Renewing bioinformatics workflow systems by using a Web 2.0 approach

Roberto Colella, Bachir Balech, Antonella Vaccina, Pietro Leo, Gaetano Scioscia

Abstract


The use of "mashups" is expanding considerably in the business environment. Business mashups are usually adopted within integrating business and data-service frameworks to provide the ability to develop new integrated services quickly. Typically, mashups provide organisations with a pronounced and flexible commodity to combine internal with external services in order to create new services, usually accessed through user-friendly Web-browser interfaces. In this study, a Web 2.0 technology was adopted to promote a key field of bioinformatics research through the management and automation of bioinformatics workflows. Consumables (widgets and services) have been developed using the Lotus Widget Factory, an Eclipse plug-in providing an easy-to-use development environment enabling developers of all skill levels to create dynamic widgets rapidly. A workflow built from widgets works as follows: the core widget receives data from one or more widgets, invokes a generic Web service, performing iteration and/or recursion, and sends the results to all other connected widgets. The number of iterations and recursions depends on the input data-set dimension and user-defined parameter values related to each specific application. Some prototype workflows have been assembled and tested with a number of widgets created with algorithms from the European Molecular Biology Open Software Suite (EMBOSS), exposed as Web services. The adoption of recent Web 2.0 technologies, such as mashup platforms, has enabled rapid generation, sharing and discovery of reusable application building-blocks (widgets, feeds, mashups), and has shown to be a plausible alternative environment for supporting bioinformatics workflow design, management and execution.

Keywords


bioinformatics workflow; mashup; bioinformatic widget; sequence analysis

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DOI: http://dx.doi.org/10.14806/ej.21.0.840

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