myGrid

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myGrid

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

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myGrid

• UK e-Science Grid programme pilot (EPSRC)
• Generic middleware
• Bioinformatics Genomics setting
• 1st October 2001 -- 31st March 2005
• (36 months funded in 42 execution period)
• 16 full-time researchers/developers

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myGrid Partners
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e-Science Biology

• Biology is a multi-faceted increasingly
  multi-disciplinary science
• Bioinformatics is an e-Science
• Discovery is done in silico on results obtained
  from experiments using a number of analysis
  data resources
• Molecular biology genomics are our particular
  focus

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Drug Discovery
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Bioinformatics Genomics

• Large amounts of data
• Highly heterogeneous
• Data types
• Data forms
• Community
• Highly complex and inter-related
• Highly volatile

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Bioinformatics Data

• Descriptive as well as numeric
• Literature
• Analogy/ knowledge-based

Text Extraction
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Bioinformatics Analysis

• Different algorithms
• BLAST, FASTA, pSW
• Different implementations
• WU-BLAST, NCBI-BLAST
• Different service providers
• NCBI, EBI, DDBJ

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In silico experimentation
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In silico experimentation

• Discovery, interoperation, fusion, sharing
• Process is as important as outcome
• Science is dynamic change happens
• Provenance and history
• Scientific discovery is personal global

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myGrid aims

• Active support of scientific practice in biology
• A e-Scientist-centric workbench
• 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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A Desiderata (cf. Grid)
A p p l i c a t i o n s

• Software development toolkits
• Standard protocols, services APIs
• A modular bag of technologies
• Enable incremental development of grid-enabled
  tools and applications
• Reference implementations
• Learn through deployment and applications
• Open source

Diverse global services
Core services
Local OS
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Approach
myGrid Stack
Personalisation
Metadata
Interoperation layer
I.E
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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
• Protocols and service descriptions
• myGrid-in-a-Box developers kit
• Re-purposing DAS, AppLab and OpenBSA
• Integrating ISYS GlaxoSmithKline platforms

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myGrid tech outcomes

• Services, service descriptions (ontologies),
  message protocols APIs
• Database access from the Grid
• Process enactment on the Grid
• Personalisation services
• Provenance services
• Metadata services DAMLOIL, OWL, RDF(S)
• Laying the foundations for Agent Services
• Grid Web Services Semantic Web

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Converging technologies
Grid Computing
Globus, Sun Grid Engine, Condor, DS (Jini, Corba)
Agents
Web Technologies
ACL, methodology
SOAP, WSDL, UDDI, DAMLOIL, OWL, RDF(S) WSFL
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myGrid Phases

• Evolution
• Incremental development rollout

6 months
Pre-prototype
12 months
Architecture
Simple services
24 months
Early toolkit trials
33 months
Extended services
Application trials

• Versions of myGrid
• Varying degrees of functionality

Developers toolkit
Release
The community commercial partners
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Pre-prototype April 2002

• User cases, Architecture Practical experiments
• Identify the different components (services) and
  their interactions
• Define common interfaces for supporting security,
  fault-tolerance, naming, etc
• Implementation showing the use of workflows,
  notifications, dynamic discovery, personalisation
• Define coding standards and repositories
  organisation

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myGrid Services
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Other Developments
Open Source Open Bio Foundation, BioPerl,
BioJava, 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.
MOBY
Distributed Computing Environments CORBA, RMI,
JavaOne
Web Services XML, SOAP, WSDL, UDDI
GRID Globus/SRB/Condor
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myGrid Summary

• myGrid aims to develop infrastructure middleware
  for an e-Biologists workbench
• The setting is bioinformatics but the results are
  intended to be generally applicable to e-Science
• A mix of standard, vanguard and bleed edge
  technologies, advanced development and (some)
  research
• Academic commercial partnership
• myGrid project is timely reflects a community
  desire to collaborate, or die

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myGrid

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

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• Presented at InfoTechPharma 2002
• London,UK
• 13th-15th February 2002