration
Simple & advanced admin.
AutoTag content(automatically adds structure)
Private Groups
Customized user profiles
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Virtual BiodiversityViBRANT
Putting itall together
- an example site
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Virtual BiodiversityViBRANT
Scratchpad structure
Taxonomybiblio
Content typesimage page
taxon page view
term 1
term 2
term 3node view
list view
custom view
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Virtual BiodiversityViBRANT
Knowledgebase on a family of flies
General Information
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Virtual BiodiversityViBRANT
Special Information
User Comments
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Virtual BiodiversityViBRANT
TaxonomyTaxonomy import,management and
navigation
Classification
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Virtual BiodiversityViBRANT
‘Content’ menu
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Virtual BiodiversityViBRANT
Image galleries
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Virtual BiodiversityViBRANT
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Virtual BiodiversityViBRANT
Link to image details
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Virtual BiodiversityViBRANT
Image details
Classificationand other tags
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Virtual BiodiversityViBRANTSpecies page
Nomenclatureand taxonomy
Images
Bibliography
Specimen
Specimen map
Links Pages
Authors &SourcesBHL
Speciesdescription
Countries map
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Virtual BiodiversityViBRANT
Glossary
Definition of term
Explanation
Character evolution
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Virtual BiodiversityViBRANT
character matrix
export to SDD and Nexus
Milichia online revision
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Virtual BiodiversityViBRANT
PhylogenyNexus / Newick import forvisualizing phylogenies
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Virtual BiodiversityViBRANT
Pages, Forums, Blogs, Newsletters
Web forums withe-mail integration
User blogs
Rich text editor
Newsletters withe-mail integration
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Virtual BiodiversityViBRANT
Paper publication
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Virtual BiodiversityViBRANT
User Support
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Virtual BiodiversityViBRANT
Getting help
http://scratchpads.eu/help
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Virtual BiodiversityViBRANT
The Sandbox
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Virtual BiodiversityViBRANT
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Built in help, the FAQ & issues queue
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Virtual BiodiversityViBRANT
• Scheduled for January 2012 (5 years after Scratchpad 1)
• Move from Drupal 6 to Drupal 7 (4 year upgrade cycle, UI + entities)
• 67 Contributed modules (31 done, 14 untested, 22 to do)
• 52 Scratchpad modules (28 done, 14 untested, 10 to do)
• Migrate current Scratchpads• New technical enhancements (hosting env., git, services, registry…)
- supporting sustainability• New user features (theme, workflow, spp. pages, mapping, services)
- supporting “publication”
Built in help, the FAQ & issues queue
http://wiki.scratchpads.eu/w/Wp2
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Virtual BiodiversityViBRANT
Scratchpads 2: user enhancements• Most sites use Garland (improves site looks)
• Idiosyncratic (colours & layouts)
• Sp2 more professional & scholarly• Some flexibility (site profiles)
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Virtual BiodiversityViBRANT
Scratchpads 2: user enhancements
• Basic vs. advanced admin• Poor findability, hard to use• Hide unnecessary items• Workflow complex functions
- Integrate complex actions- Guide the user through each step
o Adding userso Site setup functionso Groups & permissionso Edit / add content typeso Importing content & taxonomyo Creating serviceso Creating views
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Virtual BiodiversityViBRANT
Scratchpads 2: user enhancements
• 3 current map types
Areas (TDWG level 4)
Specimen point localities
GBIF occurrence records
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Virtual BiodiversityViBRANT
Scratchpads 2: user enhancementsIntegrated mapping
Areas (TDWG level 4)
TDWG area data (from Scratchpads)
Edit pointmetadata on map
Point localities (from Scratchpads)
Point localities (from GBIF)
Point localities (from flickr)
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Virtual BiodiversityViBRANT
Scratchpads: the futureA natively digital scholarly communication system
• The article was (is) the unit of scholarly comm. (350yrs)
• Research practices have moved ono Highly collaborative, data intensive & networked
• Scholarly communication has not adapted (e.g. the PDF)
• Published “knowledge” hides “dark data”• Need a natively digital scholarly communication system
o Must support end-to-end the lifecycle of data, information & knowledge
“the future scholarly communication system shouldclosely resemble—and be intertwined with—thescholarly endeavor itself, rather than beingits after-thought or annex” Van de Sompel et al 2004.
http://bit.ly/a3o9UX
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bit.ly/Carex