SlideShare a Scribd company logo
1 of 22
Biodiversity Virtual
e-Laboratory
Project Overview
BioVeL is an e-laboratory that supports research
on biodiversity using large amounts of data from
cross-disciplinary sources.

Alex Hardisty
Project Coordinator
Cardiff University                                 1
Biodiversity Virtual e-Laboratory
An international network of experts connecting 2
scientific communities: ICT and biodiversity

Offers access to a variety of data processing
services, linked as ‘workflows’ for assisting
studies in biodiversity science
   • You will hear about these during this
     workshop
   • You will be able to influence their design

Aims to foster cooperation in the community by:
   • Discussing use cases
   • Identifying important Web Services
   • Training scientists                           2
Biodiversity Virtual e-Laboratory
 BioVeL is a powerful data processing tool
 • Import data from your own research and/or from existing libraries

 • Use workflows (series of data analysis steps) for data processing

 • Build your own workflow by selecting and applying successive Web
   services (data processing techniques)

 • Access a library of workflows and re-use existing workflows

 • Cut down research time and overhead expenses




Workflow for population modelling (stage-based matrix projection models)
based on Stubben and Milligan. Journal of Statistical Software, 22(11), Sept 2007
                                                                                    3
Biodiversity Virtual e-Laboratory
Showcase study 1: create a workflow*
Study on the ecological niche of the south east Asian horseshoe crab,
an endangered species:
     • Import south east Asian data from external library
     • Apply succession of “services” = workflow
     • Result: ecological niche map




                                                                                             4
                                    * courtesy Matthias Obst, University of Gothenburg, Sweden
Biodiversity Virtual e-Laboratory
Showcase study 2: re-use a workflow
Study on the ecological niche of the American horseshoe crab
    • Import American data
    • Re-use south east Asia crab study workflow
    • Result: ecological niche map for American horseshoe crab
Compare the ecological niches of the south east Asian and American crabs.

Potential study of the ecological niche of an African animal
    • Import African data
    • Re-use horseshoe crab study workflow
    • Result: ecological niche map for African animal




                                                                       5
What does BioVeL consist of? (1)
 Biodiversity Data        Data Services        Catalogues /
User
                                               Repositories
          xls, csv         BioVeLData
                                        REST
                            Manager
        documents
                            GenBank     REST
Collections
       Genomic data        Catalogue
                                        REST
       Taxonomic data        of Life           CSW
        Observations           GBIF     REST

Spatial (Web)                           OGC
       raster    sensor      nodes
        data      data
                            BioVeL      REST
Collaboration              GeoServer    OGC
        Annotations
         Workflows

                                                              6
What does BioVeL consist of? (2)
                        Catalogues /                      Execution
Biodiversity Services
                        Repositories                      environment
Phylogenetic
       BLAST,Hmmer,




                                          Provenance
                         WebDaV Data
          MrBayes,       Management
        Blast, PAML,
         EMBOSS,…                                             Taverna
Taxonomic                                                    Workbench




                                          OpenSearch
         Synonyms
Visualization
         BioSTIF
                                                              Taverna
       Google Refine    CSW                                Workflow Engine
Modelling /




                                       Authentication /
                                        Authorisation
GeoProcessing
                R                                           Grid, Cloud, etc.

       openModeller
        WPS / WCPS
                                                                          7
Service sets driven by science
• Phylogeny and metagenomics services
   – Measures of genetic diversity and
     adaptation to changing conditions
• Taxonomy services
   – Checklists, identification, data cleaning, ...
• Niche and population modelling services
   – Processes of conservation and invasive
     species management
• Ecosystem functionality and valuation
  services
   – Modelling of ecosystem services and CO2
     sequestration
                                                      8
• Visualization and geospatial
Biospheric CO2 sequestration (1)

SCIENCE & POLICY CONTEXT
 Emission is continuously increasing – 10 GtC in 2010

 Sequestration is the only sustainable
  process to mitigate

 Terrestrial Sequestration highly depends
   on land use & climate change



SCIENTIFIC CHALLENGES
 Model improvement
 Model & data downscaling
 Model verification

   >> data-model calibration
   >> higher processing capacity

                                                        9
Biospheric CO2 sequestration (2)
REVIEW IN PROGRESS
 Collected papers                         39
 Selected and annotated papers            35

MOST RELEVANT RESEARCH GROUPS/PROJECTS
 The Global Carbon Project, Fluxnet – eddy covariance tower
 measurements, GHG Europe, ICOS, NTSG (University Montana)
 and Biome-BGC users & developers worldwide

Biome-BGC is a computer model that estimates fluxes and storage of energy,
water, carbon, and nitrogen for the vegetation and soil components of
terrestrial ecosystems.

TYPICAL „WORKFLOWS” around Biome-BGC
 Weather to Biome-BGC; Biome-BGC CARBON; Biome-BGC
 Sensitivity Analysis; Biome-BGC Data-Model Harmonization

WEB SERVICES
 no such kind of services operating yet
 new service sets identified and prioritised to develop:
   4 data retrieval services                                                 10
   6 Biome-BGC modelling services
Ecosystem functioning / valuation (1)
SCIENCE & POLICY CONTEXT
„Over the past 50 years, humans have changed ecosystems more
rapidly and extensively than … this has resulted in a substantial and
largely irreversible loss in the diversity of life on Earth.”
„… degradation of many ecosystem services [causes] increased risks
of nonlinear changes …”
„… reversing the degradation of ecosystems while meeting
increasing demands for their services can be partially met under some
scenarios …, but these involve significant changes in policies, institutions,
and practices that are not currently under way.” MEA 2005




SCIENTIFIC CHALLENGES
 Role of biodiversity and community ecology in ecosystem functioning
 How productive and effective are various ecosystem services (ES)
   - maintaining hydrologic cycles, regulating climate, cleansing air/water
 Trade offs between ecosystem functions and management regimes
   >> quantify ecosystem functioning
   >> develop ecosystem service indicators
                                                                          11
   >> potential of metagenomics in ES valuation
Ecosystem functioning / valuation (2)
REVIEW IN PROGRESS
 Collected papers                    14 (will be completed)
 Selected and annotated papers       -

MOST RELEVANT RESEARCH GROUPS/PROJECTS
 not evaluated yet

TYPICAL „WORKFLOWS”
 calculating ecosystem service indicators based on model simulation
 … will be completed

WEB SERVICES
 no such kind of applicable services operating yet
 new service sets identified and prioritised to develop:
   2 services for Stand level Ecosystems Service Indicators (SESSI)
   2 services for Landscape level ES Indicators (LESSI)

 TAXO, NICHE, META & POP services also need to be considered


                                                                      12
Invasive species management (1)
SCIENCE & POLICY CONTEXT
   Invasions of alien species are a leading cause of biodiversity loss
   and related economic damages. They degrade ecosystem services,
   generate human health problems and impact outdoor recreation
...


SCIENTIFIC CHALLENGES
 Risk assessment as climate change proceeds
   and considering the effect of different human activities
 Simulating pest control or mitigation strategy options

    >> ecological niche modelling (ENM)




                                                                         13
Invasive species management (2)
REVIEW IN PROGRESS
 Collected papers                        9 (will be completed)
 Selected and annotated papers           -

MOST RELEVANT RESEARCH GROUPS/PROJECTS
 GISIN – Global Invasive Species Information Network
 and … but not evaluated yet

TYPICAL „WORKFLOWS”
 Ecological Niche Modelling of (potential) invasive alien
 species
 Ecological Niche Modelling of (forest) pest species
 …

WEB SERVICES
 openModeller service with environmental data layers
 TAXO, NICHE, …

                                                                 14
Biodiversity Virtual e-Laboratory
BioVeL is 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. National Research Council: Institute for
    Biomedical Technologies and Institute of
    Biomembrane and Bioenergetics, Italy
10. Netherlands Centre for Biodiversity (NCB      13. University of Eastern Finland, Finland
    Naturalis), The Netherlands                   14. University of Gothenburg, Sweden
11. Stichting European Grid Initiative,           15. University of Manchester, UK
    The Netherlands
12. University of Amsterdam, Institute of
    Biodiversity and Ecosystem Dynamics,
    The Netherlands
                                                                                               15
Supported by many friends




• Become a ‘Friend of BioVeL’
  – Deploy robust (Web) services for
    biodiversity analysis and workflow
  – Encourage adoption of the workflow
    approach towards processing and
    analysis of biodiversity data        16
Fits in a portfolio of initiatives
NoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.
Projects: agINFRA, Aquamaps, ArtDataBanken, BioFresh, Envri,
EU BON, EUBrazilOpenBio, Fauna Iberica, iMarine, MicroB3,
OpenPlantBio, ViBRANT
Global: Catalogue of Life, COOPEUS, CReATIVE-B, EoL, GBIF, GSC
Biodiversity WG, TreeBase, and many more

Recognised as providing an
important contribution of
infrastructure


                                                               17
• Exploring patterns of biodiversity and
                                processes of biodiversity across time and
                                space and scales
                                     Genetic <-> Species <-> Ecosystem<-> Landscape
                                     A Systems approach

                              • A European Research Infrastructure
                                     –   Distributed observatories / sensors
                                     –   Databases, processing and analytical tools
                                     –   Computational capability and capacity
                                     –   Collaborative environments
                                     –   Support, training, partnering, fellowship
                                     –   Open access, single portal
1995                2005          2008              2011                 2016
                                                                             Operation &
 Earlier projects      Conceive     Preparations        Construction
                                                   19                  5+2   Evolution
                                         €5m                 ~ €234m
LifeWatch as a distributed
                     research infrastructure
                                    Independent
                                    entities contributing to
                                    LifeWatch operations


Distributed core
operations
owned by
LifeWatch
LifeWatch as a distributed
                                  research infrastructure
                                  Independent
                                  entities contributing to
                                  LifeWatch operations
                                                                           National contributions
                                                                           • Belgium
Distributed core
operations
                                                                           • Hungary
owned by
LifeWatch
                                                                           • Italy
                                                                           • Netherlands
                                         Core operations                   • Romania
                                         • BioVeL                          • Spain
                                         • European Taxonomic Backbone     • Sweden
                                         • Other ICT Core elements


                   Thematic contributions
                   • Population biology of migrating birds
                   • Understanding the role of marine wetlands on biodiversity migration patterns
                   • Impacts of invading alien species
                   • Assessment of regional biodiversity
                   • Preservation of ecosystem services (curing habitat destruction)
                   • Human observations of biodiversity
Finally ... ...

• White Paper initiative
  – Our community vision for biodiversity
    informatics, to inform Horizon 2020
  – http://is.gd/WhitePaperChapters


• Now,
  – Listen, enjoy the presentations
  – Network and socialise
  – Express your opinions and influence
    our work for the next months            22
Biodiversity Virtual e-Laboratory
BioVeL is funded by the European Commission
7th Framework Programme (FP7).
It is part of its e-Infrastructures activity.
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.



BioVeL is free and available via internet.




www.biovel.eu, contact Alex Hardisty: HardistyAR@cardiff.ac.uk
                                                                                               23

More Related Content

Similar to Biodiversity Virtual e-Laboratory (BioVeL)

USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3Gianpaolo Coro
 
BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...
BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...
BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...Alex Hardisty
 
10th e concertation-brussels-06march2013-v2
10th e concertation-brussels-06march2013-v210th e concertation-brussels-06march2013-v2
10th e concertation-brussels-06march2013-v2Alex Hardisty
 
Supporting researchers in the molecular life sciences Jeff Christiansen
Supporting researchers in the molecular life sciences Jeff Christiansen Supporting researchers in the molecular life sciences Jeff Christiansen
Supporting researchers in the molecular life sciences Jeff Christiansen ARDC
 
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5Gianpaolo Coro
 
Web Apollo at Genome Informatics 2014
Web Apollo at Genome Informatics 2014Web Apollo at Genome Informatics 2014
Web Apollo at Genome Informatics 2014Monica Munoz-Torres
 
Perspectives on Collaborative Research Environments offered by D4Science
Perspectives on Collaborative Research Environments offered by D4SciencePerspectives on Collaborative Research Environments offered by D4Science
Perspectives on Collaborative Research Environments offered by D4ScienceFAO
 
Advanced Bioinformatics for Genomics and BioData Driven Research
Advanced Bioinformatics for Genomics and BioData Driven ResearchAdvanced Bioinformatics for Genomics and BioData Driven Research
Advanced Bioinformatics for Genomics and BioData Driven ResearchEuropean Bioinformatics Institute
 
Introduction to bioinformatics
Introduction to bioinformaticsIntroduction to bioinformatics
Introduction to bioinformaticsMakarand Bhale
 
Talk by J. Eisen for NZ Computational Genomics meeting
Talk by J. Eisen for NZ Computational Genomics meetingTalk by J. Eisen for NZ Computational Genomics meeting
Talk by J. Eisen for NZ Computational Genomics meetingJonathan Eisen
 
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
 
PhD defense Julien Troudet (29/11/2017)
PhD defense Julien Troudet (29/11/2017)PhD defense Julien Troudet (29/11/2017)
PhD defense Julien Troudet (29/11/2017)Julien Troudet
 

Similar to Biodiversity Virtual e-Laboratory (BioVeL) (20)

iMicrobe_ASLO_2015
iMicrobe_ASLO_2015iMicrobe_ASLO_2015
iMicrobe_ASLO_2015
 
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3
 
BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...
BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...
BioVeL at IBERGRID e-Infrastructures and biodiversity workshop, 19th Septembe...
 
10th e concertation-brussels-06march2013-v2
10th e concertation-brussels-06march2013-v210th e concertation-brussels-06march2013-v2
10th e concertation-brussels-06march2013-v2
 
Supporting researchers in the molecular life sciences Jeff Christiansen
Supporting researchers in the molecular life sciences Jeff Christiansen Supporting researchers in the molecular life sciences Jeff Christiansen
Supporting researchers in the molecular life sciences Jeff Christiansen
 
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5
 
ISA - a short overview - Dec 2013
ISA - a short overview - Dec 2013ISA - a short overview - Dec 2013
ISA - a short overview - Dec 2013
 
eScience-School-Oct2012-Campinas-Brazil
eScience-School-Oct2012-Campinas-BrazileScience-School-Oct2012-Campinas-Brazil
eScience-School-Oct2012-Campinas-Brazil
 
Web Apollo at Genome Informatics 2014
Web Apollo at Genome Informatics 2014Web Apollo at Genome Informatics 2014
Web Apollo at Genome Informatics 2014
 
Perspectives on Collaborative Research Environments offered by D4Science
Perspectives on Collaborative Research Environments offered by D4SciencePerspectives on Collaborative Research Environments offered by D4Science
Perspectives on Collaborative Research Environments offered by D4Science
 
Advanced Bioinformatics for Genomics and BioData Driven Research
Advanced Bioinformatics for Genomics and BioData Driven ResearchAdvanced Bioinformatics for Genomics and BioData Driven Research
Advanced Bioinformatics for Genomics and BioData Driven Research
 
Bccvl hallgren
Bccvl hallgrenBccvl hallgren
Bccvl hallgren
 
Introduction to bioinformatics
Introduction to bioinformaticsIntroduction to bioinformatics
Introduction to bioinformatics
 
Talk by J. Eisen for NZ Computational Genomics meeting
Talk by J. Eisen for NZ Computational Genomics meetingTalk by J. Eisen for NZ Computational Genomics meeting
Talk by J. Eisen for NZ Computational Genomics meeting
 
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
 
FYP report
FYP reportFYP report
FYP report
 
OBIS introduction-for-i marine
OBIS introduction-for-i marineOBIS introduction-for-i marine
OBIS introduction-for-i marine
 
PhD defense Julien Troudet (29/11/2017)
PhD defense Julien Troudet (29/11/2017)PhD defense Julien Troudet (29/11/2017)
PhD defense Julien Troudet (29/11/2017)
 
Let's unlock UNLOCK
Let's unlock UNLOCKLet's unlock UNLOCK
Let's unlock UNLOCK
 
NETTAB 2012
NETTAB 2012NETTAB 2012
NETTAB 2012
 

More from Alex Hardisty

openDS - A new standard for digital specimens
openDS - A new standard for digital specimensopenDS - A new standard for digital specimens
openDS - A new standard for digital specimensAlex Hardisty
 
Global Research Infrastructures for Biodiversity and Ecosystems Research
Global Research Infrastructures for Biodiversity and Ecosystems ResearchGlobal Research Infrastructures for Biodiversity and Ecosystems Research
Global Research Infrastructures for Biodiversity and Ecosystems ResearchAlex Hardisty
 
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) project
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) projectApproach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) project
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) projectAlex Hardisty
 
Data accessibility and the role of informatics in predicting the biosphere
Data accessibility and the role of informatics in predicting the biosphereData accessibility and the role of informatics in predicting the biosphere
Data accessibility and the role of informatics in predicting the biosphereAlex Hardisty
 
Constructing bottomup
Constructing bottomupConstructing bottomup
Constructing bottomupAlex Hardisty
 
Mapping Research Infrastructures with the ENVRI Reference Model
Mapping Research Infrastructures with the ENVRI Reference ModelMapping Research Infrastructures with the ENVRI Reference Model
Mapping Research Infrastructures with the ENVRI Reference ModelAlex Hardisty
 
Biodiversity Informatics Horizons 2013 - Introduction and Scope
Biodiversity Informatics Horizons 2013 - Introduction and ScopeBiodiversity Informatics Horizons 2013 - Introduction and Scope
Biodiversity Informatics Horizons 2013 - Introduction and ScopeAlex Hardisty
 
Hardistyroberts190313opt 130319072407-phpapp02
Hardistyroberts190313opt 130319072407-phpapp02Hardistyroberts190313opt 130319072407-phpapp02
Hardistyroberts190313opt 130319072407-phpapp02Alex Hardisty
 
Eudat user forum-london-11march2013-biovel-v3
Eudat user forum-london-11march2013-biovel-v3Eudat user forum-london-11march2013-biovel-v3
Eudat user forum-london-11march2013-biovel-v3Alex Hardisty
 
E cconcertation lyon-22-sep2011-v3
E cconcertation lyon-22-sep2011-v3E cconcertation lyon-22-sep2011-v3
E cconcertation lyon-22-sep2011-v3Alex Hardisty
 
AH-XLDBEurope-position-09 jun2011
AH-XLDBEurope-position-09 jun2011AH-XLDBEurope-position-09 jun2011
AH-XLDBEurope-position-09 jun2011Alex Hardisty
 
XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011Alex Hardisty
 
TextofKeynote-EGIforum-15-Sep2010
TextofKeynote-EGIforum-15-Sep2010TextofKeynote-EGIforum-15-Sep2010
TextofKeynote-EGIforum-15-Sep2010Alex Hardisty
 
EGIforum-Amsterdam-15-Sep2010
EGIforum-Amsterdam-15-Sep2010EGIforum-Amsterdam-15-Sep2010
EGIforum-Amsterdam-15-Sep2010Alex Hardisty
 

More from Alex Hardisty (14)

openDS - A new standard for digital specimens
openDS - A new standard for digital specimensopenDS - A new standard for digital specimens
openDS - A new standard for digital specimens
 
Global Research Infrastructures for Biodiversity and Ecosystems Research
Global Research Infrastructures for Biodiversity and Ecosystems ResearchGlobal Research Infrastructures for Biodiversity and Ecosystems Research
Global Research Infrastructures for Biodiversity and Ecosystems Research
 
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) project
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) projectApproach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) project
Approach and outcome of the Biodiversity Virtual e-Laboratory (BioVeL) project
 
Data accessibility and the role of informatics in predicting the biosphere
Data accessibility and the role of informatics in predicting the biosphereData accessibility and the role of informatics in predicting the biosphere
Data accessibility and the role of informatics in predicting the biosphere
 
Constructing bottomup
Constructing bottomupConstructing bottomup
Constructing bottomup
 
Mapping Research Infrastructures with the ENVRI Reference Model
Mapping Research Infrastructures with the ENVRI Reference ModelMapping Research Infrastructures with the ENVRI Reference Model
Mapping Research Infrastructures with the ENVRI Reference Model
 
Biodiversity Informatics Horizons 2013 - Introduction and Scope
Biodiversity Informatics Horizons 2013 - Introduction and ScopeBiodiversity Informatics Horizons 2013 - Introduction and Scope
Biodiversity Informatics Horizons 2013 - Introduction and Scope
 
Hardistyroberts190313opt 130319072407-phpapp02
Hardistyroberts190313opt 130319072407-phpapp02Hardistyroberts190313opt 130319072407-phpapp02
Hardistyroberts190313opt 130319072407-phpapp02
 
Eudat user forum-london-11march2013-biovel-v3
Eudat user forum-london-11march2013-biovel-v3Eudat user forum-london-11march2013-biovel-v3
Eudat user forum-london-11march2013-biovel-v3
 
E cconcertation lyon-22-sep2011-v3
E cconcertation lyon-22-sep2011-v3E cconcertation lyon-22-sep2011-v3
E cconcertation lyon-22-sep2011-v3
 
AH-XLDBEurope-position-09 jun2011
AH-XLDBEurope-position-09 jun2011AH-XLDBEurope-position-09 jun2011
AH-XLDBEurope-position-09 jun2011
 
XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011
 
TextofKeynote-EGIforum-15-Sep2010
TextofKeynote-EGIforum-15-Sep2010TextofKeynote-EGIforum-15-Sep2010
TextofKeynote-EGIforum-15-Sep2010
 
EGIforum-Amsterdam-15-Sep2010
EGIforum-Amsterdam-15-Sep2010EGIforum-Amsterdam-15-Sep2010
EGIforum-Amsterdam-15-Sep2010
 

Recently uploaded

The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...Aggregage
 
Introduction to Matsuo Laboratory (ENG).pptx
Introduction to Matsuo Laboratory (ENG).pptxIntroduction to Matsuo Laboratory (ENG).pptx
Introduction to Matsuo Laboratory (ENG).pptxMatsuo Lab
 
UiPath Community: AI for UiPath Automation Developers
UiPath Community: AI for UiPath Automation DevelopersUiPath Community: AI for UiPath Automation Developers
UiPath Community: AI for UiPath Automation DevelopersUiPathCommunity
 
Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...
Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...
Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...Will Schroeder
 
20200723_insight_release_plan
20200723_insight_release_plan20200723_insight_release_plan
20200723_insight_release_planJamie (Taka) Wang
 
Introduction to Quantum Computing
Introduction to Quantum ComputingIntroduction to Quantum Computing
Introduction to Quantum ComputingGDSC PJATK
 
9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding Team9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding TeamAdam Moalla
 
Computer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and HazardsComputer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and HazardsSeth Reyes
 
UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...
UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...
UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...UbiTrack UK
 
PicPay - GenAI Finance Assistant - ChatGPT for Customer Service
PicPay - GenAI Finance Assistant - ChatGPT for Customer ServicePicPay - GenAI Finance Assistant - ChatGPT for Customer Service
PicPay - GenAI Finance Assistant - ChatGPT for Customer ServiceRenan Moreira de Oliveira
 
Machine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdfMachine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdfAijun Zhang
 
Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024D Cloud Solutions
 
COMPUTER 10: Lesson 7 - File Storage and Online Collaboration
COMPUTER 10: Lesson 7 - File Storage and Online CollaborationCOMPUTER 10: Lesson 7 - File Storage and Online Collaboration
COMPUTER 10: Lesson 7 - File Storage and Online Collaborationbruanjhuli
 
Cybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptxCybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptxGDSC PJATK
 
OpenShift Commons Paris - Choose Your Own Observability Adventure
OpenShift Commons Paris - Choose Your Own Observability AdventureOpenShift Commons Paris - Choose Your Own Observability Adventure
OpenShift Commons Paris - Choose Your Own Observability AdventureEric D. Schabell
 
Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)Commit University
 
Videogame localization & technology_ how to enhance the power of translation.pdf
Videogame localization & technology_ how to enhance the power of translation.pdfVideogame localization & technology_ how to enhance the power of translation.pdf
Videogame localization & technology_ how to enhance the power of translation.pdfinfogdgmi
 
UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7DianaGray10
 
Digital magic. A small project for controlling smart light bulbs.
Digital magic. A small project for controlling smart light bulbs.Digital magic. A small project for controlling smart light bulbs.
Digital magic. A small project for controlling smart light bulbs.francesco barbera
 
Nanopower In Semiconductor Industry.pdf
Nanopower  In Semiconductor Industry.pdfNanopower  In Semiconductor Industry.pdf
Nanopower In Semiconductor Industry.pdfPedro Manuel
 

Recently uploaded (20)

The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
 
Introduction to Matsuo Laboratory (ENG).pptx
Introduction to Matsuo Laboratory (ENG).pptxIntroduction to Matsuo Laboratory (ENG).pptx
Introduction to Matsuo Laboratory (ENG).pptx
 
UiPath Community: AI for UiPath Automation Developers
UiPath Community: AI for UiPath Automation DevelopersUiPath Community: AI for UiPath Automation Developers
UiPath Community: AI for UiPath Automation Developers
 
Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...
Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...
Apres-Cyber - The Data Dilemma: Bridging Offensive Operations and Machine Lea...
 
20200723_insight_release_plan
20200723_insight_release_plan20200723_insight_release_plan
20200723_insight_release_plan
 
Introduction to Quantum Computing
Introduction to Quantum ComputingIntroduction to Quantum Computing
Introduction to Quantum Computing
 
9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding Team9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding Team
 
Computer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and HazardsComputer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and Hazards
 
UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...
UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...
UWB Technology for Enhanced Indoor and Outdoor Positioning in Physiological M...
 
PicPay - GenAI Finance Assistant - ChatGPT for Customer Service
PicPay - GenAI Finance Assistant - ChatGPT for Customer ServicePicPay - GenAI Finance Assistant - ChatGPT for Customer Service
PicPay - GenAI Finance Assistant - ChatGPT for Customer Service
 
Machine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdfMachine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdf
 
Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024
 
COMPUTER 10: Lesson 7 - File Storage and Online Collaboration
COMPUTER 10: Lesson 7 - File Storage and Online CollaborationCOMPUTER 10: Lesson 7 - File Storage and Online Collaboration
COMPUTER 10: Lesson 7 - File Storage and Online Collaboration
 
Cybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptxCybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptx
 
OpenShift Commons Paris - Choose Your Own Observability Adventure
OpenShift Commons Paris - Choose Your Own Observability AdventureOpenShift Commons Paris - Choose Your Own Observability Adventure
OpenShift Commons Paris - Choose Your Own Observability Adventure
 
Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)
 
Videogame localization & technology_ how to enhance the power of translation.pdf
Videogame localization & technology_ how to enhance the power of translation.pdfVideogame localization & technology_ how to enhance the power of translation.pdf
Videogame localization & technology_ how to enhance the power of translation.pdf
 
UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7
 
Digital magic. A small project for controlling smart light bulbs.
Digital magic. A small project for controlling smart light bulbs.Digital magic. A small project for controlling smart light bulbs.
Digital magic. A small project for controlling smart light bulbs.
 
Nanopower In Semiconductor Industry.pdf
Nanopower  In Semiconductor Industry.pdfNanopower  In Semiconductor Industry.pdf
Nanopower In Semiconductor Industry.pdf
 

Biodiversity Virtual e-Laboratory (BioVeL)

  • 1. Biodiversity Virtual e-Laboratory Project Overview BioVeL is an e-laboratory that supports research on biodiversity using large amounts of data from cross-disciplinary sources. Alex Hardisty Project Coordinator Cardiff University 1
  • 2. Biodiversity Virtual e-Laboratory An international network of experts connecting 2 scientific communities: ICT and biodiversity Offers access to a variety of data processing services, linked as ‘workflows’ for assisting studies in biodiversity science • You will hear about these during this workshop • You will be able to influence their design Aims to foster cooperation in the community by: • Discussing use cases • Identifying important Web Services • Training scientists 2
  • 3. Biodiversity Virtual e-Laboratory BioVeL is a powerful data processing tool • Import data from your own research and/or from existing libraries • Use workflows (series of data analysis steps) for data processing • Build your own workflow by selecting and applying successive Web services (data processing techniques) • Access a library of workflows and re-use existing workflows • Cut down research time and overhead expenses Workflow for population modelling (stage-based matrix projection models) based on Stubben and Milligan. Journal of Statistical Software, 22(11), Sept 2007 3
  • 4. Biodiversity Virtual e-Laboratory Showcase study 1: create a workflow* Study on the ecological niche of the south east Asian horseshoe crab, an endangered species: • Import south east Asian data from external library • Apply succession of “services” = workflow • Result: ecological niche map 4 * courtesy Matthias Obst, University of Gothenburg, Sweden
  • 5. Biodiversity Virtual e-Laboratory Showcase study 2: re-use a workflow Study on the ecological niche of the American horseshoe crab • Import American data • Re-use south east Asia crab study workflow • Result: ecological niche map for American horseshoe crab Compare the ecological niches of the south east Asian and American crabs. Potential study of the ecological niche of an African animal • Import African data • Re-use horseshoe crab study workflow • Result: ecological niche map for African animal 5
  • 6. What does BioVeL consist of? (1) Biodiversity Data Data Services Catalogues / User Repositories xls, csv BioVeLData REST Manager documents GenBank REST Collections Genomic data Catalogue REST Taxonomic data of Life CSW Observations GBIF REST Spatial (Web) OGC raster sensor nodes data data BioVeL REST Collaboration GeoServer OGC Annotations Workflows 6
  • 7. What does BioVeL consist of? (2) Catalogues / Execution Biodiversity Services Repositories environment Phylogenetic BLAST,Hmmer, Provenance WebDaV Data MrBayes, Management Blast, PAML, EMBOSS,… Taverna Taxonomic Workbench OpenSearch Synonyms Visualization BioSTIF Taverna Google Refine CSW Workflow Engine Modelling / Authentication / Authorisation GeoProcessing R Grid, Cloud, etc. openModeller WPS / WCPS 7
  • 8. Service sets driven by science • Phylogeny and metagenomics services – Measures of genetic diversity and adaptation to changing conditions • Taxonomy services – Checklists, identification, data cleaning, ... • Niche and population modelling services – Processes of conservation and invasive species management • Ecosystem functionality and valuation services – Modelling of ecosystem services and CO2 sequestration 8 • Visualization and geospatial
  • 9. Biospheric CO2 sequestration (1) SCIENCE & POLICY CONTEXT Emission is continuously increasing – 10 GtC in 2010 Sequestration is the only sustainable process to mitigate Terrestrial Sequestration highly depends on land use & climate change SCIENTIFIC CHALLENGES Model improvement Model & data downscaling Model verification >> data-model calibration >> higher processing capacity 9
  • 10. Biospheric CO2 sequestration (2) REVIEW IN PROGRESS Collected papers 39 Selected and annotated papers 35 MOST RELEVANT RESEARCH GROUPS/PROJECTS The Global Carbon Project, Fluxnet – eddy covariance tower measurements, GHG Europe, ICOS, NTSG (University Montana) and Biome-BGC users & developers worldwide Biome-BGC is a computer model that estimates fluxes and storage of energy, water, carbon, and nitrogen for the vegetation and soil components of terrestrial ecosystems. TYPICAL „WORKFLOWS” around Biome-BGC Weather to Biome-BGC; Biome-BGC CARBON; Biome-BGC Sensitivity Analysis; Biome-BGC Data-Model Harmonization WEB SERVICES no such kind of services operating yet new service sets identified and prioritised to develop: 4 data retrieval services 10 6 Biome-BGC modelling services
  • 11. Ecosystem functioning / valuation (1) SCIENCE & POLICY CONTEXT „Over the past 50 years, humans have changed ecosystems more rapidly and extensively than … this has resulted in a substantial and largely irreversible loss in the diversity of life on Earth.” „… degradation of many ecosystem services [causes] increased risks of nonlinear changes …” „… reversing the degradation of ecosystems while meeting increasing demands for their services can be partially met under some scenarios …, but these involve significant changes in policies, institutions, and practices that are not currently under way.” MEA 2005 SCIENTIFIC CHALLENGES Role of biodiversity and community ecology in ecosystem functioning How productive and effective are various ecosystem services (ES) - maintaining hydrologic cycles, regulating climate, cleansing air/water Trade offs between ecosystem functions and management regimes >> quantify ecosystem functioning >> develop ecosystem service indicators 11 >> potential of metagenomics in ES valuation
  • 12. Ecosystem functioning / valuation (2) REVIEW IN PROGRESS Collected papers 14 (will be completed) Selected and annotated papers - MOST RELEVANT RESEARCH GROUPS/PROJECTS not evaluated yet TYPICAL „WORKFLOWS” calculating ecosystem service indicators based on model simulation … will be completed WEB SERVICES no such kind of applicable services operating yet new service sets identified and prioritised to develop: 2 services for Stand level Ecosystems Service Indicators (SESSI) 2 services for Landscape level ES Indicators (LESSI) TAXO, NICHE, META & POP services also need to be considered 12
  • 13. Invasive species management (1) SCIENCE & POLICY CONTEXT Invasions of alien species are a leading cause of biodiversity loss and related economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation ... SCIENTIFIC CHALLENGES Risk assessment as climate change proceeds and considering the effect of different human activities Simulating pest control or mitigation strategy options >> ecological niche modelling (ENM) 13
  • 14. Invasive species management (2) REVIEW IN PROGRESS Collected papers 9 (will be completed) Selected and annotated papers - MOST RELEVANT RESEARCH GROUPS/PROJECTS GISIN – Global Invasive Species Information Network and … but not evaluated yet TYPICAL „WORKFLOWS” Ecological Niche Modelling of (potential) invasive alien species Ecological Niche Modelling of (forest) pest species … WEB SERVICES openModeller service with environmental data layers TAXO, NICHE, … 14
  • 15. Biodiversity Virtual e-Laboratory BioVeL is 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. National Research Council: Institute for Biomedical Technologies and Institute of Biomembrane and Bioenergetics, Italy 10. Netherlands Centre for Biodiversity (NCB 13. University of Eastern Finland, Finland Naturalis), The Netherlands 14. University of Gothenburg, Sweden 11. Stichting European Grid Initiative, 15. University of Manchester, UK The Netherlands 12. University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics, The Netherlands 15
  • 16. Supported by many friends • Become a ‘Friend of BioVeL’ – Deploy robust (Web) services for biodiversity analysis and workflow – Encourage adoption of the workflow approach towards processing and analysis of biodiversity data 16
  • 17. Fits in a portfolio of initiatives NoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc. Projects: agINFRA, Aquamaps, ArtDataBanken, BioFresh, Envri, EU BON, EUBrazilOpenBio, Fauna Iberica, iMarine, MicroB3, OpenPlantBio, ViBRANT Global: Catalogue of Life, COOPEUS, CReATIVE-B, EoL, GBIF, GSC Biodiversity WG, TreeBase, and many more Recognised as providing an important contribution of infrastructure 17
  • 18. • Exploring patterns of biodiversity and processes of biodiversity across time and space and scales Genetic <-> Species <-> Ecosystem<-> Landscape A Systems approach • A European Research Infrastructure – Distributed observatories / sensors – Databases, processing and analytical tools – Computational capability and capacity – Collaborative environments – Support, training, partnering, fellowship – Open access, single portal 1995 2005 2008 2011 2016 Operation & Earlier projects Conceive Preparations Construction 19 5+2 Evolution €5m ~ €234m
  • 19. LifeWatch as a distributed research infrastructure Independent entities contributing to LifeWatch operations Distributed core operations owned by LifeWatch
  • 20. LifeWatch as a distributed research infrastructure Independent entities contributing to LifeWatch operations National contributions • Belgium Distributed core operations • Hungary owned by LifeWatch • Italy • Netherlands Core operations • Romania • BioVeL • Spain • European Taxonomic Backbone • Sweden • Other ICT Core elements Thematic contributions • Population biology of migrating birds • Understanding the role of marine wetlands on biodiversity migration patterns • Impacts of invading alien species • Assessment of regional biodiversity • Preservation of ecosystem services (curing habitat destruction) • Human observations of biodiversity
  • 21. Finally ... ... • White Paper initiative – Our community vision for biodiversity informatics, to inform Horizon 2020 – http://is.gd/WhitePaperChapters • Now, – Listen, enjoy the presentations – Network and socialise – Express your opinions and influence our work for the next months 22
  • 22. Biodiversity Virtual e-Laboratory BioVeL is funded by the European Commission 7th Framework Programme (FP7). It is part of its e-Infrastructures activity. 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. BioVeL is free and available via internet. www.biovel.eu, contact Alex Hardisty: HardistyAR@cardiff.ac.uk 23

Editor's Notes

  1. BioVeLfocusses on:DNA sequence-based phylogeny and metagenomics services that help link knowledge of model organisms to a broad range of species, that provide a measure of genetic diversity used in conservation planning and that help to understand adaptation in relation to climate change;Taxonomy services to provide the underpinning checklist of diversity in Europe, identification aids to native, invasive and economic species; Niche and population modelling for species, to better understand the processes of conservation and invasive species management; and, Ecosystem functionality and valuation services, to improve modelling capabilities to ecosystem services and CO2 sequestration.
  2. Terrestrial sequestration is also increasing, but only 26% of the total emission, oceans can eliminate about 24%About 50% of the total emission remains and accumulates in the atmosphere --- In 2010REF: Global Carbon Project 2010; Updated from Le Quéré et al. 2009, Nature Geoscience; Canadell et al. 2007, PNAS
  3. Fluxnet –coordinates regional and global analysis of observations from micrometeorological tower sites. The flux tower sites use eddy covariance methods to measure the exchanges of carbon dioxide (CO2), water vapor, and energy between terrestrial ecosystems and the atmosphere. NTSG : Numerical Terradynamic Simulation GroupGHG-Europe : Greenhouse Gas management in European land use systems
  4. „Over the past 50 years, humans have changed ecosystemsmore rapidly and extensively than in any comparable period oftime in human history, largely to meet rapidly growing demands forfood, fresh water, timber, fiber, and fuel. This has resulted in a substantialand largely irreversible loss in the diversity of life on Earth.”Millenium Ecosystem Assessment 2005Challenges:Role of biodiversity and community ecology in ecosystem functioning2. &quot;How much are the productivity and other services of the ecosystems in given ecological circumstances and management regimes? - maybe it would be better (provoking) to say &quot;How much (and what measure) are the other ecosystem services than productivity?&quot; - Because we know a lot about productivity of different type of ecosystems (easy to measure in agroecosystems, not so easy to measure/estimate in natural ecosystems), but what about other ecosystem services such as maintaining hydrologic cycles, regulating climate, cleansing air and water, maintaining atmospheric composition, pollination, soil genesis, storing and cycling of nutrients ...3. &quot;What is the trade off among different ecosystem functions and management regimes in various ecosystems at landscape levels?&quot; - mostly if we consider extensive and/or sustainable agriculture and/or various mosaic of landuse patterns, not massive uniform large croplands ...