Tools of a virtual laboratory
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Transcript of Tools of a virtual laboratory
TOOLS OF A VIRTUAL LABORATORY
Alex HardistyCoordinator, Cardiff University
MS11 Workshop, 6-7th June 2013, Budapest
Biodiversity Virtual e-LaboratoryAn e-Infrastructure and e-Science environment supporting research on biodiversity
Part of a workflow to study the ecological niche of the Horseshoe crab (Limulus polyphemus)
Products are “workflows” built from “services”
• Workflows allow to process vast amounts of data, repeatedly– Build your own workflow: select and
apply successive “services” (data analysis and processing steps)
– Import data from own research and/or from existing libraries(e.g., GBIF, Catalogue of Life)
• Access a library of workflowsRe-use existing workflows – Improves efficiency by reducing
research time and overhead expenses
• Aims to foster cooperation in the community by:– Discussing scientific use cases– Identifying and deploying important Web Services– Designing and offering workflows– Training scientists
• Aims to create a “Service Network”– Web services for interdisciplinary
analysis of biodiversity• And “workflows” for science
Ecological niche modellingEcosystem modellingMetagenomicsPhylogeneticsPopulation modellingTaxonomyGeospatial visualization
An international network of experts connecting 2 scientific communities: biodiversity and ICT,
to create a general purpose Virtual e-Laboratory
Biodiversity Virtual e-LaboratoryBioVeL is a consortium of 15 partners from 9 countries
1. Cardiff University, UK – Coordinator 2. Centro de Referência em Informação Ambiental, Brazil3. Foundation for Research on Biodiversity, France4. Fraunhofer-Gesellschaft, Institute IAIS, Germany5. Free University of Berlin – Botanical Gardens and
Botanical Museum, Germany6. Hungarian Academy of Sciences Institute of Ecology and
Botany, Hungary7. Max Planck Society, MPI for Marine Microbiology,
Germany8. National Institute of Nuclear Physics, Italy9. National Research Council: Institute for Biomedical
Technologies and Institute of Biomembrane and Bioenergetics, Italy
10. Netherlands Centre for Biodiversity (NCB Naturalis), The Netherlands
11. Stichting European Grid Initiative, The Netherlands12. University of Amsterdam, Institute of Biodiversity and
Ecosystem Dynamics, The Netherlands
13.University of Eastern Finland, Finland
14. University of Gothenburg, Sweden15. University of Manchester, UK
• NoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.
• Projects: 4D4Life, agINFRA, Aquamaps, ArtDataBanken, BioFresh, Envri, EU BON, EUBrazilOpenBio, Fauna Iberica, i4Life, iMarine, Micro B3, OpenPlantBio, ViBRANT
• Global: CAMERA, Catalogue of Life, COOPEUS, CReATIVE-B, EoL, GBIF, GSC Biodiversity WG, TreeBase, and many more
Fits into a portfolio of initiatives
Supported by many friends
Important contributionto infrastructure
How it worksDiscipline
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
Ferenc Horváth
Péter Ittzés
Requirements
1. Services need to be secure, scalable, reliable, and well-documented
2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows
with minimal training and assistance
Building a network of services
Users’ workflows and applications
Service and Data Providers(BioVeL, GBIF, CoL, EBI, BGBM, CRIA, etc.)
Resource Providers(EUDAT, EGI.eu, SZTAKI,commercial cloud, etc.)
Hardening and Deploying Services
• Provision of service infrastructure– Security– Data storage and staging
• Deployment on cloud and grid for better availability and scalability
• Development of best practices for improving ease of use and scalability
Requirements
1. Services need to be secure, scalable, reliable, and well-documented
2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows
with minimal training and assistance
www.biodiversitycatalogue.orgA fully curated, well-founded catalogue of
Web services for biodiversity science
Requirements
1. Services need to be secure, scalable, reliable, and well-documented.
2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows
with minimal training and assistance
Public groupsPublishing workflows and results
Private groupsLocal materialsIntra-project work and collaborations
8700 members, 318 groups, 2625 workflows, 674 files, 276 packs
repository for sharing workflowswww.myexperiment.org
Requirements
1. Services need to be secure, scalable, reliable, and well-documented
2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows
with minimal training and assistance
Tool Spectrum
TechnicalPAL
SciencePAL
DomainScientist
TavernaWorkbench
ComponentBuilder
TavernaLite / Server
Taverna Player / Domain-Specific
Website
Workflow Visibility
Concept KnowledgeWorkflow design, compute Domain science
High Low
The Portal
Taverna Lite
BioVeL Tools
• BioVeL websitehttp://www.biovel.eu
• BioVeL Portalhttp://tavlite1.biovel.eu
• BiodiversityCatalogue - Catalogue of services http://www.biodiversitycatalogue.org
• myExperiment – Catalogue of workflows http://biovel.myexperiment.org
• Taverna toolshttp://www.mygrid.org.uk
Interaction Server
Taverna Server
Server
Serv
ers
Run timeExecution
Serv
ices
COTS Shim
Domain
Cloud
DeploymentInfrastructurehosting, compute, storage
WorkflowsComponents
Catalogues & Repositories
BioCatalogueServices
BiodiversityCatalogue
Data
Mgt
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.
Questions?
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.