myGrid

1
myGrid

• 3rd Steering Meeting
• October 21st 2002, Manchester

2
Meeting Plan.

• Reminder of objectives.
• Project context.
• Review progress over past year.
• Pre-prototype Nov 2001 April 2002.
• Post Pre-prototype April 2002 October 2002.
• Review project plans and structure.
• Workbench Demonstrator.
• Provenance Personalisation.
• Industrial engagement.
• Risk assessment strategy.

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• myGridpersonalised extensible environments
  fordata-intensive in silico experiments in
  biology
• EPSRC eScience pilot project
• official start 01/10/01
• actual 01/01/02
• end 30/03/05
• 16 RAs, 9 studentships (start 09/03)

4
Circadian Rhythms

• Has anyone else studied the effect of
  neurotransmitters on the circadian rhythms in
  Drosophila?
• Ive got a cluster of proteins from my
  experiment. How do their functions interrelate?
  And what are the proteins with a particular
  function?
• Is a structure known for my protein? What other
  proteins have a similar structure?
• Can I build a homology 3D model?
• What is known about a homologous protein?

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3
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E-Science Q A

• Who else has asked this question can I
  use/adapt their approach?
• Workflow.
• What were the results at each stage?
• Dynamic Data Repositories.
• When was P12345 last updated?
• Which BLAST did I use?
• Provenance.
• Has PDB changed since I last ran this?
• Notification.

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3
5
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Personalisation.
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myGrid in silico experimentation

• Resource Interoperation.
• Workflow Coordination Database Integration
• Provenance Change Propagation.
• Improving quality of experiments data.
• Personalisation Collaborative working.
• Scientific discovery is personal global.
• Security, ownership -gt valuable assets
• Service based architecture (formally known as
  agents)
• Publication, discovery, interoperation,
  composition, decommissioning of myGrid services
• Metadata.
• Describing stuff, using ontologies, Semantic Web.

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myGrid outcomes reminder

• e-Scientists
• Workbench
• Environment built on toolkits for service access,
  personalisation community
• Application
• Gene function expression analysis using S.
  cerevisiae
• Annotation workbench for the PRINTS pattern
  database
• Developers
• myGrid-in-a-Box developers kit
• Re-purposing DAS, AppLab and OpenBSA
• Integrating ISYS GlaxoSmithKline platforms

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myGrid partners
m
Millennium Pharmaceuticals, LION BioSciences,
TurboGenomics Issue Incorporating industrial
partners.
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The myGrid team

• Carole Goble
• Norman Paton
• Brian Warboys
• Stephen Pettifer
• Alvaro Fernandes
• Luc Moreau
• Dave De Roure
• Chris Greenhalgh
• Tom Rodden
• John Brooke
• Paul Watson
• Alan Robinson
• Rob Gaizauskas
• Robert Stevens
• Ian Horrocks
• Neil Wipat

• Matthew Addis
• Nick Sharman
• Rich Cawley
• Simon Harper
• Karon Mee
• Simon Miles
• (Vijay Dailani)
• Xiaojian Liu
• Tom Oinn
• Martin Senger
• Milena Radenkovic
• Kevin Glover
• (Angus Roberts)
• Chris Wroe

• Mark Greenwood
• Phil Lord
• Neil Davis
• Darren Marvin
• Justin Ferris
• Peter Li
• Nedim Alpdemir
• Luca Toldo
• Robin McEntire
• Anne Westcott
• Tony Storey
• Bernard Horan
• Paul Smart
• Robert Haynes

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Global Grid Forum Links

• Open Grid Services Architecture
• http//www.globus.org/ogsa/
• Early Demonstrator (with AstroGrid)
• Database Access and Integration
• GGF OGSA-DAIS and OGSA-DAI project
• Norman Paton, Paul Watson, IBM (WP3)
• OGSI working group
• Tom Oinn (WP1)
• GGF-Semantic Grid Research Group
• Carole Goble, Dave De Roure
• GGF Life Sciences Working Group..

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Links with other Grid projects

• AstroGrid
• Ontologies, Databases
• Geodise
• Ontologies, Databases, Workflow
• Comb-e-Chem
• Workflow, (LabBooks)
• SCEC (USA)
• Ontologies and Service composition
• UTOPIA
• Client application of myGrid middleware.

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Potential Links with Other Projects

• MIMAIS
• Ontologies
• E-Protein
• Potential client and beta tester
• Macromolecular Structures Database
• Potential client and beta tester
• GONG
• Ontologies and ontology infrastructure
• WonderWeb
• Ontology infrastructure

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Links with Other Programmes

• I3C
• BioSciences Service Registry (Carole)
• Life Sciences ID (Martin Senger)
• BioMOBY
• Open Source Activity
• BioMOBY registry and object typing.

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Lots of links take lots of time
The Goals and Status of the e-Science Core
Programme, March 2002
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myGrid Talks

• BiGUM Bioinformatics Grid User Group, NeSC, 2001
• InfoTechPharm2002, London, Feb 2002 (mentioned by
  Novartis)
• Finland Grid workshop (via AccessGrid)
• NeSC Opening, NeSC April 2002
• Agents in Bioinformatics workshop
• Sun HPC Consortia meeting, Glasgow, July 2002
• I3C meeting, Boston, July 2002
• UK eScience All Hands, Sheffield, Sept 2002
• Genes, Proteins and Computing VII, Southampton,
  Sept 2002
• EMBL-EBI, Hinxton 30th September 2002
• Wellcome Trust UK Biological Grids Retreat,
  Hinxton. 1-3rd October 2002
• BBSRC Grant Holder workshop, 28-29th October,
  2002
• Objects in Bio and Chem Informatics, Washington
  Nov 2002
• DTI Outreach in Bioinformatics, London Nov 2002
• Sun BioGrid Symposium, Baltimore, Dec 4-5th 2002
• InforTechPharma Grids Symposium, London Feb 2003
• O'Reilly Bioinformatics Technology Conference,
  San Diego, Feb 2003

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Publications

• Comparative and Functional Genomics
• Scientific Computing article
• International Journal of Cooperative Information
  Systems
• Book chapter on Semantic Grids
• SIGMOD Record paper on Semantic Grids
• Grid Bible 2 chapter on myGrid invited
• Submission to EuroWeb 2002
• Others???

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Current programme

• Use case scenarios.
• Rolling programme of prototyping.
• April myGrid 0.0, October myGrid 0.1
• Identifying the most important services.
• Agreeing consistent interfaces.
• Integrating with other Grid services.
• Implementing core services.
• Describing services.
• Connecting with other efforts.

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Project Management

• Management structure taken a longer time than
  expected.
• Recruitment completed, and RA churn commenced
  (Lost Vijay and Angus)
• 9 PhD studentships allocated to start 2003.
  Structures taken longer than expected
• Weekly management telephone conference now a
  monthly access grid meeting
• Regular WP meetings and email lists.
• Document repository
• BSCW, WIKI, probably needs bulletin board!
• CVS code repository and software build
  environment
• Web site
• Software Development environment UML
• But common software platform still unresolved.
• Open Source license LGPL.
• Collaboration agreement

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myGrid phased development
6 months
April 2002
Pre-prototype
12 months
Architecture
Simple services
24 months
Early toolkit trials
33 months
Extended services

• Versions of myGrid
• Varying degrees of functionality

Application trials
Developers toolkit
Release
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Next Phases of development
Kick-off meeting
Nov 01
Pre-Prototype
Consolidation Architecture
Prototype Demonstrator
Pre-Release 1.0
Release 1.0
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Pre-prototype Purpose

• Requirements gathering
• Technology experimentation
• Web services
• Semantic Web
• Grid
• Not to deliver real supported software

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Pre-prototype characteristics

• A number of sequence analysis-based scenarios
• Personal data repository
• Web service-wrapped public data repositories and
  tools
• Simple Workflow enactment
• Provenance (primitive form)
• Ontology-based service discovery
• Simple Web Portal
• Decoupled text extraction
• No event notification
• No database integration (aka distributed query
  processing / instance reconciliation)

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Pre-prototype Process
Technology Personnel Induction
User Group
Architecture Group
Specifying the myGrid versions
Pre-Prototype April 2002
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Client framework
myGrid 0.0
Portal
Repository Client
Ontology Client
Workflow Client
Personal Repository
Workflow Repository
(Metadata) Ontology Server
DAMLOIL Reasoner (FaCT)
(Metadata) Service Type Directory
Workflow enactment
Matcher and Ranker
Service instance directory
Bioinformatics services
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How do the functions of a cluster of proteins
interrelate?

• Some proteins in my personal repository

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Find services that takes a protein and gives
their functions and pick the best match.
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Find another that displays the proteins base on
their function. Ontology restricts inputs
outputs
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Build a workflow of composed services linked
together
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See if a workflow that is appropriate already
exists. It could have been made anyone who will
share with you.
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Pick one and enact it.
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While its running it picks the best service
instance that can run the service at that time.
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While its running it picks the best service
instance that can run the service at that
time. Or you choose.
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The workflow finishes with the final display
service
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Results are put into your personal repository,
with a concept from the ontology to tell you and
myGrid what they mean.
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And full provenance record kept, and linked with
the results. We could redo or reuse the workflow.
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IF-2 (Hinxton, October 2002)

• Consolidated IF-1 software and builds.
• Attempted a new cut at the architecture.
• Event notification service
• Workflow enactment engine
• Personal data repository for XML data
• Ontology server
• Ontology of services
• Gateway API
• Pairwise integration.

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Overview Development

• Consolidate pre-prototype services
• Develop new services for myGrid 0.1
• Start to develop new services for myGrid 0.2

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Development Consolidation

• Bioinformatics services
• SOAPLAB Web Service access to EMBOSS tools
• Medline BQS
• BLAST Services
• Service directory
• Ported from MS Access to MySQL
• Personal repository
• Revised schema
• Specific support for XML data

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Development Consolidation

• Ontology service
• Ported from CGI to Web Service interface
• Workflow enactment engine
• Supports much richer subset of WSFL
• e-Science layer
• Refactored into web Portal and underlying Gateway
  (API Web Service)
• Text-only client for lightweight use scripting
  added

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Development For myGrid 0.1

• Use of myGrid via Talisman
• Click here to run the EMBOSS example workflow
• Notification service
• Based on EJB implementation
• Service describer client
• For introducing new service types

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Development For future

• Container-based framework
• programming model abstracts from transport
  infrastructure
• Distributed query process support
• as OGSA-DAI service
• Text extraction
• reengineered PASTA
• available via Web Service

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myGrid Framework
Portal
Work Bench
Applications UTOPIA
Bio-Medical Services Library DAS, Talisman,
workflow sets
Upper level knowledge-based Grid Common
Services Semantic integration, knowledge based
querying, workflow composition, visualisation,
provenance mgt, semantic service discovery
Middle level Grid Common Services Database
access, distributed query processing, service
discovery, workflow enactment, event notification
Low level Grid Common Services (OGSI) Co-schedulin
g, data shipping, authentication, job execution,
resource monitoring, replication
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User Agent
Custom Application
Presentation Services
Collaboration Support
Management Tools
Portal
Client Framework
Semantic Data Integration
Semantic Aspect
Information Extraction
Semantic Workflow Design
Provenance Validation Assessment
Semantic Discovery
Ontology Service
Preferences
Metadata Aspect
Availability
Preferences
Versioning
Third-party Metadata
QoS
QoS
Provenance
QoS
Coordination Services
Distributed Query
Workflow Enactment
Syntactic Discovery
Event Notification
Networked Services
White Pages Yellow Pages Discovery
Personal Repository
Database Access
JobExecution
Device Access
Device Access
Security Authentication Authorization
Distributed Resources
Database
resources data and tools
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Review

• Technology focus up until now.
• Tendency to over-develop technology without
  application focus.
• Lack of user engagement.
• Esp. from yeast and PRINTS annotators.
• Need to reassert
• application perspective
• myGrid distinctiveness provenance and
  personalisation.
• Architecture group doesnt seem to be working

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Issues (1) Work Packages

• Work package structure does not support the cross
  work package issues.
• User requirements
• Originally planned under WP6 but isnt how it
  turned out.
• Provenance
• Personalisation
• Proposed Solution
• New cross WP work packages in these areas.

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Issues (2) Application

• User requirements on workflows rather than how
  they are used.
• Lack of clarity for
• End-user application.
• End-user demonstrators for the application.
• Without this it is easy for the user scenarios to
  be simplistic and technology focused
• Forgetting how databases, workflows, services
  will be used.
• Because we dont have a bio-lead

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Who is myGrid for?
myGrid users
IS specialists
biologists
systems administrators
tool builders
infrequent
problem specific
service provider
bioinformaticians
bioinformatics tool builders
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An e-Science Workbench

• A lab book metaphor
• Strong provenance and personalisation thread.
• An integrating application
• Populated with an bio-examplar
• Andy Brass Cold Carp expression
• Macromolecular Structure Database

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Applications Framework
Sequence annotation
Cold Carp Gene Expression
MSD
App Demonstrator
Workbench Demonstrator
Application UTOPIA
Apps Builder (Talisman)
Workbench
Web Portal
Gateway API
myGrid Middleware Services
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IF-3 Proposal
Sequence annotation
Cold Carp Gene Expression
MSD
App Demonstrator
Workbench Demonstrator
Application UTOPIA
Apps Builder (Talisman)
Workbench
Web Portal
Gateway API
myGrid Middleware Services
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Issues (3) Architecture

• Difficult to get an architecture team going.
• Vested interests.
• Lack of app. focus.
• OGSA confusion.
• Architecture confusion.
• Neglect physical arch.
• Proposal build a demonstrator.
• Adopt the 41 architecture model.

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Challenges Architecture

• Use of service based architecture
• Is this enough?
• Risks stovepipe approach to cross-myGrid issues
• Need more emphasis on data model
• Resources, Services, Provenance,
• Need to address scalability across community,
  virtual organizations

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Challenges OGSA

• OGSA Grid meets Web Services
• Being define standardized by GGF
• Significant buy-in across community
• myGrid already uses Web Services
• How do we
• conform to OGSA?
• exploit OGSA?
• add value to OGSA?

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Challenges myGrid 1.0

• The myGrid proposal
• Phase 2 month 18
• First release of simple services interfaced to a
  set of biological sources.
• The first demonstration of the toolkits and
  applications toolkit trials.
• Formative assessment of the facilities using
  myGrid workshop, user meetings, and the ESNW
  Regional Centre to engage the user community.
• Third myGrid workshop.

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Challenges myGrid 1.0

• Month 18 October 2003
• myGrid iterations end of..
• January 2003
• May 2003
• September 2003 gtgtgt myGrid 0.1!

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Work Package Reports
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Work packages leaders

• WP1 fabric resources Alan Robinson, EBI
• WP2 architecture Luc Moreau,
  Southampton
• WP3 databases Paul Watson, Newcastle
  (norman paton)
• WP4 metadata Carole Goble, Manchester
  (robert stevens)
• WP5 workflow Brian Warboys, Manchester
  (matthew addis)
• WP6 toolkits Chris
  Greenhalgh, Nottingham
• WP7 information extraction Rob Gaizauskas,
  Sheffield
• WP8 management Nick Sharman, Manchester
  (carole goble)
• WP9, 10 and 11 proposed.

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WP1 Bio Services

• Leader Alan Robinson (EBI)
• Two RAs Martin Senger and Tom Oinn.
• Linking services with Grid Fabric (although this
  is done by other WP too).
• Data source preparation.
• Middleware wrapping, security and sources
  population.
• Globus deployment on hold.

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WP1 Progress Nov01-Oct02

• SOAPLAB to provide Web services for analysis
  applications EMBOSS. BLAST.
• Web services for archives MEDLINE/BQS. SRS.
  GadFly FlyBase.
• GO visualisation tool for IF-1.
• Talisman 1.4 for tool builders.
• Use cases for IF-1 IF-2 workflows.
• "Bio services" used by IF-1 IF-2.
• PR to bio community EBI/Hinxton
• Two Web services workshops.
• "What is myGrid Grid?" for non-CS.
• Participation in Users Group.
• Engaging with LION over SRS.
• caBIO of NCI, bioMOBY, I3C LSID. Participating
  in bibliographic objects effort.

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WP2 Architecture

• Leader Luc Moreau (Southampton) , Dave De Roure,
  Mike Luck
• Three Ras Simon Miles, Xiaojian Liu, (Vijay
  Dailani)
• Sub workpackages
• Service Directory WP4, WP6
• Notification Service WP3, WP5, WP6, WP11
• EJB Component Model all
• Security all
• Fault Tolerance WP11
• Issues? Risks?

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WP2 Service Directory

• A service directory offering personalised and
  customisable views of multiple existing service
  directories.
• myGrid 1.0 functionality Basic implementation of
  views (where views content is specified by
  queries over service directories or views).
• Next 4 Months View design and specification
  query language over UDDI-M
• Issue lack of Open Source UDDI who will deploy
  the demonstrator UDDI?
• Issue Link with I3C Registry.
• Link with WP4 Metadata.

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WP2 Notification Service

• A peer to peer adhoc network of OGSA compliant
  notification services offering end-to-end quality
  of service.
• MyGrid 1.0 functionality OGSA compliant
  notification service, offering elements of
  quality of service (e.g. max notification rate)
  and client feedback. Support for personalised
  views updates.
• Next 4 Months - Implementation of all the
  business logic to support OGSA interfaces (this
  includes push clients) - Syntactic compatibility
  with OGSA interface wherever technically feasible
  Framework
• Links with WP3 Info. management WP5 Workflow

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WP2 EJB based component model

• An EJB based component model that would allow us
  to deploy a service business logic as a myGrid
  service, where containers would provide default
  security, support for fault tolerance, provenance
  context, etc. Services could be exported as OGSA
  grid services, Web services or EJBs. A client
  side library would allow uniform interactions
  with any of these.
• myGrid 1.0 functionality Service deployment as
  OGSA, WS, EJB. Client API. Security container.
• Next 4 Months Client side library (with dynamic
  invocation) - Deployment of service (but no
  "added value" container provided).

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WP2 Security

• A cross-domain X509-certificate based
  authentication mechanism, and access control
  based on proxy certificates and/or role
  certificates. An API to generate non-repudiable
  provenance traces.
• myGrid 1.0 functionality Dummy implementation
  with placeholders for certificates Dummy
  implementation of authorisation based on string
  matching
• Next 4 Months (starting December) (still needs
  to be finalised)

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WP2 Fault tolerance

• A fault manager able to orchestrate, in
  collaboration with the enactment engine, the
  recovery of a workflow when faults are detected.
• myGrid 1.0 functionality to be determined.
• Next 4 Months N/A as progress needs to be made
  on the provenance personalisation front.

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WP3 Info Management

• Leader Paul Watson (Newcastle)
• Norman Paton, Alvaro Fernandes (Manchester)
• Three RAs Peter Li, ???, (Newcastle), Nedim
  Alpdemir (Manchester)
• Effective use of information
• locate, access, process, combine, share, alert
• Activities
• myGrid Information Repository
• Distributed Query Processing
• Views (personalisation)
• Notification

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Information Management Scope

• WP3 enables the scientist to make effective use
  of information
• locate, access, process, combine, share, alert
• Activities
• MyGrid Information Repository
• Distributed Query Processing
• Views
• Notification

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MyGrid Information Repository
External Bio Repositories
MyGrid Information Repository

Organisational
Analyse Data
Personal
Browse Annotate
Alert
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WP3 Progress Nov01-Oct02

• Initial MyGrid Information Repository deployed
• provenance
• data
• metadata
• workflows
• Supports XML relational
• Notification designed
• Distributed query processing prototype running on
  the Grid

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WP3 Plans

• myGrid 1.0 functionality
• Move to Open Grid Services Architecture
• distributed query processing (July)
• Next 4 Months
• requirements analysis (Nov) ? design (Dec) ?
  implementation
• Err more detail please!

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Distributed Query Processing

• select p.proteinId, Blast(p.sequence)
• from gimsprotein p, goproteinTerm t
• where
• t.termId S92 and
• p.proteinId t.proteinId
• Grid resources are acquired to run the operators
• can exploit parallelism

reduce
op_call (Blast)
exchange
hash_join (proteinId)
exchange
exchange
reduce
reduce
table_scan termIDS92 (goproteinTerm)
table_scan (gimsprotein)
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WP4 Metadata Ontologies

• Leader Carole Goble (Manchester)
• Robert Stevens (Manchester)
• One and a half RAs Phil Lord (since April 02),
• Chris Wroe, (Angus Roberts)
• The metadata requirements, services and content
  needed for publication, registration, discovery,
  matchmaking, deregistration of services
• Activities
• 1. Ontology languages services
• 2. Resource discovery WP2, WP6
• 3. Annotation with metadata WP3, WP6
• RISKS too little resource!

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WP4 Progress Jan02-Oct02

• An ontology of services for myGrid 0.0 and 0.1 in
  DAMLOIL (to be OWL). Available on web and
  accepted for publication.
• A survey of metadata requirements (not yet
  consolidated)
• Mapping service between Web Services and Ontology
  Server
• Simple service finding tool, service matcher
• SOAP Ontology server for OWL
• User requirements and scenario building
• Build environment
• DAMLOIL training for other e-Science projects
• I3C and BioMOBY tracking and participation

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WP4 Plans

• myGrid 0.1 functionality
• Integrated service publication (with WP2).
• Service discovery and publication by signature,
  types as well as ontology concepts
• OGSA compliance.
• Metadata requirements is an ontology really
  required for service discovery?
• Simple provenance annotation scheme based on
  COHSE.
• Complete provenance model.

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WP4 Plans

• Next 4 months
• Integrated service registration (with WP2).
• Types and ontologies reconciliation.
• myGrid object model and BioMOBY objects
• Extension of ontology for demonstrator
• User requirements for Cold Carp demonstrator
• Begin a provenance model.

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WP4 Issues

• Focused on describing services using ontologies.
• Information model needs attention.
• Havent looked at metadata other than ontologies.
• Too few people.

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Suite
Specialises. All concepts are subclassed from
those in the more general ontology.
Contributes concepts to form definitions.
Upper level ontology
Publishing ontology
Informatics ontology
Molecularbiology ontology
Organisationontology
Task ontology
Bioinformatics ontology
Web serviceontology
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1. User selects values from a drop down list to
create a property based description of their
required service. Values are constrained to
provide only sensible alternatives.
2. Once the user has entered a partial
description they submit it for matching. The
results are displayed below.
3. The user adds the operation to the growing
workflow.
4. The workflow specification is complete and
ready to match against those in the workflow
repository.
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Client framework
myGrid 0.0
Portal
Repository Client
Ontology Client
Workflow Client
Personal Repository
Workflow Repository
(Meta Data) Ontology Server
DAMLOIL Reasoner (FaCT)
(Meta Data) Service Type Directory
Workflow enactment
Matcher and Ranker
Service instance directory
Bioinformatics services
REGISTRY
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Uses of ontology

• Labelling data items in databases.
• Semantic typing for controlling inputs and
  outputs of workflows
• Use by distributed query processing.
• Workflow, database classification.
• Linking browsing XML-based components
• COHSE
• Soft build of portals.
• Link with the Life Science Identifier (I3C)
• BioMOBY Central service classification

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(some) Registry Issues

• Find services based on name, signature, types, a
  word (not just using the ontology).
• Registry management weeding, authorisation,
  decommissioning.
• Publishing of services. Keeping their
  descriptions up to date and faithful.
• Alternative descriptions of services.
• Staged descriptions.
• Maintenance and evolution of the ontology
• Multiple registries personal, local, enterprise

84
WP5 Workflow

• Leader Brian Warboys (Manchester), Matthew Addis
  (IT Innovation, Southampton)
• TWO RAs Mark Greenwood (Manchester), Darren
  Marvin, Justin Ferris (IT Innovation, shared)
• Activities
• 1. Workflow design and discovery WP4
• 2. Workflow enactment WP2
• Risk split over 2 sites

85
WP5 Progress Apr02-Oct02

• Post pre-prototype documentation, testing and
  support for demos
• Workflows for 0.1 use cases - both based on
  pre-prototype and EMBOSS/SOAPLab services
• Metadata for finding workflows and finding
  services for workflows
• Robust enactment engine using web service
  standards. WSDL, UDDI, WSFL
• Deployable to standard Tomcat / Axis container
  combination
• EMBOSS Workflow
• Combined two concurrent application flows
• Executing seven applications
• Forty five web service invocations
• Simple Provenance
• Date and time, Actual services used, Intermediate
  data

86
WP5 Plans

• myGrid 0.1 functionality
• Sample workflows for publicly available myGrid
• Workflow lifecycle resolution, personalisation,
  annotation, composition and development
• Workflow requirements in the context of an
  application (e.g. relationship to MATLAB,
  Talisman, )
• Provenance - are we generating the right workflow
  provenance, and how could this be used?
• Support for Secure Invocations using HTTPS and
  SOAP Digital Signatures
• Data staging for performance
• Greater control of provenance
• Personalisation
• Plug-ins to support data processing, User
  interaction during workflows, Integration with
  other tools

87
WP5 Issues

• Contacts
• no response from Frank Leymann of IBM
• after an initial positive meeting
• relationship with technology providing partners?
• When to move from WSFL to BPEL4WS (if at all)
• Technology tracking BioMOBY, OMG LAB, BPEL4WS,
  WSCI, LSID, DAML-S, OGSA/OGSI, ...
• How to manage our resources effectively - what
  alliances should we build (e.g DiscoveryNet)

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WP6 e-Science layer

• Leader Chris Greenhalgh (Nottingham)
• TWO people at Nottingham.
• Milena Radenkovic
• Kevin Glover
• Responsible for portal, workbench, collaboration
  environments and application development user
  requirements
• Propose splitting off User Requirements and
  possibly Application building.

89
WP6 e-Science layerApr02-Oct02

• Extensive discussions with other WPs, esp.
  ontology and metadata
• Major re-factoring of pre-prototype web portal to
  support multiple types of client
• Common Gateway web service/API
• Re-factored web portal as gateway client
• Sample command line clients
• Gateway job abstraction transparent direct
  invocation of web services as well as workflows
• Common build/deployment environment

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WP6 Plans

• myGrid 1.0 functionality
• Gateway personalisation enhanced user agent,
  simple workflow customisation, presentation
• Gateway provenance multiple metadata sources,
  activity logging, template workflow generation
• Direct use of ontology service/facilities
• Enhanced web portal
• Personalisation, arbitrary metadata, helper
  applications
• Other sample clients command line, GUI
  application?.
• Next 4 Months More generic gateway web
  service/API
• Enhanced web portal
• New implementation technology??
• Structured browsing, notification, complex
  operations
• Resume requirements gathering on collaboration
  support

91
WP7 Text Services

• Leader Rob Gaizauskas (Sheffield)
• TWO RAs Neil Davis ???
• Aim to provide novel text access capabilities to
  biological science researchers
• Data will be mined/extracted from text
  collections
• Entity identification (e.g. proteins, residues,
  species, etc.)
• Attribute extraction (e.g. residue function)
• Relation extraction (e.g. interactions, pathways)
• Extracted data will be provided
• Via the MyGrid portal and Via web services

92
WP7 Starting Point in myGrid

• Prototype PASTA (Protein Active Site Template
  Acquisition) System
• Terminology recognition/classification (e.g.
  proteins, genes, species, )
• Attribute extraction (e.g. residue function)
• Relation extraction (e.g. in_protein(residue,
  protein)
• Trialed on small Medline corpora (2000 texts)
• PASTAWeb browser-based interface to extraction
  results

93
WP7 Progress to Date (1)

• Relational database server for PASTA results
• Previously, extracted data held in flat text
  files indexed via Perl hashes non-scalable
  limited querying
• Relational tables for extracted results have been
  defined, implemented and tested
• Mapping procedures to map PASTA output into RDMS
• Web services (SOAP) interface to PASTA results
  RDMS
• Revised web interface to PASTA results
• Using new RDMS
• Taking into account feedback from biologists

94
WP7 Progress to Date (2)

• Resource acquisition
• UMLS and GO acquired and installed
• Negotiated full copy of MEDLINE access rights
  for MyGrid partners via web services to arrive
  December 02
• Baseline PASTA system (nearly) integrated in
  GATE-II text engineering architecture

95
WP7 Activities Underway

• Work begun on significant revision/extension to
  terminology acquisition/management/recognition
• Redesigning lexical databases to include
  synonym/term variant information
• Investigating automatic term acquisition
  algorithms
• The views of biological scientists being sought
• To ensure information being extracted is useful
  and relevant
• To extend system to new domains
• To refine interface/searching capabilities over
  extracted data
• To elicit novel text-related requirements

96
WP7 Technical Issues

• Text extraction is currently a slow procedure
  not feasible in real-time
• Re-indexing the data post text extraction
  increases it by roughly a factor of 10
• It is proposed to pre-process all (or at least a
  sizeable fraction) of MEDLINE which will be
  computationally very intensive

97
WP7 Text Services and myGrid

• How text services will be integrated in myGrid
  still not clear
• Text services could be integrated at the simplest
  level as another web service
• A more ambitious idea is an ambient text system
  where potential search terms are gleaned from the
  workflow to silently provide a library of useful
  texts on the users desktop

98
Extra Work Packages

• WP9 User Requirements
• Robert Stevens, Anil Wipat, Peter Li, EBI, Phil
  Lord
• Scenarios, interviews, web pages
• Issue getting GSK/AZ/Merck requirements
• Issue getting user requirements into the other
  work packages
• Solution IF-3 demonstrator.

99
Extra Work Packages

• WP10 Application
• Part of WP6, but WP6 doesnt have any biologists.
  
• Suggestion New WP responsible for producing the
  application on top of the workbench.
• IF-3 demonstrator for Cold Carp.

100
Extra Work Packages

• W11 Provenance
• Hidden in WP4 but pervades the whole of myGrid
• Provenance model
• Simple provenance demonstrators using annotation.

101
Top 10 thoughts

• Application driven by use cases.
• Open Source.
• Data object types, APIs, protocols, ontologies
  have longer life span that s/w.
• Components are useful dont have to buy into
  the whole shooting match.
• Dont reinvent the wheel.
• Get others to build services / applications.
• Lower barriers of entry.
• Keep it simple.
• Its distributed and global.
• One solution wont work.