Workflows in bioinformactics: Meta-analysis and prototype implementation of a workflow generator

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Abstract

BACKGROUND: Computational methods for problem solving need to interleave<br />information access and algorithm execution in a problem-specific<br />workflow. The structures of these workflows are defined by a scaffold<br />of syntactic, semantic and algebraic objects capable of representing<br />them. Despite the proliferation of GUIs (Graphic User Interfaces)<br />in bioinformatics, only some of them provide workflow capabilities;<br />surprisingly, no meta-analysis of workflow operators and components<br />in bioinformatics has been reported. RESULTS: We present a set of<br />syntactic components and algebraic operators capable of representing<br />analytical workflows in bioinformatics. Iteration, recursion, the<br />use of conditional statements, and management of suspend/resume tasks<br />have traditionally been implemented on an ad hoc basis and hard-coded;<br />by having these operators properly defined it is possible to use<br />and parameterize them as generic re-usable components. To illustrate<br />how these operations can be orchestrated, we present GPIPE, a prototype<br />graphic pipeline generator for PISE that allows the definition of<br />a pipeline, parameterization of its component methods, and storage<br />of metadata in XML formats. This implementation goes beyond the macro<br />capacities currently in PISE. As the entire analysis protocol is<br />defined in XML, a complete bioinformatic experiment (linked sets<br />of methods, parameters and results) can be reproduced or shared among<br />users. Availability: http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html<br />(interactive), ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download).<br />CONCLUSION: From our meta-analysis we have identified syntactic structures<br />and algebraic operators common to many workflows in bioinformatics.<br />The workflow components and algebraic operators can be assimilated<br />into re-usable software components. GPIPE, a prototype implementation<br />of this framework, provides a GUI builder to facilitate the generation<br />of workflows and integration of heterogeneous analytical tools.

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APA

Garcia Castro, A., Thoraval, S., Garcia, L. J., & Ragan, M. A. (2005). Workflows in bioinformactics: Meta-analysis and prototype implementation of a workflow generator. BMC Bioinformatics, 6. https://doi.org/10.1186/1471-2105-6-87

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