Developing and supporting eScience at the University of Cambridge

Centre for Scientific Computing

Michael Simmons, Development Manager, eScience

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, high-perfomance 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

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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

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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

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CamGrid

• Started in Jan 2005 by five groups (now up to eleven; 13 pools).

• UCS has its own, separate Condor facility known as “PWF Condor”.

• Each group sets up and runs its own pool, and flocks to/from other pools.

• Hence a decentralised, federated model.

• Strengths:

• No single point of failure

• Sysadmin tasks shared out

• Free to join

• Free middleware

• Weaknesses:

• Debugging is complicated, especially networking issues.

• Many linux variants: can cause library problems.

Mark Calleja (Michael Simmons)

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 PukalaDepartment of Chemistry

Modelling the evolution of the influenza virus

David BurkeAntigenic Cartography GroupDepartment of Zoology

Modelling the evolution of the influenza virus

David BurkeAntigenic Cartography GroupDepartment of Zoology

Structure PredictionComparative 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?

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?

• 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

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What have we done?

• 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

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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

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Camtology

• •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

mps48@cam.ac.uk

+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