biovel at ibergrid e-infrastructures and biodiversity workshop, 19th september 2013, madrid
DESCRIPTION
Talk about workflows, service network and human aspects of the Biodiversity Virtual e-Laboratory (BioVeL) project.TRANSCRIPT
A PILOT IMPLEMENTATION INVESTIGATING LIFEWATCH IDEAS
Alex HardistyCoordinator, Cardiff University
e-Infrastructures and Biodiversity WorkshopIBERGRID, 19th September 2013, Madrid
Biodiversity Virtual e-LaboratoryAn e-Infrastructure and e-Science environment supporting research on biodiversity
What is a Virtual e-Laboratory?
• Like a physical laboratory– A place “inside computers”
where you can analyse data and do digital experiments
– Like a physical lab, it’s equipped with everything you need
• Project investigates:– Workflows approach– Service network approach– Human aspects
Part of a workflow to study the ecological niche of the Horseshoe crab (Limulus polyphemus)
Workflows, pipelines and other applications are built from “services”
• Workflows allow to run studies and experiments to process vast amounts of data, repeatedly– Select and apply successive “services”
(data analysis and processing steps)– Import data from own research and/or
from existing public sources– Choose input parameters
• Access a library of workflows– Re-using existing workflows improves
efficiency by reducing research time and overhead expenses
Public groupsPublishing workflows and results
Private groupsLocal materialsIntra-project work and collaborations
8700 members, 318 groups, 2625 workflows, 674 files, 276 packs
Workflows must be shareable and discoverable www.myexperiment.org
A grouping of Web services having related functionality is called a ‘Service Set’
Taxonomy Metagenomics and metagenetics
Ecological niche and population modelling
Ecosystem functioning and valuation
Mapping, visualization, transformation
Catalogue of Life name lookup
QIIME ENM (openModeller)
Get meteor-ological data
Spatio-temporal visualization
GBIF occurrence data retrieval
BOLD PopBio Weather to Biome-BGC data
GeoServer WMS/WFS/WCS
GBIF ChecklistBank
BlastX Biome-BGCmonte carlo
Raster Diff
WoRMS aphia name
Sequence (OTU) clustering
Biome-BGC sensitivity anal.
ISO Country Code
PESI name Functional diversity
Data-Model harmonization
DwC-A to JSON shim
Checklist Cross-mapping
Taxonomic diversity
Biome-BGC CARBON
DwC-A to CSV shim
?
Taxonomy &Systematics
Ecological niche andpopulation modelling
Ecosystem functioningand valuation
?
Genes-Species-Specimens(multi-scale linkages)
Citizen Science &Observations
Mapping, visualization andtransformation services
Service sets driven by science and policy needs
• CO2 emissions continuously increasing– 10 GtC in 2010; Sequestration is the sustainable
process to mitigate the effects
• Over the past 50 years, humans have changed ecosystems– resulting in a substantial and largely irreversible loss
of biodiversity
• Invasions of alien species– A leading cause of biodiversity loss and related
economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation.
“transportation with ships is a high risk to
spread the species to these spots”
Stelzer et al 2013
Source: NOAA
Service sets driven by science and policy needs
• CO2 emissions continuously increasing– 10 GtC in 2010; Sequestration is the sustainable
process to mitigate the effects
• Over the past 50 years, humans have changed ecosystems– resulting in a substantial and largely irreversible loss
of biodiversity
• Invasions of alien species– A leading cause of biodiversity loss and related
economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation.
“transportation with ships is a high risk to
spread the species to these spots”
Stelzer et al 2013
Source: NOAA
Modellingecosystem services
ModellingCO2 sequestration
Calculating measures of genetic diversity
Assessing adaptationto changing conditions
Supporting processesof conservation
Assisting invasivespecies management
An international network connecting 2 communities: biodiversity and ICT
Discipline
Scientists
Scientific PAL
Technical PAL
Scientific and Technical Service Providers
ScientificRequirements
Translation
TechnicalRequirements
TechnicalCapabilities
ScientificCapabilities
ApplicationServices Team
Prioritisation
Support Centre
Training &Issue Resolution
Service LevelRequirements
Sustainability
Community
Community
Secure, scalable, reliable, and well-documentedin a geographically distributed network of services
Users’ workflows and applications
Sustained Service and Data ProvidersGBIF, CoL, ITIS, OBIS, WoRMS,EBI, BGBM, CRIA, EoL, BHL, ALA, etc. + many many more
Recognised and stable Resource ProvidersNational, EGI.eu, PRACE, commercial, etc.
Services must be discoverable
www.biodiversitycatalogue.orgA fully curated, well-founded catalogue of
Web services for biodiversity science
• Connecting biology and IT communities– Distinct languages, different understandings– Service Network approach connects them
• Supporting use cases we know today ...– … and use cases in the future that we cannot
yet imagine
• Different Service Providers are good (competent) at different things
• Deals with multiple jurisdictions and supports a business model– Leading to sustainability
Why do we need this approach?
Scientists’ perspectives
Info
rmati
on T
echn
olog
ists
’pe
rspe
ctive
s
Biodiversity studies & experiments
Services for biodiversity science
compose to support
ICT Technical Capabilities
ICT Technical Elements
combine to deliver
combine to support
Users need to be able to build and use workflows
TechnicalPAL
SciencePAL
DomainScientist
TavernaWorkbench
ComponentBuilder
TavernaLite / Server
Taverna Player / Domain-Specific
Website
Workflow Visibility
Concept KnowledgeWorkflow design, compute Domain science
High Low
http://portal.biovel.eu/
Interaction Server
Taverna Server
Server
Serv
ers
Run timeExecution
Serv
ices
COTS Shim
Domain
Cloud
DeploymentInfrastructurehosting, compute, storage
WorkflowsComponents
Catalogues & Repositories
BioCatalogue
Services
BiodiversityCatalogue
Dat
a M
gt
Data Mgt Workspace
AuthenticationManagement System
Local FileStores
Local DataSets
Local Public BioVeL
Curators
TavernaWorkbench
ProMakers
In the FieldUsers Third Party
Channels
InterfacesDesign & Launch tools Lite, Player, Portal
BioVeL is funded by the European Commission 7th Framework Programme (FP7).It is part of its e-Infrastructures activity.
BioVeL contributes to LifeWatch and GEO BON.
BioVeL products are free to access.
www.biovel.eu
Under FP7, the e-Infrastructures activity is part of the Research Infrastructures programme, funded under the FP7 'Capacities' Specific Programme. It focuses on the further development and evolution of the high-capacity and high-performance communication network (GÉANT), distributed computing infrastructures (grids and clouds), supercomputer infrastructures, simulation software, scientific data infrastructures, e-Science services as well as on the adoption of e-Infrastructures by user communities.