Transcript Slide 1

Developing and supporting eScience at the
University of Cambridge
Michael Simmons, Development Manager, eScience
Centre for Scientific Computing
eScience at Cambridge
• who we are
• what is eScience?
• our model
• what we do
• what we want to do
Centre for Scientific Computing
•CRC: Professor Mike Payne FRS
•eScience
Director: Mark Hayes
Grid Specialist: Mark Calleja
Development Manager: Michael Simmons
• HPC
•Director: Paul Calleja, two colleagues
• MPhil in Scientific Computing
•Director: Nikos Nikiforakis
•Deputy Director: Julian Huppert
What is eScience?
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•eScience is "research into new ways of using the Internet to do science".
•access to web-enabled scientific applications
•compute grids based on software such as Condor
•data grids based on web-friendly technologies such as REST
•multi-party video conferencing and telepresence e.g. AccessGrid,
•remote graphical visualisation
eScience at Cambridge
•To support e-Science projects involving scientists and industry in the
Cambridge region. (and beyond)
•To enable new scientific advances by using Grid-enabled applications to
tackle Terascale problems.
• To develop new generic Grid-based tools for massive data handling, highperfomance computing and visualisation applications on wide area
networks.
eScience model
• identify academics with need for scientific computing
• propose or join project funding bids
• promote eScience support for researchers
• develop extended networks inside and outside the University
• develop collaborative bids with industry
• Services: CamGrid, data issues inc semantic web, interoperability,
specialist web applications
• We need to:
• Recover costs
• Demonstrate added value
•Metrics: resulting publications, academic satisfaction
Collaborators and funders include
• UK Research Funding Councils: EPSRC, STFC, NERC
• Technology Strategy Board (formerly DTI Technology Programme)
•UK eScience programme; SRIF
• JISC
• UK Department for Transport
• O2
• Nokia
• Symbian
• Siemens
• Rolls-Royce
Universities and industry
• Fruitful meetings/engagements, results orientated, to develop
• Good personal contacts, enthusiasm (cf Lambert Report 2005)
• Knowledge exchange
• mini projects to test the water
• Universities need to understand company drivers and vice versa
• Different companies do things differently, so do universities, but
neither are homogenous masses
• Collaborative funding projects leveraging eg TSB, European, PIPSS
etc
What do we do?
• CamGrid
• GridPP
• Mobile Environmental Sensing System Across a Grid
Environment (MESSAGE): monitoring pollution exposure for
individual cyclists and pedestrians.
• Telemedicine on the Grid: demonstrating the capability of Grid
technology to support multi-disciplinary meetings for the review of
cancer diagnoses and treatment
• CancerGrid: open standards for clinical cancer informatics
What do we do?
• MaterialsGrid: a large scale dynamic database of materials
properties
• SciBorg: extracting the science from scientific publications
• National Transport Data Framework: providing access to
distributed sources of transport data
• EU-IndiaGrid: joining European and Indian Grids
• CCPNGrid: grid-enabled NMR structure calculations
CamGrid
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Started in Jan 2005 by five groups (now up to eleven; 13 pools).
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UCS has its own, separate Condor facility known as “PWF Condor”.
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Each group sets up and runs its own pool, and flocks to/from other pools.
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Hence a decentralised, federated model.
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Strengths:
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No single point of failure
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Sysadmin tasks shared out
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Free to join
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Free middleware
Weaknesses:
Mark Calleja (Michael Simmons)
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Debugging is complicated, especially networking issues.
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Many linux variants: can cause library problems.
Mark Calleja
CamGrid: participating departments
• Astrophysics
•Biological Sciences
•Biological and Soft Systems
•Cambridge eScience Centre
•Chemical Informatics
•Earth Sciences (2)
•High Energy Physics
•Materials Science
•National Institute for Environmental eScience (2)
•Oncology
•Semiconductor Physics
41 refereed publications to date
Credit: Mark Calleja
Computational Strategies for the Study of Protein
Complex Structure and Assembly by Ion Mobility
Mass Spectrometry
Tara Pukala
Department of Chemistry
Modelling the evolution of the influenza virus
David Burke
Antigenic Cartography Group
Department of Zoology
Modelling the evolution of the influenza virus
Structure Prediction
Comparative modelling
Based on xray structure of a
strain of HA from 1968
Molecular Dynamics
Monte Carlo simulations
Which features of the protein structure
change as the virus evolves?
Can we quantify the antigenic change
given the amino acid substitutions and
subsequent structure prediction?
David Burke
Antigenic Cartography Group
Department of Zoology
Genomic arrrays: tools for cancer gene discovery
Ian Roberts Hutchison MRC Research Centre
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www.ntdf.org.uk
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MESSAGE PROJECT in
Cambridge (eScience,
Chemistry, Computer
Laboratory)
•Develop portable
systems to collect data
on pollution
•Collaborators: O2,
Nokia, Symbian,
Alphasense
•Build sensor grid
infrastructure
•Query database,
personal look up
•With Imperial College,
Southampton, Leeds,
Newcastle universities
•Asthma peak flow metre
trial
Credit: Iq Mead
What have we done?
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• EMGrid - Electromagnetic Scattering From Aircraft: visualising
complex 3D EM data
• Molecular Informatics - Molecular Standards for the Grid:
exploiting modern methods of information management to discover
new molecular information
• CosmoGrid: enabling UK cosmologists to make world class
contributions from observation of the cosmic microwave sky
What have we done?
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• GROWL: a light-weight Grid services toolkit and applications
• FutureGrid: a program for long-term research into Grid systems
architecture
• Multicast Transport for Grid Computing: reliable high-speed
bulk data delivery using IP multicast
• Distance CFD Supercomputing for Industry: understanding
turbulent flow patterns in complex systems like gas turbines and
aero engines
What do we want to do?
• Develop eScience model 2.0 with stakeholders
• • Create grid collaborations with industry (including help develop more
‘imense.coms’, ‘bridging the gap between commercial requirements and
publically-funded eScience resources’
• Develop networks and collaborative projects with industry leveraging
appropriate funding
• Extend CamGrid to support more research projects, extend range
• Application of new technologies, eg GPUs, pilot/feasibility
• Virtualisation imense various virtual platforms, vm’s….
• ‘Mobile grid’; sensors grid infrastructure
Camtology
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•Project to create start up specialising in ontological search
•Joint venture between imense.com and iLexIR
•Will use grid via joint venture partners
Constellation
New company to commercialise GLite
STFC support
What do we want to do?
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Fold.it
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reCaptcha
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Akogrimo
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Contact
Michael Simmons, Development Manager
[email protected]
+44 7764 199 221
+44 1223 765518
eScience: www.escience.cam.ac.uk with links to past and current
projects and to CamGrid technical details
Presentations from CamGrid users’ meeting:
http://www.dspace.cam.ac.uk/handle/1810/197075/browse-title
Centre for Scientific Computing: www.csc.cam.ac.uk