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Tools of a virtual laboratory

B iodiversity V irtual e- L aboratory. An e-Infrastructure and e-Science environment supporting research on biodiversity. Alex Hardisty Coordinator, Cardiff University MS11 Workshop, 6-7 th June 2013, Budapest. Tools of a virtual laboratory.

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Tools of a virtual laboratory

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  1. Biodiversity Virtual e-Laboratory An e-Infrastructure and e-Science environment supporting research on biodiversity Alex Hardisty Coordinator, Cardiff University MS11 Workshop, 6-7th June 2013, Budapest Tools of a virtual laboratory

  2. 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 Part of a workflow to study the ecological niche of the Horseshoecrab (Limuluspolyphemus)

  3. An international network of experts connecting 2 scientific communities: biodiversity and ICT,to create a general purpose Virtual e-Laboratory • 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 interdisciplinaryanalysis of biodiversity • And “workflows” for science Ecological niche modelling Ecosystem modelling Metagenomics Phylogenetics Population modelling Taxonomy Geospatial visualization

  4. BioVeL is a consortium of 15 partners from 9 countries Cardiff University, UK – Coordinator Centro de ReferênciaemInformaçãoAmbiental, Brazil Foundation for Research on Biodiversity, France Fraunhofer-Gesellschaft, Institute IAIS, Germany Free University of Berlin – BotanicalGardens and BotanicalMuseum, Germany HungarianAcademy of Sciences Institute of Ecology and Botany, Hungary Max Planck Society, MPI for Marine Microbiology, Germany National Institute of NuclearPhysics, Italy National Research Council: Institute for Biomedical Technologies and Institute of Biomembrane and Bioenergetics, Italy Netherlands Centre for Biodiversity (NCB Naturalis), The Netherlands StichtingEuropeanGrid Initiative, The Netherlands University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics, The Netherlands University of EasternFinland, Finland University of Gothenburg, Sweden University of Manchester, UK

  5. Supported by many friends Fits into a portfolio of initiatives • 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 Important contributionto infrastructure

  6. How it works Discipline Scientists Community Scientific Requirements Scientific Capabilities FerencHorváth Training & Issue Resolution Scientific PAL Services Team Support Centre Translation Application PéterIttzés Prioritisation Service Level Requirements Technical PAL Sustainability Technical Requirements Technical Capabilities Community Scientific and Technical Service Providers

  7. Requirements • Services need to be secure, scalable, reliable, and well-documented • Services need to be discoverable • Workflows need to be storable and discoverable • Users need to be able to build their own workflows with minimal training and assistance

  8. 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.)

  9. 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

  10. Requirements • Services need to be secure, scalable, reliable, and well-documented • Services need to be discoverable • Workflows need to be storable and discoverable • Users need to be able to build their own workflows with minimal training and assistance

  11. www.biodiversitycatalogue.org A fully curated, well-founded catalogue ofWeb services for biodiversity science

  12. Requirements • Services need to be secure, scalable, reliable, and well-documented. • Services need to be discoverable • Workflows need to be storable and discoverable • Users need to be able to build their own workflows with minimal training and assistance

  13. Public groups Publishing workflows and results Private groups Local materials Intra-project work and collaborations repository for sharing workflowswww.myexperiment.org 8700 members, 318 groups, 2625 workflows, 674 files, 276 packs

  14. Requirements • Services need to be secure, scalable, reliable, and well-documented • Services need to be discoverable • Workflows need to be storable and discoverable • Users need to be able to build their own workflows with minimal training and assistance

  15. Tool Spectrum Workflow design, compute Concept Knowledge Domain science Technical PAL Science PAL Domain Scientist Taverna Workbench Component Builder Taverna Lite / Server Taverna Player / Domain-Specific Website High Workflow Visibility Low

  16. The Portal

  17. Taverna Lite

  18. 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

  19. Third Party Channels TavernaWorkbench Local File Stores Server Interaction Server Taverna Server Cloud Biodiversity Catalogue Catalogues & Repositories Workflows Services Components BioCatalogue Curators Pro Makers In the Field Users Interfaces Design & Launch tools Lite, Player, Portal Local Public BioVeL COTS Shim Services Servers Data Mgt Data Mgt Workspace Run time Execution Local Data Sets Authentication Management System Domain Deployment Infrastructure hosting, compute, storage

  20. Questions? BioVeL is funded by the European Commission 7th Framework Programme (FP7).It is part of its e-Infrastructures activity. BioVeLcontributes to LifeWatch and GEO BON. BioVeL products are free to access. Under FP7, the e-Infrastructuresactivityis part of the Research Infrastructures programme, fundedunder the FP7 'Capacities' Specific Programme. It focuses on the furtherdevelopment and evolution of the high-capacity and high-performance communication network (GÉANT), distributedcomputing 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.

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