wp5 overview (data services)

Virtual BiodiversityViBRANT

Identification and Analysis Toolsfor Scratchpads

NEIL CAITHNESSUniversity of Oxford

[email protected]

ViBRANTVirtual Biodiversity

Workpackage 5Interaction and ServicesOverview

TaxonTaxon DataData

External Computing Services


Who we are & what we do

Who we are What we do

4 UOXF Oxford Neil CaithnessMilo Thurston

e-Sciencee-Science

2.636

3%41%

6 JKI Berlin Gregor Hagedorn Standards 19 22%

11 VIZZ Madrid Javier de la Torre Visualization 12 14%

13 UPMC Paris Régine Vignes-LebbeTo be appointed

IdentificationIdentification

312

3%14%

16 ULR Reunion Noël Conruyt Identification 3 3%

87.6 100%

2 of 10


Brief bio

South Africa – Zoology (UCT & Wits University)• Teaching: evolution and speciation• Field work on African Antelope:

South Africa, Zimbabwe, Botswana (sometimes on horseback)• (Hugh Paterson, Elisabeth Vrba, Robin Crewe)

USA – Post-doc (American Museum of Natural History)• Ornithology: bioclimatic modelling of African Passerine birds• (Joel Cracraft, George Barrowclough, Gary Nelson)

UK – • NHM (zoology, entomology, botany)• Reading – grid pilot project for computational workflows supporting biodiversity science • Oxford – research facilitator for general e-Science, now moving more towards biology with

collaborations in Oxford Zoology

3 of 10


What we will do in ViBRANT

1. Design and implement a mechanism for Scratchpads to send jobs to external computing services and to receive the results …a) Design and maintain the Tools API

b) Implement and maintain a working system

4 of 10



2. Provide a series of working services …a) Phylogenetic services

• GARLI, PAUP, TNT, Mr Bayes …

b) Bioclimatic modelling services

• GARP, MaxEnt, CSM …

c) Identification services for molecular data

• NCBI BLAST, Barcode of Life Database (BOLD) …

d) Identification services for morphological descriptions (UPMC)

• Xper2, Lucid …

5 of 10



3. Work behind the scenes …a) Computing platforms deployment infrastructure

• Oxford Supercomputing Centre

• NGS Campus Grids

• Volunteer computing (e.g. BOINC)

• Amazon cloud-like services

b) Job description and metadata repository

• A complete history of jobs shown to the user via the Enhanced Scratchpad User Interface

c) Enhanced user interface and matrix editor (JKI)

d) Enhanced visualization services (VIZZ)

e) Biodiversity patterns and indices (VIZZ)

6 of 10


WP5WP5

WP5


… Schematic Summary

ScratchpadScratchpadScratchpadScratchpadScratchpadScratchpadScratchpadScratchpadScratchpadScratchpad

ServiceServiceServiceServiceServiceService

API(BB)

7 of 10

VisualizationData tools

ServiceServiceService


Linking workpackage activities within ViBRANT

WP1. for project management

WP2. for dependent engineering of core Drupal systems

WP3. for user feedback on desired tools and services

WP4. for linkage between data API and tools API

WP5. … that’s us

WP6. (none planned – consider metatdata to aid markup)

WP7. (none planned – consider data mining as a service)

WP8. for linkage with biodiversity patterns and indices work

8 of 10


Who are our users & how will they engage?

• Scratchpad users

• Service providers anyone providing a new computational service to Scratchpads

• Admin usersproviding usage tracking for external services

9 of 10


Risk & Mitigation

•We may not do what we said we were going to do.

•We will always do what we say we will do.

IN OTHER WORDS•Be agile enough to do what is considered best.•Communication and mutual agreement are the key.

10 of 10

RISKRISK

MITIGATION MITIGATION


Schedule of Talks

12:05 WP5 Overview (Data analysis services) Neil Caithness, WP leader

12:15 Distributed services Milo Thurston

12:20 Identification keys Régine Vignes-Lebbe

12:25 Ontologies for description, classification and identification processes

Noël Conruyt

12:30 Descriptive data supporting keys – SDD Gregor Hagedorn

12:35 Mobile phone apps monitoring biodiversity Javier de la Torre

12:40 Biodiversity indices Javier de la Torre

12:45 WP5 general discussion and questions Facilitator: Neil Caithness

12:50 LUNCH Museum Canteen

wp5 overview (data services)

Documents