Architectural issues in a

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myGrid

• Architectural issues in a
• bioinformatics Grid
• http//www.mygrid.org.uk
• Luc Moreau,
• University of Southampton, UK

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Overview

• Bioinformatics background
• myGrid facts
• Service oriented architecture
• Architectural issues
• Notification service
• Grid component model
• Service directory
• Conclusions

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Bioinformatics Genomics

• Large amounts of data
• Highly heterogeneous
• Data types
• Data forms
• Community
• Highly complex and inter-related
• 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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The Human Genome Project

• Many genes will be linked with diseases
• Cancer
• HIV
• Parkinsons
• Asthma
• Malaria
• Autoimmune (arthritis)
• Cardiovascular
• Antibacterial antifungal

• The HGP will make available potentially thousands
  of targets for
• Understanding biology genetics
• Drug discovery
• Diagnostics

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Drug Discovery
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In silico experimentation

• Discovery of resources and tools, staging of
  operations, sharing of results
• Process is as important as outcome
• Science is dynamic change happens
• Scientific discovery is personal global
• Provenance and history

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Overview

• Bioinformatics background
• myGrid facts
• Service oriented architecture
• Architectural issues
• Notification service
• Grid component model
• Service directory
• Conclusion

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myGrid

• EPSRC funded pilot project
• Generic middleware within application setting
• 36 month in 42 month performance period
• Start 1st October
• 16 full-time post docs altogether
• 6 DTA studenships
• 1 technical project manager
• 1 system manager
• 1 secretarial post

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myGrid consortium

• Scientific Team
• Biologists and Bioinformaticians
• 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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myGrid outcomes

• e-Scientists
• Bioinformatics demonstrator (on cold carp)
• Developers
• myGrid-in-a-Box developers kit
• Integrating some existing bioinformatics tools
  with myGrid

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Overview

• Bioinformatics background
• myGrid facts
• Service oriented architecture
• Architectural issues
• Notification service
• Grid component model
• Service directory
• Conclusions

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Overview

• Bioinformatics background
• myGrid facts
• Service oriented architecture
• Architectural issues
• Notification service
• Grid component model
• Service directory
• Conclusions

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Architectural Issues
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Architectural Issues

• Notification service

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Vision

• Asynchronous delivery and persistence of messages
• Topics can be created and discovered on the fly
• Subscribers can subscribe to topics, publishers
  can publish messages on a given topic
• Peer to peer network of notification services
• Topology can be re-organized to enhance
  reliability
• Subscribers and publishers can negotiate over QoS

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A notification service instance
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Federated notification services

• Strong communication links between hubs
• Efficient data replication
• Simple notification routing

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QoS Negotiation Protocol
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Current status

• Push and pull messaging
• Topic,message and publisher filter
• WSDL interface
• Workflow interaction
• Integration with mySQL, openJMS, tomcat and Axis
• Federated service (undergraduate project)
• QoS negotiation (PhD work underway)
• OGSA compliance

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Experimentation

• Windows and Unix platforms with Tomcat 4.0.5,
  Axis beta 3.0, OpenJMS 0.7.2 and mySQL 3.23.51
• Aggregation test with 500 topics, 2,000
  subscribers, 2,000 publishers and 10,000
  registered subscriptions, 10,000 notifications
• 72 hours non-stop subscribing/publishing with the
  above populations

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Architectural Issues

• Notification service

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Architectural Issues

• Notification service
• Grid component model

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Grid Component Model

• The myGrid framework is a component model for
  flexible, simple and future-proof deployment and
  use of services on the Grid.

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Problems Addressed

• For service developers and deployers
• Ease of development of sophisticated services by
  separation of concerns and re-use of third party
  functionality.
• Consistent distribution of functionality over a
  set of services, e.g. access control, support for
  fault-tolerance.
• Application of solutions to the above to services
  deployed using technologies such as OGSA Grid
  Services, Web Services and Enterprise JavaBeans.

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Problems Addressed

• For service clients
• Development of service clients that are not
  limited by the range of standards known at
  deployment time.
• Control over how service operations are invoked,
  so that they can make use of the most suitable
  protocols supported by a service.
• Provision of a standard client interface hiding
  the differences in deployment philosophy that
  each middleware technology brings.
• Application of solutions to the above to services
  deployed using technologies such as OGSA Grid
  Services, Web Services and Enterprise JavaBeans.

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Nested Component Model
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Framework
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Current Status

• Startpoints for Web Services
• Deployment within nested containers
• Facades for exposing EJBs as Web Services
• Performance tests

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Current Implementation
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Current Work

• Automated deployment in nested containers
• Definition of containers for deployment-time
  configuration
• Using containers to provide minimal functionality
  of OGSA Grid Services
• Startpoints for EJBs, Grid Services

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Experimentation

• Our experiments have shown that nesting in our
  containers is not costly compared to method
  invocation and nested inner classes
• The cost of calling EJBs via the Web Service
  façade comes mostly from the use of SOAP, and the
  consequential requirement for conversion to/from
  objects

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Architectural Issues

• Notification service
• Grid component model

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Architectural Issues

• Notification service
• Grid component model
• Service directory

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Service Directory Views

• Multiple service directories will co-exist (IBM,
  Microsoft, EBI, local institutions)
• Need to attach metadata to service directory
  entries
• Metadata is personal to the scientist trust,
  perceived QoS, ontological description
• Need for a mechanism to allow scientists to add
  their metadata and to make it available to other
  users as a regular service directory.

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Views status

• Currently in design phase
• Use cases in the process of being finalized
• Preliminary specification of interfaces
• More work is needed on policy languages
• Design to be finalized by end of January
• First prototype of core functionality 4 months
  later

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Overview

• Bioinformatics background
• myGrid facts
• Service oriented architecture
• Architectural issues
• Notification service
• Grid component model
• Service directory
• Conclusions

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Conclusions

• More architectural issues being addressed
• Security (GSI, RBAC), but where is the community
  going?
• Fault tolerance

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• Workflow enactment
• WSFL compatible enactment engine
• Support for fault tolerance, checkpointing,
  migration
• Editor

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Conclusions

• 4 months development cycle with integration
  fest
• Our roadmap is based on a layered organisation of
  functionality

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myGrid in Southampton

• Luc Moreau, Michael Luck, David DeRoure
• Terry Payne, Keith Decker
• Simon Miles, Juri Papay, John Dickman, Xiaojian
  Liu, Claudia di Napoli, Vijay Dialani, Richard
  Lawley

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www.mygrid.org.uk
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