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Dr Richard Sinnott Dr Dave Berry 5 th February 2004 National e-Science Centre Local Developments Technical Director National e-Science Centre ||| Deputy.

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Presentation on theme: "Dr Richard Sinnott Dr Dave Berry 5 th February 2004 National e-Science Centre Local Developments Technical Director National e-Science Centre ||| Deputy."— Presentation transcript:

1 Dr Richard Sinnott Dr Dave Berry 5 th February 2004 National e-Science Centre Local Developments Technical Director National e-Science Centre ||| Deputy Director (Technical) Bioinformatics Research Centre University of Glasgow Research Manager National e-Science Centre University of Edinburgh

2 Overview NeSC Role in UK e-Science NeSC Edinburgh developments e-Science Institute Infrastructure/set-up Projects Plans NeSC Glasgow developments Infrastructure/set-up Projects Plans Conclusions

3 NeSCs Role Help coordinate and lead the UK e-Science Programme Community building activities, regional support & outreach Grid building as a member of the Engineering Task Force Skill building through training events & support centre Help establish the UKs international role International meetings, standardisation work & presentations Undertake R&D projects To deliver reliable middleware To engage industry To stimulate the uptake of e-Science technology and methods Run the e-Science Institute Knowledge building through workshops and conferences Research visitors and events

4 NeSC at Edinburgh: Recent Developments Globus Alliance Digital Curation Centre Edinburgh, Glasgow, UKOLN, CCLRC New e-Science Lecturer (Particle Physics) Training Team PPARC and EGEE funding Manager + 4 trainers Europe-wide role DAI Two (Extension of OGSA-DAI) OGSA Test Grid

5 Digital Curation Centre Industry research collaborators standards bodies testbeds & tools communities of practice: users communit y support & outreach research development services management & co- ordination curation organisations Collaborative Associates Network of Data Organisations

6 e-Science Institute A meeting place The focus for presenting UK e-Science Visiting researchers Collaborate in our research and development Engage in and develop our event programme Build bridges with their community Visits last between one week and six months Research-oriented event programme e-Science research topics Training to e-Science research teams

7 eSI Workshops Space for real work Crossing communities Creativity: new strategies and solutions Written reports Scientific Data Mining, Integration and Visualisation Grid Information Systems Portals and Portlets Virtual Observatory as a Data Grid Imaging, Medical Analysis and Grid Environments Open Issues in Grid Scheduling Data Provenance & Annotation e-Science Workflow Services GeoSciences & Scottish Bioinformatics Forum Suggestions always welcome!

8 Projects OGSA-DAI/DAIT, MS.NETGrid, SunDCG, GridWeaver, BRIDGES, PGPGrid, FirstDIG, ODD-Genes EGEE, NextGrid OGSA Test Grid, IBM Early Evaluation edikt Publishing Scientific Data GridPP, AstroGrid, QCDGrid, RealityGrid Portal Biological Spatio-Temporal Databases CoAKTinG, Grid-enabled Modelling Tools and Databases for Neuroinformatics, e-Diamond Dynamic Configuration of Grid Fabrics, Dependable Grid Services, Deductive Synthesis Techniques, Inferring QoS Properties for Grid Applications, Mobile Resource Guarantees TIES, TIES-II

9 The Virtual Observatory International Virtual Observatory Alliance UK, Australia, EU, China, Canada, Italy, Germany, Japan, Korea, US, Russia, France, India How to integrate many multi-TB collections of heterogeneous data distributed globally? Sociological and technological challenges to be met

10 Data Services GGF Data Access and Integration Svcs (DAIS) OGSI-compliant interfaces to access relational and XML databases Needs to be generalized to encompass other data sources (see next slide…) Generalized DAIS becomes the foundation for: Replication: Data located in multiple locations Federation: Composition of multiple sources Provenance: How was data generated?

11 1a. Request to Registry for sources of data about x 1b. Registry responds with Factory handle 2a. 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 RegistryFactory 2b. Factory creates GridDataService to manage access Grid Data Service Client XML / Relationa l database Data Access & Integration Services

12 edikt The team: 8 professional software engineers, support staff, project manager, commercialisation manager, architect, and SAB SHEFC funded research and development grant 3 years funding: May 2002 – 2005 +3 years funding upon successful project and review Standards Edikt project Requirements analysis Technology matchmaking Gap fillingRigorous engineering CS Research Grid Services for e-Science Data Management Commercial SW components and skills E-Science Apps

13 Java Framework ELDAS – Data Access Service Implemented using Enterprise Java Beans Data Access Components interface to distinct DBMSs Accessible as a grid data service or a web data service ELDAS DB2 DBMySQL DBXindice DB Web User1 Oracle 9i DB EJB - DAS DAC ELDAS runs anywhere Web Servlet Grid Proxy Grid User1Grid User2 Suitable for grid & web

14 e-Science Application Binary Data File BinX – accessing legacy binary data The Problem: Many binary data files Applications must know the data format Binary data formats are machine-specific BinX Library The Solution: Write a stand-aside format description in XML Provide a library to Interpret the description Provide file access across different machines Build higher-level services BinX file describes binary file structure simulations

15 NeSC at Glasgow E-Science Hub Externally Glasgow end of NeSC –Involved in UK wide activities »ETF: In May 2003 became first UK e-Science Centre to run integration tests across every site of the UK (Level 2) Grid. Therefore 100% access to UK Grid resources at this time –Public visibility of NeSC »responsible for NeSC web site Internally Focal point for e-Science research/activities at Glasgow Work closely with foundation departments –Department of Computing Science –Department of Physics & Astronomy Also working closely with other groups including –Bioinformatics Research Centre –Electronics and Electrical Engineering –Biostatistics, …

16 Glasgow e-Science Investment Major investment by university 230m 2 of newly renovated floor space in Kelvin Building offices access grid facility training room –equipped with 20PCs/server for training courses Funding Technical Director

17 Resource Consolidation at Glasgow Building around ScotGrid Providing shared Grid resource for wide variety of scientists inside/outside Glasgow Particle physicists, computer scientists, electronic engineers, bioinformaticians, … Focal point, knowledge pool, primary resource for e-Science activity at Glasgow Target shares –60% PP, 20% Bioinf, 20% open share… Hardware 59 IBM X Series 330 dual 1 GHz Pentium III with 2GB memory 2 IBM X Series 340 dual 1 GHz Pentium III with 2GB memory 3 IBM X Series 340 dual 1 GHz Pentium III with 2GB memory and 100 + 1000 Mbit/s ethernet 1TB disk LTO/Ultrium Tape Library Cisco ethernet switches IBM X Series 370 PIII Xeon with 32 x 512 MB RAM 5TB FastT500 disk 70 x 73.4 GB IBM FC Hot-Swap HDD eDIKT 28 IBM blades dual 2.4 GHz Xeon with 1.5GB memory eDIKT 6 IBM X Series 335 dual 2.4 GHz Xeon with 1.5GB memory CDF 10 Dell PowerEdge 2650 2.4 GHz Xeon with 1.5GB memory CDF 7.5TB Raid disk Shared Resources: Disk ~15TB CPU ~ 330 1GHz CDF LHC BIO

18 Projects with NeSC Glasgow Involvement DCC National Digital Curation Centre AMUSE Autonomous Management of Ubiquitous Systems for e-Health P2Popt Performance measurement & mgt of 2-Layer Peer to Peer NWs… PGPGrid Peppers Ghost Productions Equator Environmental e-Science Interdisciplinary Research Project BPS Biochemical Pathway Simulator BRIDGES

19 Overview of BRIDGES Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) NeSC (Edinburgh and Glasgow) and IBM 2 year project started 1 st October 2003 Supporting project for CFG project Generating data on hypertension Rat, Mouse, Human genome databases Variety of tools used BLAST, FASTA, MPsrch, BLAT, Gene Prediction, visualisation, … Variety of data sources and formats Microarray data, genome DBs, project partner research data, medical records, … Aim is integrated infrastructure supporting Data federation Security

20 Shared data CFG Partner Distribution Glasgow Edinburgh Leicester Oxford London Netherlands Public curated data Private data Private data Private data Private data Private data Private data

21 Problems specific to Bio- 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, …) …

22 More genomes …... Arabidopsis thaliana mouse rat Caenorhabitis elegans Drosophila melanogaster Mycobacterium leprae Vibrio cholerae Plasmodium falciparum Mycobacterium tuberculosis Neisseria meningitidis Z2491 Helicobacter pylori Xylella fastidiosa Borrelia burgorferi Rickettsia prowazekii Bacillus subtilis Archaeoglobus fulgidus Campylobacter jejuni Aquifex aeolicus Thermotoga maritima Chlamydia pneumoniae Pseudomonas aeruginosa Ureaplasma urealyticum Buchnerasp. APS Escherichia coli Saccharomyces cerevisiae Yersinia pestis Salmonella enterica Thermoplasma acidophilum

23 Complexity of Biological Data Nucleotide sequences Nucleotide structures Gene expressions Protein Structures Protein functions Protein-protein interaction (pathways) Cell Cell signalling Tissues Organs Physiology Organisms

24 BRIDGES Data Integration/Federation Local repository being developed Populated with data that cannot be federated e.g. public data sets with no programmatic interface Shared data sets of CFG scientists Security through X.509 PKI (authentication) PERMIS (authorisation) Will make use of e-Science technologies (OGSA- DAI/DAIT, ELDAS, IBMs DiscoveryLink) Automatically keep fresh/updated data Web (Grid) services offered that allow to make use of these local data sets For example for visualising, searching, querying, … Example usage scenario …

25 System Usage Scenario BRIDGES Portal Client Site X Secure access for CFG VO Shared/ Private Data Sets Personalised Services BLAST Smith W SV DL OGSA-DAI Authorisation Per user, per site Remote data in Oracle, DB2,Sybase, Excel, flat files, XML... Browser based clients… Java App downloaded (via WebStart) Push relevant data onto ScotGrid for BLASTing Secure Data Repository Up to date results input to DB wrappers Generic services used by other projects

26 Conclusions NeSC continues to provide leadership in UK e-Science Difficult with multitude of scientific research areas, heterogeneity of systems and fluidity of technologies, GT2, GT3, WSRF, GT4…? Closer working with GridPP beneficial for everyone move towards Production Grid ScotGrid a good model for co-operation Planning for soft landing through diversification and more integration into university MRC bids, BBSRC bids, EPSRC bids, … UK e-Science operating as community for upcoming DTI funding opportunities Plans for developing Grid Computing teaching modules as part of advanced MSc

27 Website National e-Science Centre Mission, Background, Foundation Locations, Staff, Resources, Projects Register interest, Mailing lists, NeSCForge Regional associations and Collaborations News, Notices Presentations & Lectures e-Science Institute Mission, Events (Future and Past) Register for Events, Visitor Programme UK e-Science Map and Index of Centres Technical Papers Index of >100 Projects Task Forces General Information Glossary, Bibliography, Whos who E-Science job vacancies

28 Questions…?

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