chris jones moving forward with e-science in pharma october 2002 1 moving forward with e-science in...

Chris JonesMoving Forward with e-Science in Pharma

October 20021

Moving Forward with

e-Science in Pharma

@

The PRISM ForumChris Jones

October 2002


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


October 20023

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


October 20024

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


October 20025

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:


October 20026

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


October 20027

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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October 20028

GRID

MIDDLEWARE

Visualising

Supercomputer, PC-Cluster

Data-storage, Sensors, Experiments, Grid enabled Applications

Internet, networks

Workstation

Mobile Access

Grids, continued

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October 20029

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)


October 200210

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


October 200211

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


October 200212

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…


October 200213

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!


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…


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


October 200216

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


October 200217

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


October 200218

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


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

http://www.cordis.lu/FP6


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…


October 200221

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)

…


October 200222

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


October 200223

Databases in the Grid

Computational Complexity

DataComplexity


October 200224

MyGridPersonalised

extensible environments for

data-intensive

in silico experiments

IBM

in biology

Professor Carole Goble,

University of Manchester

Dr Alan Robinson,

EBI


October 200225

Consortium

Scientific TeamBiologists and Power BiologistsGlaxoSmithKline, AstraZeneca, Merck KGaA, Manchester, EBI

Technical TeamManchester, Southampton, Newcastle, Sheffield, EBI, NottinghamIBM, SUNGeneticXchangeNetwork Inference, Epistemics Ltd


October 200226

Comparative Functional Genomics

Vast amounts of data & escalating

Highly heterogeneousData typesData formsCommunity

Highly complex and inter-related

Volatile


October 200227

myGrid Project

Imminent ‘deluge’ of data

Highly heterogeneous

Highly complex and inter-

related

Convergence of data and

literature archives


October 200228

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


October 200230

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?


October 200231

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


October 200232

So would you like me to try to organise such a

“Retreat”?


October 200233

BioGRIDS ?

See Rick Steven's Presentation

chris jones moving forward with e-science in pharma october 2002 1 moving forward with e-science in...

Documents

escience science

escience slide

uk escience vision escience

science grids

uk escience programme

way science

uk escience pilot projects

key areas of science