Scratchpads Intro: Swiss Orchid Foundation

Ed Baker!Natural History Museum, London, UK!

Virtual Biodiversity ViBRANT!

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


The problem

Science is global •  It needs global standards •  Global workflows •  Cooperation of global players

Science is carried out �locally� •  By local scientists •  Being part of local infrastructures •  Having local funders


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


Goal

�a scholarly communication system that is intertwined with the pursuit of natural history, rather than an after-

thought or annex�


Your data 1

“Published” & reviewed on your site

3 Uploaded &

tagged

2

Fast Intuitive Fit for use

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


Scratchpads Overview

•  Hosted websites for taxonomists •  Research & publication platform •  Modular (Drupal) & flexible •  Supports the taxonomic workflow •  Bottom-up design, agile dev. •  Ecosystem of communities (330+) •  7,350+ users (unpaid) from 2007


Scratchpad Application Form Free to any individual or community


Categories of Scratchpads

Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic,

genotypic & morphometric datasets, keys, phylogenies)

Projects Conservation Regions Societies


Flexible Template Site With easy navigation


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

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


Scratchpad Technical Overview


Scratchpad management Scalable & 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/

Scratchpads Intro: Swiss Orchid Foundation

Technology

Transcript of Scratchpads Intro: Swiss Orchid Foundation