progress with uk e-science bcs anglia ruskin university chelmsford malcolm atkinson director...

Progress with UK e-Science

BCSAnglia Ruskin University

Chelmsford Malcolm Atkinson

Director e-Science Institute & e-Science Envoy

www.nesc.ac.uk20th February 2007

OverviewHistory of e-Science in UK

Three Significant Strengths Established

ESFRI, EGEE, et al. thriving in Europee-Science & Cyberinfrastructure everywhere

e-Science definition & historyPropose an e-Science FrameworkTest drive framework on 3 UK projectThe framework in today’s technical context

Communities & Breadth

Projects e-Infrastructure

Defining e-Science

e-Science: Systematic Support for Collaborative Research

Multi-disciplinary, Multi-Site & Multi-NationalAll disciplines contribute & benefitEnabling wider engagementBuilding with and demanding advances in Computing Science

Using advances in computing to support research, design, diagnosis

Dates back 50 yearsPrevalent in branches of biology 20 yearsPrevalent in Engineering for >40 years

UK e-Science

e- Science and the Grid‘e- Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it.’

‘e- Science will change the dynamic of the way science is undertaken.’

J ohn TaylorDirector General of Research Councils

Offi ce of Science and Technology

From presentation by Tony Hey

NERC (£15M)7%

CLRC (£10M)5%

ESRC (£13.6M)6%

PPARC (£57.6M)27%

BBSRC (£18M)8%

MRC (£21.1M)10%

EPSRC (£77.7M)37%

Staff costs -Grid Resources

Computers & Networkfunded separately

Applied (£35M)45%

HPC (£11.5M)15%

Core (£31.2M)40%

EPSRC Breakdown

UK e-Science Budget (2001-2006)

Source: Science Budget 2003/4 – 2005/6, DTI(OST)

Total: £213M

+ Industrial Contributions £25M

+ £100M via JISC

Slide from Steve Newhouse

UK e-Science Diversity

Thriving CommunityAll disciplines & all Research CouncilsIndustry & AcademiaMany universities & research institutesUK e-Science All Hands MeetingsProductive collaboration

e-Infrastructure

A shared resourceThat enables science, research, engineering, medicine, industry, …It will improve UK / European / … productivity

Lisbon Accord 2000 E-Science Vision SR2000 –

John Taylor

Commitment by UK government

Sections 2.23-2.25

Always there c.f. telephones, transport,

power

OSI report www.nesc.ac.uk/documents/

OSI/index.html

National Centre for e-Social Science

ColchesterColchester

University of EssexUniversity of Essex

LancasterLancaster

BristolBristol

LeedsLeeds

University of ManchesterUniversity of Manchester

ManchesterManchester

NottinghamNottingham

LondonLondon

OxfordOxford

AberdeenAberdeen

EdinburghEdinburgh

Edinburgh

CardiffCardiff

BristolBristol

LancasterLancaster

WestminsterWestminster

National Grid Service and partners

EdinburghEdinburgh

YorkYork


DidcotDidcot

CCLRC RutherfordAppleton LaboratoryCCLRC RutherfordAppleton Laboratory

LeedsLeeds

SheffieldSheffield

UK e-Infrastructure

LHC

I SI S TS2

HPCx + HECtoR

Users get common access, tools, inf ormation, Nationally supported services, through NGS

I ntegratedinternationally

VRE, VLE, IE

Regional and Campus grids

Community Grids

Slide: Neil Geddes

e-Science Centres in the UK

LeicesterLeicester

LeSCLeSC

BirminghamBirmingham

White Rose GridWhite Rose Grid

BristolBristol

LancasterLancaster

ReadingReading

OxfordOxford

EdinburghEdinburgh

BelfastBelfast

CambridgeCambridgeCCLRC DaresburyCCLRC Daresbury


UCLUCL

NewcastleNewcastle

SouthamptonSouthampton

CardiffCardiff

CCLRC RALCCLRC RAL

Access GridSupport CentreAccess GridSupport Centre

Digital Curation CentreDigital Curation Centre

National GridService

National GridService

National Centre fore-Social Science

National Centre fore-Social Science

National Centre forText Mining

National Centre forText Mining

National Institute forEnvironmental e-Science

National Institute forEnvironmental e-Science

Open MiddlewareInfrastructure Institute

Open MiddlewareInfrastructure Institute

GlasgowGlasgow

YorkYorkLeedsLeeds

SheffieldSheffield

Coordinated by:Directors’ Forum

& NeSC

+2 years

OMII-UK nodes

EdinburghEdinburgh

EPCC & National e-Science CentreEPCC & National e-Science Centre


School of Computer ScienceUniversity of Manchester

School of Computer ScienceUniversity of Manchester

SouthamptonSouthampton

School of Electronics andComputer Science

University of Southampton

School of Electronics andComputer Science

University of Southampton

Digital Curation Centre and partners

GlasgowGlasgow

Humanities Advanced Technology and

Information Institute

Humanities Advanced Technology and

Information Institute

BathBathUKOLN (formerly UK Office for Library Networking)

UKOLN (formerly UK Office for Library Networking)

WarringtonWarrington

DidcotDidcot

Rutherford Appleton (Didcot) and Daresbury

(Warrington) Laboratories

Rutherford Appleton (Didcot) and Daresbury

(Warrington) Laboratories

EdinburghEdinburgh

Database Research Group, School of Informatics

AHRC Research Centre for Studies in Intellectual Property

and Technology LawEDINA

National e-Science Centre

Database Research Group, School of Informatics

AHRC Research Centre for Studies in Intellectual Property

and Technology LawEDINA

National e-Science Centre

Office of Cyberinfrastructure

D. E. Atkins

Office of Cyberinfrastructure

D. E. Atkins

Transformative Application - to

enhance discovery & learning

R&D to enhance technical and social dimensions of future CI

systems

Provisioning -Creation,

deployment and operation of advanced CI

Achieving the CI Vision requiressynergy between 3 types of Foundation

wide activities

Framework for e-Science

Motivation for collaborationSocio-economic value identifiedImpediments recognisedAll participants agree & cooperate

Challenge and InsightsArticulated & demanding challengeCreative new approachPotentially feasible

Technical advancesNew models, new methods, collaboration supportEconomic changes - e.g. shared computingCultural changes - e.g. shared information

The NERC Success

Professor Robert GurneyDirector, Environmental Systems Science Centre, Reading

The NERC e-Science experience 11 papers in NatureEnthusiastic uptake of ensemble methods

Predicting Climate ChangeThrough Volunteer Computing

University of Oxford

Department of Atmospheric Physics

climateprediction.net

Slide: Robert Gurney

climateprediction.net Users Worldwide>300,000 users total (90% MS Windows): >60,000 active~17 million model-years simulated (as of September '06)

~180,000 completed simulations

The world's largest climate modelling supercomputer!(NB: a black dot is one or more computers running climateprediction.net)

Slide: Robert Gurney

Impact:New ScienceUnderstanding of scienceEngaging schoolsBBC follow on

Climateprediction.net – Volunteer computing – Myles Allen, Atmospheric Physics

- More than 10 Million models calculated- Uses BOINC – portal for broader community- Used in schools- Interesting distributed data analysis problems


Motivation for collaborationSocio-economic value?

Better global warming prediction public understanding of GW

Impediments? Reaching enough participants Gaining attention & resources

Participants cooperate? Volunteers “buy in” Boinc culture helps Good PR media interest BBC involved more incentives motivated by cause, by visualisation and by wiki Global net of data collection centres needed - storage & compute! Why should they contribute?


Challenge and InsightsChallenge?

Explore effects of uncertainty in models & physics of climate Infeasible amounts of supercomputing time

New approach? Run simpler model Use ensemble computing - Monte Carlo parameter exploration Analyses and integration over all results

Feasible? BOINC from SETI suggest computation resource feasible But large volumes of data per model run Needs to be stored and later analysed

http://climateprediction.net


Technical advancesNew model?

Simplified Hadley + …

New method? Ensemble methods Distributed using BOINC Distributed data collection Distributed data integration and analysis

http://www.allhands.org.uk/2006/proceedings/papers/595.pdfCollaboration support?

Built on BOINC collaboration support Improved visualisation

Economic change? Free model runs > 21 million model hours How were the data centres financed?

Cultural change? Explicit use of media NERC support for community integration

6th September 2006 24

NERC centres

SwindonSwindon ReadingReadingUniversity of ReadingUniversity of Reading

CambridgeCambridge

National Institute forEnvironmental e-Science, University of Cambridge

National Institute forEnvironmental e-Science, University of Cambridge

Construct in silico experiments, find and adapt others, manage the experiment lifecycleTaverna Workflow workbenchOGSA-DQPSemantic TechnologiesWilliams-Beuren Syndrome, Grave’s Disease, Trypanosomiasis in cattle.

OMII-UK Node, GRIMOIRE Registry, Taverna Workflow workbench12000+ Downloads of TavernaWide transfer to BBSRC (e-Fungi, ISPIDER, ComparaGrid) & MRC projects (PsyGrid, CLEF, CLEFS)Semantic Grid pioneerWBS gene identificationOutstanding international linksGreat deal of open source s/wLinks into BOSC & HGMPKT to BT, ComparaGrid, OntoGrid, BBSRC Systems Biology Centre, MIASGrid, Rice Institute etc

• Carole Goble (Comp Sci, Manchester)• 7 Universities and institutes (incl. EBI)• 8 Companies

Middleware for data intensive in silico biology by bioinformaticians

In silico biology http://www.mygrid.org.uk

Slide: Carole Goble & Jim Fleming


Motivation for collaborationSocio-economic value?Impediments?Participants cooperate?

Challenge and InsightsChallenge?New approach?Feasible?

Technical advancesNew model? New method? Collaboration support?Economic change?Cultural change?

Taverna Workflow WorkbenchCarole Goble

David De Roure

Slide: Dave De Roure & Jeremy Frey

X-Raye-Lab

Analysis

Properties

Propertiese-Lab

SimulationVideo

Diff

ract

omet

er

Grid Middleware

StructuresDatabase

CombeChem Semantic Datagrid


Learning & Teaching workflows

Research & e-Science workflows

Aggregator services: national, commercial

Repositories : institutional, e-prints, subject, data, learning objects

Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules

Harvestingmetadata

Data creation / capture / gathering: laboratory experiments, Grids, fieldwork, surveys, media

Resource discovery, linking, embedding

Deposit / self-archiving

Peer-reviewed publications: journals, conference proceedings

Publication

Validation

Data analysis, transformation, mining, modelling


Deposit / self-archiving

Learning object creation, re-use

Searching , harvesting, embedding

Quality assurance bodies

Validation

Presentation services: subject, media-specific, data, commercial portals


The scholarly knowledge cycle.

Liz Lyon, Ariadne, July 2003.

This work is licensed under a Creative Commons LicenseAttribution-ShareAlike 2.0

© Liz Lyon (UKOLN, University of Bath), 2003

http://creativecommons.org/licenses/by-sa/2.0/


Motivation for collaborationSocio-economic value?Impediments?Participants cooperate?

Challenge and InsightsChallenge?New approach?Feasible?

Technical advancesNew model? New method? Collaboration support?Economic change?Cultural change?

Data capture


1 1 2 2 1 3 1 4

Sample of 4-flourinatedbiphenyl

Add CoolReflux

Butanone Sample ofK2CO3Powder

Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text

3 5

Add

g

Sample ofBr11OCB

2 6

Reflux

2 7

Cool

Water

Measure

30 ml

9

Liquid-liquid

extraction

DCM

Measure

3 of 40 ml

10

Dry

MgSO4

11

Filter(Buchner)

12

RemoveSolvent

by RotaryEvaporation

13

Fuse

Silica

14

ColumnChromatography

Ether/PetrolRatio

Butanone dried via silica column andmeasured into 100ml RB flask.

Used 1ml extra solvent to wash outcontainer.

Started reflux at 13.30. (Had tochange heater stirrer) Only reflux

for 45min, next step 14:15.

Inorganics dissolve 2layers. Added brine

~20ml.

Organics are yellowsolution

Washed MgSO4 withDCM ~ 50ml

Measure

excess

Observation Types

weight - grammes

measure - ml, drops

annotate - text

temperature - K, °C

Key

Process

Input

Literal

Observation

Add CoolRefluxAddAdd Reflux Cool Dry Filter Remove

Solventby Rotary

Evaporation

Fuse ColumnChromatography

Dissolve 4-flourinatedbiphenyl inbutanone

Add K2CO3powder

Heat at refluxfor 1.5 hours

Cool and addBr11OCB

Heat atreflux untilcompletion

Cool and addwater (30ml)

Combine organics,dry over MgSO4 &filter

Removesolvent invacuo

Liquid-liquid

extraction

Extract withDCM(3x40ml)

Fuse compound to silica &column in ether/petrol

4 8

Add

Add

text

Annotate

Annotate

text

Weigh

Annotate

g

Annotate Annotate

text text

Future Questions

Whether to have many subclasses of processes or fewer with annotations

How to depict destructive processes

How to depict taking lots of samples

What is the observation/process boundary? e.g. MRI scan

1.5918

Combechem

30 January 2004gvh, hrm, gms

Ingredient List

Fluorinated biphenyl 0.9 gBr11OCB 1.59 gPotassium Carbonate 2.07 gButanone 40 ml

image

To

Do

Lis

tP

lan

Pro

ce

ss

Re

co

rd

CombeChem Semantic Datagrid


ecrystals.chem.soton.ac.uk


http://ecrystals.chem.soton.ac.uk/

TimelineTimeline

Today

BroadcastingBroadcasting100 years100 years

BroadcastingBroadcasting100 years100 years

TelecommunicationsTelecommunications170 years170 years

TelecommunicationsTelecommunications170 years170 years

PrintingPrinting600 years600 yearsPrintingPrinting

600 years600 years

WritingWriting5,000 years5,000 years

WritingWriting5,000 years5,000 years

Grunts andGrunts andbody languagebody language500,000 years500,000 years

Grunts andGrunts andbody languagebody language500,000 years500,000 years

SpeechSpeech300,000 years300,000 years

SpeechSpeech300,000 years300,000 years

Home ComputersHome ComputersInternet and WWWInternet and WWW

Mobile phonesMobile phonesGrid and Web 2.0Grid and Web 2.0

Web 3.0 and Ubiquitous connected devicesWeb 3.0 and Ubiquitous connected devices30 years30 years

Home ComputersHome ComputersInternet and WWWInternet and WWW

Mobile phonesMobile phonesGrid and Web 2.0Grid and Web 2.0

Web 3.0 and Ubiquitous connected devicesWeb 3.0 and Ubiquitous connected devices30 years30 years

“Wellbeing” the global-scale killer app., Sir Robin Saxby Oct. 2006

PatientHome-mobile-clinic

via TV-PDA-laptop-PC-Paper

Diabetes Specialist / Other Specialist Nurses

Home-mobile-clinicvia TV-PDA-laptop-PC-Paper

Dietitian

DiabeticianHome-mobile-clinic

via PDA-laptop-PC-Paper

Biochemist

GPHome-mobile-clinic

via PDA-laptop-PC-Paper

Various Clinical Specialists (Distributed)e.g. Ophthalmologist, Podiatrist, Vascular

Surgeons, Renal Specialists, Wound clinic, Foot care clinic, Neurologists, Cardiologists

ILLNESS

REFERRAL REFERRAL

REFERRAL

CASE

Community Nurses / Health Visitors

VARIABLESACCESSMATRIX

Healthcare @ Home

DAME http://www.cs.york.ac.uk/dame/

● Aims to manage >1Tb per year of Aero Engine vibration and maintenance data.

● Interlinks with search and reasoning services.

● Defined and evaluated a distributed search system.

● GSI enabled secure engine performance simulation

● CBR advisor for diagnostic engineer● A data architecture defined based

on Globus and SRB.

● BROADEN DTI Project (£3.9M)● Spun out technology exploited

through Cybula Ltd., Oxford Biosignals and DS&S.

● Successful mid-term demonstrator well received by Rolls Royce

● White Rose Grid: experience of building & using production Grids

● In Grid Blue Print 2 edition 2

• Jim Austin (Comp Sci, York)• 4 Universities and institutes• 3 Companies

Aircraft healthcare diagnosis

Slide: Carole Goble, Jim Fleming & Jim Austin

6th September 2006 40

Timeline (years ago)

300,000300,000 1701706006005,0005,000 303010010050,00050,000Up to Up to 1,500,0001,500,000

Homo erectus lived between 1.8 million and 300,000

years ago. It was a successful species for over a

million years. The brain grew steadily during its reign.

The species definitely had speech.

Homo habilis existed between 2.4 and 1.5 million years ago and the species’

brain shape shows evidence that some speech had

developed.

Arrival of ‘modern man’.

The first commercial electrical telegraph was

constructed and opened on 9 April 1839.

Home ComputersInternet and WWW

Mobile phonesGrid and Web 2.0

Web 3.0 and Ubiquitous connected devices

First ‘writing’ system developed in ancient Sumeria (cuneiform).

Johannes Gutenberg invented the first printing

press in 1440.In the US, Charles Herrold

sent out broadcasts as early as April 1909.

In the UK, the first experimental broadcasts

from Marconi’s factory began in 1920.

The Semantic Web layer cake

XML + Namespaces

URI Unicode

Sig

natu

re

En

cry

pti

on

Rules

Proof

Trust

RDF

RDF Schema

OWL

Identity

Standard syntax

Metadata

Ontologies +Inference

Explanation

Attribution

SPARQL(queries)

User Interface and Applications

S-OGSA Model

Knowledge Resource

Knowledge Entity

Ontology Service

Is-a

Reasoning Service

Annotation Tool/Service

Metadata Store/Service

Knowledge Service

Is-a

Ontology

Rule set

Knowledge

Grid Entity

Grid Service

VOManager

Policy

SatelliteImage File

JSDL file

Grid Resource

IntelligentMonitoring

Filemgt

Is-a

Is-a

Grid

Semantic ProvisioningService

Semantic Binding

Is-a

0..m

0..m

1..m1..m

Semantic aware Grid Service

produce

0..m0..m

consume

Is-a

Is-a

Semantic BindingProvisioning Service

Is-a

Is-a

Semantic Grid

Semantic Entity

Is-a

Is-a

Carole Goble

What’s Web2.0 ?

“Web 2.0, a phrase coined by O'Reilly Media in 2004, refers to a supposed second-generation of Internet-based services such as social networking sites, wikis, communication tools, and folksonomies that let people collaborate and share information online in previously unavailable ways.” - Wikipedia

Pamela Fox

So what’s a mashup anyway?

A mashup is a website or application that combines content from more than one source into an integrated experience. Content used in mashups is typically sourced from a third party via a public interface or API. Other methods of sourcing content for mashups include Web feeds (e.g. RSS or Atom) and JavaScript.” – WikipediaA mashup is the ultimate user-generated content: user likes data source A, data source B, & puts them together how they like.* There are also music & video mashups Pamela

Fox

Amazon Web Services

Web 2.0 APIshttp://www.programmableweb.com/apis currently (Jan 10 2007) 356 Web 2.0 APIs with GoogleMaps the most used in MashupsThis site acts as a “UDDI” for Web 2.0

Geoffrey Fox

Take Home

UK e-Science investment built 3 interdependent strengths:

Communities & collaborationProjects delivering & demandinge-Infrastructure: organisation, support & technology

Three success factors for projectsEngagement & value for all participantsCreativity & insight addressing a well-posed challengeTechnology adoption and innovation

Research, design or diagnosis is the driverIntegrate whatever technology you needInvent new technology only if you have to

progress with uk e-science bcs anglia ruskin university chelmsford malcolm atkinson director...

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