comb-e-chem jeremy frey sept 2003 from e-science to publication@source jeremy frey school of...

Jeremy FreyJeremy FreySept 2003Sept 2003

Comb-e-Chem

From From ee-Science to -Science to Publication@SourcePublication@Source

Jeremy FreyJeremy FreySchool of Chemistry School of Chemistry

University of Southampton, UKUniversity of Southampton, UK

X-ray single Mol

STM

Ram

an

Ocean Monolayer

19 Feb 2004 OAI Meeting19 Feb 2004 OAI Meeting Jeremy G. Frey & Mike HursthouseJeremy G. Frey & Mike Hursthouse

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 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."


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

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


•Bristol •Chemistry

•ECS

•Stats

•Chemistry

•Combi •Centre

•Southampton

•NCS

•IUPAC•RSC

•IBM

•CCDC

•Pfizer

•IT •Innovation

•Comb-e-Chem Partners

•GSK

•AZ


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


Comb-e-Chem Project - Comb-e-Chem Project - AutomationAutomation

X-Raye-Lab

Analysis

Properties

Propertiese-Lab

SimulationVideo

Diff

ract

omet

er

Grid

StructuresDatabase


HPC

HPCAnalysis

Storage

Storage

Analysis

Experiment

ExperimentComputing

HPC

Scientist

Scientist at the Centre of an Information WebBy access variable and difficult


The Future

The Grid Model - Information Utilities

Uniform access

MIDLEWARE

Experiment

Experiment

Computing

Computing

Computing

Storage

Storage

Storage

Analysis

Analysis

Scientist

Remember that you contribute to other people’s information web


End - to - end connectivityEnd - to - end connectivity

• Provide the smooth connection between Provide the smooth connection between the sources of data & informationthe sources of data & information

• From literature to the laboratory bench From literature to the laboratory bench and back via all stages of analysis and and back via all stages of analysis and discussiondiscussion

• Thus the need for a Data Grid or GridsThus the need for a Data Grid or Grids

• Al steps need to be Grid awareAl steps need to be Grid aware


Plan & COSHH

Digital Model

InformationIntegration

Report

Knowledge

Goal

Literature

Synthesis

Smart Laboratory

Analysis

Generate information within & for the grid context


0

0.2

0.4

0.6

0.8

1

1.2

1 15 29 43 57 71 85 99 113

127

141

155

169

183

197

211

225

239

SN

O

NH

NH2

O Variety of data


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

– Complexity of dataComplexity of data– 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)


Dissemination & Publication

•A different approach is required to provide data to the community

•The grid provides the necessary medium

•What & How do we want to make available


Journals: Journals: Publication @ sourcePublication @ source

JournalJournal

Materials

Database

Multimedia

Laboratory Data

Paper

“Full” record


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

• Need URIs for everythingNeed URIs for everything


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!


Publication ChainPublication Chain

Institution Laboratory

Student

Journal

Bibliography

Professional Body Archive


Sample

Raw images

Processed diffractionpattern

Structure

CIF Database

Validation

Journal

Synthesis

Smart Labs NCS Archive

CCDC

metadataAutomated structuredetermination

Jeremy FreyJeremy FreySept 2003Sept 2003

Comb-e-Chem

Chemical Crystallography: A Chemical Crystallography: A Suitable Case for OA TherapySuitable Case for OA Therapy

Mike HursthouseMike HursthouseDepartment of Chemistry and Department of Chemistry and

Combinatorial Centre of Excellence,Combinatorial Centre of Excellence,

EPSRC National Service for EPSRC National Service for Crystallography Crystallography

University of Southampton, UKUniversity of Southampton, UK


• Characterisation technique for Chemical Characterisation technique for Chemical Structure. Structure.

• Use XRD.Use XRD.• Provides high level of chem knowledgeProvides high level of chem knowledge• Structure – molecular or crystalStructure – molecular or crystal• Previously focussed on molecular structure – Previously focussed on molecular structure –

chemical propschemical props• Now focus on crystal structure – physical propsNow focus on crystal structure – physical props• Change in interest facilitated by availability of Change in interest facilitated by availability of

database archive.database archive.• However, woefully incompleteHowever, woefully incomplete

ChemCryst


• Database Archive – ca 300000 entries – allDatabase Archive – ca 300000 entries – all

• published structurespublished structures

• >10M chemical compounds known>10M chemical compounds known

• Probably 1.5M structures knownProbably 1.5M structures known

• Why shortfall? Archaic publishing methods.Why shortfall? Archaic publishing methods.

• Solution? Solution?

ChemCryst


• ChemCryst results New dissemination strategyChemCryst results New dissemination strategy

• E-Prints of “Structure Reports”E-Prints of “Structure Reports”

• Can be created automatically.Can be created automatically.

• Work can be validated automatically.Work can be validated automatically.

• All data (raw, processed, meta…) included.All data (raw, processed, meta…) included.

• Hence bypass Journal sponsored “refereeing Hence bypass Journal sponsored “refereeing

• Still need to decide on “publication” of “science”Still need to decide on “publication” of “science”

ChemCryst


ee-Bank Project JISC project with -Bank Project JISC project with UKOLNUKOLN

• 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

comb-e-chem jeremy frey sept 2003 from e-science to publication@source jeremy frey school of...

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