Toward Reproducible Analysis and Exploration of High-Throughput Biological Datasets

Abstract

This dissertation argues that we can develop unified systems for reproducible exploration and analysis of high-throughput biological datasets. We propose an approach, Small Modular Entities (SME), that orchestrates the execution of analysis pipelines and data exploration applications. We realize SMEs using software container technologies together with well-defined interfaces, configuration, and orchestration. It simplifies the development of such applications, and provides detailed information to reproduce the analyses.