Comb-e-Chem Jeremy Frey Sept 2004 Drug Design & Delivery: The role of e-Science Jeremy Frey School...

Jeremy FreyJeremy FreySept 2004Sept 2004

Comb-e-Chem

Drug Design & Delivery:Drug Design & Delivery:The role of The role of ee-Science-Science

Jeremy FreyJeremy FreySchool of Chemistry School of Chemistry

University of Southampton, UKUniversity of Southampton, UK

X-ray single Mol

STM

Ram

an

Ocean Monolayer

Jeremy G. FreyJeremy G. Frey

ee-Science-Science• ‘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.’

John Taylor, DG of UK OST

• ‘[The Grid] intends to make access to computing power, scientific data repositories and experimental facilities as easy as the Web makes access to information.’

Tony Blair, 2002


The UK e-Science The UK e-Science ChallengeChallenge

• £120M over a 3 Year Programme to £120M over a 3 Year Programme to create the next generation IT create the next generation IT infrastructure to support e-Science infrastructure to support e-Science and Businessand Business

• Essential that UK plays a leading role Essential that UK plays a leading role in Global Grid development with the in Global Grid development with the USA and EUUSA and EU

• Phase 1: Started roll out of plan for Phase 1: Started roll out of plan for Grid Research, Development and Grid Research, Development and Support of e-Science Pilot Projects Support of e-Science Pilot Projects


Cambridge

Newcastle

Edinburgh

Oxford

Glasgow

Manchester

Cardiff

Southampton

London

Belfast

DL

RAL Hinxton

UK e-Science Grid


National e-Science Centre National e-Science Centre (NeSC)(NeSC)

• NeSC is in EdinburghNeSC is in Edinburgh

• Provides Courses & MeetingsProvides Courses & Meetings

• Also has some funding for fellowships Also has some funding for fellowships to visit NeSCto visit NeSC


The Collaboratory ConceptThe Collaboratory Concept

• In 1989, William Wulf, then with the U.S. In 1989, William Wulf, then with the U.S. National Science Foundation, defined a National Science Foundation, defined a collaboratorycollaboratory as as

"a center without walls, in which the nation's "a center without walls, in which the nation's

researchers can perform their research without researchers can perform their research without regard to geographical location, interacting with regard to geographical location, interacting with colleagues, accessing instrumentation, sharing colleagues, accessing instrumentation, sharing data and computational resources, and accessing data and computational resources, and accessing information in digital libraries."information in digital libraries."


HPC

HPCAnalysis

Storage

Storage

Analysis

Experiment

ExperimentComputing

HPC

Scientist

The Current “Client – Server ad hock” model


The Future

The Grid Model - Information Utilities

MIDLEWARE

Experiment

Experiment

Computing

Computing

Computing

Storage

Storage

Storage

Analysis

Analysis

Scientist


Access GridAccess Grid

• Full multi-site video conferencing Full multi-site video conferencing over the IP networkover the IP network

• Many sites now in the UK all running Many sites now in the UK all running the same systemthe same system

• System originated in the USA so also System originated in the USA so also sites there.sites there.


Access Grid nodesAccess Grid nodes

Access Grid


The GridThe Grid• Grid is needed because Grid is needed because

– Volume of data (real time data, images, Volume of data (real time data, images, video)video)

– Scale of computation (analysis, simulation)Scale of computation (analysis, simulation)– Complexity of process (automation)Complexity of process (automation)– Variable demands on computationVariable demands on computation– Provenance (audit trials, timestamps, Provenance (audit trials, timestamps,

process)process)


•Bristol •Chemistry

•ECS

•Stats

•Chemistry

•Combi •Centre

•Southampton

•NCS

•IUPAC•RSC

•IBM

•CCDC

•Pfizer

•IT •Innovation

•Comb-e-Chem Partners

•GSK

•AZ

Jeremy G. FreyJeremy G. FreyCom

beC

hem

People

& P

lace

s

IBM

GSK

Pfizer

AZ


People• Chemistry (Southampton & Bristol)

– Mike Hursthouse, Chris Frampton, Jon Essex, Jeremy Frey, Guy Orpen, Stephan Christensen, Thomas Gelbrich, Sam Peppe, Hongchen Fu, Graham Tizard, Suzanna Ward, Lefteris Danos

• National Crystallography Service (NCS)– Simon Coles, Mark Light, Ann Bingham

• Electronics and Computer Science (Southampton)– Dave De Roure, Luck Moreau, Mike Luck, Hugo Mills, Graham Smith,

Simon Miles, Nicky Harding, Gareth Hughes, monica Schraefel, Terry Payne

• It-Innovation (Southampton)– Mike Surridge, Ken Meacham, Steve Taylor, Daren Marvin

• Statistics (Southampton)– Alan Welsh, Sue Lewis, Ralph Manson, Dave Woods

• Rutherford Appleton Laboratory


Synthesis

Structure

Analysis &Correlation

Modelling

Dissemination

Prediction

Design

Plan Goal

Properties

All steps must be Grid Aware

I will illustrate the application of e-Science to some of these stages using examples from the Comb-e-Chem Project


Synthesis

Structure

Analysis &Correlation

Modelling

Dissemination

Prediction

Design

Plan Goal

Properties

All steps must be Grid Aware

Salt Selection

Smart Lab

Crystallography

Structural SimilaritiesNon-linear optical effects

Simulations

Publication@SourceCombinatorial Chemistry

Semantic Grid

Descriptors

With examples…….


The Comb-e-Chem Project• The exponential world of

Combinatorial Synthesis and High throughput analysis meets the exponentially growing power of computing

• FundingEPSRC, IBM, GSK, AZ, Southampton


The CombThe Comb-e- -e- Chem VisionChem Vision

Structures DB

Properties DB

Structure + Properties Knowledge + Prediction

Automation & Remote interaction

Co-LaboratoryInteraction between users & “Dark Labs”

Simulation and

calculation


Design

AutomationAnalysis

Structures

Models

Properties

Experiment


All about AutomationAll about Automation

ExperimentsExperiments

Information & Information & KnowledgeKnowledge

• DesignDesign

• SynthesisSynthesis

• MeasurementMeasurement

• AnalysisAnalysis

• DatabasesDatabases

• AgentsAgents


Plan & COSHH

Digital Model

InformationIntegration

Report

Knowledge

Goal

Literature

Synthesis

Smart Laboratory

Analysis


Plan & COSHH

Digital Model

InformationIntegration

Report

Knowledge

Goal

Literature

Synthesis

not just one laboratory but many co-laboratories

working together

Analysis

Smart Laboratory


Making best use of the Plan Making best use of the Plan COSHHCOSHH


Smart LabSmart Lab http://smarttea.org


Smart HelpSmart Help http://smarttea.org


Laboratory ContextLaboratory Context

COSHH Plan Record

Annotation

Guide

Experimenters

Digital Context


Chemistry Starts in the LabChemistry Starts in the Lab

Lab Lab Lab

NCS

StructureRaw data

Database Publication

URI

URI

URI URI

URI

URI URI

URI


Semantic Grid ProjectSemantic Grid Project

• Inference based on the semantics

• Importance of Ontology

•But problem of contradictions even within a domain

•This is not an avoidable issue


XMLXML

Gaussian ab initio program

Gaussian ab initio program

XML wrapper

XML wrapper

Simulation program

Simulation program

XML wrapper

XML wrapper

InterfaceInterface

Personal Agent

Personal Agent

But need more general descriptions for servicesRDF – resource description frameworkDAML-S (for describing services)


DatabasesDatabases

• Database will become the key Database will become the key method of handling all datamethod of handling all data

• Metadata must be generated at Metadata must be generated at inception and added as data inception and added as data traverses the workflowtraverses the workflow

• Version control, audit and backup Version control, audit and backup handled at the database level.handled at the database level.


Talk

•The UK e-Science Programme

•The Comb-e-Chem Project

•“Smart Lab”

•NCS Grid Service

•Structure Analysis Services

•Dissemination & Publication


Users Users Users

Experiment Expert

Data & control links

Access Grid links

ExperimentRemote (Dark) Laboratory

Centralised remote equipment, multiple users, few experts

•Model for National crystallographic Service NCSModel for National crystallographic Service NCS


Expert

Manufacturer Support Service

Users

Experiment

Users

Experiment

Users

Experiment

Local link

“External” linkAccess grid & control links

Expert is the centralresource in short supply

•Model for Combinatorial Raman ProjectModel for Combinatorial Raman Project


Sample

Raw images

Processed diffractionpattern

Structure

CIF Database

Validation

Journal

Synthesis

Smart Labs NCS Archive

CCDC

metadataAutomated structuredetermination


Archiving of DataArchiving of Data

RAW DATA:

Automatic archiving and retrieval with Atlas Datastore (RAL)

Development of schema for retrieval of crystallographic metadata from relational databases (ISIS Data analysis group)

Storage Resource Broker (SRB): Uniform access interface to different types of storage devices

RESULTS DATA:

Automatic deposition of CIF data with CCDC GRID-enabled pre-deposition database


Data TrailData Trail

• Drill down through the analysis path Drill down through the analysis path

• Look at increasingly raw dataLook at increasingly raw data

• Often large expansion in quantity Often large expansion in quantity and variety at each stageand variety at each stage


Publication@SourcePublication@Source• Must be able to track back to the original dataMust be able to track back to the original data

• Primary reason is to allow new analysis in the Primary reason is to allow new analysis in the future by other researchers.future by other researchers.

• In a university environment this may be In a university environment this may be viewed as a public responsibility in business viewed as a public responsibility in business environment ensuring maximum value from environment ensuring maximum value from investment.investment.

• Does have implications for provenance and Does have implications for provenance and even fraud!even fraud!


Journals: Journals: Publication @ sourcePublication @ source

JournalJournal

Materials

Database

Multimedia

Laboratory Data

Paper

“Full” record


Publication ChainPublication Chain

Institution Laboratory

Student

Journal

Bibliography

Professional Body Archive


ee-Bank Project-Bank Project

• Link comb-Link comb-ee-chem and other -chem and other semantic grid science projects to the semantic grid science projects to the e-print system at Southamptone-print system at Southampton

• Provide dissemination and Provide dissemination and provenanceprovenance


Changing the way we workChanging the way we work

DataProvenance

QuantumMechanical

AnalysisPropertiesPrediction Data Mining,

QSAR, etc Design ofExperiment

E-Lab:Combinatorial

Synthesis

E-Lab:Properties

Measurement

E-Lab:X-Ray

Crystallography

LaboratoryProcesses

LaboratoryProcesses

StructuresDB

PropertiesDB

Data StreamingAuthorship/Submission

VisualisationAgent Assistant

LaboratoryProcesses

Samples Samples

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Comb-e-Chem Jeremy Frey Sept 2004 Drug Design & Delivery: The role of e-Science Jeremy Frey School...

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