A marine Virtual Laboratory inthe 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.

Constructing LifeWatch

Reminders

“The mission of LifeWatch is to construct and operatea distributed infrastructure for biodiversity andecosystem science based upon Europe-widestrategies implemented at the local level:individuals, research groups, institutions, countries.”

See my slideshares• www.slideshare.net/hardisty/egiforumamsterdam15sep2010• ww.slideshare.net/hardisty/textofkeynoteegiforum15sep2010

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

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

Info

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Tec

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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

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

Organisation – role of national initiativesNational 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

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

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• www.biodiversitycatalogue.org

• A first version of the Portal / Dashboard• www.biovel.eu; integrative efforts in progress e.g., with Scratchpads; R in Greece

• Services to support the Release 1 focus• 49 services registered today; docs at: https://wiki.biovel.eu/x/QID7

• Procedure for the admission of new data resources• Draft procedure exists

• Helpdesk and training• support@biovel.eu• tender in progress in Italy for LifeWatch SC platform

Hard to know completely, because so much is in progress across Europe

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?

Sourcing the right ingredients

Service Network:Sourcing the right ingredients for the finished meal

• Connecting biology and IT communitiesDistinct 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 (http://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons

• 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• www.biodiversitycatalogue.org

– Services can be “managed” to a greateror lesser extent

WS1 WS2WS4

WS5

WS3

A Virtual Lab connects services of the ServiceNetwork into useful applications and workflows

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 Infrastructure ProvidersNational, EGI.eu, PRACE, commercial, EUDAT, etc.

Steps towards building Virtual Laboratories

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

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

18 questions towards equipping a Virtual Lab(Original concept by Lourens Veen, University of Amsterdam, November 2010)

Questions?