A PILOT IMPLEMENTATION INVESTIGATING
LIFEWATCH IDEAS
Alex Hardisty
Coordinator, Cardiff University
e-Infrastructures and B...
What is a Virtual e-Laboratory?
• Like a physical laboratory
– A place “inside computers”
where you can analyse data
and d...
Part of a workflow to study the
ecological niche of the Horseshoe crab
(Limulus polyphemus)
Workflows, pipelines and other...
Public groups
– Publishing
workflows and
results
Private groups
– Local
materials
– Intra-project
work and
collaborations
...
A grouping of Web services having related
functionality is called a ‘Service Set’
Taxonomy Metagenomics
and
metagenetics
E...
Service sets driven by science and policy needs
• CO2 emissions continuously increasing
– 10 GtC in 2010; Sequestration is...
Service sets driven by science and policy needs
• CO2 emissions continuously increasing
– 10 GtC in 2010; Sequestration is...
An international network connecting 2
communities: biodiversity and ICT
Discipline
Scientists
Scientific PAL
Technical PAL...
Secure, scalable, reliable, and well-documented
in a geographically distributed network of services
Users’ workflows and
a...
Services must be discoverable
www.biodiversitycatalogue.org
A fully curated, well-founded catalogue of
Web services for bi...
• Connecting biology and IT communities
– Distinct languages, different understandings
– Service Network approach connects...
Users need to be able to build and use
workflows
Technical
PAL
Science
PAL
Domain
Scientist
Taverna
Workbench
Component
Bu...
http://portal.biovel.eu/
Interaction Server
Taverna Server
Server
Servers
Run time
Execution
Services
COTS Shim
Domain
Cloud
Deployment
Infrastruct...
BioVeL is funded by the
European Commission
7th Framework Programme (FP7).
It is part of its e-Infrastructures activity.
B...
BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th September 2013, Madrid
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BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th September 2013, Madrid

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Talk about workflows, service network and human aspects of the Biodiversity Virtual e-Laboratory (BioVeL) project.

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Transcript of "BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th September 2013, Madrid"

  1. 1. A PILOT IMPLEMENTATION INVESTIGATING LIFEWATCH IDEAS Alex Hardisty Coordinator, Cardiff University e-Infrastructures and Biodiversity Workshop IBERGRID, 19th September 2013, Madrid Biodiversity Virtual e-Laboratory An e-Infrastructure and e-Science environment supporting research on biodiversity
  2. 2. What is a Virtual e-Laboratory? • Like a physical laboratory – A place “inside computers” where you can analyse data and do digital experiments – Like a physical lab, it’s equipped with everything you need • Project investigates: – Workflows approach – Service network approach – Human aspects
  3. 3. Part of a workflow to study the ecological niche of the Horseshoe crab (Limulus polyphemus) Workflows, pipelines and other applications are built from “services” • Workflows allow to run studies and experiments to process vast amounts of data, repeatedly – Select and apply successive “services” (data analysis and processing steps) – Import data from own research and/or from existing public sources – Choose input parameters • Access a library of workflows – Re-using existing workflows improves efficiency by reducing research time and overhead expenses
  4. 4. Public groups – Publishing workflows and results Private groups – Local materials – Intra-project work and collaborations 8700 members, 318 groups, 2625 workflows, 674 files, 276 packs Workflows must be shareable and discoverable www.myexperiment.org
  5. 5. A grouping of Web services having related functionality is called a ‘Service Set’ Taxonomy Metagenomics and metagenetics Ecological niche and population modelling Ecosystem functioning and valuation Mapping, visualization, transformation Catalogue of Life name lookup QIIME ENM (openModeller) Get meteor- ological data Spatio-temporal visualization GBIF occurrence data retrieval BOLD PopBio Weather to Biome-BGC data GeoServer WMS/WFS/WCS GBIF ChecklistBank BlastX Biome-BGC monte carlo Raster Diff WoRMS aphia name Sequence (OTU) clustering Biome-BGC sensitivity anal. ISO Country Code PESI name Functional diversity Data-Model harmonization DwC-A to JSON shim Checklist Cross-mapping Taxonomic diversity Biome-BGC CARBON DwC-A to CSV shim ? Taxonomy & Systematics Ecological niche and population modelling Ecosystem functioning and valuation ? Genes-Species-Specimens (multi-scale linkages) Citizen Science & Observations Mapping, visualization and transformation services
  6. 6. Service sets driven by science and policy needs • CO2 emissions continuously increasing – 10 GtC in 2010; Sequestration is the sustainable process to mitigate the effects • Over the past 50 years, humans have changed ecosystems – resulting in a substantial and largely irreversible loss of biodiversity • Invasions of alien species – A leading cause of biodiversity loss and related economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation. “transportation with ships is a high risk to spread the species to these spots” Stelzer et al 2013 Source: NOAA
  7. 7. Service sets driven by science and policy needs • CO2 emissions continuously increasing – 10 GtC in 2010; Sequestration is the sustainable process to mitigate the effects • Over the past 50 years, humans have changed ecosystems – resulting in a substantial and largely irreversible loss of biodiversity • Invasions of alien species – A leading cause of biodiversity loss and related economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation. “transportation with ships is a high risk to spread the species to these spots” Stelzer et al 2013 Source: NOAA Modelling ecosystem services Modelling CO2 sequestration Calculating measures of genetic diversity Assessing adaptation to changing conditions Supporting processes of conservation Assisting invasive species management
  8. 8. An international network connecting 2 communities: biodiversity and ICT Discipline 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
  9. 9. Secure, scalable, reliable, and well-documented in a geographically distributed network of services 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 Resource Providers National, EGI.eu, PRACE, commercial, etc.
  10. 10. Services must be discoverable www.biodiversitycatalogue.org A fully curated, well-founded catalogue of Web services for biodiversity science
  11. 11. • 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 Why do we need this approach? Scientists’ perspectives InformationTechnologists’ perspectives Biodiversity studies & experiments Services for biodiversity science compose to support ICT Technical Capabilities ICT Technical Elements combine to deliver combine to support
  12. 12. Users need to be able to build and use workflows Technical PAL Science PAL Domain Scientist Taverna Workbench Component Builder Taverna Lite / Server Taverna Player / Domain-Specific Website Workflow Visibility Concept KnowledgeWorkflow design, compute Domain science High Low
  13. 13. http://portal.biovel.eu/
  14. 14. Interaction Server Taverna Server Server Servers Run time Execution Services COTS Shim Domain Cloud Deployment Infrastructure hosting, compute, storage Workflows Components Catalogues & Repositories BioCatalogue Services Biodiversity Catalogue DataMgt Data Mgt Workspace Authentication Management System Local File Stores Local Data Sets Local Public BioVeL Curators Taverna Workbench Pro Makers In the Field Users Third Party Channels Interfaces Design & Launch tools Lite, Player, Portal
  15. 15. 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. www.biovel.eu 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.
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