YAMP is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerisation to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system, and offers seamless support for multiple job schedulers as well as for Amazon AWS cloud. Although YAMP has been developed to be ready-to-use by non-experts, bioinformaticians will appreciate its flexibility, modularisation, and simple customisation. The YAMP script, parameters, and documentation are available at https://github.com/alesssia/YAMP.
The ability to independently regenerate published computational claims is widely recognized as a key component of scientific reproducibility. In this article we take a narrow interpretation of this goal, and attempt to regenerate published claims from author-supplied information, including data, code, inputs, and other provided specifications, on a different computational system than that used by the original authors. We are motivated by Claerbout and Donoho's exhortation of the importance of providing complete information for reproducibility of the published claim. We chose the Elsevier journal, the Journal of Computational Physics, which has stated author guidelines that encourage the availability of computational digital artifacts that support scholarly findings. In an IRB approved study at the University of Illinois at Urbana-Champaign (IRB #17329) we gathered artifacts from a sample of authors who published in this journal in 2016 and 2017. We then used the ICERM criteria generated at the 2012 ICERM workshop "Reproducibility in Computational and Experimental Mathematics" to evaluate the sufficiency of the information provided in the publications and the ease with which the digital artifacts afforded computational reproducibility. We find that, for the articles for which we obtained computational artifacts, we could not easily regenerate the findings for 67% of them, and we were unable to easily regenerate all the findings for any of the articles. We then evaluated the artifacts we did obtain (55 of 306 articles) and find that the main barriers to computational reproducibility are inadequate documentation of code, data, and workflow information (70.9%), missing code function and setting information, and missing licensing information (75%). We recommend improvements based on these findings, including the deposit of supporting digital artifacts for reproducibility as a condition of publication, and verification of computational findings via re-execution of the code when possible.
Conference and journal publications increasingly require experiments associated with a submitted article to be repeatable. Authors comply to this requirement by sharing all associated digital artifacts, i.e., code, data, and environment configuration scripts. To ease aggregation of the digital artifacts, several tools have recently emerged that automate the aggregation of digital artifacts by auditing an experiment execution and building a portable container of code, data, and environment. However, current tools only package non-distributed computational experiments. Distributed computational experiments must either be packaged manually or supplemented with sufficient documentation. In this paper, we outline the reproducibility requirements of distributed experiments using a distributed computational science experiment involving use of message-passing interface (MPI), and propose a general method for auditing and repeating distributed experiments. Using Sciunit we show how this method can be implemented. We validate our method with initial experiments showing application re-execution runtime can be improved by 63% with a trade-off of longer run-time on initial audit execution.
We describe the four publications we have tried to make reproducible and discuss how each paper has changed our workflows, practices, and collaboration policies. The fundamental insight is that paper artifacts must be made reproducible from the start of the project; artifacts are too difficult to make reproducible when the papers are (1) already published and (2) authored by researchers that are not thinking about reproducibility. In this paper, we present the best practices adopted by our research laboratory, which was sculpted by the pitfalls we have identified for the Popper convention. We conclude with a "call-to-arms" for the community focused on enhancing reproducibility initiatives for academic conferences, industry environments, and national laboratories. We hope that our experiences will shape a best practices guide for future reproducible papers.
A recent widespread realization that software experiments are not as easily replicated as once believed brought software execution preservation to the science spotlight. As a result, scientists, institutions, and funding agencies have recently been pushing for the development of methodologies and tools that preserve software artifacts. Despite current efforts, long term reproducibility still eludes us. In this paper, we present the requirements for software execution preservation and discuss how to improve long-term reproducibility in science. In particular, we discuss the reasons why preserving binaries and pre-built execution environments is not enough and why preserving the ability to replicate results is not the same as preserving software for reproducible science. Finally, we show how these requirements are supported by Occam, an open curation framework that fully preserves software and its dependencies from source to execution, promoting transparency, longevity, and re-use. Specifically, Occam provides the ability to automatically deploy workflows in a fully-functional environment that is able to not only run them, but make them easily replicable.
Psychology is currently experiencing a "renaissance" where the replication and reproducibility of published reports are at the forefront of conversations in the field. While researchers have worked to discuss possible problems and solutions, work has yet to uncover how this new culture may have altered reporting practices in the social sciences. As outliers can bias both descriptive and inferential statistics, the search for these data points is essential to any analysis using these parameters. We quantified the rates of reporting of outliers within psychology at two time points: 2012 when the replication crisis was born, and 2017, after the publication of reports concerning replication, questionable research practices, and transparency. A total of 2235 experiments were identified and analyzed, finding an increase in reporting of outliers from only 15.7% of experiments mentioning outliers in 2012 to 25.0% in 2017. We investigated differences across years given the psychological field or statistical analysis that experiment employed. Further, we inspected whether outliers mentioned are whole participant observations or data points, and what reasons authors gave for stating the observation was deviant. We conclude that while report rates are improving overall, there is still room for improvement in the reporting practices of psychological scientists which can only aid in strengthening our science.