Related papers: Reproducing software environments: a prerequisite …
Due to the growing complexity of software systems, there has been a dramatic increase and industry demand for tools and techniques on software refactoring in the last ten years, defined traditionally as a set of program transformations…
Reproducibility should be a cornerstone of scientific research and is a growing concern among the scientific community and the public. Understanding how to design services and tools that support documentation, preservation and sharing is…
Complex software can be hard to read, adapt, and maintain. Refactoring it can create cleaner and self-explanatory code. Refactoring tools try to guide developers towards better code, with more quality. However, most of them take too long to…
Reproducible builds are a set of software development practices that establish an independently verifiable path from source code to binary artifacts, helping to detect and mitigate certain classes of supply chain attacks. Although quantum…
Research methods are essential parts in conducting any research project. Although they have been theorized and summarized based on best practices, every field of science requires an adaptation of the overall approaches to perform research…
The vast majority of scientific contributions in the field of computational systems biology are based on mathematical models. These models can be broadly classified as either dynamic (kinetic) models or steady-state (constraint-based)…
High-quality research software is a cornerstone of modern scientific progress, enabling researchers to analyze complex data, simulate phenomena, and share reproducible results. However, creating such software requires adherence to best…
In recent years, the research community, but also the general public, has raised serious questions about the reproducibility and replicability of scientific work. Since many studies include some kind of computational work, these issues are…
A growing number of researchers suggest that software process must be tailored to a project's context to achieve maximal performance. Researchers have studied 'context' in an ad-hoc way, with focus on those contextual factors that appear to…
We introduce Repro, an open-source library which aims at improving the reproducibility and usability of research code. The library provides a lightweight Python API for running software released by researchers within Docker containers which…
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…
Computational tools for data analysis are being released daily on repositories such as the Comprehensive R Archive Network. How we integrate these tools to solve a problem in research is increasingly complex and requiring frequent updates.…
Software systems are getting more complex as the system grows where maintaining such system is a primary concern for the industry. Code clone is one of the factors making software maintenance more difficult. It is a process of replicating…
Replication packages are crucial for enabling transparency, validation, and reuse in software engineering (SE) research. While artifact sharing is now a standard practice and even expected at premier SE venues such as ICSE, the practical…
Context: Research software is essential for developing advanced tools and models to solve complex research problems and drive innovation across domains. Therefore, it is essential to ensure its correctness. Software testing plays a vital…
The ability to repeat the experiments from a research study and obtain similar results is a corner stone in experiment-based scientific discovery. This essential feature has been often ignored by the distributed computing and networking…
Increased reproducibility of machine learning research has been a driving force for dramatic improvements in learning performances. The scientific community further fosters this effort by including reproducibility ratings in reviewer forms…
Results of simulation studies evaluating the performance of statistical methods are often considered actionable and thus can have a major impact on the way empirical research is implemented. However, so far there is limited evidence about…
The reproduction and replication of reported scientific results is a hot topic within the academic community. The retraction of numerous studies from a wide range of disciplines, from climate science to bioscience, has drawn the focus of…
Computational methods and associated software implementations are central to every field of scientific investigation. Modern biological research, particularly within systems biology, has relied heavily on the development of software tools…