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091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
091020 E Research Otago
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091020 E Research Otago

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Update on BeSTGRID project to regional eResearch even eResearch@Otago '09.

Update on BeSTGRID project to regional eResearch even eResearch@Otago '09.

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  • GRISU is a Job Execution Manager
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    • 1. BeSTGRID: Developing NZ research infrastructure
      www.bestgrid.org
      Nick Jones
      Director, BeSTGRID
      Co-DirectoreResearch, Centre for eResearch
      University of Auckland
      n.jones@auckland.ac.nz
    • 2. ... was a Pilot
      $2.5million: Sep 2006 – March 2008
      “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 infrastructurewith some capital investment at key institutions”
      BeSTGRID:intial three years
    • 3. Collaboration Services
      • Advanced Video Conferencing (Access GRID, EVO - Enabling Virtual Organizations, HD, H.323)
      • 4. Telemedicine – APAN 26
    • Collaboration Services
      • Sakai VRE (Virtual Research Environment) – collaboration space (wikis, mailing lists, event calendars, file sharing)
      • 5. “VRE” development by UK e-Science group at Hartree Centre, Daresbury
      • 6. BeSTGRID IAM Federation
      • 7. Pilot integration with Australian AAF
      • 8. Auckland, Canterbury, Lincoln, Open
      • 9. Wikis, SLCS (Grid Certificates)
    • Computation Grid Tools
      Grid Computing interfaces
      Grisu GUI, Grisu CLI
      Bioportal (Phylogenetics)
      x.509 Certificates
      Grix certificate issuing tools
      SLCS Shibboleth issued certificates (Canterbury)
    • 10. Bioinformatics
      Steven Stones-Havas1 and Allen Rodrigo2
      1Biomatters Ltd
      2The Bioinformatics Institute (New Zealand)
    • 11. Data Services
      • 30TB storage at each foundation BeSTGRIDsite
      • 12. Auckland, Canterbury, Massey
      • 13. Local mirrors of research databases
      • 14. NZ BioMirror
      • 15. Ecology and Human Behaviour
      • 16. Whole Genome Association Studies
      • 17. NZ Social Sciences Data Service
      • 18. Ocean Biogeographic Information System
      • 19. Austronesian Basic Vocabulary and Bantu Language Database
      • 20. Data services (GridFTP, NFS, Samba, FTP)
    • Successes: within NZ
      First grid infrastructure in NZ, focused on BioInformatics, with Industry collaboration with BioMatters and New Zealand Supercomputing Centre
      Implementation of first federated identity management framework in NZ
      contribution to a multi-sector working group to further evolve identity management across research and education (IMAGER, http://www.morst.govt.nz/current-work/science-infrastructure/imager/)
      Established the foundations of a shared infrastructure service delivery model across institutions
      Recognition from MoRST of need for eResearch support, with $4.2M in ‘08/’09 budget for eResearch infrastructure
    • 21. 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: $540M ++ over 5 years alongside State and Institutional investments
      EU FP7 e-Infrastructure call + National Grid Initiatives + Identity + HPC + Networks in member states
      US Office of Cyberinfrastructure, NSF, NIH, DoE all funding major Cyberinfrastructure initiatives
      Education programs lacking
      Who is training the next generation?
    • 22. BeSTGRID 2009 - 2010
      MoRST GRID Computing Middleware Initiative
    • 23. MoRSTeResearchprogramme
      Review:
      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
      • 24. Federated Identity and Access Management
      • 25. Towards a Federated Approach – strategy development
      • 26. Technical Support and Resources
      • 27. Semantic Data and Public Access to Research
      • 28. Grid Middleware Initiative
      • 29. Hardship fund for remote site connection to KAREN
    • Advanced Video Collaboration Centre
      • Advanced Video Collaboration Centre
      • 30. Helpdesk 0800 666 889
      • 31. http://avcc.karen.net.nz/
      • 32. Event calendar
      • 33. Quality Assurance for end points
      • 34. Nathan Gardiner
    • NZ Identity Federation
      Towards a Federated Identity
      https://nzfed.auckland.ac.nz/
      Strategy consultation – Q3 – Q4 2009
      Resources, Toolkit, and examplar services – 2010
      Governance and Ownership discussion underway – NZVCC IT, CRI IT, supported by MoRST
      IMAGER – http://www.morst.govt.nz/current-work/science-infrastructure/imager/
      Matthew Cocker
    • 35. Semantic public research data
      Public research data – semantic interoperability
      Integration of Geoscience related data holdings
      University of Auckland, Landcare Research
      Mark Gahegan, Robert Gibb
    • 36. BeSTGRID2009 – 2010
      • MoRST Dec 2008 funding request forMiddleware development for eResearch in NZ
      $840k approved 24 Dec 2008, initiated April 2009
      • Provides ongoing support for BeSTGRID
      • 37. Widened from founders: Auckland, Canterbury & Massey
      • 38. by active participation of new Universities and CRIsVictoria, Otago, Lincoln, Landcare Research, AUT
      • 39. Aim: coordinate national grid middleware; use best-practice tools & services; focus on sustainability
    • BeSTGRID2009 – 2010
      Form collaborations with related Science Infrastructure programmes
      • SCENZ Grid
      • 40. New Zealand Genomics Limited
      • 41. Virtual Institute of Statistical Genetics and MapNet
      • 42. Social Sciences Data Archive and Services
      • 43. Auckland Cancer Society Research Centre
      Support Science Gateways, applications and services
      infrastructure supports science communities with own specialised needs
      • Bio – Extension of scope from phylogenetics to other areas of Bioinformatics and Biomolecular sciences
      • 44. Geo – collaboration with Canadian geoscience infrastructure
      Add in new Data and HPC sites and services:
      • Otago University
      • 45. Victoria University Wellington
      • 46. Landcare Research
      • 47. Auckland University Technology
    • Auckland
      Massey, Albany
      AUT
      Landcare Research
      Victoria
      Lincoln
      Canterbury
      Otago
      Computation
      Cluster
      Identity provider
      Planned
      Storage
      Virtual Applications
      Current
    • 48. Computation Grid Resources
    • 49. NZ eResearch Infrastructure
    • 50. Key Milestones
      Winter Retreat 2009
      Geo, Bio, Grid strategy workshops – Auckland
      29 June – 1 July
      Spring Retreat 2009
      Technical Working Group working session – Canterbury
      14 September
      Strategies and plans
      Geo and Bio strategy drafts – near completion
      Initial projects kicking off in parallel
      National workshop – planning underway for 2010
      Coordinating with KAREN, Federated IAM, and others
      Grid Middleware strategy – Q3 2010
    • 51. BeSTGRID Winter Retreat 2009
      Geoscience WG
      Middleware WG
    • 52. Bioscience theme
      Leadership
      Dr. Mik Black, Biochemistry Department, University of Otago
      The Team
      MikBlack, AnetteBecher, Cris Print, Jack Flanagan, Mike Cooling, Mike Eccles, NeilGemmell, Phil Wilcox, Robert Hickson, George Slim, Mark Gahegan, Nick Jones, Richard Li
      Research Communities
      Virtual Institute of Statistical Genetics, MapNet, NZ Genomics Ltd, Centre for Reproduction and Genomics, Auckland Bioengineering Institute, Auckland Cancer Society Research Centre, Bioinformatics Institute
      Initial Goals – Genetics/Genomics
      • Storage and management of high-throughput data (e.g., microarray and sequence data).
      • 53. Distributed analysis of large data sets (analysis via GenePattern).
    • GenePattern: a platform for integrative genomics
      GenePattern provides access to a broad array of computational methods used to analyze genomic and proteomic data. It is designed to be easy for computational biologists to add their own analysis and visualizations, which enables access to new computational methods on a regular basis.
      Imaging
      Clinical Research
      Pathology
      Molecular Biology
      Slide adapted from Ted Liefeld
      The Broad Institute of MIT and Harvard
    • 54. Geoscience theme
      Leadership
      Prof. Mark Gahegan, Centre for eResearch, University of Auckland
      The Team
      Mark Gahegan, Kevin Buckley, Isabella Cawthorn,
      Robert Gibb, Niels Hoffmann,FemkeReitsma,
      Nick Jones, Richard Li, Mik Black
      Research Communities
      Invasive species modelling, surface and ground water modelling, ecosystem services modelling, carbon emissions, landcover and landuse databases, drill core integration, taxonomy reconcilliation, nationally significant databases development
      Initial Goals
      • Invasive Species Modelling (R on the grid with workflows, mapping)
      • 55. Surface and Ground Water modelling (Lidar processing and workflows, mapping)
      • 56. Taxonomy Reconcilliation (Data and Collections Management)
    • WS
      Data
      Paul Grimwood & colleagues, GNS
    • 57. User Interface: Portal
      Robert Gibb, Niels Hoffmann, Landcare
    • 58. Technology (future)
      Workflow
      Kepler
      currently issue with proxies
      Triana
      Taverna
      No spatial components
      Robert Gibb, Niels Hoffmann, Landcare
    • 59. Grid Middleware Planning
    • 60. Technical Working Group
      Deliver on needs of Bio and Geo themes
      Meet monthly, to present and discuss proposals, progress reports, and services and applications deployed
      Membership
      Institutions formally contracted to BeSTGRID + collaborators
      Terms of Reference, Meeting notes, etc on BeSTGRID website
      http://www.bestgrid.org/index.php/Grid_Technical_Working_Group
    • 61. Summary
      What do we have, where are we going?
    • 62. What do we have?
      A good high-speed network with capacity for growth
      The foundations of a sophisticated infrastructure, some HPC and massive storage silos,
      Authentication, some grid middleware and basic services (but not nationally coordinated)
      Good links to e-research development communities: e.g. Australian National Collaborative Research Infrastructure Committee (NCRIS), Argonne (Globus), San Diego Supercomputer Center (SDSC), eScienceUK, UK NGS, OMII-UK (Edinburgh, Manchester)
    • 63. BeSTGRID2009 – 2010
      • MoRST Dec 2008 funding request forMiddleware development for eResearch in NZ
      $840k approved 24 Dec 2008, initiated April 2009
      • Provides ongoing support for BeSTGRID
      • 64. Widened from founders: Auckland, Canterbury & Massey
      • 65. by active participation of new Universities and CRIsVictoria, Otago, Lincoln, Landcare Research, AUT
      • 66. Aim: coordinate national grid middleware; use best-practice tools & services; focus on sustainability
    • BeSTGRID2009 – 2010
      Form collaborations with related Science Infrastructure programmes
      • SCENZ Grid
      • 67. New Zealand Genomics Limited
      • 68. Virtual Institute of Statistical Genetics and MapNet
      • 69. Social Sciences Data Archive and Services
      • 70. Auckland Cancer Society Research Centre
      Support Science Gateways, applications and services
      infrastructure supports science communities with own specialised needs
      • Bio – Extension of scope from phylogenetics to other areas of Bioinformatics and Biomolecular sciences
      • 71. Geo – collaboration with Canadian geoscience infrastructure
      Add in new Data and HPC sites and services:
      • Otago University
      • 72. Victoria University Wellington
      • 73. Landcare Research
      • 74. Auckland University Technology
    • What next?Aligning with the NZ science community
      Developing a RIAG bid for a long-term integrated landscape of eResearch including Federated IAM and HPC, as a National eResearch Infrastructure
      What are the research needs, tools, applications, environments, computing capabilities that we will need in New Zealand, over the next 10 - 20 years?
      Please get in touch if you would like to include your ideas and needs:
      m.gahegan@auckland.ac.nz
      n.jones@auckland.ac.nz
      tim.david@canterbury.ac.nz
    • 75. Thanks !!!
    • 76. End
      Questions, comments

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