Scratchpads has been developed for the last 5 years as a e-structure for facilitating the development of virtual research environments.
Intuitive professional looking layout.Easy to compile taxon pages without any knowledge of web design.Taxonomy provides the crucial backbone, linking content together and is easily updateable.On this page you can see the classification browser in the side bar, detailed nomenclatural information, images and a diagnostic summary.
Scratchpads training course introduction
An Introduction to Scratchpads:Making your data work for you Koureas D.N., Van deVelde I., Roberts D.
keep the discussion going@vbrant @scratchpads &@dimitriskoureasat#piblei
What are Scratchpads?• Hosted websites for biodiversity data• Virtual research & publication platform• Completely open access & open source• Modular & flexible
What are Scratchpads?Facilitate the development of online research communitiesProvide a standardized environment of entering and curating dataEnable users in sharing and interlinking their dataAccelerate publication process & dissemination of research products
The Scratchpads conceptA Scratchpad is a website that holds data for you and your community Your data External data & services
What Scratchpads are not!A single biodiversity databaseRestricted thematically, geographically or taxonomicallyA tool just for taxonomists
How are Scratchpads doing?464 Scratchpads Communitiesby 6,407 active registered users In total more thancovering 52,661 taxain 559,488 pages. 1,200,000 visitorsPer month unique visitors to Scratchpads sites 65000 unique visitors/month
How are Scratchpads funded?2007 2011 2014 ViBRANT Virtual Biodiversity Research &
Why Scratchpads? Our informatics grand challenge…“Link together evolutionary This requires data, information & knowledgedata… by developing analytical to be…tools and proper • Digitaldocumentation and then use Not printed paperthis framework to conduct • Openly accessiblecomparative analyses, studies Not behind barriersof evolutionary process and • Linked-upbiodiversity analyses” Not in silosCyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page.TREE. doi:10.1016/j.tree.2011.11.001
Why Scratchpads? Our current taxonomic data production • 15-20k new spp. described annually (2M total)1 • 30k nomenclatural acts (12M total) 1 • 20k phylogenies (750k total)2 • 31k taxa sequenced (360k taxa total)3 • 800k BioMed papers (40M total pp. of taxonomy) 4 • Countless specimens, images, maps, keys and datasets Typically generated by small communities for “local” research projectsFigures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.
Why Scratchpads?Vast amounts of unpublished taxonomic “knowledge” OrPublished knowledge cannot easily be mobilised
Why Scratchpads?This leads to:• A complex, fragmented & hard to navigate landscape• Dispersed data sources• Difficulties for collecting information for research
Why Scratchpads?• Science is global• It needs global standards• Global workflows• Cooperation of large institutes and organisations
ScratchpadsVirtual Research Environments Making taxonomy digital, open & linked
Scratchpads are an integrated system toEnter, Curate, Mark-up, Link and Publish data workflow taxonomic in a single virtual environment
Help & Support • In-site Support - One click help within your site • Wiki - Training manuals, videos & glossary • Training Courses (12 in 2012) - UK (6), Sweden, (2) Greece (1), Bulgaria (1), South Africa (1), Brazil (1) • Ambassadors Programme - Enthusiastic experienced users - Local support • Embedded Issues Queue - Bug reports - Feature requests • Sandbox Site - http://sandbox.scratchpad.euhttp://help.scratchpad.eu
AcknowledgementsScratchpad technical development - Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine BoutonScratchpad outreach - Isa van deVelde, Laurence Livermore & Dimitris KoureasE-Monocot - Paul Wilkin & the Kew team, Charles Godfray & the Oxford teamViBRANT - Vince Smith, Dave Roberts & Lucy ReeveOur 7,000+ users
and now…hands-on timeyour training site:http://pro-ibioXX.taxon.namesome dummy data:http://help.scratchpads.eu/w/Introduction_to_basic_Scratchpad_training_course