100503 bioinfo instsymp

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100503 bioinfo instsymp

  1. 1. The Impact of BeSTGRID Developing NZ research infrastructure www.bestgrid.org twitter: @bestgrid Nick Jones Director, BeSTGRID Co-Director eResearch, Centre for eResearch University of Auckland [email_address]
  2. 2. “ 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
  3. 3. KAREN
  4. 4. Current Planned Identity provider Virtual Applications Computation Cluster Storage
  5. 5. People <ul><li>The University of Auckland </li></ul><ul><li>Stephen Cope </li></ul><ul><li>Mark Gahegan </li></ul><ul><li>Yuriy Halytskyy </li></ul><ul><li>Nick Jones </li></ul><ul><li>Andrey Kharuk </li></ul><ul><li>Auckland University Technology </li></ul><ul><li>Slava Kitaev </li></ul><ul><li>Gene Soudlenkov </li></ul><ul><li>Canterbury University </li></ul><ul><li>Tim David </li></ul><ul><li>Vladimir Mencl </li></ul><ul><li>Industrial Research Limited </li></ul><ul><li>John Burnell </li></ul><ul><li>Peter McGavin </li></ul><ul><li>Landcare Research </li></ul><ul><li>Robert Gibb </li></ul><ul><li>Aaron Hicks </li></ul><ul><li>Landcare Research (continued) </li></ul><ul><li>Niels Hoffmann </li></ul><ul><li>David Medyckyj-Scott </li></ul><ul><li>Lincoln University </li></ul><ul><li>Stuart Charters </li></ul><ul><li>Massey University </li></ul><ul><li>Martin Johnson </li></ul><ul><li>Guy Kloss </li></ul><ul><li>Otago University </li></ul><ul><li>Mik Black </li></ul><ul><li>Marcus Davy </li></ul><ul><li>Matthew Grant </li></ul><ul><li>Victoria University Wellington </li></ul><ul><li>Kevin Buckley </li></ul><ul><li>John Hine </li></ul><ul><li>Waikato University </li></ul><ul><li>Joseph Lane </li></ul>
  6. 6. Successes: within NZ <ul><li>National grid infrastructure , primarily focused on Bioscience and Geoscience applications & services, data storage and sharing, computation, along with many others </li></ul><ul><li>Established the foundations of a shared research infrastructure service delivery model (governance, management, services) across research sector institutions (Universities, CRIs) </li></ul><ul><li>Piloted first federated identity management service in NZ, now moving to production through the NZ Access Federation (nzfed.auckland.ac.nz) </li></ul><ul><li>Acting as the basis for sector wide HPC and eResearch programme: </li></ul><ul><ul><li>National eScience Infrastructure proposal : 2010 – 2015 </li></ul></ul>
  7. 7. What did we learn? <ul><li>Stay Connected, Collaborate </li></ul><ul><ul><li>With Scientists, Administrators, Technologists, Policy makers, Funders </li></ul></ul><ul><ul><li>Locally AND Internationally </li></ul></ul><ul><li>Buy (Translate) - don’t build </li></ul><ul><ul><li>Development where necessary – others have been here before </li></ul></ul><ul><ul><li>Source from international community: technologies, approaches, strategies, configurations, programmes </li></ul></ul>
  8. 8. * 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 – JISC Shibboleth – JISC, SWITCH SLCS - Switch Sakai - JISC * Grisu – ARCS * Confluence - Atlassian * NCRIS - DIISR * QFAB - QCIF
  9. 9. What did we learn? <ul><li>Change difficult within Institutions </li></ul><ul><ul><li>Medium to Long term timeframes required with researchers, ITS, SMT, research support units </li></ul></ul><ul><ul><li>“ Final Report: A Workshop on Effective Approaches to Campus Research Computing Cyberinfrastructure ” Klingenstein, Morooney, Olshansky. 2006 </li></ul></ul><ul><li>Collaboration seen as critical, yet complex and expensive </li></ul><ul><ul><li>Working with user communities essential to mutual understand of needs and opportunities, and developing capabilities </li></ul></ul><ul><ul><li>Need significant capability before international collaborations (and related learning) possible </li></ul></ul><ul><ul><li>New forms of organisation and support required </li></ul></ul><ul><ul><li>“ Beyond Being There: A Blueprint for Advancing the Design, Development, and Evaluation of Virtual Organization ” Cummings, Finholt, Foster, Kesselman, Lawrence. 2008 </li></ul></ul><ul><ul><li>“ The Importance of Long-Term Science and Engineering Infrastructure for Digital Discovery ” Wilkins-Diehr, Alameda, Droegemeier, Gannon. 2008 </li></ul></ul><ul><li>Government and Institutional Investment well below international levels </li></ul><ul><ul><li>Australia NCRIS + Super Science </li></ul></ul><ul><ul><li>EU FP7 e-Infrastructure call + National Grid Initiatives + Identity + HPC + Networks in member states </li></ul></ul><ul><ul><li>UK JISC + NGS + DCC + AAA </li></ul></ul><ul><ul><li>US Office of Cyberinfrastructure, NSF, NIH, DoE all funding major Cyberinfrastructure initiatives </li></ul></ul><ul><li>Education programs lacking </li></ul><ul><ul><li>Who is training the next generation? </li></ul></ul><ul><ul><li>Need to grow awareness of career paths in computational and data intensive sciences for computer science and software engineering graduates </li></ul></ul>
  10. 10. BeSTGRID: since 2006 “ 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 hypen Issue 09 September 2009
  11. 11. MoRST eResearch programme <ul><li>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: </li></ul><ul><li>Advanced Video Conferencing Collaboration and Support Centre </li></ul><ul><li>Federated Identity and Access Management </li></ul><ul><ul><li>Towards a Federated Approach – strategy development </li></ul></ul><ul><ul><li>Technical Support and Resources </li></ul></ul><ul><li>Semantic Data and Public Access to Research </li></ul><ul><li>BeSTGRID Grid Middleware Initiative </li></ul><ul><li>Hardship fund for remote site connection to KAREN </li></ul>
  12. 12. BeSTGRID 2009 – 2010 <ul><li>MoRST Dec 2008 funding request for Middleware development for eResearch in NZ </li></ul><ul><li>Provides ongoing support for BeSTGRID </li></ul><ul><ul><li>Widened from founders through active participation of new Universities and CRIs </li></ul></ul><ul><li>Aims: </li></ul><ul><ul><li>Coordinate access to compute and data resources </li></ul></ul><ul><ul><li>Provide discipline specific services and applications </li></ul></ul><ul><ul><li>Build a sustainable resource administration, middleware and applications & services development community </li></ul></ul>
  13. 13. Compute and storage platforms Shared investment Heterogeneous architectures Scale up science Create new opportunities Grid Middleware Provides simplified & secure access to job queues & data sharing Common across compute and storage platforms Applications and tools Managed, secure, stable, reliable Improve collaboration ‘ Science as a service’ Research communities Deep engagement to map problems onto HPC and Grid Increased throughput, efficient Governance / Priorities Nimble, responsive, focused & fair By member institutions
  14. 14. Site admin Site admin Site admin Site admin Site admin Faculty IT Institution IT Technical Working Group Geoscience Leads eResearch Centres eResearch Centres eResearch Centres Bioscience Leads eResearch Centres Steering Committee Project Management Compute and storage platforms Shared investment Heterogeneous architectures Scale up science Create new opportunities Grid Middleware Provides simplified & secure access to job queues & data sharing Common across compute and storage platforms Applications and tools Managed, secure, stable, reliable Improve collaboration ‘ Science as a service’ Research communities Deep engagement to map problems onto HPC and Grid Increased throughput, efficient Governance / Priorities Nimble, responsive, focused & fair By member institutions
  15. 15. Take lead from community <ul><li>Lead Users from each community </li></ul><ul><ul><li>Define requirements </li></ul></ul><ul><ul><li>Evaluate developments </li></ul></ul><ul><ul><li>Promote services </li></ul></ul><ul><ul><li>Disseminate learning </li></ul></ul><ul><li>Technology group </li></ul><ul><ul><li>“ User needs” lead requirements </li></ul></ul><ul><ul><li>Scans undertaken for technologies to acquire </li></ul></ul><ul><ul><li>Incremental development iterations </li></ul></ul><ul><li>Aligned with national research & economic growth agenda </li></ul>
  16. 16. Virtual servers Shibboleth Service Provider Databases 3D Docking libraries <ul><li>GenePattern – MIT Broad </li></ul><ul><li>Local Analysis Modules </li></ul><ul><li>Auckland </li></ul><ul><li>Otago </li></ul>Data Storage Computation Grid Jack Flanagan: Drug discovery Virtual screening pipeline Maurice Wilkins Centre ? Molecular docking Gene sequence DB Shared Storage X ray crystallography Shaun Lott: Biological Structure
  17. 17. Bioscience projects <ul><li>BioMirror </li></ul><ul><ul><li>Service: Database hosting, 5TB storage, FTP </li></ul></ul><ul><ul><li>Partner: Bioinformatics Institute </li></ul></ul><ul><ul><li>A public service in New Zealand for high-speed access to up-to-date DNA & protein biological sequence databanks </li></ul></ul><ul><li>GenePattern: </li></ul><ul><ul><li>Service: Genomics processing portal </li></ul></ul><ul><ul><li>Partners: Integration Genomics, Otago </li></ul></ul><ul><ul><li>Reuse existing and deploy custom genomics processing codes </li></ul></ul><ul><ul><li>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. </li></ul></ul><ul><li>CellML Simulator </li></ul><ul><ul><li>Service: Run simulations of CellML models on computational cluster </li></ul></ul><ul><ul><li>Partner: Auckland Bioengineering Institute </li></ul></ul><ul><li>GOLD Protein Docking </li></ul><ul><ul><li>Service: GOLD protein docking on computational cluster </li></ul></ul><ul><ul><li>Partner: Auckland Cancer Society Research Centre </li></ul></ul><ul><ul><li>Molecular Mechanics and Structural Biology </li></ul></ul>
  18. 18. Any questions..? www.bestgrid.org @bestgrid Nick Jones Director, BeSTGRID Co-Director eResearch, Centre for eResearch University of Auckland [email_address]

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