Using BioDepot-workflow-Builder to Create and Execute Reproducible Bioinformatics Workflows

Abstract

Reproducibility is essential for the verification and advancement of scientific research. It is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results of computational analyses. Software containers like Docker, that distribute the entire computing environment are rapidly gaining popularity in bioinformatics. Docker not only allows for the reproducible deployment of bioinformatics workflows, but also facilitates mix-and-match of components from different workflows that have complex and possibly conflicting software requirements. However, configuration and deployment of Docker, a command-line tool, can be exceedingly challenging for biomedical researchers with limited training in programming and technical skills. We developed a drag and drop GUI called the Biodepot-Workflow-Builder (Bwb) to allow users to assemble, replicate, modify and execute Docker workflows. Bwb represents individual software modules as widgets which are dragged onto a canvas and connected together to form a graphical representation of an analytical pipeline. These widgets allow the user interface to interact with software containers such that software tools written in other languages are compatible and can be used to build modular bioinformatics workflows. We will present a case study using the Bwb to create and execute a RNA sequencing data workflow.