Scratchpad training

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


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

2

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 new sites/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 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.


14 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


SERVICEWP5. Data

WP6. Publishing

WP4. StandardsWP8. Mobilisation

RESEARCHWP2. Architecture

WP7. Literature

NETWORKINGWP3. Training

ViBRANT Project planThe “chromosome”


ScratchpadTechnicalOverview


Scratchpad Object Model

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


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://dev.scratchpads.eu/


Scratchpad SVN

http://svn.scratchpads.eu/viewvc


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


Putting itall together

- an example site


Scratchpad structure

Taxonomybiblio

Content typesimage page

taxon page view

term 1

term 2

term 3

node 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

Classification and other tags

Virtual BiodiversityViBRANTSpecies page

Nomenclatureand 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


PhylogenyNexus / 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


53 of

Built in help, the FAQ & issues queue


Screencasts, but…

Questions?


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

Technology

Scratchpad training