scratchpad training
DESCRIPTION
2011 Scratchpad training course presentation.TRANSCRIPT
Vince Smith & Ed BakerNatural History Museum, London, UK
Training session
Virtual BiodiversityViBRANT
Overview of the day
• Expectations, introductions & goals• Overview presentation (30-40 minutes)
• Overview of http://scratchpads.eu (10 minutes)
• Training course options- Basic training (2-5 hours)
- Advanced training (3 hours)
- Publication tool (1 hour)
• Final Q&A• Feedback form
Virtual BiodiversityViBRANT
Why Scratchpads?
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
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
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
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
Virtual BiodiversityViBRANT
http://scratchpads.eu
ScratchpadsA multisite implementation of Drupal
Virtual BiodiversityViBRANT
Scratchpad Application FormFree to any individual or community
Virtual BiodiversityViBRANT
Flexible Template SiteWith easy navigation
Virtual BiodiversityViBRANT
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
Virtual BiodiversityViBRANT
Virtual BiodiversityViBRANT
Sustaining 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.
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
Virtual BiodiversityViBRANT
SERVICEWP5. Data
WP6. Publishing
WP4. StandardsWP8. Mobilisation
RESEARCHWP2. Architecture
WP7. Literature
NETWORKINGWP3. Training
ViBRANT Project planThe “chromosome”
Virtual BiodiversityViBRANT
ScratchpadTechnicalOverview
Virtual BiodiversityViBRANT
Scratchpad Object Model
http://scratchpads.eu/sites/scratchpads.eu/files/Scratchpad_Object_Model.pdf
Virtual BiodiversityViBRANT
Scratchpad managementScalable & 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
Virtual BiodiversityViBRANT
Scratchpad Developers Site
http://dev.scratchpads.eu/
Virtual BiodiversityViBRANT
Scratchpad SVN
http://svn.scratchpads.eu/viewvc
Virtual BiodiversityViBRANT
ScratchpadFunctionality
Summary
Virtual BiodiversityViBRANT
TaxonomyTaxonomy import, management and
navigation
Virtual BiodiversityViBRANT
Bibliographic data
Reference manager / Endnote support for bibliographies
Virtual BiodiversityViBRANT
Images
Image galleries,image upload & annotation
Virtual BiodiversityViBRANT
Phylogeny
Nexus / Newick import for visualizing phylogenies
Virtual BiodiversityViBRANT
Character Matricies
Molecular & morphological character matricies (discrete, morphometric and text characters)
Virtual BiodiversityViBRANT
Distribution Maps
Presence absence country maps
Virtual BiodiversityViBRANT
Specimens & locations
Specimen & location records (DwC)
Virtual BiodiversityViBRANT
Pages, Forums, Blogs, Newsletters
Web fora with e-mail integration
User blogs
Static web pages
Newsletters with e-mail integration
Virtual BiodiversityViBRANT
Mass Import
Import from CSV text file to any content type
Virtual BiodiversityViBRANT
Create & switch between content in any language
Multilingual Support
Virtual BiodiversityViBRANT
Administration
Simple & advanced admin.
AutoTag content(automatically adds structure)
Private Groups
Customized user profiles
Virtual BiodiversityViBRANT
Putting itall together
- an example site
Virtual BiodiversityViBRANT
Scratchpad structure
Taxonomybiblio
Content typesimage page
taxon page view
term 1
term 2
term 3
node view
list view
custom view
Virtual BiodiversityViBRANT
Knowledgebase on a family of flies
General Information
Virtual BiodiversityViBRANT
Special Information
User Comments
Virtual BiodiversityViBRANT
TaxonomyTaxonomy import, management and
navigation
Classification
Virtual BiodiversityViBRANT
‘Content’ menu
Virtual BiodiversityViBRANT
Image galleries
Virtual BiodiversityViBRANT
Virtual BiodiversityViBRANT
Link to image details
Virtual BiodiversityViBRANT
Image details
Classification and other tags
Virtual BiodiversityViBRANTSpecies page
Nomenclatureand taxonomy
Images
Bibliography
Specimen
Specimen map
Links Pages
Authors & Sources
BHL
Species description
Countries map
Virtual BiodiversityViBRANT
Glossary
Definition of term
Explanation
Character evolution
Virtual BiodiversityViBRANT
character matrix
export to SDD and Nexus
Milichia online revision
Virtual BiodiversityViBRANT
PhylogenyNexus / Newick import for visualizing phylogenies
Virtual BiodiversityViBRANT
Pages, Forums, Blogs, Newsletters
Web forums with e-mail integration
User blogs
Rich text editor
Newsletters with e-mail integration
Virtual BiodiversityViBRANT
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
Virtual BiodiversityViBRANT
Paper publication
Virtual BiodiversityViBRANT
User Support
Virtual BiodiversityViBRANT
Getting help
http://scratchpads.eu/help
Virtual BiodiversityViBRANT
The Sandbox
Virtual BiodiversityViBRANT
53 of
Built in help, the FAQ & issues queue
Virtual BiodiversityViBRANT
Screencasts, but…
Questions?
Virtual BiodiversityViBRANT
Scratchpad Training
http://training[X].taxon.name
Username: usernamePassword: password
Sites will be available for 2 weeks
Scratchpad Log-in
http://scratchpads.eu/scratchpad-training-filesScratchpad Training Files
http://carnidae.myspecies.info/Example Completed Site - Carnidae