Published research, particularly in silico research, should contain sufficient information to completely reproduce the research results. By capturing the analysis methods, parameters, and data used to produce the research results, GenePattern pipelines enable reproducible research. By versioning every pipeline and its methods, GenePattern ensures that each version of a pipeline (and its results) remain static, even as your research and the pipeline continue to evolve.
GenePattern uses Life Science Identifiers (LSIDs) to uniquely identify objects, such as analysis methods and pipelines. When you create an object, GenePattern automatically assigns the object an LSID with a version number of one (1). When you update an object, GenePattern automatically updates the version number of the object’s LSID. This careful versioning process allows you to accurately reproduce analysis results by rerunning the precise version of the pipeline that previously generated those results.