http:www'qub'ac'ukescience

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Health Technologies and Grid Computing
http//www.qub.ac.uk/escience
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The UK e-Science Programme

• Ron Perrott
• Director
• Belfast e-Science Centre
• Queens University
• Belfast
• r.perrott_at_qub.ac.uk
• http//www.qub.ac.uk/escience

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Grid The Web on Steroids
Grid Flexible access to significant resources
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Why now?

• The Internet as infrastructure
• Increasing bandwidth, advanced services
• Advances in storage capacity
• Price reduction
• Increased availability of compute resources
• Clusters, supercomputers, etc.
• Advances in application concepts
• Simulation-based design, collaborative
  engineering, ...

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UK e-Science Grid

• Provide a national grid resource
• Industrial and pilot projects advance grid
  middleware
• Act as information centres

Edinburgh
Glasgow
Newcastle
Belfast
Manchester
Cambridge
Oxford
Cardiff
London
Southampton
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e-Science Phase 2

• Key e-Science Infrastructure components
• Persistent National e-Science Research Grid
• Grid Operations Centre
• Open Middleware Infrastructure Institute
• National e-Science Institute
• National Digital Curation Centre
• e-Science/Grid Legal Service
• International Standards Activity

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Where is this all leading?
e-Science and the Grid
e-Business - Grid Services
Industrial Strength Infrastructure and Middleware
e-Science
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Belfast e-Science Centre Projects

• GridCast Television/Radio broadcasting
• Business change, resilience, reliability, cost,
  customisation, interoperability
• RiskGrid Financial Services
• Business change, performance, cost, resilience,
  reliability, interoperability
• Geddm High-performance data mining
• Performance, cost, business change, resilience,
  interoperability
• GeneGrid Bioinformatics
• Performance, cost, business change,
  interoperability
• GridMil Military infrastructures
• Resilience, reliability, performance,
  interoperability, agility, cost

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The GeneGrid Project

• Dr Paul DonachyCommercial Director

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GeneGrid

• GeneGrid Business Drivers
• Architecture
• GeneGrid Benefits

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GeneGrid

• Collaborative Industrial RD project
• Stakeholders
• Fusion Antibodies
• Amtec Medical
• Support from BT plc
• 820,000 (DTI Link funding)

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Business Drivers

• Multi site organisation with little
  collaboration.
• Little dedicated HPC resource
• Economic advantage (peak demand/supply min)
• Composite analysis manual cut paste
• No single application
• Iterative analysis
• Technical Issues
• Data sources formats
• Federated view
• Lack common model
• Skills set

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Aim

• Create "virtual Bioinformatics laboratory
• Platform for Biologists and Scientists to access
  collective skills, experiences and results in
  secure, reliable and scaleable manner.
• Integrate Biological Software Applications
• Data Sources Public / Private
• High Performance Computing facilities
• Tools
• aid multi sited federated database integration
• Workflow create, submission, monitoring
• Intuitive portal , non-programmer dependant

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Why use Grid Technology

• Access to vast computing and data resources
• Reduce TCO of IT infrastructure
• Increased business agility
• to tackle large-scale problems on-demand
• Empowers organisations
• towards better collaboration within and between
  organisations

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Architecture
GeneGrid Environment
GeneGrid Portal Manager
GeneGrid Security Manager
GDM Service
GeneGrid Environment 2
GeneGrid Environment n
GeneGrid Workflow Manager
GDM Service
GeneGrid Admin Manager
GAM Service
GAM
GAM
TMHMM
bl2seq
GAM Service
SignalP
TMHMM
GAM Service
GAM Service
SignalP
RP
TMHMM
bl2seq
RP
EMBOSS
Primer3
GeneWise
EMBOSS
ClustalW
HMM
BLAST
DB query
6p SMP sparc (solaris 7)
DB query
RP
Eliminator
I686 Linux Sparc (Solaris 8)
QUB
4p SMP linux
4p SMP linux
BT Data Centre
University Melbourne
32 x Sun Blade linux
SDSC
Belfast e-Science Centre
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SOA OGSA

• Service Oriented Architecture (SOA)
• reuse
• interoperability
• dynamic services
• Open Grid Services Architecture (OGSA)
• GT4 based on WS-RF
• IT vendors
• GGF,OASIS

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GeneGrid Benefits

• A - Identification of Novel Protein Family
  Members
• B Automated Antigenic Region Detection

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A - Results

• 6 uncharacterised and potentially new siglecs
• Current business process - 1 day
• GeneGrid 20 mins
• Different applications were accessed from
  different resources
• BLAST Linux Cluster at BeSC
• TMHMM Linux Cluster at SDSC
• SignalP Sun SMP machine at QUB

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B - Results

• Current business process 30/60mins per Gene
• GeneGrid 90mins for 100 Genes
• Resources used
• BeSC, BT Datacentre, Uni Melbourne, SDSC
• Individual task execution and overall experiment
  execution times reduced
• High throughput analysis of genes for potential
  antigenic regions

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GeneGrid Benefits

• SOA recycling software
• Open Extensible (EAI framework)
• Security
• Data Management
• Lower CAPEX, variable OPEX
• Biologically meaningful experiments as workflows

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Commercial Use Cases
Dr Shane McKee Amtec Medical
http//www.qub.ac.uk/escience
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Target discovery

• Functional characterisation
• Sequence analysis
• Pattern recognition
• GeneOntology
• Gene annotation
• Cross-species comparison

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GeneGrid in action

• Ion channel identification
• Cancer gene characterisation
• Infectious disease investigation
• Novel SIGLEC family members (Fusion Antibodies)

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Ion channels

• Transmembrane proteins involved in ion flux into
  out of cells
• Regulate electrical activity in brain
• Mutated in several forms of epilepsy
• Prime targets for novel anti-epilepsy drugs

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Example Procedure

• Identify all ion channels (GeneOntology)
• Identify transmembrane pore domains (TMHMM)
• Filter list (LOCAL)
• Compare list against whole genome sequences
  intra trans-species (BLAST)
• Identify novel genes in chromosomal regions of
  interest (LOCAL)
• Screen genes for mutations in families

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Analysis of ANKH

• BLAST against other sequences
• Human
• Other organisms
• CLUSTAL view of sequence alignments
• Confirmation of transmembrane elements
• Detection of protein domains

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Using the Virtual Bioinformatics Laboratory

• Practice makes perfect
• Open source means transparency
• Legacy and vanilla file formats allow
  integration of Grid technologies with local
  applications
• Streamlining of hypothesis-testing
• Still needs smart hypotheses!

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GeneGrid Demo
P.V. Jithesh Belfast e-Science Centre
http//www.qub.ac.uk/escience
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Discussion Forum
Dr Peter Donnelly BioBusinessNI