A FRAMEWORK BASED ON WEB SERVICES ORCHESTRATION FOR BIOINFORMATICS WORKFLOW MANAGEMENT Laboratory...
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A FRAMEWORK BASED ON WEB SERVICES ORCHESTRATION FOR BIOINFORMATICS WORKFLOW
MANAGEMENT
Laboratory for Bioinformatics (LBI), Institute of Computing (IC) - UNICAMP
Luciano Antonio Digiampietri
João Carlos Setubal
Cláudia Bauzer Medeiros
PhD Student:
Advisor:
Co-advisor:
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Motivation
Genome assembly and annotation pipeline
assemblyreads contigs human
validation
incrementalassembly
new reads generation
assembly OK annotation
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Motivation
The growth of bioinformatics activities– Data– Services
Data and services don’t use public standards
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Goals
Specification and development of a framework that allows:– Data integration;– Service integration;– Modeling of complex tasks as workflows;– Coordination of workflow execution
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This talk
Work in progress– no results yet
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Overview: user interaction
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Related issues
Web services– “a software application identified by a URI,
whose interfaces and bindings are capable of being defined, described, and discovered as XML artifacts” [W3C:webservices]
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Related issues
Workflows– Workflows represent a set of activities
to be executed, their interdependencies relations, inputs and outputs.
activity1
activity2
activity3input data1
input data2
input data3
activity4
output data
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Related issues
Service coordination– Service orchestration is a centralized
mechanism that describes how diverse services can interact. This interaction includes message exchange, business logic and order of execution;
– We are using PBEL4WS as the specification language for service orchestration
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Related issues
Bioinformatics tools and data– Selection of basic bioinformatics tools for
genomic assembly and annotation;– Selection of some important data sources;– Use of tools and data ontology.
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Related issues
Example of part of a tool ontology:
Alignment service
Local Alignment Global Alignment
Heuristic Alignment
Non-Heuristic Alignment
Non-Heuristic Alignment
Heuristic Alignment
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The framework
Workflow management
Service layer
Service discovery Service request
application1 application2
Workflow discovery
Workflow repository
Workflow design Workflow engine
User interface
Service Catalog application3
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The framework
Service layer – bioinformatics basic Web services
• assembly,• matching,• consensus, • etc
Service catalog layer – stores Web services'
• syntactical description;• semantical description;• URI.
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The framework
Service discovery – search by:
• functionality,• context,• syntax.
Service request layer – management of each Web service solicitation:
• Sending input data;• Receiving results;• Detecting service failure.
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The framework
Workflow engine layer – controls execution of all workflow tasks, via orchestration. – The main functions:
• interpretation of the process (or task) definition,• creation and management of process instances,• navigation between activities,• supervisory functions.
Workflow design layer – supports workflow specification and edition. – The facilities provided are:
• graphical interface for workflow edition,• service list,• interface description of selected services,• syntactical check of workflow.
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Methodology
A bottom-up approach:
Service1
Service2
Service3
Workflow design and
engine
Workflow management
Service discovery
and requisition
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Methodology
Services– bioinformatics basic services
• specification• development.
– metadata types definition Service discovery
– development of techniques for service discovery and request using syntactic and semantic search mechanisms.
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Methodology
Workflow– specification and development of methods
for workflow design and execution;– Design of workflows is being done using
WOODS*; – Specification and implementation of an
orchestration mechanism.
*Seffino, L.A., Medeiros, C.B., Rocha, J.V.R., Yi, B.:WOODS- a spatial decision support system based on workflows. Decision Support Systems 27 (1999) 105-123
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Conclusions
The main contribution is the framework itself:– It allows multi-institutional cooperation,
sharing:• Data• Tools• Workflows
– It can be the interface among various kinds of users of different research centers
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Conclusions
Other contributions lie in– Scientific workflows specification and
publishing (using Web services as basic units);
– Semantic specification of bioinformatics tasks;
– Definition of a generic methodology for data and tools integration.
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Thank you!Laboratory for Bioinformatics www.lbi.ic.unicamp.br
Institute of Computation (IC) www.ic.unicamp.br
University of Campinas (UNICAMP) www.unicamp.br
Luciano Antonio Digiampietri [email protected]