introduction to scratchpads & vibrant

Ed BakerNatural History Museum, London, UK

Training session

Virtual BiodiversityViBRANT

Why Scratchpads?


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


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


Your data1

“Published” & reviewedon your site

3Uploaded &

tagged

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Fast Intuitive Fit for use

What is a Scratchpad?A website for you & your community


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


http://scratchpads.eu

ScratchpadsA multisite implementation of Drupal


Scratchpad Application FormFree to any individual or community


Flexible Template SiteWith easy navigation


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


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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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


SERVICEWP5. Data

WP6. Publishing

WP4. StandardsWP8. Mobilisation

RESEARCHWP2. Architecture

WP7. Literature

NETWORKINGWP3. Training

ViBRANT Project planThe “chromosome”


ScratchpadTechnicalOverview


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


Scratchpad Developers Site

http://dev.scratchpads.eu/


ScratchpadFunctionality

Summary


TaxonomyTaxonomy import,management and

navigation


Bibliographic data

Reference manager /Endnote support forbibliographies


Images

Image galleries,image upload &annotation


Phylogeny

Nexus / Newick import forvisualizing phylogenies


Character Matricies

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


Distribution Maps

Presence absencecountry maps


Specimens & locations

Specimen & locationrecords (DwC)


Pages, Forums, Blogs, Newsletters

Web fora with e-mail integration

User blogs

Static web pages

Newsletters withe-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 itall together

- an example site


Scratchpad structure

Taxonomybiblio

Content typesimage page

taxon page view

term 1

term 2

term 3node view

list view

custom view


Knowledgebase on a family of flies

General Information


Special Information

User Comments


TaxonomyTaxonomy import,management and

navigation

Classification


‘Content’ menu


Image galleries


Link to image details


Image details

Classificationand other tags

Virtual BiodiversityViBRANTSpecies page

Nomenclatureand taxonomy

Images

Bibliography

Specimen

Specimen map

Links Pages

Authors &SourcesBHL

Speciesdescription

Countries map


Glossary

Definition of term

Explanation

Character evolution


character matrix

export to SDD and Nexus

Milichia online revision


PhylogenyNexus / Newick import forvisualizing phylogenies


Pages, Forums, Blogs, Newsletters

Web forums withe-mail integration

User blogs

Rich text editor

Newsletters withe-mail integration


Paper publication


User Support


Getting help

http://scratchpads.eu/help


The Sandbox


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Built in help, the FAQ & issues queue


• 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


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

• Idiosyncratic (colours & layouts)

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


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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3

4

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Scratchpads 2: user enhancements

• 3 current map types

Areas (TDWG level 4)

Specimen point localities

GBIF occurrence records


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)


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

introduction to scratchpads & vibrant

Technology

taxonomy taxonomy import

european biodiversity

virtual research communities

research database

scratchpad training

century taxonomy

mass import import

software user support