The National e-Science Centre:Role and Activities

Dave Berry, Research Manager

Indo-UK Workshop on e-ScienceDelhi, February 2004

Outline: The National e-Science Centre

The National e-Science Centre Role and missionThe e-Science Institute

NeSC projects

NeSC Roles

Help coordinate and lead the UK e-Science Programme

Community building activities, regional support & outreachSkill building through training events & support centre

Help establish the UK’s international roleInternational meetings, standardisation work & presentations

Run the e-Science InstituteKnowledge building through workshops and conferencesResearch visitors and events

Undertake R&D projectsTo deliver reliable middlewareTo engage industryTo stimulate the uptake of e-Science technology and methodsEmphasis on scientific data management

e-Science Institute

A meeting placeThe focus for presenting UK e-Science

Visiting researchersCollaborate in our research and developmentEngage in and develop our event programmeBuild bridges with their communityVisits last between one week and six months

Research-oriented event programmee-Science research topics Training to e-Science research teams

eSI Events held in the 2nd Year(from 1 Aug 2002 to 31 Jul 2003)

We have had 86 events: 11 project meetings 11 research meetings 25 workshops2 “summer” schools15 training sessions12 outreach events5 international meetings5 e-Science management meetings

(though the definitions are fuzzy!)

eSI Workshops

Space for real workCrossing communitiesCreativity: new strategies and solutionsWritten reports

Scientific Data Mining, Integration and VisualisationGrid Information SystemsPortals and PortletsVirtual Observatory as a Data GridImaging, Medical Analysis and Grid EnvironmentsOpen Issues in Grid SchedulingData Provenance & Annotatione-Science Workflow ServicesGeoSciences & Scottish Bioinformatics Forum

http://www.nesc.ac.uk/events/

Suggestionsalways

welcome!

eSI Industrial Involvement

194 registered users from 97 companies133 different delegates have attended events (169 event registrations) from 64 companies including not only

IBM, Microsoft, Oracle, Sun, Hewlett-Packard

but also …Apple, Astra Zeneca, BAE, Cisco, Honeywell, Motorola, Organon, Pfizer, Siemens

Research visitors

Establish a collaboration with NeSCPre-established mutual interests

We encourage diversity of disciplines and interests

Complementary experience, knowledge and skillsWe can help match interests and develop a plan

Visitors must already be engaged in relevant R&D

This is not a training opportunity

Our support depends on the length and value of visit

Typically covers travel and/or local living costsApplication via our web site

eSI in Edinburgh

National e-Science Centre

Outline: NeSC Projects

The National e-Science Centre Role and missionThe e-Science Institute

NeSC Projects

e-Science Projects

OGSA-DAI/DAIT, MS.NETGrid, SunDCG, GridWeaver, BRIDGES, PGPGrid, FirstDIG, ODD-GenesEGEE, NextGridOGSA Test Grid, IBM Early EvaluationediktDigital Curation Centre, Publishing Scientific DataGridPP, AstroGrid, QCDGrid, RealityGrid PortalBiological Spatio-Temporal DatabasesCoAKTinG, Grid-enabled Modelling Tools and Databases for Neuroinformatics, e-DiamondDynamic Configuration of Grid Fabrics, Dependable Grid Services, Deductive Synthesis Techniques, Inferring QoS Properties for Grid Applications, Mobile Resource GuaranteesTIES, TIES-II

Digital Curation Centre

Industry

research collaborators

standards bodies

testbeds& tools

communities of practice:

users

community support & outreach

research

development

servicesmanagement

& co-ordination

curation organisations

Collaborative Associates Network of DataOrganisations

The Virtual Observatory

International Virtual Observatory Alliance

UK, Australia, EU, China, UK, Australia, EU, China, Canada, Italy, Germany, Japan, Canada, Italy, Germany, Japan, Korea, US, Russia, France, IndiaKorea, US, Russia, France, India

How to integrate manymulti-TB collections ofheterogeneous data distributed globally?

Sociological and technological challenges to be met

Data Services

GGF Data Access and Integration Svcs(DAIS)OGSI-compliant interfaces to access relational and XML databasesNeeds to be generalized to encompass other data sources

Generalized DAIS becomes the foundation for:

Replication: Data located in multiple locationsFederation: Composition of multiple sourcesProvenance: How was data generated?

1a. Request to Registry for sources of data about “x”

1b. Registry responds with

Factory handle2a. Request to Factory for access to database

2c. Factory returns handle of GDS to client

3a. Client queries GDS with XPath, SQL, etc

3b. GDS interacts with database

3c. Results of query returned to client as XML

SOAP/HTTP

service creation

API interactions

Registry

Factory

2b. Factory creates GridDataService to manage access

Grid Data Service

Client

XML / Relational database

Data Access & Integration Services

edikt

The team: 8 professional software engineers, support staff, project manager, commercialisation manager, architect, and SABSHEFC funded research and development grant

3 years funding: May 2002 – 2005+3 years funding upon successful project and review

Standards

Edikt project

Requirementsanalysis

Technologymatchmaking

Gap filling Rigorousengineering

CS Research

Grid Services fore-Science Data Management

Commercial SW components

and skills

E-Science Apps

JavaFramework

ELDAS – Data Access Service

Implemented using Enterprise Java BeansData Access Components interface to distinct DBMSsAccessible as a grid data service or a web data service

ELDAS

DB2 DBMySQL DBXindice DB

Web User1

Oracle 9i DB

EJB - DAS

DACDACDACDAC

ELDAS runs anywhereWeb ServletGrid Proxy

Grid User1 Grid User2

Suitable for grid & web

e-ScienceApplication

BinaryData File

BinaryData FileBinary

Data File

BinaryData FileBinary

Data File

BinaryData File

BinX – accessing legacy binary data

The Problem:Many binary data filesApplications must “know”the data formatBinary data formats are machine-specific

BinX Library

The Solution:Write a “stand-aside” format description in XMLProvide a library to

Interpret the description Provide file access across

different machines

Build higher-level services

BinX file describes binary file structure

BinX file describes binary file structure

simulations

Shared data

BRIDGES

Glasgow Edinburgh

Leicester

Oxford

London

Netherlands

Public curated

data

Private data

Private data

Private data

Private data

Private data

Private data

Problems specific toBio-Informatics Community

PDB Content Growth

•DBs growing exponentially!!!•Biobliographic (MedLine, …)

•Amino Acid Seq (SWISS-PROT, …)

•3D Molecular Structure (PDB, …)

•Nucleotide Seq (GenBank, EMBL, …)

•Biochemical Pathways (KEGG, WIT…)

•Molecular Classifications (SCOP, CATH,…)

•Motif Libraries (PROSITE, Blocks, …)

More genomes …...

Arabidopsis thaliana

mouse

rat

Caenorhabitis elegans

Drosophilamelanogaster

Mycobacteriumleprae

Vibrio cholerae

Plasmodiumfalciparum

Mycobacteriumtuberculosis

Neisseria meningitidis

Z2491

Helicobacter pylori

Xylella fastidiosa

Borrelia burgorferi

Rickettsia prowazekii

Bacillus subtilis

Archaeoglobusfulgidus

Campylobacter jejuni

Aquifex aeolicus

Thermotoga maritima

Chlamydiapneumoniae

Pseudomonasaeruginosa

Ureaplasmaurealyticum

Buchnerasp. APS

Escherichia coli

Saccharomycescerevisiae

Yersinia pestis

Salmonellaenterica

Thermoplasmaacidophilum

System Usage Scenario

BRIDGES Portal

ClientSite X

Secure access for CFG VO

Shared/Private

Data Sets

Personalised Services

BLASTSmith

WSV

DLO

GS

A-

DA

I

Re

mo

te d

ata

in O

racle

, DB

2,

Syb

ase

, Exce

l, flat file

s, XM

L...

Brow

ser based clients…

Authorisation

Per user, per siteJava App downloaded (via WebStart)

Push relevant data onto ScotGrid for BLAST’ing

Secure Data Repository

Up to date results input to DB

wrappers

wrappers

Generic services used by other

projects

Website

National e-Science Centre http://www.nesc.ac.uk/

Mission, Background, FoundationLocations, Staff, Resources, ProjectsRegister interest, Mailing lists, NeSCForgeRegional associations and CollaborationsNews, NoticesPresentations and Lectures http://www.nesc.ac.uk/presentations/

e-Science Institute http://www.nesc.ac.uk/esi/

Mission, Events (Future and Past)Register for Events, Visitor Programme

UK e-ScienceMap and Index of Centres http://www.nesc.ac.uk/centres/Technical Papers http://www.nesc.ac.uk/technical_papers/Index of >100 Projects http://www.nesc.ac.uk/projects/Task Forces http://www.nesc.ac.uk/teams/

General InformationGlossary, Bibliography,Who’s whoE-Science job vacancies

Questions?

daveb@nesc.ac.uk