BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th September 2013, Madrid
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Transcript of BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th September 2013, Madrid
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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
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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
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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
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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
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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
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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
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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
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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
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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.
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Services must be discoverable
www.biodiversitycatalogue.orgA fully curated, well-founded catalogue of
Web services for biodiversity science
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• 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
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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
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http://portal.biovel.eu/
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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
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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.