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:

Topics Motivation Goals Related issues The framework Methodology Conclusions Future work

Motivation Genome assembly and annotation pipeline assembly reads contigs human validation incremental assembly new reads generation assembly OK annotation

Motivation The growth of bioinformatics activities –Data –Services Data and services don’t use public standards

Goals Specification and development of a framework that allows: –Data integration; –Service integration; –Modeling of complex tasks as workflows; –Coordination of workflow execution

This talk Work in progress –no results yet

Overview: user interaction

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]

Related issues Workflows –Workflows represent a set of activities to be executed, their interdependencies relations, inputs and outputs. activity1 activity2 activity3 input data1 input data2 input data3 activity4 output data

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

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.

Related issues Example of part of a tool ontology: Alignment service Local AlignmentGlobal Alignment Heuristic Alignment Non-Heuristic Alignment Heuristic Alignment

The framework Workflow management Service layer Service discoveryService request application1application2 Workflow discovery Workflow repository Workflow design Workflow engine User interface Service Catalog application3

The framework Service layer –bioinformatics basic Web services assembly, matching, consensus, etc Service catalog layer –stores Web services' syntactical description; semantical description; URI.

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.

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.

Methodology A bottom-up approach: Service1 Service2Service3 Workflow design and engine Workflow management Service discovery and requisition

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.

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)

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

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.

Thank you! Laboratory for Bioinformatics Institute of Computation (IC) University of Campinas (UNICAMP) Luciano Antonio Digiampietri