Constructing bottomup

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Presentation to meeting, Heraklion, 4th June 2014 on constructing a marine virtual laboratory from the bottom up in the context of LifeWatch. Covers: - Constructing LifeWatch reminders of what we are doing - Sourcing the right ingredients - The Service Network idea - Steps towards building Virtual Laboratories.


  • 1. A marine Virtual Laboratory in the context of LifeWatch Constructing from the bottom up My talk is in several parts: - Constructing LifeWatch reminders of what we are doing - Sourcing the right ingredients - The Service Network idea - Steps towards building Virtual Laboratories Alex Hardisty, Cardiff University, 4th June 2014.

2. Constructing LifeWatch 3. Reminders The mission of LifeWatch is to construct and operate a distributed infrastructure for biodiversity and ecosystem science based upon Europe-wide strategies implemented at the local level: individuals, research groups, institutions, countries. See my slideshares BioVeL is a pilot implementation of LifeWatch Connecting biodiversity science and ICT LifeWatch as a community driven distributed e-Infrastructure Organisation of LifeWatch the role of national initiatives Release 1 description and progress to date Getting to sustainable outcomes 4. Specific use cases, applications and workflows: now and future Biodiversity analytical tasks, modelling, data transformations, discovery, etc. Common computing functions, workspace management, authn/authz, etc. Scientists perspectives InformationTechnologists perspectives Biodiversity studies & experiments Services for biodiversity science compose to support ICT Technical Capabilities ICT Technical Elements deliver combine to support Physically deployed compute & storage resources, databases, tools, etc. Connecting biodiversity science and ICT 5. A community driven e-Infrastructure Centres, distributed across countries offer services to users ICT oriented (computer centres, data centres), human oriented (service centres), or a combination (National) projects create their own e- laboratories or e-services They share their data and algorithms with others, while controlling access 6. Organisation role of national initiatives National functions Acting as focal point(s) for coordinating national contributions to LifeWatch Consortium development to organise the national contributions If necessary, managing the national financial investments in LifeWatch Functions for LifeWatch Construct / operate parts of the LifeWatch research infrastructure Focus on national, regional and/or thematic services, e.g.: Operate specific thematic services, Increase targeted data generation 7. Release 1 product description Focus: Data discovery, retrieval and visualization of species occurrence data, with support for the R statistical environment and ecological niche modelling. Virtual Lab(s) The Data Catalogue The Tools and Services Catalogue A first version of the Portal / Dashboard Services to support the Release 1 focus Procedure for the admission of new data resources Helpdesk and training 8. Release 1 progress to date (today) Virtual Lab(s) General purpose biodiversity analyses (BioVeL) Bird movement modelling (Netherlands) Ecosystem fragility to alien and invasive species (Italy) Others . The Data Catalogue Not available yet (but data is available through various services) The Tools and Services Catalogue A first version of the Portal / Dashboard; integrative efforts in progress e.g., with Scratchpads; R in Greece Services to support the Release 1 focus 49 services registered today; docs at: Procedure for the admission of new data resources Draft procedure exists Helpdesk and training tender in progress in Italy for LifeWatch SC platform Hard to know completely, because so much is in progress across Europe 9. Getting to sustainable outcomes My beliefs: Sustainability is based on commitment of institutions to each sustain pieces of the jigsaw as part of their core business Everyone has to play their part so that the whole functions coherently What we need to do Ask Friends of BioVeL and others to take this on Identify, adopt and join the jigsaw pieces Nurture and extend the community of biologists and ICT experts to strengthen this sense of ownership and responsibility Manage the pieces to support the VLs we want How? 10. Sourcing the right ingredients 11. Service Network: Sourcing the right ingredients for the finished meal 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 Danny Robinson [CC-BY-SA-2.0 (], via Wikimedia Commons 12. A Service Network is a set of Web service (WS) instances that interact together to perform an application objective In our case: multiple objectives, varying over time and from one user to another Usage and hence composition needs to be dynamic In a Service Network: Instances may join and leave Instances are discoverable Services can be managed to a greater or lesser extent WS1 WS2 WS4 WS5 WS3 13. A Virtual Lab connects services of the Service Network into useful applications and workflows Users workflows and applications Sustained Service and Data Providers GBIF, CoL, ITIS, OBIS, WoRMS, EBI, BGBM, CRIA, EoL, BHL, ALA, etc. + many many more Recognised and stable Infrastructure Providers National,, PRACE, commercial, EUDAT, etc. 14. Steps towards building Virtual Laboratories 15. Many different kinds of VL General purpose laboratory as in a general purpose chemistry laboratory for creating and executing any kind of workflow (e.g., BioVeL) Somewhat specialised thematic laboratory a forensics lab, soils lab, aquaculture lab for example for dealing with niche modelling problems or with population modelling problems organised around specific geographical areas, such as Waddenzee wetlands in Northern Netherlands/ NW Germany/S Denmark organised around general ecological themes, such as studies on invasive alien species for analysing and processing data from Ocean Sampling Day Highly specialised laboratory dedicated to the pursuit of a single scientific objective such as developing a vaccine for HIV to find an optimal way of sequestering carbon in a forest using essential biodiversity variables to predict the biosphere 16. What kind of marine VL do we want? First, decide the theme: Themes are subsets of the natural world or subsets of the field of biodiversity research Scientists effort is organised to pursue a theme Second, decide how to equip it (as for a real lab) to support the theme Can offer 18 questions arranged at the intersections of two orthogonal sets of 3 axes Functionality is about what the Virtual Lab does: Making data available Offering processing facilities for those data Facilitating interacting with users. Aspects are the cross-cutting issues that play a role for every theme and every piece of functionality: Collaboration, the Science, the ICT 17. 18 questions towards equipping a Virtual Lab (Original concept by Lourens Veen, University of Amsterdam, November 2010) 18. Questions?