Roberts, D and Smith, VS. 2011. ViBRANT: linking communities and services. TDWG 2011 Annual Conference, at the Astor Crown Plaza Hotel, New Orleans, Louisiana, USA. 16 - 21st October 2011.

1. ViBRANT
Virtual Biodiversity
ViBRANT: linking communities and services
Dave Roberts, Simon Rycroft & Vince Smith
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

2. ViBRANT
Virtual Biodiversity
Pre-ViBRANT landscape
Complex ESFRI
Fragmented E Journal
LifeWatch
EMBRC
ELIXIR
Occurrence & Community Data Platform Standards
vocabulary tools
Aggregation EU projects
Portal
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

3. ViBRANT
Virtual Biodiversity
Post-ViBRANT landscape
INTEGRATED ESFRI
SUPPORT
(Support for marine research communities)
Code compliant e-publishing
Support Services (help desks, courses, networking)
from Scratchpads
LifeWatch (Prototype service centre)
ELIXIR (EBI metadata services)
Sociological research & feedback
biowikifarm
Mirroring & load balancing, phylogenetic
Occurrence & vocab. & ID services, literature services Integration &
data publishing networking
EMBRC
Aggregation portal, gap analysis,
quality control, API data services
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

4. ViBRANT
Virtual Biodiversity
“overall objective”
to increase the mobility of data and to make use of shared web resources wherever
possible using the Scratchpads as a hub to link a community's data with a range of
services.
“making the Scratchpads better”
More reliable & sustainable (e.g., distribute the servers, simple administration, distribute
developers, development sandbox)
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)
“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)
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

5. ViBRANT
Virtual Biodiversity
5000
4000
Sites
350 Users
300 Active Users 3000
250
Virtual machine hosted on VMWare vSphere 4
200 2000
8GB Ram
Intel Xeon E5630 (4 x Cores) 150
260GB of Storage
Tivoli Backup every 24 hours 100 1000
Debian 6.0.3
PHP - 5.3.3 50
MySQL - 5.1.49
0 0
Apache - 2.2.16 2007 2008 2009 2010 2011
Nodes: 390,092 on 14 Oct 2011
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

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

7. ViBRANT
Virtual Biodiversity
irtual
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

8. ViBRANT
Virtual Biodiversity
Can we use web data to identify the range of audiences for the Scratchpads?**
Myspecies.info (1 Oct 10 - 31 Mar 11) Number %
All ISPs* 9212 100
ISPs* excluding commercial providers 2316 25
* Average time on site >4 sec.
Categories of ISPs Number %
Research/Education/R&D 1933 83
Government 204 9
Company 50 2
Non-profit 41 2
Health 39 2
Art/culture/media/publishing 25 1
Travel 23 1
Other 1 0.04
** Data presented at Altmetrics workshop of the ACM WebSci ‘11
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

9. ViBRANT
Virtual Biodiversity
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

10. ViBRANT
Virtual Biodiversity
Mark up, publication, dissemination and use of taxonomic information
NEW PUBLICATIONS | LEGACY LITERATURE (FLORAS, FAUNAS)
TaxPub XML schema TaxonX XML schema
TaXMLit XML schema
PENSOFT MARK UP tool PLAZI’ GOLDEN GATE
Marked up publications EDIT European
Distributed
PDF, HTML and XML
Institute of
Taxonomy
Automated submission;
peer-review
Unified marked up final output
Taxon treatments, keys, images, localities
End WIKIs Indexing Aggregators
Electronic archives; Species-ID, biowikifarm, (IPNI, ZooBank, (EOL, GBIF,
User Data centers Wikispecies,Wikipedia
MycoBank, GNA) PLAZI)
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

11. ViBRANT
Virtual Biodiversity
irtual
http://www.gopetition.com/petitions/support-the-hellenic-centre-for-marine-research-hcmr.html
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

12. ViBRANT
Virtual Biodiversity
Oxford Batch Operations Engine
https://oboe.oerc.ox.ac.uk/
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

13. ViBRANT
Virtual Biodiversity
Taxonomic Concept Nexus
Schema XML Newick
CSV/tab Excel file
EoL Transfer schema (SPM) XML
SDD, Lucid, CSV, XLS,
DwCA RDF
Nexus Microsoft Word
.DOC, TXT
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

14. ViBRANT
Virtual Biodiversity
Citation and credit
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

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