Automation and
Semantics:
The CombeChem
Experience
Oct 2004
Jeremy Frey
CombeDay
Feb 2005
Jeremy Frey
Informatics1
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.’
Tony Blair, 2002
 What is the web?
Feb 2005
J G Frey
Workshop
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
Feb 2005
J G Frey
Workshop
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
Feb 2005
J G Frey
Workshop
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
Feb 2005
J G Frey
Workshop
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
Feb 2005
J G Frey
Workshop
•CombeChem Partners
•IT
•Innovation
•IBM
•U. Indiana
Crystallography
•GSK
Feb 2005
•ECS
•Chemistry
•Stats
•Combi
•Centre
•Southampton
•AZ
•NCS
•UKOLN
J G Frey Bath
•Bristol
Chemistry
•CCDC
•IUPAC
•RSC
•IUCr
EPSRC
JISC
Workshop
Feb 2005
J G Frey
Workshop
Design
(statistics)
Experiments
Smart Labs
Plan
Access to data
CombeChem Data and Knowledge Cycle
High End-to-End Management
Throughput
Literature
measurement
Dissemination
Analysis
E-Bank
Statistics
Data
Feb 2005
J G Frey
Workshop
Feb 2005
J G Frey
•Network Dangers?
Workshop
Chemists and programming
 Many Chemists
think that they can
program
You still use FORTRAN!!
Feb 2005
J G Frey
Workshop
e-Workflow
Some Chemists
can
What about that! His brain still uses perl scripts
Feb 2005
J G Frey
Workshop
Much more automation in modern chemistry
Feb 2005
“That is so cool Dave, you
J G Freyonly need a palm pilot”
Workshop
Make sure the computer scientists know what you
actually do
“No, I don’t want to play chess, I just want to reheat the lasagne”
Feb 2005
J G Frey
Workshop
Pub/Sub for Laboratory data
using a broker and ultimately
delivered over GPRS
Feb 2005
J G Frey
Workshop
Annotation@source
Feb 2005
J G Frey
Workshop
Semantic (Pervasive) Grid
Grid
Feb 2005
J G Frey
Workshop
Security
and trust
for
experiments
and data
Feb 2005
J G Frey
Workshop
e-worries
Standards – now not just at the data level but
metadata level as well
WSRF
GTi
Feb 2005
J G Frey
Must ensure this is
not a problem for
applications
Workshop