This document provides an overview of constructing a marine virtual laboratory within the context of LifeWatch. It discusses sourcing the right ingredients to build virtual laboratories through a service network approach. This connects biology and IT communities to support current and future use cases. Different service providers offer distinct competencies. The document outlines steps towards building virtual laboratories, including deciding on a theme and equipping the lab to support that theme through questions at the intersection of functionality and cross-cutting aspects like collaboration, science, and ICT. The goal is to design sustainable virtual laboratories that meet the needs of marine scientists.

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
• 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

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
• 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

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
(http://creativecommons.org/licenses/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
• www.biodiversitycatalogue.org
– 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, EGI.eu, 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?