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Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Digital computational outputs are now ubiquitous in the research workflow and the way in which these data are stored and cataloged is becoming more standardized across fields of research. However, even with accessible data and code, the…
Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…
In recent years, the research community has raised serious questions about the reproducibility of scientific work. In particular, since many studies include some kind of computing work, reproducibility is also a technological challenge, not…
This paper investigates the reproducibility of computational science research and identifies key challenges facing the community today. It is the result of the First Summer School on Experimental Methodology in Computational Science…
Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years sustainable software development practices have made progress in being considered as an integral component of research.…
Meta-analysis is routinely performed in many scientific disciplines. This analysis is attractive since discoveries are possible even when all the individual studies are underpowered. However, the meta-analytic discoveries may be entirely…
As software has become an integral part of scientific workflows, reproducible research practices must take it into account. In what way? Archiving source code is a necessary but insufficient condition. The ability to redeploy software…
The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers. Since sharing materials reproducibly is challenging, several…
Ensuring the reproducibility of scientific work is crucial as it allows the consistent verification of scientific claims and facilitates the advancement of knowledge by providing a reliable foundation for future research. However,…
With the advent of Open Science, researchers have started to publish their research artefacts (i. e., data, software, and other products of the investigations) in order to allow others to reproduce their investigations. While this…
Replication crises have shaken the scientific landscape during the last decade. As potential solutions, open science practices were heavily discussed and have been implemented with varying success in different disciplines. We argue that…
Computer science is also an experimental science. This is particularly the case for parallel computing, which is in a total state of flux, and where experiments are necessary to substantiate, complement, and challenge theoretical modeling…
An essential part of research and scientific communication is researchers' ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
This paper investigates the conceptual relationship between openness and reproducibility using a model-centric approach, heavily informed by probability theory and statistics. We first clarify the concepts of reliability, auditability,…
Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the…
Transparency and reproducibility are often seen in opposition to privacy and confidentiality. Data that need to be kept confidential are seen as an impediment to reproducibility, and privacy would seem to inhibit transparency. I bring a…
Reproducibility is a crucial aspect of scientific research that involves the ability to independently replicate experimental results by analysing the same data or repeating the same experiment. Over the years, many works have been proposed…
Being able to duplicate published research results is an important process of conducting research whether to build upon these findings or to compare with them. This process is called "replicability" when using the original authors'…