The association between the bacterium Fusobacterium nucleatum and human colon cancer is more complicated than it first appeared.
Here we present the Scientific Filesystem (SCIF), an organizational format that supports exposure of executables and metadata for discoverability of scientific applications. The format includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within. SCIF makes it easy to expose metadata, multiple environments, installation steps, files, and entrypoints to render scientific applications consistent, modular, and discoverable. A SCIF can be installed on a traditional host or in a container technology such as Docker or Singularity. We will start by reviewing the background and rationale for the Scientific Filesystem, followed by an overview of the specification, and the different levels of internal modules (“apps”) that the organizational format affords. Finally, we demonstrate that SCIF is useful by implementing and discussing several use cases that improve user interaction and understanding of scientific applications. SCIF is released along with a client and integration in the Singularity 2.4 software to quickly install and interact with Scientific Filesystems. When used inside of a reproducible container, a Scientific Filesystem is a recipe for reproducibility and introspection of the functions and users that it serves.
While reproducibility has been a requirement in natural sciences for centuries, computational experiments have not followed the same standard. Often, there is insufficient information to reproduce computational results described in publications, and in the recent past, this has led to many retractions. Although scientists are aware of the numerous benefits of reproducibility, the perceived amount of work to make results reproducible is a significant disincentive. Fortunately, much of the information needed to reproduce an experiment can be obtained by systematically capturing its provenance. In this paper, we give an overview of different types of provenance and how they can be used to support reproducibility. We also describe a representative set of provenance tools and approaches that make it easy to create reproducible experiments.
Science is conducted collaboratively, often requiring the sharing of knowledge about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers (DOIs). An experiment, however, seldom includes only datasets, but more often includes software, its past execution, provenance, and associated documentation. The Research Object has recently emerged as a comprehensive and systematic method for aggregation and identification of diverse elements of computational experiments. While a necessary method, mere aggregation is not sufficient for the sharing of computational experiments. Other users must be able to easily recompute on these shared research objects. Computational provenance is often the key to enable such reuse. In this paper, we show how reusable research objects can utilize provenance to correctly repeat a previous reference execution, to construct a subset of a research object for partial reuse, and to reuse existing contents of a research object for modified reuse. We describe two methods to summarize provenance that aid in understanding the contents and past executions of a research object. The first method obtains a process-view by collapsing low-level system information, and the second method obtains a summary graph by grouping related nodes and edges with the goal to obtain a graph view similar to application workflow. Through detailed experiments, we show the efficacy and efficiency of our algorithms.
A heated debate surrounds the significance of reproducibility as an indicator for research quality and reliability, with many commentators linking a "crisis of reproducibility" to the rise of fraudulent, careless and unreliable practices of knowledge production. Through the analysis of discourse and practices across research fields, I point out that reproducibility is not only interpreted in different ways, but also serves a variety of epistemic functions depending on the research at hand. Given such variation, I argue that the uncritical pursuit of reproducibility as an overarching epistemic value is misleading and potentially damaging to scientific advancement. Requirements for reproducibility, however they are interpreted, are one of many available means to securere liable research outcomes. Furthermore, there are cases wherethe focus on enhancing reproducibility turns out not to foster high-quality research. Scientific communities and Open Science advocates should learn from inferential reasoning from irreproducible data, and promoteincentives for all researchers to explicitly and publicly discuss (1) their methodological commitments, (2) the ways in which they learn from mistakes and problems in everyday practice, and (3) the strategies they use to choose which research component of any project needs to be preserved in the long term, and how.
A paper which analyzes terminologies related to reproducible research -- exploring differences and patterns among them -- aiming to resolve some contradictions.