Scratchpad training

Vince Smith & Ed Baker Natural History Museum, London, UK Training session

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

Why Scratchpads?

21st Century taxonomy
Inventory the Earth’s species
Document their relationships
“ Publish” & apply these data
Goal… The challenge for modern taxonomists
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?

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

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

Scratchpads Overview
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

http://scratchpads.eu Scratchpads A multisite implementation of Drupal

Scratchpad Application Form Free to any individual or community

Flexible Template Site With easy navigation

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

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.

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
of 14 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

ViBRANT Project plan The “chromosome” SERVICE WP5. Data WP6. Publishing WP4. Standards WP8. Mobilisation RESEARCH WP2. Architecture WP7. Literature NETWORKING WP3. Training

Scratchpad Technical Overview

Scratchpad Object Model http://scratchpads.eu/sites/scratchpads.eu/files/Scratchpad_Object_Model.pdf

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

Scratchpad Developers Site http://dev.scratchpads.eu/

Scratchpad SVN http://svn.scratchpads.eu/viewvc

Scratchpad Functionality Summary

Taxonomy Taxonomy import, management and navigation

Bibliographic data Reference manager / Endnote support for bibliographies

Images Image galleries, image upload & annotation

Phylogeny Nexus / Newick import for visualizing phylogenies

Character Matricies Molecular & morphological character matricies (discrete, morphometric and text characters)

Distribution Maps Presence absence country maps

Specimens & locations Specimen & location records (DwC)

Pages, Forums, Blogs, Newsletters Web fora with e-mail integration User blogs Static web pages Newsletters with e-mail integration

Mass Import Import from CSV text file to any content type

Create & switch between content in any language Multilingual Support

Administration Simple & advanced admin. AutoTag content (automatically adds structure) Private Groups Customized user profiles

Putting it all together - an example site

Scratchpad structure Taxonomy biblio Content types image page taxon page view term 1 term 2 term 3 node view list view custom view

Knowledgebase on a family of flies General Information

User Comments Special Information

Taxonomy Taxonomy import, management and navigation Classification

‘ Content’ menu

Image galleries

Link to image details

Image details Classification and other tags

Species page Nomenclature and taxonomy Images Bibliography Specimen Specimen map Links Pages Authors & Sources BHL Species description Countries map

Glossary Definition of term Explanation Character evolution

character matrix export to SDD and Nexus Milichia online revision

Phylogeny Nexus / Newick import for visualizing phylogenies

Pages, Forums, Blogs, Newsletters Web forums with e-mail integration User blogs Rich text editor Newsletters with e-mail integration

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

Paper publication

User Support

Getting help http://scratchpads.eu/help

The Sandbox

of Built in help, the FAQ & issues queue

Screencast s, but…

Questions?

Scratchpad Training http://training[X].taxon.name Username: username Password: password Sites will be available for 2 weeks Scratchpad Log-in http://scratchpads.eu/scratchpad-training-files Scratchpad Training Files http://carnidae.myspecies.info/ Example Completed Site - Carnidae

Scratchpad training

by Vincent Smith

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Scratchpad training Presentation Transcript