GenePattern pipelines allow you to capture, automate, and share the complex series of steps required to analyze genomic data. By providing a way to create and distribute an entire computational analysis methodology in a single executable script, pipelines enable a form of in silico reproducible research.
Pipelines capture computational analysis methods, modules and/or other pipelines, and their parameters. They allow you to “chain” methods by using the output of one as the input of another. You can use a simple form-based interface to build a pipeline from scratch, or have GenePattern work backward from an analysis results file to create a pipeline that contains the analysis methods used to generate that file. You can create a pipeline to reproduce an exact set of events, or parameterize the pipeline to run an analysis methodology against variable data.
Since pipelines are easily exported and imported from GenePattern, you can share them with colleagues who would like to reproduce your results or use them to document published research. By versioning every pipeline and each of its methods, GenePattern ensures that you can reproduce previous analysis results even if you modify the pipeline.