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Automation and Semantics: The CombeChem Experience. Jeremy Frey CombeDay Feb 2005. e -Science. ‘e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it.’ John Taylor, DG of UK OST

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Automation and semantics the combechem experience

Automation and Semantics: The CombeChem Experience

Jeremy Frey

CombeDay

Feb 2005

Jeremy Frey


E science
e-Science

  • ‘e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it.’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.’ TonyBlair, 2002

  • What is the web?

J G Frey


Publication@source
Publication@Source

  • Trace all the way back from publication to the original data – provenance CombeChem

  • Who needs provenance? Bush, Blair The JIC, MI5, CIA & Hutton 2004

J G Frey


The comb e chem project
The CombeChem Project

  • The exponential world of combinatorial synthesis and high throughput analysis meets the exponentially growing power of computing

    • Automation, Semantics & the Grid”

  • End to End linking of data and information

    • In chemistry this can be a very long chain –from a lab to inside a mouse

J G Frey


The comb e chem project1
The CombeChem Project

  • Collect data with regard to how it could eventually be used

    • Make sure the metadata is of high quality

    • Record properly at source

  • The Chemistry Lab

    • People & Machines working together

J G Frey


People
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, Jamie Robinson, Kieron Taylor

  • 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 –Atlas Datastore

J G Frey


Automation and semantics the combechem experience

  • U. Indiana Crystallography

  • IUPAC

  • RSC

  • IUCr

  • CombeChem Partners

  • IT

  • Innovation

  • NCS

  • Bristol Chemistry

  • ECS

  • Chemistry

  • CCDC

  • Combi

  • Centre

  • Stats

  • GSK

  • Southampton

  • AZ

  • UKOLN Bath

EPSRC

JISC

J G Frey



Automation and semantics the combechem experience

Design

(statistics)

Experiments

Smart Labs

Plan

Access to data

CombeChem Data and Knowledge Cycle

End-to-End Management

High

Throughput

measurement

Literature

Dissemination

E-Bank

Data

Analysis

Statistics

J G Frey



Chemists and programming

You still use FORTRAN!!

Chemists and programming

  • Many Chemists think that they can program

J G Frey


Automation and semantics the combechem experience

e-Workflow

Some Chemistscan

What about that! His brain still uses perl scripts

J G Frey


Automation and semantics the combechem experience

Much more automation in modern chemistry

“That is so cool Dave, you only need a palm pilot”

J G Frey


Automation and semantics the combechem experience

Make sure the computer scientists know what you

actually do

J G Frey

“No, I don’t want to play chess, I just want to reheat the lasagne”



Automation and semantics the combechem experience

Annotation@source delivered over GPRS

J G Frey


Automation and semantics the combechem experience

Semantic (Pervasive) Grid delivered over GPRS

Grid

J G Frey


Automation and semantics the combechem experience

Security and trust for experiments and data delivered over GPRS

J G Frey


Automation and semantics the combechem experience

Standards – now not just at the data level but metadata level as well

e-worries

WSRF

Must ensure this is not a problem for applications

GTi

J G Frey