A FRAMEWORK BASED ON WEB SERVICES ORCHESTRATION FOR BIOINFORMATICS WORKFLOW MANAGEMENT

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A FRAMEWORK BASED ON WEB SERVICES ORCHESTRATION
FOR BIOINFORMATICS WORKFLOW MANAGEMENT

• Laboratory for Bioinformatics (LBI), Institute of
  Computing (IC) - UNICAMP

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Topics

• Motivation
• Goals
• Related issues
• The framework
• Methodology
• Conclusions
• Future work

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Motivation

• Genome assembly and annotation pipeline

human validation
assembly
assembly OK
annotation
contigs
reads
incremental assembly
new reads generation
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Motivation

• The growth of bioinformatics activities
• Data
• Services
• Data and services dont 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 W3Cwebservices

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Related issues

• Workflows
• Workflows represent a set of activities to be
  executed, their interdependencies relations,
  inputs and outputs.

activity1
input data1
activity3
output data
activity2
input data2
input data3
activity4
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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
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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

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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.b
r Institute of Computation (IC)
www.ic.unicamp.br University of Campinas
(UNICAMP) www.unicamp.br Luciano Antonio
Digiampietri luciano_at_ic.unicamp.br