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
Apr 01, 2015
1
Biodiversity Virtual e-LaboratoryProject OverviewBioVeL is an e-laboratory that supports research on biodiversity using large amounts of data from cross-disciplinary sources.
Alex HardistyProject CoordinatorCardiff University
2
Biodiversity Virtual e-LaboratoryAn 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
3
Biodiversity Virtual e-Laboratory
• 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
BioVeL is a powerful data processing tool
Workflow for population modelling (stage-based matrix projection models) based on Stubben and Milligan. Journal of Statistical Software, 22(11), Sept 2007
4
Biodiversity Virtual e-Laboratory
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
Showcase study 1: create a workflow*
* courtesy Matthias Obst, University of Gothenburg, Sweden
5
Biodiversity Virtual e-LaboratoryStudy 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
Showcase study 2: re-use a workflow
6
What does BioVeL consist of? (1)
User
Collections
Biodiversity Data
Spatial (Web)
OGC
BioVeLDataManager
xls, csv
Catalogueof Life
Observations
Annotations
Taxonomic data
Data Services Catalogues /Repositories
Collaboration
raster data
REST
REST
REST
sensor data BioVeL
GeoServer
CSWREST
OGCnodes
GBIF
Workflows
Genomic data
documents
GenBank
REST
7
What does BioVeL consist of? (2)
Phylogenetic
Taxonomic
Biodiversity Services
Visualization
WebDaV Data Management
BLAST,Hmmer,MrBayes,
Blast, PAML,EMBOSS,…
R
Synonyms
Execution environment
Catalogues /Repositories
Modelling / GeoProcessing
BioSTIFGoogle Refine CSW
openModeller
WPS / WCPS Auth
entic
ation
/ A
utho
risati
onO
penS
earc
hPr
oven
ance
TavernaWorkbench
TavernaWorkflow Engine
Grid, Cloud, etc.
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
• 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
UnstableEarth systems
SCIENTIFIC CHALLENGES Model improvement Model & data downscaling Model verification
>> data-model calibration >> higher processing capacity
10
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 6 Biome-BGC modelling services
Biospheric CO2 sequestration (2)
11
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 >> potential of metagenomics in ES valuation
Ecosystem functioning / valuation (1)
12
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
Ecosystem functioning / valuation (2)
13
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)
Invasive species management (1)
14
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, …
Invasive species management (2)
15
Biodiversity Virtual e-LaboratoryBioVeL is a consortium of 15 partners from 9 countries1. Cardiff University, UK – Coordinator 2. Centro de Referência em Informação
Ambiental, Brazil3. Foundation for Research on Biodiversity,
France4. Fraunhofer-Gesellschaft, Institute IAIS,
Germany5. Free University of Berlin – Botanical
Gardens and Botanical Museum, Germany6. Hungarian Academy of Sciences Institute of
Ecology and Botany, Hungary7. Max Planck Society, MPI for Marine
Microbiology, Germany8. National Institute of Nuclear Physics, Italy9. National Research Council: Institute for
Biomedical Technologies and Institute 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, The Netherlands
13.University of Eastern Finland, Finland14. University of Gothenburg, Sweden15. University of Manchester, UK
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
17
Fits in a portfolio of initiatives
Recognised as providing an important contribution of infrastructure
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
• Exploring patterns of biodiversity and processes of biodiversity across time and space and scales
Genetic <-> Species <-> Ecosystem<-> LandscapeA 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
Earlier projects Conceive Preparations Construction Operation &Evolution
€5m ~ €234m19 5 + 2
Core operations• BioVeL• ICT Core• European Taxonomic Backbone
LifeWatch as a distributed research infrastructure
National contributions• Belgium• Hungary• Italy• Netherlands• Romania• Spain• Sweden
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
Distributed coreoperationsowned by LifeWatch
Independententities contributing to LifeWatch operations
Distributed coreoperationsowned by LifeWatch
Independententities contributing to LifeWatch operations
22
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
23
Biodiversity Virtual e-LaboratoryBioVeL 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: [email protected]