myGrid

1
myGrid

• Personalised
• extensible environments for
• data-intensive
• in silico experiments in biology
• http//www.mygrid.org.uk
• Professor Carole Goble,
• University of Manchester,UK

2
Welcome myGrid kick-off

• Objectives
• Team building
• Technology and skills sharing
• Work towards the myGrid pre-prototype
• Use cases
• Strawman architecture
• Work plan setting

3
myGrid

• EPSRC funded pilot project
• Generic middleware within application setting
• 36 month in 42 month performance period
• Start 1st October
• 1 full-time funded individual
• 16 full-time post docs altogether
• 1 secretarial post
• 1 technical project manager (advertised)
• 1 system manager (to be advertised)

4
myGrid partners
m
Visitors EPSRC, Open University KMI, Millennium
Pharmaceuticals
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myGrid consortium

• Scientific Team
• Biologists and Power Biologists
• GSK, AZ, Merck KGaA, Manchester, EBI
• Technical Team
• Manchester, Southampton, Newcastle, Sheffield,
  EBI, Nottingham
• IBM, SUN
• GeneticXchange
• Network Inference, Epistemics Ltd

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In silico experimentation

• Discovery, interoperation, fusion, sharing
• Process is as important as outcome
• Science is dynamic change happens
• Scientific discovery is personal global
• Provenance
• Versatile, people-powered

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e-Science viewpoint
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myGrid e-Science objectives

• Active support of scientific practice in biology
• Straightforward discovery, interoperation,
  sharing
• information AND processes AND best practice
• Improving quality of both experiments and data
• provenance through information lt-gt process
  linkage
• propagating change
• Individual creativity collaborative working
• personalisation
• Cottage Industry to an Industrial Scale

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myGrid operational environment
Open Source Open Bioinformatics Foundation, Bio
Consortium Expertise View propagation,
reasoning, workflow
(DeFacto) Standards OMG LSR, I3C, MGED, Gene
Ontology
Semantic Web RDF, RDFS, DAMLOIL
Bioinformatics integration platforms DAS,
OpenBSA, ISYS, OpenMMS, Kleisli, Ensembl, AppLab,
SRS, BioNavigator, DiscoveryLink, GX TAMBIS
Distributed Computing Environments CORBA, RMI,
Jini, JXTA, DCOM
Web Services XML, SOAP, WSDL, UDDI
GRID Globus/SRB/Condor
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Approach
myGrid stack
Personalisation
Metadata
Interoperation protocols descriptions
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1. Resource management 2. Middleware technologies
incl. Globus 3. Incorporating existing resources
Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Communication fabric
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1. Integration distributed queries 2. View
management3. Personal repositories
Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Data mgt
Process mgt
Context mgt
Communication fabric
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1. Process description storage 2. Process
enactment 3. Process personalisation
Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Data mgt
Process mgt
Context mgt
Communication fabric
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• Security Confidentiality
• Provenance Attribution
• Versioning

Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Data mgt
Process mgt
Context mgt
Communication fabric
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1. Ontology languages services 2. Resource
service descriptions 3. Annotation with metadata
Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Communication fabric
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1. Agent based communication abstraction 2.
Software engineering paradigm for extensible
distributed services 3. Foundation for
architectural evolution
Dynamically Composable Cooperating Services
Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Communication fabric
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• Personal data repositories
• Personal processes
• Models of sharing

Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Communication fabric
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1. User interfaces visualisation 2.
Collaboration environments 3. Environment
development 4. User-centred application
development
Shared Virtual Environments for Collaboration
Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Communication fabric
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1. Specialist process information extraction
Applications
Toolkits
Personalisation
Metadata
Interoperation layer
Communication fabric
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myGrid outcomes

• e-Scientists
• Environment built on toolkits for service access,
  personalisation community
• 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 generic technologies

• Database access from the Grid
• Process enactment on the Grid
• Personalisation services
• Metadata services
• Laying the foundations for Agent Services
• Ontologies, Protocols APIs
• Grid Services Semantic Web

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myGrid phased development
6 months
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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Phase 1 Getting our act together
Technology Induction
User Requirements Chris Greenhalgh
Architecture Mark Greenwood
Specifying the MyGrid versions
Pre-Prototype April 2002
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myGrid work package leaders

• WP1 fabric resources Alan Robinson, EBI
• WP2 architecture Luc Moreau, Southampton
• WP3 databases Paul Watson, Newcastle (norman
  paton)
• WP4 metadata Carole Goble, Manchester
• WP5 workflow Brian Warboys, Manchester
  (matthew addis)
• WP6 toolkits Chris Greenhalgh, Nottingham
• WP7 information extraction Rob Gaizauskas,
  Sheffield
• WP8 management Carole Goble Brian Warboys

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myGrid project management
Project director
Management team
Steering Committee
Support Team
Technical manager
Administrator
Sys Prog
WP Managers



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myGrid desiderata

• Keep it simple
• Its the linking of the pieces, not the pieces
  themselves
• Evolution and incremental development
• Standardsand emerging dominant technologies are
  to be embraced not ignored
• This is not a green field site
• This is a platform not an application
• This is advanced development not research
• In 3.5 years time the community will have to
  support this.

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myGrid

• Personalised
• extensible environments for
• data-intensive
• in silico experiments in biology
• http//www.mygrid.org.uk
• Professor Carole Goble,
• University of Manchester,UK

29
Questions for working groups

• What functionality should the pre-prototype have?
• What should the services of the pre-prototype be?
• What architecture language should we adopt?
• Extent of person interaction
• Provision for provenance, security, change mgt,
  personalisation
• What technologies/systems are available and
  suitable/adoptable?
• Web Services for pre-prototype?
• How to get to the pre-prototype
• Commercial/academic interface?

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• myGrid Kick-off meeting introduction
• 5th-7th November, 2001
• Manchester, UK