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Software now lies at the heart of scholarly research. Here we argue that as well as being important from a methodological perspective, software should, in many instances, be recognised as an output of research, equivalent to an academic…
Context: Software systems are in continuous evolution through source code changes to fixing bugs, adding new functionalities and improving the internal architecture. All these practices are recorded in the version history, which can be…
Data management, which encompasses activities and strategies related to the storage, organization, and description of data and other research materials, helps ensure the usability of datasets -- both for the original research team and for…
With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
As a newly designated professional title, research software engineers (RSEs) link the two worlds of software engineering and research science. They lack clear development and training opportunities, particularly in the realm of mentoring.…
Institutional repositories are deposits of different types of digital files for access, disseminate and preserve them. This paper aims to explain the importance of repositories in the academic field of engineering as a way to democratize…
The reuse of research software is central to research efficiency and academic exchange. The application of software enables researchers with varied backgrounds to reproduce, validate, and expand upon study findings. Furthermore, the…
Software Heritage is the largest public archive of software source code and associated development history, as captured by modern version control systems. As of July 2023, it has archived more than 16 billion unique source code files coming…
Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities…
Scientific software projects evolve rapidly in their initial development phase, yet at the end of a funding period, the completion of a research project, thesis, or publication, further engagement in the project may slow down or cease…
Although computer science papers are often accompanied by software artifacts, connecting research papers to their software artifacts and vice versa is not always trivial. First of all, there is a lack of well-accepted standards for how such…
Research software is an integral part of most research today and it is widely accepted that research software artifacts should be accessible and reproducible. However, the sustainable archival of research software artifacts is an ongoing…
The proliferation of open-source scientific software for science and research presents opportunities and challenges. In this paper, we introduce the SciCat dataset -- a comprehensive collection of Free-Libre Open Source Software (FLOSS)…
The purpose of scholarly peer review is to evaluate the quality of scientific manuscripts. However, study after study demonstrates that peer review neither effectively nor reliably assesses research quality. Empirical standards attempt to…
Research software is crucial in the research process and the growth of Open Science underscores the importance of accessing research artifacts, like data and code, raising traceability challenges among outputs. While it is a clear principle…
In software development, the identification of source code file experts is an important task. Identifying these experts helps to improve software maintenance and evolution activities, such as developing new features, code reviews, and bug…
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…
Writing complex computer programs to study scientific problems requires careful planning and an in-depth knowledge of programming languages and tools. In this chapter the importance of using the right tool for the right problem is…
Research Software Engineering is the application of professional software skills to research problems. Those who do this are called Research Software Engineers or RSEs for short. RSEs work closely with researchers in a collaborative fashion…
In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily…