An introduction to Docker for reproducible research, with examples from the R environment

As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge. In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers. I review current approaches to these issues, including virtual machines and workflow systems, and their limitations. I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a `DevOps' philosophy, to address these challenges. I illustrate this with several examples of Docker use with a focus on the R statistical environment

Urban Street Network Analysis in a Computational Notebook

Computational notebooks offer researchers, practitioners, students, and educators the ability to interactively conduct analytics and disseminate reproducible workflows that weave together code, visuals, and narratives. This article explores the potential of computational notebooks in urban analytics and planning, demonstrating their utility through a case study of OSMnx and its tutorials repository. OSMnx is a Python package for working with OpenStreetMap data and modeling, analyzing, and visualizing street networks anywhere in the world. Its official demos and tutorials are distributed as open-source Jupyter notebooks on GitHub. This article showcases this resource by documenting the repository and demonstrating OSMnx interactively through a synoptic tutorial adapted from the repository. It illustrates how to download urban data and model street networks for various study sites, compute network indicators, visualize street centrality, calculate routes, and work with other spatial data such as building footprints and points of interest. Computational notebooks help introduce methods to new users and help researchers reach broader audiences interested in learning from, adapting, and remixing their work. Due to their utility and versatility, the ongoing adoption of computational notebooks in urban planning, analytics, and related geocomputation disciplines should continue into the future

A Grammar for Reproducible and Painless Extract-Transform-Load Operations on Medium Data

Many interesting data sets available on the Internet are of a medium size---too big to fit into a personal computer's memory, but not so large that they won't fit comfortably on its hard disk. In the coming years, data sets of this magnitude will inform vital research in a wide array of application domains. However, due to a variety of constraints they are cumbersome to ingest, wrangle, analyze, and share in a reproducible fashion. These obstructions hamper thorough peer-review and thus disrupt the forward progress of science. We propose a predictable and pipeable framework for R (the state-of-the-art statistical computing environment) that leverages SQL (the venerable database architecture and query language) to make reproducible research on medium data a painless reality.Comment: 30 pages, plus supplementary material