comb-e-chem jeremy frey sept 2004 drug design & delivery: the role of e-science jeremy frey...
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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
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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
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
Cambridge
Newcastle
Edinburgh
Oxford
Glasgow
Manchester
Cardiff
Southampton
London
Belfast
DL
RAL Hinxton
UK e-Science Grid
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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."
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Jeremy G. FreyJeremy G. Frey
HPC
HPCAnalysis
Storage
Storage
Analysis
Experiment
ExperimentComputing
HPC
Scientist
The Current “Client – Server ad hock” model
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Jeremy G. FreyJeremy G. Frey
The Future
The Grid Model - Information Utilities
MIDLEWARE
Experiment
Experiment
Computing
Computing
Computing
Storage
Storage
Storage
Analysis
Analysis
Scientist
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Jeremy G. FreyJeremy G. Frey
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.
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Jeremy G. FreyJeremy G. Frey
Access Grid nodesAccess Grid nodes
Access Grid
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Jeremy G. FreyJeremy G. Frey
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)
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Jeremy G. FreyJeremy G. Frey
•Bristol •Chemistry
•ECS
•Stats
•Chemistry
•Combi •Centre
•Southampton
•NCS
•IUPAC•RSC
•IBM
•CCDC
•Pfizer
•IT •Innovation
•Comb-e-Chem Partners
•GSK
•AZ
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Jeremy G. FreyJeremy G. FreyCom
beC
hem
People
& P
lace
s
IBM
GSK
Pfizer
AZ
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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…….
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
Design
AutomationAnalysis
Structures
Models
Properties
Experiment
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Jeremy G. FreyJeremy G. Frey
All about AutomationAll about Automation
ExperimentsExperiments
Information & Information & KnowledgeKnowledge
• DesignDesign
• SynthesisSynthesis
• MeasurementMeasurement
• AnalysisAnalysis
• DatabasesDatabases
• AgentsAgents
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Jeremy G. FreyJeremy G. Frey
Plan & COSHH
Digital Model
InformationIntegration
Report
Knowledge
Goal
Literature
Synthesis
Smart Laboratory
Analysis
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Jeremy G. FreyJeremy G. Frey
Plan & COSHH
Digital Model
InformationIntegration
Report
Knowledge
Goal
Literature
Synthesis
not just one laboratory but many co-laboratories
working together
Analysis
Smart Laboratory
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Jeremy G. FreyJeremy G. Frey
Making best use of the Plan Making best use of the Plan COSHHCOSHH
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Jeremy G. FreyJeremy G. Frey
Smart LabSmart Lab http://smarttea.org
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Jeremy G. FreyJeremy G. Frey
Smart HelpSmart Help http://smarttea.org
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Jeremy G. FreyJeremy G. Frey
Laboratory ContextLaboratory Context
COSHH Plan Record
Annotation
Guide
Experimenters
Digital Context
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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)
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Jeremy G. FreyJeremy G. Frey
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.
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Jeremy G. FreyJeremy G. Frey
Talk
•The UK e-Science Programme
•The Comb-e-Chem Project
•“Smart Lab”
•NCS Grid Service
•Structure Analysis Services
•Dissemination & Publication
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
Sample
Raw images
Processed diffractionpattern
Structure
CIF Database
Validation
Journal
Synthesis
Smart Labs NCS Archive
CCDC
metadataAutomated structuredetermination
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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!
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Jeremy G. FreyJeremy G. Frey
Journals: Journals: Publication @ sourcePublication @ source
JournalJournal
Materials
Database
Multimedia
Laboratory Data
Paper
“Full” record
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Jeremy G. FreyJeremy G. Frey
Publication ChainPublication Chain
Institution Laboratory
Student
Journal
Bibliography
Professional Body Archive
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Jeremy G. FreyJeremy G. Frey
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
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Jeremy G. FreyJeremy G. Frey
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