Eudat user forum-london-11march2013-biovel-v3
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The document discusses the Biodiversity Virtual e-Laboratory (BioVeL), which provides an e-infrastructure and e-science environment to support biodiversity research. It offers web services and workflows to allow researchers to process large amounts of biodiversity data. Researchers can access libraries of existing workflows and services from databases like GBIF and the Catalogue of Life. The BioVeL aims to foster collaboration between biodiversity and information and communications technology researchers.
Eudat user forum-london-11march2013-biovel-v3
- 1. Biodiversity Virtual e-Laboratory An e-Infrastructure and e-Science environment supporting research on biodiversity WEB SERVICES INFRASTRUCTURES FOR BIODIVERSITY SCIENCE Alex Hardisty Coordinator, Cardiff University EUDAT User Forum, 11-12th March 2013, London
- 3. Products are “services” and “workflows” • 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 one’s own research and/or from existing libraries (i.e. GBIF, Catalogue of Life) • Access a library of workflows and re-use existing workflows. – Improves efficiency by reducing Part of a workflow to study the ecological niche of the horseshoe crab research time and overhead expenses
- 4. Creates powerful data processing tools Ecological Niche Modelling Biogeochemical modelling for biodiversity research Metagenomics • Carbon Sequestration Phylogenetics Population Modelling • Ecosystem Functioning and Valuation Taxonomy Geospatial Visualization • Invasive Species Management An international virtual network of experts connecting 2 scientific communities: biodiversity and ICT • Aims to foster cooperation in the community by: – Discussing scientific use cases – Identifying and deploying important Web Services – Designing and offering workflows – Training scientists
- 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 contribution to infrastructure
- 6. BioVeL Tool Spectrum Workflow design, compute Concept Knowledge Domain science Technical Science Domain PAL PAL Scientist Taverna Component Taverna Domain-Specific Workbench Builder Lite / Server Website (Taverna Player) High Workflow Visibility Low
- 7. Biodiversity Catalogues & Catalogue Workflows Repositories Components Services BioCatalogue Curators Pro In the Interfaces Makers Field Design & Launch Users Third Party tools Taverna Lite Channels Workbench Local Public BioVeL Services Data Mgt Servers COTS Shim Local Taverna Server File Data Mgt Run time Stores Workspace Execution Local Authentication Data Management Sets Domain Server Interaction Server System Deployment Infrastructure Cloud hosting, compute, storage
- 8. We’re at the halfway point • Several workflows maturing nicely – Public Shared: Data refinement, Population modelling, Ecol. niche modelling – Beta: Phylogenetic inferencing – In the pipe: Biogeochemical process modelling, metagenomics, … • Using Web services from GBIF, CoL, CRIA, Fraunhofer, INFN, …. – Developing new services: viz and data selection, phylo, metagenomics, Biome-BGC modelling, pop modelling • A curated public catalogue of Web services – www.biodiversitycatalogue.org • AWS cloud infrastructure, new user interfaces (tavlite1.biovel.eu) • Growing profile in community – Steady enquiries from potential users and public training workshops
- 9. 4 questions to address 1. How to use distributed centres to efficiently run distributed processing chains? 2. Is there a problem of data exchange? (And how to solve this) 3. Deploying codes close to data 4. Access and security issues around managing protected services
- 10. How to use distributed centres to efficiently run distributed processing chains? Users’ workflows and applications Service and Data Providers (INFN, BioVeL, GBIF, CoL, EBI, BGBM, etc.) Resource Providers (EUDAT, EGI.eu, PRACE, commercial cloud, etc.)
- 11. Is there a problem of data exchange? (And how to solve this) • At simplest level, we need for the user: – A "starting place", where a workflow can find the data it needs – An "ending place", where a workflow can put its results – A "transient place" where temporary data / intermediate results can be put and retrieved • For services we need: – Temporary spaces associated with specific services, supporting data movements between services – Separation of users and separation of workflow runs • Summarise as : – A replicated distributed storage space, accessible to BioVeL services, (hence workflows) for both reading and writing; which presents to the user as a filespace, native to the user’s local environment. • = Dropbox for services, with fast replication between known service locations. Today, typically GB not TB
- 12. Deploying codes close to data • BioVeL Appliance – A service packaged for DCI, deployed on-demand – Working with EGI Fedcloud on this – Could be deployed close to data but this only makes sense if this would be quicker than moving the data • So where is the break-even point? • Taverna Server deployments – In connection with Web Services hosting Taverna Server
- 13. Access and security issues around managing protected services • We need a lightweight and standard solution for – User management & single sign-on to our Service Network – Permissions system for authorizing access to services • Same for Workspace Access Service (user workspace) User Contract SP Contract RP
- 14. Access and security issues around managing protected services • We need a lightweight and standard solution for – User management & single sign-on to our Service Network – Permissions system for authorizing access to services • Same for Workspace Access Service (user workspace) • 3-legged OAuth, extended – resource / service is independent of BioVeL OAuth provider • Adopt from megx.net – marine ecological genomics
- 15. Questions? 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. 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.