Vincent S. Smith& Simon Rycroft

ScratchpadsA standard implementation using Drupal

Macro taxonomyThe foundation for biodiversity research

• 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?

Micro taxonomyThe process of taxonomic research

• Parochial• Specialised experts• Fragmented & distributed

Sociology…

• Different (domain specific)• Communities of practice• Non transferable skills

Methodology…

Output…• Heterogeneous & scattered• High volume, low impact• Hard to find (use)

Managed Web Support

Pros • High quality• Bespoke • Branded*

Cons • Limited control • Limited updates• NHM centric• No services• No ownership• No connectivity• Protracted & slow

The NHM experience

Lepidoptera

Solanaceae

Chalcid Wasps

Spanish Sandflies

British Fleas

Martian Meteorites

Loch Ness Worms Bumble bees

Managed Web SupportThe NHM experience

Web Bottlenecks • Technology• Management

Explosion of Web 2.0Solutions to technical and management bottlenecks

Content Management SystemsProvide the basic web publishing functions

Joomla WordPress

DrupalPlone

Drupal’s strength - “community”Support the social processes of web

publishing

Drupal - social networkingComparing CMS systems

http://www.idealware.org/comparing_os_cms/

http://scratchpads.eu

ScratchpadsA multi-site implementation of Drupal

Scratchpad Application FormFree to any individual or community

Flexible Template SiteWith easy navigation

An ecosystem of communities

Sites: 130+

Users: 1500+

Pages: 170k

Circa 2 new sites/wk.

March 2007

ScratchpadTechnicalOverview

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

Scratchpad Developers Site

http://home.scratchpads.eu/

Scratchpad SVN

http://svn.scratchpads.eu/viewvc

Scratchpad Object Model

http://scratchpads.eu/sites/scratchpads.eu/files/Scratchpad_Object_Model.pdf

ScratchpadFunctionality

Summary

TaxonomyTaxonomy 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

Dynamically built species pages

Integrating data & “publishing” in a Scratchpad

Taxon Pages

Browsed through a taxonomy

Integrating data & “publishing” in a Scratchpad

Taxon Pages

Including 3rd party content

Integrating data & “publishing” in a Scratchpad

Taxon Pages

With data curation toolsWith data curation tools

Integrating data & “publishing” in a Scratchpad

Taxon Pages

Listing all “authors”

Integrating data & “publishing” in a Scratchpad

Taxon Pages

Dated, permanent & citable

Integrating data & “publishing” in a Scratchpad

Taxon Pages

Control what to display

Adjusting the layout

Taxon Pages

n.b. Taxon page tools have since been updated

User Support

Sandbox Site

Uservoice

Screencasts

Future Directions

BMC Bioinformatics

BMC Bioinformatics 2009, 10 (Suppl 14)S6doi:10.1186/1471-2105-10-S14-S6

Published: 10 November 2009

ViBRANT

INFRA-2010-1.2.3 (VRC)17 PartnersApprox €4M

• Distribute hosting infrastructure• Web services on major data types• Registry of sites and data services• Common data portal• New services (keys / phylog.)• Vocab. / ontology site (GBIF)• User support• Sociological research

Questions?