tools of a virtual laboratory

TOOLS OF A VIRTUAL LABORATORY

Alex HardistyCoordinator, Cardiff University

MS11 Workshop, 6-7th June 2013, Budapest

Biodiversity Virtual e-LaboratoryAn e-Infrastructure and e-Science environment supporting research on biodiversity

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 workflowsRe-use existing workflows – Improves efficiency by reducing

research time and overhead expenses

• 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 modellingEcosystem modellingMetagenomicsPhylogeneticsPopulation modellingTaxonomyGeospatial visualization

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

to create a general purpose Virtual e-Laboratory

Biodiversity Virtual e-LaboratoryBioVeL is a consortium of 15 partners from 9 countries

1. 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 Netherlands12. University of Amsterdam, Institute of Biodiversity and

Ecosystem Dynamics, The Netherlands

13.University of Eastern Finland, Finland

14. University of Gothenburg, Sweden15. 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 contributionto infrastructure

How it worksDiscipline

Scientists

Scientific PAL

Technical PAL

Scientific and Technical Service Providers

ScientificRequirements

Translation

TechnicalRequirements

TechnicalCapabilities

ScientificCapabilities

ApplicationServices Team

Prioritisation

Support Centre

Training &Issue Resolution

Service LevelRequirements

Sustainability

Community

Community

Ferenc Horváth

Péter Ittzés

Requirements

1. Services need to be secure, scalable, reliable, and well-documented

2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows

with minimal training and assistance

Building a network of services

Users’ workflows and applications

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

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

Hardening and Deploying Services

• Provision of service infrastructure– Security– Data storage and staging

• Deployment on cloud and grid for better availability and scalability

• Development of best practices for improving ease of use and scalability

Requirements

1. Services need to be secure, scalable, reliable, and well-documented

2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows

with minimal training and assistance

www.biodiversitycatalogue.orgA fully curated, well-founded catalogue of

Web services for biodiversity science

Requirements

1. Services need to be secure, scalable, reliable, and well-documented.

2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows

with minimal training and assistance

Public groupsPublishing workflows and results

Private groupsLocal materialsIntra-project work and collaborations

8700 members, 318 groups, 2625 workflows, 674 files, 276 packs

repository for sharing workflowswww.myexperiment.org

Requirements

1. Services need to be secure, scalable, reliable, and well-documented

2. Services need to be discoverable3. Workflows need to be storable and discoverable4. Users need to be able to build their own workflows

with minimal training and assistance

Tool Spectrum

TechnicalPAL

SciencePAL

DomainScientist

TavernaWorkbench

ComponentBuilder

TavernaLite / Server

Taverna Player / Domain-Specific

Website

Workflow Visibility

Concept KnowledgeWorkflow design, compute Domain science

High Low

The Portal

Taverna Lite

BioVeL Tools

• BioVeL websitehttp://www.biovel.eu

• BioVeL Portalhttp://tavlite1.biovel.eu

• BiodiversityCatalogue - Catalogue of services http://www.biodiversitycatalogue.org

• myExperiment – Catalogue of workflows http://biovel.myexperiment.org

• Taverna toolshttp://www.mygrid.org.uk

Interaction Server

Taverna Server

Server

Serv

ers

Run timeExecution

Serv

ices

COTS Shim

Domain

Cloud

DeploymentInfrastructurehosting, compute, storage

WorkflowsComponents

Catalogues & Repositories

BioCatalogueServices

BiodiversityCatalogue

Data

Mgt

Data Mgt Workspace

AuthenticationManagement System

Local FileStores

Local DataSets

Local Public BioVeL

Curators

TavernaWorkbench

ProMakers

In the FieldUsers Third Party

Channels

InterfacesDesign & Launch tools Lite, Player, Portal

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.