Introduction to Scratchpads & ViBRANT

Ed BakerNatural History Museum, London, UK

Training session

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 newsites/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 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.

Virtual BiodiversityViBRANT

13 of

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

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

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 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

Virtual BiodiversityViBRANT

Scratchpad Developers Site

http://dev.scratchpads.eu/

Virtual BiodiversityViBRANT

ScratchpadFunctionality

Summary

Virtual BiodiversityViBRANT

TaxonomyTaxonomy import,management and

navigation

Virtual BiodiversityViBRANT

Bibliographic data

Reference manager /Endnote support forbibliographies

Virtual BiodiversityViBRANT

Images

Image galleries,image upload &annotation

Virtual BiodiversityViBRANT

Phylogeny

Nexus / Newick import forvisualizing phylogenies

Virtual BiodiversityViBRANT

Character Matricies

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

Virtual BiodiversityViBRANT

Distribution Maps

Presence absencecountry maps

Virtual BiodiversityViBRANT

Specimens & locations

Specimen & locationrecords (DwC)

Virtual BiodiversityViBRANT

Pages, Forums, Blogs, Newsletters

Web fora with e-mail integration

User blogs

Static web pages

Newsletters withe-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 3node 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

Classificationand other tags

Virtual BiodiversityViBRANTSpecies page

Nomenclatureand taxonomy

Images

Bibliography

Specimen

Specimen map

Links Pages

Authors &SourcesBHL

Speciesdescription

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 forvisualizing phylogenies

Virtual BiodiversityViBRANT

Pages, Forums, Blogs, Newsletters

Web forums withe-mail integration

User blogs

Rich text editor

Newsletters withe-mail integration

Virtual BiodiversityViBRANT

Paper publication

Virtual BiodiversityViBRANT

User Support

Virtual BiodiversityViBRANT

Getting help

http://scratchpads.eu/help

Virtual BiodiversityViBRANT

The Sandbox

Virtual BiodiversityViBRANT

49 of

Built in help, the FAQ & issues queue

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

Virtual BiodiversityViBRANT

Scratchpads 2: user enhancements• Most sites use Garland (improves site looks)

• Idiosyncratic (colours & layouts)

• Sp2 more professional & scholarly• Some flexibility (site profiles)

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

12

3

4

5

Virtual BiodiversityViBRANT

Scratchpads 2: user enhancements

• 3 current map types

Areas (TDWG level 4)

Specimen point localities

GBIF occurrence records

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)

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

bit.ly/Carex