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cfgPres

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to quite IT savvy individuals. None of them. knew much about the Grid ... Idea of asking them to get X.509 certificates a complete non-starter ... – PowerPoint PPT presentation

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Title: cfgPres


1
Development of Usable Grid Services for the
Biomedical Community Prof Richard
Sinnott Technical Director National e-Science
Centre Deputy Director (Technical)
Bioinformatics Research Centre University of
Glasgow 26th January 2006
...or the customer is always right!
2
Overview of BRIDGES
  • Biomedical Research Informatics Delivered by Grid
    Enabled Services (BRIDGES)
  • NeSC (Edinburgh and Glasgow) and IBM
  • Started October 2003 successfully concluded end
    of 2005!
  • Supporting project for CFG project
  • Generating data on hypertension
  • Rat, Mouse, Human genome databases
  • Variety of tools used
  • BLAST, visualisation,
  • Variety of data sources and formats
  • Microarray data, genome DBs, project partner
    research data,
  • Aim is integrated infrastructure supporting
  • Data federation
  • Security

3
IT background of scientists
  • From
  • whats a browser?
  • to quite IT savvy individuals
  • None of them
  • knew much about the Grid
  • had the time or inclination to really want to
    learn about how to use the Grid
  • Idea of asking them to get X.509 certificates a
    complete non-starter
  • They were largely sceptical
  • fairly tough customers who had research to do
  • wanted software to solve problems not add to them
    or distract them from their daily work

4
BRIDGES Project
5
Bridges Portal
6
MagnaVista
www.nesc.ac.uk
7
MagnaVista
8
Seriously clever solution
  • Dealing with complex remote data sets where
    schemas were often not given and they changed at
    arbitrary times
  • (normally during live demos!)
  • But they hated it!
  • User interface was far too complicated
  • Pull down menus, tabs, options,
  • Few of them (actually none!) ever used the
    profile capabilities
  • In short a general dont have time to read the
    manual attitude
  • They used and were comfortable with Google
  • hence we decided to give them a Google-like
    solution

9
GeneVista
10
Better solution
  • But still suffers from changing schemas
  • Requires constant monitoring
  • Remote schema changes manifest as cryptic SQL
    exceptions to users
  • This used to fix client wrappers to remote
    databases
  • Off-putting for users
  • Discourages wider take-up

11
Grid Blast Interface
  • Allows genome scale blasting
  • Transparently uses NGS, ScotGrid, other GU
    clusters, Condor pools
  • Many databases already deployed across nodes
  • No user certificates
  • Fine grained security at
  • back-end

but really need to support large jobs...
12
Lessons learned
  • The customer is always right!
  • There has to be less middleware push and more
    scientific pull
  • Understanding requirements crucial
  • Rapid prototyping, feedback best model but need
    time to do this!
  • Public data resource openness
  • Often cannot query directly
  • Often not easy/possible to find schemas
  • Grid middleware still painful experience
  • But ok for us - should not be for scientists
  • Why should biologist go on training course to run
    BLAST on the NGS?
  • Take the certificates away from end users

13
Conclusions
  • BRIDGES experiences helping to shape MANY other
    projects in Glasgow
  • Clinical Trials
  • Genetics Healthcare
  • Scottish Bioinformatics Research Network
  • Occupational Data
  • Numerous security oriented projects
  • Access to and usage of Grid via Shibboleth
  • ...
  • Happy to discuss in more detail... probably
    off-line though

14
Scientific Pull (Work!)
  • Once we have (securely) connected all relevant
    data sets simplified access to and usage of HPC
    resources, wrapped your favourite bioinformatics
    applications as Grid services...
  • what questions would you like to ask?
  • How does a cell work?
  • Why do people who eat less tend to live longer?
  • How many people across Scotland had a heart
    attack in the last 5 years took drug X, and of
    those that did where genes A or B influenced by
    this drug?
  • Who has performed an experiment similar to mine
    and where their results similar?
  • We need to be thinking about these things now and
    making sure the infrastructures we are developing
    will allow to answer these questions!!!
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