chris jones moving forward with e-science in pharma october 2002 1 moving forward with e-science in...
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Chris JonesMoving Forward with e-Science in Pharma
October 20021
Moving Forward with
e-Science in Pharma
@
The PRISM ForumChris Jones
October 2002
Chris JonesMoving Forward with e-Science in Pharma
October 20022
Summary
Reminder! What do we mean by e-Science?
So what is the current status of e-Science (GRIDS)?
And where is this going?
Standards and Middleware
EU 6th Framework Programme
Joint Wellcome Trust – UK e-Science Retreat
Different types of GRIDS
How to move forward with e-Science in Pharma?
Some UK e-Science Pilot Projects
EU 6th Framework Programme Integrated Projects
Chris JonesMoving Forward with e-Science in Pharma
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What do we mean by “e-Science”?
e-Sciencescience increasingly done through distributed global collaborations enabled by the internet
using very large data collections, terascale computing resources and high performance visualisation
Gridnew generation information utility
middleware, software and hardware to access, process, communicate and store huge quantities of data
infrastructure enabler for e-science
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The UK e-Science Vision
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.
“[The UK 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, 23rd May 2002
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Why we need a UK e-Science programme?
health and medicinegenomics and bioscienceparticle physics and astronomyenvironmental scienceengineering designchemistry and material sciencesocial sciences
To provide infrastructure and facilities needed for next major stages of collaborative research in:
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Why we need an e-Science programme?
One national information utility infrastructure not one per discipline,
in silico experimentation, huge data collections,
global col-laboratories, not individual client-
server
integrated campus infrastructure for all disciplines
To provide the UK-wide national infrastructure and facilities needed for the UK’s participation in world wide science research across all disciplines
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Supercomputer
PC-ClusterArchive
Analysis
Experiment
PC-Cluster SupercomputerScientist/user
Middleware
Archive
Supercomputer
PC-ClusterArchive Analysis
Experiment
PC-Cluster Supercomputer
Scientist/user
Archive
Analysis
Often monolithic, “vertical”, proprietary solutions
Through open, standard interfaces: flexible, adaptable, interchangeable, multiple vendor solutions
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GRID
MIDDLEWARE
Visualising
Supercomputer, PC-Cluster
Data-storage, Sensors, Experiments, Grid enabled Applications
Internet, networks
Workstation
Mobile Access
Grids, continued
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The GRID Vision
Computing resources
Data
Knowledge
Instruments
People
Solution
Complex problem
GRID
„Eventually, users will be unaware they are using any computer but the one on their desk, because it will have the capabilities
to reach out across the (inter-) national network and obtain whatever computational resources are necessary”
(Larry Smarr and Charles Catlett, 1992)
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From the Sublime to the Ridiculous
From Tony Blair to the universal inclusion of the word GRID in all applications for resources…
Grid and e-Science have come a long way:
..\enterthegrid.htm
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A (rough) Timeline of the Web
1988 Internet established1989 first idea and paper from TBL1990 development begun on Next computers, CERN Web
server1991 character-mode browsers on VM and VM/CMS (saving
remote logins)1992 Physics uses Web extensively and groupies gather1993 MOSAIC browser UNIX primarily, PCs and Macs second1994 May, NETSCAPE formed, Bay Area pilots, “World”
impact vision appears. Web pages for IT companies.1995 Windows 95, MS file formats more acceptable. TBL
left CERN for MIT1996 Java.Web well established in large companies1997 Battle of the browsers1998 ….1999 ….fairly ubiquitous in homes
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Timeline of the GRID
1998 and before, “Metacomputing” S/C community, early adopters e.g. NASA IPG
1999 “The Bible” from Foster and Kesselman, Taylor plants idea for UK pending Review, first words to PRISM
2000 UK spending review in November, DataGRID discusions
2001 UK money, EU money, GGF1, computer industry2002 OGSA, industry role and commitment, GLOBUS 2,
heavy involvement by IBM et al2003 EU FP6, OGSA implementations…
One has to chose the moment to move forward…
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Global GRID Forum
First Meeting, joining separate Grid Forum initiatives, Amsterdam in April 2001, sold out with 350 people
Subsequent meetings in Washington, Rome, Toronto, Edinburgh, excellent attendance
And growing industry attendance
As the role that industry will play in this open source - open interface unfolds
Next Meeting, October 2002, (this week)Chicago. First Meeting with Working Groups only(have a look to see if you have someone thatshould be there)
So far everyone is still playing the same game!
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October 200214
Globus and other Middleware
Globus isn’t good enough, but its what we have…(Why only one Web?)
So let’s develop Globus (release 2 available, release 3 under specification)
It needs functionality, and it needs hardening!
White Papers:The Anatomy of the GRIDThe Physiology of the GRID
Open Services GRID Architecture – OGSAConvergence with Web ServicesComputer Industry involvementDefine API’s and protocols
So industry may produce alternative middleware, written to these interfaces…
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October 200215
OGSA – DAI Project
Key middleware project for UK Program
- Total Budget £3M (CP £1.5M)
Three Centres involved:
- Edinburgh, Manchester and Newcastle
Industrial partners:
- IBM US, IBM Hursley and Oracle UK
Develop high-quality data-centric middleware
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OGSA – DAI Project
Design Specification completedPaper for WG on Database Access and Integration Services
Three Prototypes delivered:Distributed Query ServiceXML Database InterfaceRelational Database Interface
Final versions by November 2002Integrated with Globus GT3
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EU 6th Framework Programme
Introduces new components of
Networks of Excellence and
Integrated Projects
Within the European Research Space
Perhaps correcting funding asymmetry with e.g NSF
Delegation of management of major ambitious projects to key players
Will pay 100% management costs!
Opportunity for EIROFORUM Institutions
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FP6 Integrated Projects (seen in April 2002)
Very ambitious
Tens of millions of Euros € over 3 to 5 years
Group of key players, typically 20 rather than 5
Solicitation for Expressions of Interest, April 7th
until June 7th 2002
Call for Proposals ~ around end 2002
Money not before second half of 2003
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October 200219
FP6 in October 2002
Expressions of Interest in May 2002. (Also NoIs)
Analysis of EoI and NoI’s October 2002, www.cordis.lu/FP6
EU Meetings now to discuss plans
…maybe not so much money for IP’s
For GRIDS/e-Science/(Ambient Intelligence?)Overall “some time to mature needed”Early call for proposals around Infrastructure Dec. 2002 for say € 50 M.Later a call for EU Networking, son of GEANT, € 100 MLater a call for e-Science Application money for € 50-100 M
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October 200220
Joint Wellcome – UK e-Science Retreat on GRIDS for
BioinformaticsA distinguished collection including the usual main suspects!In Hinxton Hall on Wellcome Trust Genome Campus, with the same facilities used for the PRISM founding meeting
Revealed the “tension” between the service providers and the front-line developers
Revealed the lack of IT architects in bioinformatics community (rather application driven)
Revealed that Hinxton Campus has no planned IT infrastructure…
Nonetheless the objective of launching the bioinformatic community into GRIDS was achieved
Looking at ways to start with Hinxton GRID, start to adapt EBI services to GRID, extend to e.g. 3D mouse database…
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Types of GRIDS ?
Cycle Scavenging GRIDS
Supercomputer GRIDS
Compute intensive GRIDS (e.g. distributed
farms/clusters, simulations, fast interactive response…)
Data GRID (very large amounts of distributed data, data tends to move to be computed)
Service GRID (Astronomical combined data, BLAST search on genome, protein databases)
Integration GRID (of many distributed heterogeneous dbs)
…
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Three Layer GRID Abstraction
Information Grid
Knowledge Grid
Computation/Data Grid
Data to
Knowledge
Control
•Data Un-interpreted bits and bytes
•Information Data equipped with meaning
•Knowledge Information applied to achieve a goal, solve a problem or enact a decision
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Databases in the Grid
Computational Complexity
DataComplexity
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MyGridPersonalised
extensible environments for
data-intensive
in silico experiments
IBM
in biology
Professor Carole Goble,
University of Manchester
Dr Alan Robinson,
EBI
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Consortium
Scientific TeamBiologists and Power BiologistsGlaxoSmithKline, AstraZeneca, Merck KGaA, Manchester, EBI
Technical TeamManchester, Southampton, Newcastle, Sheffield, EBI, NottinghamIBM, SUNGeneticXchangeNetwork Inference, Epistemics Ltd
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Comparative Functional Genomics
Vast amounts of data & escalating
Highly heterogeneousData typesData formsCommunity
Highly complex and inter-related
Volatile
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myGrid Project
Imminent ‘deluge’ of data
Highly heterogeneous
Highly complex and inter-
related
Convergence of data and
literature archives
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myGrid Generic Technologies
Database access from the Grid
Process enactment on the Grid
Personalisation services
Metadata services
Development of Agent Services
Ultimate goal is to put Grid Services together
with Ontologies to develop ‘Semantic Grid’
Comb-e-Chem Project
X-Raye-Lab
Analysis
Properties
Propertiese-Lab
SimulationVideo
Diff
ract
omet
er
Grid Middleware
StructuresDatabase
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A Pharma-GRID Retreat?In which way(s) should Pharma get involved with GRIDS? And at what times?“Cycle scavenging” is entry level with low resistance for approvalCan we use this technology for better integration?Can we do things with GRIDS we couldn’t do before?Can we ask question we considered impossible before?Can we play interactively with ideas that were batch jobs before and hence not tried?Is there work on GRIDS that the pharma industry needs done specially for them?Are there pre-competitive projects?Can this technology speed up the famous time to market?What about GRIDS in the clinical arena, regulatory domain?Etc...A host of questions..can we gain competitive advantage?
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A Pharma-GRID Retreat?
Participation of distinguished GRID experts? - probably OKHow many participants per company? One, two, more?Where?
Pharma company CERN National UK E-Science Centre in Edinburghother?
Finances? As PRISM? How long? One day, 1.5, 2?
The objective of the review and brainstorming should be to clarify relevance to pharma of this technology in which time-frames, and to determine which ways one could move forward in bringing e-Science to Pharma
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So would you like me to try to organise such a
“Retreat”?
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BioGRIDS ?
See Rick Steven's Presentation