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?