This book contains a collection of 31 case studies of reproducible research workflows, written by academic researchers in the data-intensive sciences. Each case study describes how the author combined specific tools, ideas, and practices in order to complete a real-world research project. Emphasis is placed on the practical aspects of how the author organized his or her research to make it as reproducible as possible.

We present a toolchain for computational research consisting of Sacred and two supporting tools. Sacred is an open source Python framework which aims to provide basic infrastructure for running computational experiments independent of the methods and libraries used. Instead, it focuses on solving universal everyday problems, such as managing configurations, reproducing results, and bookkeeping. Moreover, it provides an extensible basis for other tools, two of which we present here: Labwatch helps with tuning hyperparameters, and Sacredboard provides a web-dashboard for organizing and analyzing runs and results.

Replication of scientific experiments is critical to the advance of science. Unfortunately, the discipline of Computer Science has never treated replication seriously, even though computers are very good at doing the same thing over and over again. Not only are experiments rarely replicated, they are rarely even replicable in a meaningful way. Scientists are being encouraged to make their source code available, but this is only a small step. Even in the happy event that source code can be built and run successfully, running code is a long way away from being able to replicate the experiment that code was used for. I propose that the discipline of Computer Science must embrace replication of experiments as standard practice. I propose that the only credible technique to make experiments truly replicable is to provide copies of virtual machines in which the experiments are validated to run. I propose that tools and repositories should be made available to make this happen. I propose to be one of those who makes it happen.

We present noWorkflow, an open-source tool that systematically and transparently collects provenance from Python scripts, including data about the script execution and how the script evolves over time. During the demo, we will show how noWorkflow collects and manages provenance, as well as how it supports the analysis of computational experiments.We will also encourage attendees to use noWorkflow for their own scripts.

Achieving research reproducibility is challenging in many ways: there are social and cultural obstacles as well as a constantly changing technical landscape that makes replicating and reproducing research difficult. Users face challenges in reproducing research across different operating systems, in using different versions of software across long projects and among collaborations, and in using publicly available work. The dependencies required to reproduce the computational environments in which research happens can be exceptionally hard to track – in many cases, these dependencies are hidden or nested too deeply to discover, and thus impossible to install on a new machine, which means adoption remains low. In this paper, we present ReproZip, an open source tool to help overcome the technical difficulties involved in preserving and replicating research, applications, databases, software, and more. We examine the current use cases of ReproZip, ranging from digital humanities to machine learning. We also explore potential library use cases for ReproZip, particularly in digital libraries and archives, liaison librarianship, and other library services. We believe that libraries and archives can leverage ReproZip to deliver more robust reproducibility services, repository services, as well as enhanced discoverability and preservation of research materials, applications, software, and computational environments.

Presentation slides for the 2017 Workshop on Reproducibility Taxonomies for Computing and Computational Science