BIODIVERSITY VIRTUAL LABORATORY (BIOVEL) PILOT PROJECT AND OTHER BIODIVERSITY E-SCIENCE PROJECTS

Alex Hardisty Cardiff University

Biodiversity Forum, 4th April 2013, Beijing

Biodiversity monitoring and research networks

• LTER, Genomic Observatories, EMBRC, Natural

History Museums, EU BON, EMBOS, BioSOS

Biodiversity information systems

• ViBRANT, i4Life, PESI, WORMS, OBIS, GBIF,

GeneBank, AquaMaps, agINFRA, pro-iBioSphere,

OpenUp!, BioFresh, etc.

Biodiversity e-science infrastructures

• LifeWatch, BioVeL, iMarine, EUBrazilOpenBio

European e-Science Infrastructures for Biodiversity and Ecosystem Research

Data analysis

Data curation and access

Data generation

AN E-INFRASTRUCTURE AND E-SCIENCE ENVIRONMENT SUPPORTING RESEARCH ON BIODIVERSITY

Alex Hardisty Coordinator, Cardiff University

Biodiversity Forum, 4th April 2013, Beijing

Biodiversity Virtual e-Laboratory

• Aims to foster cooperation in the community by:

– Discussing scientific use cases

– Identifying and deploying important Web Services

– Designing and offering workflows

– Training scientists

• Aims to create a “Service Network”

– Web services for interdisciplinary analysis of biodiversity

• And “workflows” for science

Ecological Niche Modelling Biogeochemical modelling Metagenomics Phylogenetics Population Modelling Taxonomy Geospatial Visualization

An international network of experts connecting 2 scientific communities: biodiversity and ICT,

to create a general purpose Virtual e-Laboratory

The Service Network idea

Users’ workflows and applications

Service and Data Providers (LifeWatch, BioVeL, GBIF, CoL, EBI, etc.)

Resource Providers (EUDAT, EGI.eu, PRACE, commercial cloud, etc.)

www.biodiversitycatalogue.org A fully curated, well-founded catalogue of

Web services for biodiversity science

Part of a workflow to study the

ecological niche of the Horseshoe crab

(Limulus polyphemus)

Products are “workflows” built from “services”

• Workflows allow to process vast amounts of data, repeatedly

– Build your own workflow: select and apply successive “services” (data analysis and processing steps)

– Import data from own research and/or from existing libraries (e.g., GBIF, Catalogue of Life)

• Access a library of workflows Re-use existing workflows

– Improves efficiency by reducing research time and overhead expenses

www.myexperiment.org A repository for sharing workflows

• Niche modelling of interactions between forest insects and their host trees under various climate change scenarios

• Quantifying taxonomic and geographical change over seven decades of anthropogenic pressures in the North East Atlantic

• Deriving quantitative ecosystem service indicators and developing a new IT tool based on terrestrial ecosystem simulations

• Studying microbial communities through metagenomics and a functional trait-based ecology

• Spatial-Temporal Visualisation of Biodiversity Data: an integrative Tool for Ecologists

• Large scale modelling of the distribution and impact of invasive species in the Baltic Sea

• Carbon Sequestration • Ecosystem Functioning and Valuation • Invasive Species Management

6 submissions to INTECOL 2013 (waiting)

Creates powerful data processing tools for biodiversity research

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 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, Finland

14. University of Gothenburg, Sweden 15. University of Manchester, UK

• NoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.

• Projects: 4D4Life, agINFRA, Aquamaps, ArtDataBanken, BioFresh, Envri, EU BON, EUBrazilOpenBio, Fauna Iberica, i4Life, iMarine, Micro B3, OpenPlantBio, ViBRANT

• Global: CAMERA, Catalogue of Life, COOPEUS, CReATIVE-B, EoL, GBIF, GSC Biodiversity WG, TreeBase, and many more

Fits into a portfolio of initiatives

Supported by many friends

Important contribution to infrastructure

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.

Questions?

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.

A Data e-Infrastructure and specialised Virtual Laboratory initiative for Fisheries Management and Conservation of Marine Living Resources – based on a managed Ecosystem Approach

www.i-marine.eu

i-Marine

“The creation of the marine knowledge begins with the observation of the sea and oceans. Data from these observations are assembled, then analysed to create information and knowledge. Subsequently, the knowledge can be applied to deliver smart sustainable growth, to assess the health of the marine ecosystem or to protect coastal communities.”

Source: EC Communication on Marine Knowledge 2020

Multiple apps across integrated information

14

FIGIS (reports)

MyOcean (environmental data)

GENESI-DEC (earth observations)

DRIVER (publications)

OBIS (marine species data)

GBIF (occurrence points)

Catalogue of Life (taxonomy)

WoRMS (marine taxonomy)

ITIS (taxonomy)

AO SDMX Registry (stat. data)

AquaMaps (species maps)

FLOD (open linked data)

Geonetwork (georefenced data)

…Everything accessible through TAPIR, DigiR, OAI-PMH, OpenSearch, OGC W*S ,SDMX,….

software system)

Open e-Infrastructure capabilities to enhance Biodiversity community research

CRIA, SP

UFF, RJ CESAR, PE

RNP, RJ

BSC, Spain

CNR-ISTI, Italy

SP2000, UK

Trust-IT, UK

UPVLC, Spain

www.eubrazilopenbio.eu

Combining Biodiversity Science and Open Access to deploy a joint European and Brazilian e-Infrastructure

• Use case 1: Integration between Regional & Global Taxonomies – Cross-map the regional List of Species of Brazilian Flora with the Global

Catalogue of Life

• Use Case II: Data usability and ecological niche modelling – Use of openModeller in a distributed environment to run the models

• Open Access project e-Infrastructure – Research resources (HW, SW, Data) can be shared and exploited on-

demand in collaborative way (in virtual laboratory applications)

– Integration of resources from Brazil and Europe for benefit of both scientific communities

www.scratchpads.eu

The Catalogue of Life

4D4Life

Many information systems have a taxonomic (name) component. Before 1996 no single authoritative index of valid names, synonyms, common names was available. Authorized species names are important for reliable information services in society. The Catalogue of Life was set up to provide that service.

CoL

INDEX

Legislation: Species protection

Import/export Observations

Literature Reference systems

E-publications

Chemical substances: Source species

Medical information: E.g. medicinal plants

Image libraries: Images, videos, sounds

Molecular data: Sequences

Protein data

Identification data: Identification keys

Identification characters

Biological collections: (type) specimen

Historical data

Type strains

Ecological relations: E.g. Food web structures

Host-parasite relations

Taxonomic dbs

Hierarchies, names

What is the Catalogue of Life?

A Resource…

• an electronic synonymic species checklist,

• a tightly integrated taxonomic hierarchy,

• intended for all 1.9 M extant known species.

….constructed through international networking

• both checklist and hierarchy constructed from sectors from

many networked databases around the world

• and integrated using an international review panel of experts

www.catalogueoflife.org

Developments 2009-2013

Two e-infrastructure projects funded by the EC: 4D4Life: improving the internal infrastructure and services i4Life: building a virtual community of users

The 4D4Life Project (2009 – 2012)

builds a state-of-the art e-infrastructure that: • modernized information management tools • partly automated tasks; more efficient CoL production • structured information exchange in the project networks • synthesises a globally significant resource for science • dissemination in an array of web-services and e-products • multi-hub structure for regional deployment

4D4Life: Distributed Dynamic Diversity Databases for Life

4D4Life

The i4Life project (2010 – 2013) Establish a Virtual Research Community to integrate the indexing of biological species between the world’s major biodiversity programmes

• It uses the Catalogue of Life as a yardstick with which to compare and unify what is known

• will for the first time provide a summary of all species known on earth

• It will create a global standard for taxonomic data integration in electronic infrastructures world-wide

i4Life: Indexing for Life

More questions?