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The evidence-based approach has increasingly been employed to synthesize empirical findings from the primary research in software engineering. Nevertheless, the reproducibility of evidence-based software engineering (EBSE) studies seems to…
Ecosystems are complex and dynamic systems. Over billions of years, they have developed advanced capabilities to provide stable functions, despite changes in their environment. In this paper, we argue that the laws of organization and…
Publishing reproducible analyses is a long-standing and widespread challenge for the scientific community, funding bodies and publishers. Although a definitive solution is still elusive, the problem is recognized to affect all disciplines…
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…
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…
Recent developments in the commercial open source community have catalysed the use of Linux containers for scalable deployment of web-based applications to the cloud. Scientific software can be containerized with dependencies, configuration…
Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a…
In Open Source Software, the source code and any other resources available in a project can be viewed or reused by anyone subject to often permissive licensing restrictions. In contrast to some studies of dependency-based reuse supported…
The traditional foundation of science lies on the cornerstones of theory and experiment. Theory is used to explain experiment, which in turn guides the development of theory. Since the advent of computers and the development of…
So far, the relationship between open science and software engineering expertise has largely focused on the open release of software engineering research insights and reproducible artifacts, in the form of open-access papers, open data, and…
Dedicated software search engines that index open source software repositories or in-house software assets significantly enhance the chance of finding software components suitable for reuse. However, they still leave the work of evaluating…
Open source software ecosystems consist of thousands of interdependent libraries, which users can combine to great effect. Recent work has pointed out two kinds of risks in these systems: that technical problems like bugs and…
Building software that can support the huge growth in data and computation required by modern research needs individuals with increasingly specialist skill sets that take time to develop and maintain. The Research Software Engineering…
Science depends heavily on reliable and easy-to-use software packages, such as mathematical libraries or data analysis tools. Developing such packages requires a lot of effort, which is too often avoided due to the lack of funding or…
This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducibility and the avoidance of pitfalls. It details practical applications from website management using…
Many software engineering studies or tasks rely on categorizing software engineering artifacts. In practice, this is done either by defining simple but often imprecise heuristics, or by manual labelling of the artifacts. Unfortunately,…
In the ever-changing realm of research software development, it is crucial for the scientific community to grasp current trends to identify gaps that can potentially hinder scientific progress. The adherence to the FAIR (Findable,…
Ascertaining the feasibility of independent falsification or repetition of published results is vital to the scientific process, and replication or reproduction experiments are routinely performed in many disciplines. Unfortunately, such…
The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…
In this paper, we discuss the need for an integrated software stack that unites artificial intelligence (AI) and modeling and simulation (ModSim) tools to advance scientific discovery. The authors advocate for a unified AI/ModSim software…