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Presentation on the work we've done within BeSTGRID as it relates to bioinformatics in NZ, for the 2010 Bioinformatics Symposium https://www.bestgrid.org/NZ-Bioinformatics-Symposium-2010
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The Impact of BeSTGRIDDeveloping NZ research infrastructure
www.bestgrid.orgtwitter: @bestgrid
Nick JonesDirector, BeSTGRID
Co-Director eResearch, Centre for eResearchUniversity of [email protected]
“BeSTGRID aims to enhance e-Research capability in New Zealand by providing the skill base to help the various research disciplines engage with new eResearch services”
“BeSTGRID aims to kick start centralised infrastructure with some capital investment at key institutions”
BeSTGRID: since 2006
KAREN
CurrentPlanned
Identity provider
Virtual Applications
ComputationCluster
Storage
PeopleThe University of Auckland• Stephen Cope• Mark Gahegan• Yuriy Halytskyy• Nick Jones• Andrey Kharuk
Auckland University Technology• Slava Kitaev• Gene Soudlenkov
Canterbury University• Tim David• Vladimir Mencl
Industrial Research Limited• John Burnell• Peter McGavin
Landcare Research• Robert Gibb• Aaron Hicks
Landcare Research (continued)• Niels Hoffmann• David Medyckyj-Scott
Lincoln University• Stuart Charters
Massey University• Martin Johnson• Guy Kloss
Otago University• Mik Black• Marcus Davy• Matthew Grant
Victoria University Wellington• Kevin Buckley• John Hine
Waikato University• Joseph Lane
Successes: within NZNational grid infrastructure, primarily focused on Bioscience and Geoscience
applications & services, data storage and sharing, computation, along with many others
Established the foundations of a shared research infrastructure service delivery model (governance, management, services) across research sector institutions (Universities, CRIs)
Piloted first federated identity management service in NZ, now moving to production through the NZ Access Federation (nzfed.auckland.ac.nz)
Acting as the basis for sector wide HPC and eResearch programme:– National eScience Infrastructure proposal : 2010 – 2015
What did we learn?Stay Connected, Collaborate
• With Scientists, Administrators, Technologists, Policy makers, Funders
• Locally AND Internationally
Buy (Translate) - don’t build• Development where necessary – others have been
here before• Source from international community:
technologies, approaches, strategies, configurations, programmes
* VDT - OpenScienceGrid* Globus – Argonne* Shibboleth – Internet2* iRODS – DICE / RENCI* Sakai – Sakai Foundation* OCI - NSF * PRAGMA – UCSD* EVO – CalTech* AccessGrid - Argonne* GenePattern – MIT Broad* caBIG - NIH
* VDT - OpenScienceGrid* Globus – Argonne* Shibboleth – Internet2* iRODS – DICE / RENCI* Sakai – Sakai Foundation* OCI - NSF * PRAGMA – UCSD* EVO – CalTech* AccessGrid - Argonne* GenePattern – MIT Broad* caBIG - NIH
* UK eScience - JISC* eFramework – JISCShibboleth – JISC, SWITCHSLCS - SwitchSakai - JISC
* UK eScience - JISC* eFramework – JISCShibboleth – JISC, SWITCHSLCS - SwitchSakai - JISC
* Grisu – ARCS* Confluence - Atlassian* NCRIS - DIISR* QFAB - QCIF
* Grisu – ARCS* Confluence - Atlassian* NCRIS - DIISR* QFAB - QCIF
What did we learn?Change difficult within Institutions
– Medium to Long term timeframes required with researchers, ITS, SMT, research support units– “Final Report: A Workshop on Effective Approaches to Campus Research Computing Cyberinfrastructure” Klingenstein,
Morooney, Olshansky. 2006
Collaboration seen as critical, yet complex and expensive– Working with user communities essential to mutual understand of needs and opportunities, and developing capabilities– Need significant capability before international collaborations (and related learning) possible– New forms of organisation and support required– “Beyond Being There: A Blueprint for Advancing the Design, Development, and Evaluation of Virtual Organization ”
Cummings, Finholt, Foster, Kesselman, Lawrence. 2008– “The Importance of Long-Term Science and Engineering Infrastructure for Digital Discovery” Wilkins-Diehr, Alameda,
Droegemeier, Gannon. 2008
Government and Institutional Investment well below international levels– Australia NCRIS + Super Science– EU FP7 e-Infrastructure call + National Grid Initiatives + Identity + HPC + Networks in member states– UK JISC + NGS + DCC + AAA– US Office of Cyberinfrastructure, NSF, NIH, DoE all funding major Cyberinfrastructure initiatives
Education programs lacking– Who is training the next generation?– Need to grow awareness of career paths in computational and data intensive sciences for computer science and software
engineering graduates
“BeSTGRID could well be New Zealand’s earliest dedicated eResearch infrastructure providers – even predating KAREN. Since 2006, BeSTGRID has been delivering services and tools to support research and research collaboration on shared data sets, and in accessing computational resources.”
KAREN hypenIssue 09September 2009
BeSTGRID: since 2006
MoRST eResearch programme
In Vote RS&T 2008/09, funding was appropriated to develop capability within the Kiwi Advanced Research and Education Network user group to make effective use of KAREN:
• Advanced Video Conferencing Collaboration and Support Centre
• Federated Identity and Access Management• Towards a Federated Approach – strategy development• Technical Support and Resources
• Semantic Data and Public Access to Research
• BeSTGRID Grid Middleware Initiative
• Hardship fund for remote site connection to KAREN
BeSTGRID 2009 – 2010
• MoRST Dec 2008 funding request forMiddleware development for eResearch in NZ
• Provides ongoing support for BeSTGRID– Widened from founders through active participation of new
Universities and CRIs
• Aims:• Coordinate access to compute and data resources• Provide discipline specific services and applications• Build a sustainable resource administration, middleware
and applications & services development community
Compute and storage platformsShared investmentHeterogeneous architecturesScale up scienceCreate new opportunities
Compute and storage platformsShared investmentHeterogeneous architecturesScale up scienceCreate new opportunities
Grid MiddlewareProvides simplified & secure access to job queues & data sharingCommon across compute and storage platforms
Grid MiddlewareProvides simplified & secure access to job queues & data sharingCommon across compute and storage platforms
Applications and toolsManaged, secure, stable, reliableImprove collaboration‘Science as a service’
Applications and toolsManaged, secure, stable, reliableImprove collaboration‘Science as a service’
Research communitiesDeep engagement to map problems onto HPC and GridIncreased throughput, efficient
Research communitiesDeep engagement to map problems onto HPC and GridIncreased throughput, efficient
Governance / PrioritiesNimble, responsive, focused & fairBy member institutions
Governance / PrioritiesNimble, responsive, focused & fairBy member institutions
Site admin
Site admin
Site admin
Site admin
Site admin
Site admin
Site admin
Site admin
Site admin
Site admin
Faculty ITInstitution IT
Faculty ITInstitution IT
Technical Working GroupTechnical Working Group
GeoscienceLeads
GeoscienceLeads
eResearch Centres
eResearch Centres
eResearch Centres
eResearch Centres
eResearch Centres
eResearch Centres
BioscienceLeads
BioscienceLeads
eResearch Centres
eResearch Centres
Steering CommitteeSteering Committee
Project ManagementProject Management
Compute and storage platformsShared investmentHeterogeneous architecturesScale up scienceCreate new opportunities
Compute and storage platformsShared investmentHeterogeneous architecturesScale up scienceCreate new opportunities
Grid MiddlewareProvides simplified & secure access to job queues & data sharingCommon across compute and storage platforms
Grid MiddlewareProvides simplified & secure access to job queues & data sharingCommon across compute and storage platforms
Applications and toolsManaged, secure, stable, reliableImprove collaboration‘Science as a service’
Applications and toolsManaged, secure, stable, reliableImprove collaboration‘Science as a service’
Research communitiesDeep engagement to map problems onto HPC and GridIncreased throughput, efficient
Research communitiesDeep engagement to map problems onto HPC and GridIncreased throughput, efficient
Governance / PrioritiesNimble, responsive, focused & fairBy member institutions
Governance / PrioritiesNimble, responsive, focused & fairBy member institutions
Take lead from community• Lead Users from each community
– Define requirements– Evaluate developments– Promote services– Disseminate learning
• Technology group– “User needs” lead requirements– Scans undertaken for technologies to acquire– Incremental development iterations
Aligned with national research & economic growth agenda
Jack Flanagan: Drug discovery
Virtual screening pipeline
Virtual screening pipeline
Maurice Wilkins Centre ?
Molecular dockingMolecular dockingGene sequence
DB
Shared Storage
X ray crystallograph
y
Shaun Lott: Biological Structure
Virtual serversShibboleth Service ProviderDatabases3D Docking libraries
Virtual serversShibboleth Service ProviderDatabases3D Docking libraries
GenePattern – MIT BroadLocal Analysis Modules• Auckland• Otago
GenePattern – MIT BroadLocal Analysis Modules• Auckland• Otago
Data StorageComputation GridData StorageComputation Grid
Bioscience projects• BioMirror
– Service: Database hosting, 5TB storage, FTP– Partner: Bioinformatics Institute– A public service in New Zealand for high-speed access to up-to-date DNA & protein biological
sequence databanks
• GenePattern: – Service: Genomics processing portal– Partners: Integration Genomics, Otago– Reuse existing and deploy custom genomics processing codes– Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501
doi:10.1038/ng0506-500.
• CellML Simulator– Service: Run simulations of CellML models on computational cluster– Partner: Auckland Bioengineering Institute
• GOLD Protein Docking– Service: GOLD protein docking on computational cluster– Partner: Auckland Cancer Society Research Centre– Molecular Mechanics and Structural Biology
Any questions..?
www.bestgrid.org@bestgrid
Nick JonesDirector, BeSTGRIDCo-Director eResearch, Centre for eResearchUniversity of [email protected]