Integrative Biology
Overview of Progress
Sharon Lloyd and David Gavaghan
Computing Laboratory
University of Oxford
EPSRC Conference - Edinburgh
April 21-22nd 2005
12 July, 2005
Integrative Biology Confidential
1
Status Update
•
..Evolving Partners
• ..Evolving Science
• ..Evolving Technology
• ..Evolving Projects
• Dissemination
• Training
• Demonstrations at this meeting
• 2005-6 Targets
12 July, 2005
Integrative Biology Confidential
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Evolving Partners
ƒ Intial Partners : CCLRC, Oxford (Denis Noble), Nottingham, Leeds, UCL,
Birmingham, and Sheffield in the UK, Auckland (Peter Hunter) and IBM
ƒ New Heart Modelling Partners:
USA: Tulane (Natalia Trayanova), Washington Lee (Jamie Eason), UCSD
(Andrew McCulloch), UCLA (Alan Garfinkel)
Europe: Graz, Austria (Gernot Plank), Utrecht (Sasha Panfilov) and Sheffield
(Richard Clayton)
ƒ New Cancer Modelling Partners:
USA: Arizona (Bob Gatenby)
Europe: Oxford (Walter Bodmer), Birmingham (Simon Grummett)
‘Readiness’ varies… Matlab to monolithic Delphi to MPI….
12 July, 2005
Integrative Biology Confidential
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Evolving Partners
Optimal Parallel
Codes
Basic Models
12 July, 2005
Graz
Sheffield CVC
Utrecht
Tulane
Auckland
Oxford Heart
UCSD
……
Cancer Modelling
Integrative Biology Confidential
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Evolving Science
ƒ Well-advanced with the various heart modelling groups.
ƒ “Rules of engagement” established
¾
¾
¾
¾
Executables and any data generated must be stored within IB system
Open source must be available to allow incorporation of steering and
visualisation libraries
All data is available to IB team for use in development of visualisation and
data analysis tools
Groups must provide an outline scientific agenda
ƒ Short term assistance approach to advance science in parallel to
technology development
12 July, 2005
Integrative Biology Confidential
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HPCx – parallel optimal codes
CSAR Shared
Memory Compute
UCL Altix
Test Machine
Atlas Data
Store
NGS
RAL
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
How do I use all this complex technology?
How do I move from running my models on a
personal machine?
Global Users
12 July, 2005
Integrative Biology Confidential
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CSAR Shared
Memory Compute
UCL Altix
Test Machine
HPCx – parallel optimal codes
Atlas Data
Store
NGS
RAL
Stage 1:
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Assist!
Global Users
12 July, 2005
Integrative Biology Confidential
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CSAR Shared
Memory Compute
UCL Altix
Test Machine
HPCx – parallel optimal codes
Atlas Data
Store
NGS
RAL
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Step 1:
Get eScience
Certificate!
Gernot (Austria)
Code Parallel Heart Model
12 July, 2005
Integrative Biology Confidential
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CSAR Shared
Memory Compute
UCL Altix
Test Machine
HPCx – parallel optimal codes
Step 2:
Compile model
On NGS compute
nodes
Atlas Data
Store
NGS
RAL
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Gernot (Austria)
Code Parallel Heart Model
12 July, 2005
Integrative Biology Confidential
9
CSAR Shared
Memory Compute
UCL Altix
Test Machine
HPCx – parallel optimal codes
Step 3:
Setup account
On IB data
Management
System (SRB)
Atlas Data
Store
NGS
RAL
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Gernot (Austria)
Code Parallel Heart Model
12 July, 2005
Integrative Biology Confidential
10
CSAR Shared
Memory Compute
UCL Altix
Test Machine
HPCx – parallel optimal codes
Step 4:
Benchmark
Code and store
Data results in
SRB
Atlas Data
Store
NGS
RAL
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Gernot (Austria)
Code Parallel Heart Model
12 July, 2005
Integrative Biology Confidential
11
CSAR Shared
Memory Compute
UCL Altix
Test Machine
HPCx – parallel optimal codes
Atlas Data
Store
NGS
RAL
Stage 2:
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Migrate to HPCx to progress
Science faster!
Gernot (Austria)
Code Parallel Heart Model
12 July, 2005
Integrative Biology Confidential
12
HPCx – parallel optimal codes
Step 3:
Run
Simulation
Real time data
Results feed
CSAR Shared
Memory Compute
UCL Altix
Test Machine
Data
Results
Atlas Data
Store
Control
NGS
RAL
Step 3:
Generate
Geometry
12 July, 2005
NGS
Ox Compute
Ship
And visualise
Geometry
NGS
Man
NGS
Leeds Compute
Computational Steering
Capability – longer term
(> 12 months)
Gernot (Austria)
Code Parallel Heart Model
Integrative Biology Confidential
13
Step 1:
Run
Simulation
Real time data
Results feed
HPCx – parallel optimal codes
CSAR Shared
Memory Compute
UCL Altix
Test Machine
Coupled
Models
Data
Results
Atlas Data
Store
Control
NGS
RAL
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Coupled Models– longer term
(> 12 months)
Step 3:
Generate
Geometry
12 July, 2005
Ship
And visualise
Geometry
Gernot (Austria)
Code Parallel Heart Model
Integrative Biology Confidential
14
HPCx – parallel optimal codes
CSAR Shared
Memory Compute
UCL Altix
Test Machine
Atlas Data
Store
NGS
RAL
NGS
Ox Compute
NGS
Man
NGS
Leeds Compute
Integrative Biology
Global Users
Stage 3:
12 July, 2005
Integrative Biology Confidential
Hide the complexity from
The users through the use
Of an IB portal or client
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Evolving Technology
ƒ Two-pronged approach
¾
Pragmatic: enable users as quickly as possible to get full engagement using
whatever tools are currently available and straightforward to use
¾
IB: become early adopters of OMII’s underlying architecture and work
with them to ensure that it meets the needs of IB
– Rationale: OMII have been entrusted with providing a robust infrastructure for the NGS
and we will therefore need to adopt this infrastructure in due course in any case.
¾
12 July, 2005
More details from Damian Mac Randall
Integrative Biology Confidential
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Evolving Projects
ƒ myGrid Best Practise (EPSRC)
ƒ gLite Best Practise (EPSRC)
ƒ Sister Project for US travel (EPSRC)
ƒ
IB VRE (JISC)
ƒ
Uklight
ƒ .. Adaptive FEM proposal (looking at some of the mathematical issues)
ƒ ..SAN modelling proposal (with Denis Noble’s group)
12 July, 2005
Integrative Biology Confidential
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IB VRE (Jisc)
ƒ
IB consortium has been awarded £300K from JISC to develop a Virtual Research
Environment as a front-end to the IB system
ƒ
Will be built on the OGCE platform
ƒ
Will be undertaken in collaboration with Oxford University Computing Services (Mike
Fraser and Matthew Dovey) and Rob Allan’s group at CCLRC
ƒ
Start date March 2005 (planning)
ƒ
Recruitment process just completed (yesterday)
12 July, 2005
Integrative Biology Confidential
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Dissemination
ƒ
Demonstrations at All Hands
¾ Implementation of GEODISE job submission middleware (via MATLAB) using
the Oxford JISC cluster on the NGS
¾ Computational steering demonstration using tools developed in the gViz Project
¾ Grid-enabled visualisation demonstration using tools developed at CCLRC
ƒ
First Annual workshop in September
¾ Attended by over 60 people in total
¾ Peter Hunter and five colleagues for Auckland
¾ Natalia Trayanova from Tulane
¾ Representatives from MyGrid, ReG, gViz
¾ Excellent progress made in project planning
12 July, 2005
Integrative Biology Confidential
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Training
ƒ
We currently have eight IB PhD students in the Doctoral Training Centre
¾ Two from Oxford Computing Laboratory (one an IBM CASE award)
¾ Two from Oxford Mathematics
¾ One from Oxford biochemistry
¾ Two from Nottingham Mathematics
¾ One from Birmingham Mathematics
ƒ
Core training now completed
ƒ
Students now undertaking a four-week module in collaboration with the Computational
Biology Group in the Computing Laboratory in software engineering for complex
systems biology (DG is module leader)
12 July, 2005
Integrative Biology Confidential
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Demonstrations at this conference
ƒ Richard Clayton – Cardiac Heart Modelling on the White Rose
Grid, recently parallelised with Matlab interface
ƒ Gernot Plank, Utrecht – Heart Modelling on NGS via
visualisation front end (user selected environment)
ƒ Blanca Rodriguez, Oxford – Heart Modelling in NGS via portal
and visualisation via meshalyser
12 July, 2005
Integrative Biology Confidential
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2005-6 Targets
ƒ Release of portal and Meshalyser interfaces and services to
selected users
ƒ Refinement and extension of services through review
ƒ Usability review
ƒ Advance move to HPCx and CSAR machines
ƒ IB VRE development
ƒ Workflow development for IB through best practise project
ƒ Advance US collaborative links through workshops and adoption
of technology
12 July, 2005
Integrative Biology Confidential
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Summary
ƒ User engagement well established
ƒ Technology development incremental – evaluation and
integration
ƒ Any Questions?
12 July, 2005
Integrative Biology Confidential
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