SYNERGY Framework and Architecture OVERVIEW

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SYNERGY Framework and ArchitectureOVERVIEW
Scott Markel 20 May 1999 lifesci/99-05-05
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What is CORBA?

• A specification for a vendor neutral software
  architecture that is
• Distributed
• Object-oriented
• Language Independent
• Hardware neutral

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Using CORBA for Bioinformatics

• IDL for data types
• DNA sequences
• Sequence Assemblies
• IDL for analyses
• Get restriction map for a given sequence
• Get PCR primers for a given sequence
• IDL for databases
• Get GenBank entry by accession number
• Your relational, object or flat file data here!

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Using CORBA to Find ORFs
ORFFinder
ORFService
DNA
Client
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Using CORBA to Find ORFs
Persistence
ORFFinder
ORFService
DNA
Client
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Using CORBA to Find ORFs
Persistence
ORFFinder
ORFService
DNA
DNA
Project Manager
Client
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Using CORBA to Find ORFs and Perform BLAST
Persistence
Persistence
BLAST
ORFFinder
ORFService
BLAST Service
DNA
DNA
Analysis Manager
Project Manager
Client
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Using CORBA to Find ORFs and Perform BLAST
Persistence
Persistence
BLAST
ORFFinder
ORFService
BLAST Service
BLAST-ORF Service
DNA
DNA
Analysis Manager
Project Manager
Client
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Developing a Framework

• Make the framework ignorant of data types and
  services.
• Allow objects and services to rendezvous and
  collaborate without compile-time knowledge.
• Facilitate real-time evolution and upgrade of
  objects and services.
• Facilitate re-use of components through
  delegation.

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Developing a Framework

• CORBA provides part of the solution
• The Interface Repository allows introspection of
  interface details.
• The Naming and Trading Services provide a
  flexible model for service registration and
  location.
• Collection and Query services allow manipulation
  of collections of objects and querying of
  collections.
• Event service provides distributed event model.

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Developing a Framework

• Additional elements enhance the solution
• The GenericService interface
• meta-data describing the input and output
• execution interface
• An AnalysisManager and ServiceFinder
• uses GenericService meta-data
• collaboration between objects and services
• A FactoryFinder and GenericItem interface
• manage object creation and life cycle

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Developing a Framework

• Additional elements enhance the solution
• Distributed Synergy
• Federated services support multiple node
  installations and easy addition of new nodes.
• Globally unique object identifiers
• Externalization of single objects and graphs of
  objects
• Implementation of CosExternalization
• CORBA, XML or custom formats supported

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Why Synergy?

• Pattern-based framework facilitates integration
  of new components
• Technologies that can effectively leverage a wide
  variety of compute resources
• Fully distributed architecture that is designed
  to leverage existing data and systems
• Emerging OMG LSR standards
• Outsourcing and consulting support

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Synergy SDK

• Work in progress
• Java-based SYNERGY development
• Java Server Framework simplifies development of
  Java based services.
• IDL and stubs generated from the IDL
• JavaDoc reference documentation (tutorials and
  example code provided to be used as templates)
• Cookbook tutorials using example code

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SDK Future Direction

• Easy integration of algorithms into the SYNERGY
  framework
• Plug and play integration of databases into
  SYNERGY
• User-defined pipelines
• Integration of component technology
• JFC and JavaBeans
• CORBA Components/Enterprise JavaBeans