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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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091020 E Research Otago 091020 E Research Otago Presentation Transcript

  • 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
  • ... 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
  • Collaboration Services
    • Advanced Video Conferencing (Access GRID, EVO - Enabling Virtual Organizations, HD, H.323)
    • Telemedicine – APAN 26
  • Collaboration Services
    • Sakai VRE (Virtual Research Environment) – collaboration space (wikis, mailing lists, event calendars, file sharing)
    • “VRE” development by UK e-Science group at Hartree Centre, Daresbury
    • BeSTGRID IAM Federation
    • Pilot integration with Australian AAF
    • Auckland, Canterbury, Lincoln, Open
    • 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)
  • Bioinformatics
    Steven Stones-Havas1 and Allen Rodrigo2
    1Biomatters Ltd
    2The Bioinformatics Institute (New Zealand)
  • Data Services
    • 30TB storage at each foundation BeSTGRIDsite
    • Auckland, Canterbury, Massey
    • Local mirrors of research databases
    • NZ BioMirror
    • Ecology and Human Behaviour
    • Whole Genome Association Studies
    • NZ Social Sciences Data Service
    • Ocean Biogeographic Information System
    • Austronesian Basic Vocabulary and Bantu Language Database
    • 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
  • 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?
  • BeSTGRID 2009 - 2010
    MoRST GRID Computing Middleware Initiative
  • 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
    • Federated Identity and Access Management
    • Towards a Federated Approach – strategy development
    • Technical Support and Resources
    • Semantic Data and Public Access to Research
    • Grid Middleware Initiative
    • Hardship fund for remote site connection to KAREN
  • Advanced Video Collaboration Centre
    • Advanced Video Collaboration Centre
    • Helpdesk 0800 666 889
    • http://avcc.karen.net.nz/
    • Event calendar
    • Quality Assurance for end points
    • 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
  • Semantic public research data
    Public research data – semantic interoperability
    Integration of Geoscience related data holdings
    University of Auckland, Landcare Research
    Mark Gahegan, Robert Gibb
  • 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
    • Widened from founders: Auckland, Canterbury & Massey
    • by active participation of new Universities and CRIsVictoria, Otago, Lincoln, Landcare Research, AUT
    • Aim: coordinate national grid middleware; use best-practice tools & services; focus on sustainability
  • BeSTGRID2009 – 2010
    Form collaborations with related Science Infrastructure programmes
    • SCENZ Grid
    • New Zealand Genomics Limited
    • Virtual Institute of Statistical Genetics and MapNet
    • Social Sciences Data Archive and Services
    • 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
    • Geo – collaboration with Canadian geoscience infrastructure
    Add in new Data and HPC sites and services:
    • Otago University
    • Victoria University Wellington
    • Landcare Research
    • Auckland University Technology
  • Auckland
    Massey, Albany
    AUT
    Landcare Research
    Victoria
    Lincoln
    Canterbury
    Otago
    Computation
    Cluster
    Identity provider
    Planned
    Storage
    Virtual Applications
    Current
  • Computation Grid Resources
  • NZ eResearch Infrastructure
  • 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
  • BeSTGRID Winter Retreat 2009
    Geoscience WG
    Middleware WG
  • 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).
    • 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
  • 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)
    • Surface and Ground Water modelling (Lidar processing and workflows, mapping)
    • Taxonomy Reconcilliation (Data and Collections Management)
  • WS
    Data
    Paul Grimwood & colleagues, GNS
  • User Interface: Portal
    Robert Gibb, Niels Hoffmann, Landcare
  • Technology (future)
    Workflow
    Kepler
    currently issue with proxies
    Triana
    Taverna
    No spatial components
    Robert Gibb, Niels Hoffmann, Landcare
  • Grid Middleware Planning
  • 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
  • Summary
    What do we have, where are we going?
  • 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)
  • 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
    • Widened from founders: Auckland, Canterbury & Massey
    • by active participation of new Universities and CRIsVictoria, Otago, Lincoln, Landcare Research, AUT
    • Aim: coordinate national grid middleware; use best-practice tools & services; focus on sustainability
  • BeSTGRID2009 – 2010
    Form collaborations with related Science Infrastructure programmes
    • SCENZ Grid
    • New Zealand Genomics Limited
    • Virtual Institute of Statistical Genetics and MapNet
    • Social Sciences Data Archive and Services
    • 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
    • Geo – collaboration with Canadian geoscience infrastructure
    Add in new Data and HPC sites and services:
    • Otago University
    • Victoria University Wellington
    • Landcare Research
    • 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
  • Thanks !!!
  • End
    Questions, comments