biovel at ibergrid e-infrastructures and biodiversity workshop, 19th september 2013, madrid

A PILOT IMPLEMENTATION INVESTIGATING LIFEWATCH IDEAS

Alex HardistyCoordinator, Cardiff University

e-Infrastructures and Biodiversity WorkshopIBERGRID, 19th September 2013, Madrid

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

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

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

Public groupsPublishing workflows and results

Private groupsLocal materialsIntra-project work and collaborations

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

Workflows must be shareable and discoverable www.myexperiment.org

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-BGCmonte 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 andpopulation modelling

Ecosystem functioningand valuation

?

Genes-Species-Specimens(multi-scale linkages)

Citizen Science &Observations

Mapping, visualization andtransformation services

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

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

Modellingecosystem services

ModellingCO2 sequestration

Calculating measures of genetic diversity

Assessing adaptationto changing conditions

Supporting processesof conservation

Assisting invasivespecies management

An international network connecting 2 communities: biodiversity and ICT

Discipline

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

Secure, scalable, reliable, and well-documentedin a geographically distributed network of services

Users’ workflows and applications

Sustained Service and Data ProvidersGBIF, CoL, ITIS, OBIS, WoRMS,EBI, BGBM, CRIA, EoL, BHL, ALA, etc. + many many more

Recognised and stable Resource ProvidersNational, EGI.eu, PRACE, commercial, etc.

Services must be discoverable

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

Web services for biodiversity science

• 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

Info

rmati

on T

echn

olog

ists

’pe

rspe

ctive

s

Biodiversity studies & experiments

Services for biodiversity science

compose to support

ICT Technical Capabilities

ICT Technical Elements

combine to deliver

combine to support

Users need to be able to build and use workflows

TechnicalPAL

SciencePAL

DomainScientist

TavernaWorkbench

ComponentBuilder

TavernaLite / Server

Taverna Player / Domain-Specific

Website

Workflow Visibility

Concept KnowledgeWorkflow design, compute Domain science

High Low

http://portal.biovel.eu/

Interaction Server

Taverna Server

Server

Serv

ers

Run timeExecution

Serv

ices

COTS Shim

Domain

Cloud

DeploymentInfrastructurehosting, compute, storage

WorkflowsComponents

Catalogues & Repositories

BioCatalogue

Services

BiodiversityCatalogue

Dat

a M

gt

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.

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.