The document summarizes the BioVeL project, which created a biodiversity virtual e-laboratory infrastructure. It discusses (1) the background and objectives of providing web services and workflows for cross-disciplinary biodiversity analysis, (2) the key achievements including 50 services, several workflow families, and an operational virtual laboratory portal, and (3) lessons learned regarding focusing on high-value assets, better promoting the project, and addressing scalability challenges.

1. Funded by the
BioVeL - Approach and outcome of
the Biodiversity Virtual e-Laboratory project
Alex Hardisty, Coordinator
Cardiff University, United Kingdom
13th November 2014
Paris, France
Final event
BioVeL In Practice and In Future
Funded by the

2. Funded by the
Overview
1. What we did: Background, objectives and approach
2. What was achieved: Infrastructure and important
outcomes
3. What did we learn: Lessons and future development
13th November 2014
Paris, France
Final event
BioVeL In Practice and In Future
Funded by the

3. Funded by the
Background to the work
2001 GRAB demonstrator links climate, species and
geographic data in an “e‐Science environment”
with a simple static workflow
2003‐2006 Biodiversity World prototype applied workflow
techniques to model climate preferences for the
Leguminosae
European Networks of Excellence make case for
LifeWatch in ESFRI 2006 roadmap
2008‐2011 ESFRI LifeWatch research infrastructure:
“Preparatory Phase” project adopts Service
Network (“as a Service” model) and workflow
paradigms as basis of architecture
2011‐2014 BioVeL project explores the practicalities and
offers a pilot service for scientists 3
Parallel developments in the USA, of course

4. Funded by the
Important contribution
to infrastructure
Where we fit in
Data curation
Biodiversity monitoring and research networks
• LTER / NEON, Genomic Observatories, EMBRC,
Natural History Museums, GEO BON / EU BON,
EMBOS, BioSOS, citizen observatories
Data acquisition
Biodiversity information systems
• ViBRANT Scratchpads, CoL i4Life, PESI,
WORMS, OBIS, GBIF, BExIS, BOLD, AquaMaps,
agINFRA, pro-iBioSphere, OpenUp!, BioFresh,
Dryad, Pangaea, GFBio, ALA, SiBBr/SpeciesLink,
GBoWS/CAS, SANBI, etc.
Biodiversity e-science infrastructures
• LifeWatch, BioVeL, iMarine, EUBrazilOpenBio
• DataONE
Data processing
and analysis
Data access
Synthesis Centres

5. Funded by the
Objectives of the project
• Provide (web)services for the interdisciplinary analysis of
biodiversity
• Provide analytical pipelines (workflows) based on these services
• Desired functionalities
– Access data from cross‐disciplinary resources (data mining)
– Access analytical methods from a range of disciplines (interoperability)
– Digest large data (scalability)
– Repeat complex analytical processes (reproducibility)
– Access to virtual communities (sociability)
Overall: Build an infrastructure to facilitate cross-disciplinary and
holistic analytical approaches in biodiversity and ecosystem research

6. Funded by the
6
Users’ workflows and
applications
Sustained Service and
Data Providers
GBIF, CoL, OBIS, WoRMS,
EMBL‐EBI, BGBM, CRIA, EoL,
BHL, ALA, LTER, etc. & more.
www.biodiversitycatalogue.org
Recognised and stable
Infrastructure Providers
National, EGI.eu, PRACE,
commercial, EUDAT, etc.
Building a heterogeneous Service Network
Technical objective: An informatics infrastructure for the next decade

7. Funded by the
e.g., Study ecological niche of south east Asian horseshoe crab
• Import south east Asian data from external library
• Apply succession of “services” = workflow
• Result: ecological niche map
Study 1: create a workflow
7
Creating powerful data virtual laboratories
Technical objective: Flexible, re-usable, adjustable workflows
e.g., Study niche of American horseshoe crab
• Import American data
• Re-use south east Asian crab study workflow
Study 3: modify a workflow
e.g., substitute a different model validation method
or produce the output in a different format
Study 2: re-use a workflow
S
e
r
v
i
c
e
Z

8. Funded by the
Develop a portfolio of data access and processing
services, composed into ‘workflows’
• Toolbox of many different Web services.
• Connect in sequence to perform required analysis task.
• Workflows can be shared and re‐used.
• ‘Pre‐cooked’ workflows for users that don’t want to
create their own.
Foster cooperation in the community by
• Discussing scientific use cases
• Identifying important Web Services
• Offering workflows
• Training scientists
Development guided by use cases
Science objective: Achieve new research publications and impact
TaxonomyTaxonomy
Ecosystem modellingEcosystem modelling
Population modellingPopulation modelling
Ecological niche modellingEcological niche modelling
GenomicsGenomics
PhylogeneticsPhylogenetics
……
Carbon
sequestration
Carbon
sequestration
Ecosystem
function
Ecosystem
function
Invasive
species
Invasive
speciesMethods
Research

9. Funded by the
DisciplineDiscipline
Scientists
Scientific PAL
Technical PAL
Scientific and Technical Service Providers
Scientific
Requirements
Translation
Technical
Requirements
Technical
Capabilities
Scientific
Capabilities
Application
Services Team
Prioritisation
Support Centre
Training &
Issue Resolution
Service Level
Requirements
Sustainability
Community
Community
Source: J Giddy
Connecting two communities
Social objective: Building an international social network
connecting biodiversity scientists and computing technologists

10. Funded by the
Overview
1. What we did: Background, objectives and approach
2. What was achieved: Infrastructure and important
outcomes
3. What did we learn: Lessons and future development
13th November 2014
Paris, France
Final event
BioVeL In Practice and In Future
Funded by the

11. 1. 50 Services and a community catalogue for
discovery www.biodiversitycatalogue.org
– includes 3rd party services, best practice guidance
2. Several families of workflows, shared via
www.myexperiment.org
3. Public virtual laboratory (portal.biovel.eu) as
operational service
– users can execute workflows with their own data,
– incl. data/parameter sweeps and keeping details of
their experiments, and sharing with colleagues,
– helpdesk and associated training
4. Taverna Player plug‐in for website integration
– e.g., for Scratchpads, National LifeWatch, Fisheries
and Oceans Canada
5. VRE/VL image: Research groups can take our
stuff and create their own virtual labs, under
own control
– still using our workflows and services if they like
As an international network cooperating together
day‐to‐day, we deliver:

12. Funded by the
Biodiversity Catalogue
www.biodiversitycatalogue.org
Web service provider community
• How can I advertise my web services?
• What information do people need about
them?
Web service provider community
• How can I advertise my web services?
• What information do people need about
them?
Scientific user community
• How can I find the right web service?
• What can this web service do?
• How do I use it?
• How do I know this service is working?
Scientific user community
• How can I find the right web service?
• What can this web service do?
• How do I use it?
• How do I know this service is working?
Relevant
analytical and
processing code
Web Service
wrapper
Multiple and systematic
execution of the service in
scientific workflows and
other applications
Discoverable, scalable,
and robust service
STANDARDS

13. Funded by the
Biodiversity Catalogue
Curation: Annotation
• Scientific annotations
– Description
– Links to publications
• About the service
• About the algorithms
– How to cite
• Technical annotations
– How to use the service
– Endpoints
– Data formats
– Sample data

14. Funded by the
BioVeL Workflow
Repository
http://biovel.myexperiment.org
• Hosted on the myExperiment
public site in a branded space
• Includes scientific and technical
specifications
• Internal group:
– Develop
– 44 members, 148 workflows
• Public group: curated content
– Publish
– 39 workflows
• Established workflow approval
process

15. Funded by theSign up on the portal
https://portal.biovel.eu/

16. Funded by the
16
Linking services and workflows at the user documentation site
https://wiki.biovel.eu

17. BioVeL portal myExperiment
User documentation Biodiversity
Catalogue
services
DeveloperScientist

18. Scientists and
stakeholders
Scientists and
stakeholders
Workflow buildersWorkflow builders
Service providersService providers
Service
Centre
User documentation
BioVeL portal
BiodiversityCatalogue
Taverna workbench
myExperiment
BioVeLinfrastructure
Helpdesk: triage
advise
troubleshoot
escalate
resolve
Solving more than 70% of
problems in less than 5 days
Training

19. Funded by the
Achievement in numbers
• International network cooperating together
– >50 ICT and ecology experts, 18 ‘friends’, 20+ EC FP7 projects and
national LifeWatch initiatives alongside; Wider biodiversity informatics
community of 80 persons + many others
• 135 products (assets) arising from the project
– 36 web services deployed in use; 24 R libraries
• BiodiversityCatalogue.org – 58 services registered (21 BioVeL representing
36 deployed). 37 external to BioVeL. 160,000 discovery queries
– 45 workflows, in several families
• Niche modelling (5), Population modelling (25), Phylogenetics (7),
Metagenomics (3), Ecosystem functionality & CO2 sequestration (5)
• ~30 regular users. Steady stream of new sign‐ups (>105)
• 12 training workshops. 15 papers published
19

20. Funded by the
Overview
1. What we did: Background, objectives and approach
2. What was achieved: Infrastructure and important
outcomes
3. What did we learn: Lessons and future development
13th November 2014
Paris, France
Final event
BioVeL In Practice and In Future
Funded by the

21. Funded by the
What have we learnt? (doing well)
• Our approach works
– “It’s promising for the future” is the view of world‐class experts
• It impresses
– The ideas it demonstrates are widely supported
– We have won many friends
• Positive multiplier effects
– From embedding workflows into other applications and websites
• It can deliver new science
– More quickly, more cheaply, more effectively
• It makes the LifeWatch vision more tangible
– Laying the basis for the decadal objectives to be achieved i.e., “as a
Service” model, calculating EBVs, towards predicting the biosphere
21

22. Funded by the
What have we learnt? (to help and guide us)
• We have to focus more on the key / most valuable assets
• We need to better promote what is really cool and
unique about BioVeL
• We need to refine target audience segmentation into
different kinds of users and developers, and to address
each with more appropriate services and capabilities
(e.g., better support for R users)
• Data management capabilities needs to be more obvious
• Need to scale up the science to show something that
cannot be done on the desktop or with R alone 22

23. Funded by the
What have we learnt? (operational issues)
• Delivering “professional quality” operational service is hard
• Technical challenges
– Delegated authentication and authorization of service use
– Long‐running asynchronous jobs have to be handled
– Difficult to maintain large number of services/workflows robust & operational
• Sociological challenges
– Pals (buddy) approach works well but is expensive
– Professionalization of service delivery (long road to ITSM certification)
– Achieving sustainability is still difficult
• Scalability challenges
– Multiple issues: e.g. files in BioSTIF, large data retrievals in DRW
– Peaks of multiple simultaneous usage; presently managed “by hand”

24. Funded by the
Future activity focus
• Promoting biodiversity workflows and services
through Friends, National LifeWatch initiatives,
LifeWatch ERIC, Horizon 2020 opportunities
• Coordinate, sustain and integrate existing workflows
and service initiatives
• Ramp‐up the service to gain a broad user base

25. Funded by the
A consortium of 15 partners from 9 countries
1. Cardiff University, UK – Coordinator
2. Centro de Referência em Informação Ambiental, Brazil
3. Foundation for Research on Biodiversity, France
4. Fraunhofer‐Gesellschaft, Institute IAIS, Germany
5. Free University of Berlin – Botanical Gardens and Botanical Museum, Germany
6. Hungarian Academy of Sciences Institute of Ecology and Botany, Hungary
7. Max Planck Society, MPI for Marine Microbiology, Germany
8. National Institute of Nuclear Physics, Italy
9. CNR: Inst. for Biomedical Technologies / Inst. of Biomembrane and Bioenergetics, Italy
10. Netherlands Centre for Biodiversity (NCB Naturalis), The Netherlands
11. Stichting European Grid Initiative, The Netherlands
12. University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics, NL
13. University of Eastern Finland, Finland
14. University of Gothenburg, Sweden
15. University of Manchester, UK
Thank you for your attention