The Reproducibility Project: Cancer Biology launched in 2013 as an ambitious effort to scrutinize key findings in 50 cancer papers published in Nature, Science, Cell and other high-impact journals. It aims to determine what fraction of influential cancer biology studies are probably sound — a pressing question for the field. In 2012, researchers at the biotechnology firm Amgen in Thousand Oaks, California, announced that they had failed to replicate 47 of 53 landmark cancer papers2. That was widely reported, but Amgen has not identified the studies involved.
A large portion of scientific results is based on analysing and processing research data. In order for an eScience experiment to be reproducible, we need to able to identify precisely the data set which was used in a study. Considering evolving data sources this can be a challenge, as studies often use subsets which have been extracted from a potentially large parent data set. Exporting and storing subsets in multiple versions does not scale with large amounts of data sets. For tackling this challenge, the RDA Working Group on Data Citation has developed a framework and provides a set of recommendations, which allow identifying precise subsets of evolving data sources based on versioned data and timestamped queries. In this work, we describe how this method can be applied in small scale research data scenarios and how it can be implemented in large scale data facilities having access to sophisticated data infrastructure. We describe how the RDA approach improves the reproducibility of eScience experiments and we provide an overview of existing pilots and use cases in small and large scale settings.
A strong movement towards openness has seized science. Open data and methods, open source software, Open Access, open reviews, and open research platforms provide the legal and technical solutions to new forms of research and publishing. However, publishing reproducible research is still not common practice. Reasons include a lack of incentives and a missing standardized infrastructure for providing research material such as data sets and source code together with a scientific paper. Therefore we first study fundamentals and existing approaches. On that basis, our key contributions are the identification of core requirements of authors, readers, publishers, curators, as well as preservationists and the subsequent description of an executable research compendium (ERC). It is the main component of a publication process providing a new way to publish and access computational research. ERCs provide a new standardisable packaging mechanism which combines data, software, text, and a user interface description. We discuss the potential of ERCs and their challenges in the context of user requirements and the established publication processes. We conclude that ERCs provide a novel potential to find, explore, reuse, and archive computer-based research.
Scientific research is published in journals so that the research community is able to share knowledge and results, verify hypotheses, contribute evidence-based opinions and promote discussion. However, it is hard to fully understand, let alone reproduce, the results if the complex data manipulation that was undertaken to obtain the results are not clearly explained and/or the final data used is not available. Furthermore, the scale of research data assets has now exponentially increased to the point that even when available, it can be difficult to store and use these data assets. In this paper, we describe the solution we have implemented at the National Computational Infrastructure (NCI) whereby researchers can capture workflows, using a standards-based provenance representation. This provenance information, combined with access to the original dataset and other related information systems, allow datasets to be regenerated as needed which simultaneously addresses both result reproducibility and storage issues.
Improving the reliability and efficiency of scientific research will increase the credibility of the published scientific literature and accelerate discovery. Here we argue for the adoption of measures to optimize key elements of the scientific process: methods, reporting and dissemination, reproducibility, evaluation and incentives. There is some evidence from both simulations and empirical studies supporting the likely effectiveness of these measures, but their broad adoption by researchers, institutions, funders and journals will require iterative evaluation and improvement. We discuss the goals of these measures, and how they can be implemented, in the hope that this will facilitate action toward improving the transparency, reproducibility and efficiency of scientific research.
In this talk I will review a few examples of reproducibility challenges in computational environments and discuss their potential effects. Based on discussions in a recent Dagstuhl seminar we will identify different types of reproducibility. Here, we will focus specifically on what we gain from them, rather than seeing them merely as means to an end. We subsequently will address two core challenges impacting reproducibility, namely (1) understanding and automatically capturing process context and provenance information, and (2) approaches allowing us to deal with dynamically evolving data sets relying on recommendation of the Research Data Alliance (RDA). The goal is to raise awareness of reproducibility challenges and show ways how these can be addressed with minimal impact on the researchers via research infrastructures offering according services.