Paths to a Reference Architecture for an Open Bio Grid

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Paths to a Reference Architecture for an Open Bio
Grid

• Rick Stevens

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Determining Requirements for the Open BioGrid

• Model for Community Involvement
• MPEG-7 process
• Call for proposals
• Technologies
• Architectures
• Interfaces and APIs
• Requirements Collection
• Input for an eventual RFP
• Scope the components of a Standard
• Related to existing Standards

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Open BioGrid Architecture

• Core database(s)
• Extensible core schemas
• Object model support
• Language independence
• Distributed curation environment
• High-performance interfaces
• Peer-to-Peer synchronization/updates

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Principal Partners and Stakeholders

• Biology and Biomedical Communities
• Computer Science Community
• Industry
• User community
• Technology providers
• Agencies (NIH, NSF, DOE, etc.)
• Standards Organizations
• Professional Societies

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Proposed Process

• Start with the LSG Survey
• Create a database/inventory of stakeholders
• Issue a RFI (request for information)
• Requirements for reference an architecture
• 3-4 meetings resulting in a RFP document
• RFP announcement
• 90 days (proposals tech/arch/interface)
• Evaluation of proposals ? criteria/reviewers
• Draft standard open architecture LSG
• 3-4 meetings digest-negotiation/compromise
• Chapters in a standards document
• Reference Implementation(s)
• Interoperability
• Publication open source

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Open Issues

• Determining scope of The Standard
• Core team
• Fast track (meeting every 6 weeks (2-3 days))
• Buy-in from stakeholders
• Sponsorship
• Open Source (license issues)
• Time Frame for completion

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Scope of a Proposed Standard

• SW platform for biological data integration
• Distributed curation with versioning
• Support rapid update cycle
• Conduits for synchronization
• major community databases
• Peer-to-peer servers (instances)
• Open architecture
• Open source
• DB independent
• Language independent
• Extensible APIs
• Grid/Web services
• Flexible data sharing
• Publish/subsciption model of data sharing

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Scope II

• Supports multiple views and proprietary data
• Private data integrated with public data
• Public data
• Interfaces
• Transactions
• High-throughput data paths, bulk transfers
• Simulation/DB connections
• Import/export APIs
• Scalability
• Security
• Portability

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Scalability Goals

• Millions of genes and gene products
• GBs-TBs of annotation per gene
• 100,000s of genomes
• Many close variants
• Millions of phenomes
• Instances of k
• Thousands of cooperating sites
• Update Channels (pub/sub)
• Thousands (some private, some open)

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Model III

• Kernel server
• Services registry
• Computation on the DB
• External representation of objects
• Security
• Versioning
• Transaction support
• Update (local) support
• Schema extensions
• Import/Export engine
• Portable formats
• Interfaces to external sources/sinks
• Synchronization engine
• Publish and subscription services
• Update channels

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Thoughts on a Architectural Model
Web Portal/Presentation
External DBs

SE
SE
I/E
Kernel
Plug-Ins
DB
Local apps
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Model II

• OLSG Services
• Directory services
• Namespace/ontology services
• Brokering
• Channel Services
• Computing services
• Grid service
• Security
• Transport
• Etc.