Automatic Synthesis of Bioconductor Pipelines: A Domain Modeling Challenge

GNU R is a widely used programming language and software environment for statistical data analysis and visualization. Bioconductor [1] is a collection of bioinformatics packages that extends R’s standard range of functionality by comprehensive libraries of functions and meta-data predominantly for the analysis of data from high-throughput genomics and molecular biology experiments, and additionally provides several example data sets that are useful for testing, benchmarking and demonstration purposes. Reference manuals and additional manuscripts provided with the packages at the Bioconductor web site describe a variety of data analysis procedures based on the available functionality. The described bioinformatics procedures or workflows are typically referred to as data analysis pipelines, as they typically have a simple, in fact mostly linear, structure. (This is largely due to the fact that the often considerable complexity of the individual analysis steps is encapsulated by a services with a simple interface, and hence hidden from the user at the provided level of abstraction.) Thus, automatic workflow composition functionality like the method described in [6], which is based on a linear-time logic synthesis algorithm, can be easily applied here to generate the complete analysis pipelines automatically. Making use of the constraint-driven workflow composition functionality of the PROPHETS framework [5], which is based on such a linear-time logic synthesis algorithm, we created a prototype of a corresponding synthesis framework [3]. Focusing on DNA microarray analysis, this prototype comprises around 30 services and provides a framework for user-level construction of analysis pipelines based on appropriately wrapped and integrated Bioconductor functionality. It helps handling the variability that is inherent in microarray data analysis at an useraccessible level and emphasizes the agility of a model-driven and service-oriented approach to workflow design. PROPHETS is the current reference implementation of the loose programming paradigm [4], aiming to simplify workflow development in order to reach application experts without programming background. Working with PROPHETS consists of two major phases: