Presented by Dave Roberts and coauthored by Simon Rycroft and Vince Smith at the GBIF European Nodes workshop at the National Muséum of Natural History (MNHN) in Paris, France. 4-6 April, 2011.

1. ViBRANT
Virtual Biodiversity
Community web sites: small pieces loosely joined
Dave Roberts, Simon Rycroft & Vince Smith
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

2. ViBRANT
Virtual Biodiversity
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

3. ViBRANT
Virtual Biodiversity
Small pieces loosely joined
Has many potential meanings:
Joining contributors together to form
communities
Joining the data together that go towards
forming a Scratchpad
Joining Scratchpad content with the landscape of
biodiversity informatics data on the web
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

4. ViBRANT
Virtual Biodiversity
Addressing the challenges of taxonomy
Goal ...
Inventory the Earth’s species
Document their relationships
“Publish” & apply these data
Data set ...
1.8 M described spp. (10M names)
300M pages (over last 250 years)
1.5-3B specimens
People ...
4-6,000 taxonomists
30-40,000 “pro-amateurs”
Many more citizen scientists?
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

5. ViBRANT
Virtual Biodiversity
A website for you & your community
Magic
Your data Your web site
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

6. ViBRANT
Virtual Biodiversity
Dynamic web pages
Taxonomy import, management and navigation
Reference manager / Endnote support for
bibliographies
Image galleries, image upload & annotation
Nexus / Newick import for visualising
phylogenies
Character matricies (discrete, morphometric
and text characters)
Presence / absence country maps
Specimen & location records (DwC)
Newsletters & Web fora with e-mail integration
User blogs
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

7. ViBRANT
Virtual Biodiversity
Import from CSV text file to any
content type
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PROGRAMME -infrastructure

8. ViBRANT
Virtual Biodiversity
Taxonomy & Literature Characters, Phylogeny & Specimens
Lice, mosquitos, freeloader flies, ... Termites, bryozoa, ...
(rapid upload and management of names, synonyms & bibliographic data) (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps)
3000
Sites Registered Users 2500
240
Sites
200 2000
Users
160
1500
Taxon descriptions & Publications Image Galleries
Freeloader Flies, fungus gnats, ... 120 Dragon trees, nanno fossils, cockroaches, fungi, polychaetes, ...
(rapid upload, annotation & display of images)
(publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life)
1000
80
500
40
0 0
Year 1 Year 2 Year 3 Year 4
eJournals Societies, Organisations & Projects
European Mosquito Bulletin, Phasmid Studies, ... ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ...
(submission, review & dissemination of articles) (space for data collection, services, discussion & organisation)
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PROGRAMME -infrastructure

9. ViBRANT
Virtual Biodiversity
ViBRANT Products
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 compile taxonomic manuscripts automatically from their site.
A portal
for users to access public 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 biodiversity research community.
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

10. ViBRANT
Virtual Biodiversity
Training Biodiversity
& outreach data
programme standards
Networking
User Controlled
feedback vocabulary
The “chromosome” systems platform
WP3. Training
User
sociology
Data
aggregation
WP4. Standards
study portal
WP8. Mobilisation
Field GBIF
recording integration
support activities
Citizen
Biodiversity
science
visualisation
programme
layers
Scratchpads
Virtual Research
Service Research
Environment Distributed
Phylogenetic
Scratchpad
analysis
hosting
Bioclimatic Software
WP5. Data modelling
& metrics
module
integration
WP2. Architecture
WP6. Publishing WP7. Literature
Identification Sustainability
tools plan
Communal
Matrix data
biodiversity
editor
literature
Biodiversity Biodiversity
data literature
publishing markup
Scholarly
Biodiversity
manuscript
datamining
publishing
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

11. ViBRANT
Virtual Biodiversity
Training Biodiversity
& outreach data
programme standards
GBIF
Networking
User Controlled
feedback vocabulary
The “chromosome” systems
GBIF
platform
WP3. Training
User
sociology
Data
aggregation
WP4. Standards
study portal
WP8. Mobilisation
Field GBIF
recording integration
support activities
GBIF GBIF
Citizen
Biodiversity
science
visualisation
programme
layers
GBIF
Scratchpads
Virtual Research
Service Research
Environment Distributed
Phylogenetic
Scratchpad
analysis
hosting
Bioclimatic Software
WP5. Data modelling
& metrics
module
integration
WP2. Architecture
WP6. Publishing WP7. Literature
Identification Sustainability
tools plan
Communal
Matrix data
biodiversity
editor
literature
Biodiversity Biodiversity
data literature
publishing markup
Scholarly
Biodiversity
manuscript
datamining
publishing
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

12. ViBRANT
Virtual Biodiversity
“making the Scratchpads better”
More reliable (e.g., distribute the servers)
More functional (e.g., phylogenetic & publication services)
Easier to use (better workflows)
Prettier (better graphical design - more intuitive)
More integrated (for data stored inside & outside the Scratchpad framework)
More sustainable (simple administration, distribute developers, development sandbox)
“making natural history better”
Easier to compile, manage and reuse your data
Easier to find and reuse other peoples data
Promoting your data inside & outside the taxonomic community
Getting people to work for you (crowdsourcing)
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PROGRAMME -infrastructure

13. ViBRANT
Virtual Biodiversity
Author
Manuscript Public Enhanced
preparation on HTML
a Scratchpad
PDF
Submit as XML
Enhanced XML Printed paper
Produce PDF
Send to Register with
reviewers ZooBank,
Publisher GBIF, EoL etc.
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PROGRAMME -infrastructure

14. ViBRANT
Virtual Biodiversity
https://git.scratchpads.eu/viewgit
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PROGRAMME -infrastructure

15. ViBRANT
Virtual Biodiversity
Thank you for your
attention.
Any questions
e-mail: enquiries@vbrant.eu
http://vbrant.eu http://scratchpads.eu
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PROGRAMME -infrastructure