Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

Background: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. Results: We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Alexander García Castro, Samuel Thoraval, Leyla Jael García-Castro, Mark A. Ragan
• Keywords: Bioinformatic, BMCBI 2005, Graphic User Interfaces, Workflows