Related papers: Biomedical Open Source Software: Crucial Packages …
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…
Software systems have grown as an indispensable commodity used across various industries, and almost all essential services depend on them for effective operation. The software is no longer an independent or stand-alone piece of code…
In computational science and in computer science, research software is a central asset for research. Computational science is the application of computer science and software engineering principles to solving scientific problems, whereas…
This research analyzes complex networks in open-source software at the inter-package level, where package dependencies often span across projects and between development groups. We review complex networks identified at ``lower'' levels of…
Modern software development is increasingly dependent on components, libraries and frameworks coming from third-party vendors or open-source suppliers and made available through a number of platforms (or forges). This way of writing…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
While open-source software has enabled significant levels of reuse to speed up software development, it has also given rise to the dreadful dependency hell that all software practitioners face on a regular basis. This article provides a…
The integration of medical devices in the patient treatment process becomes increasingly important due to the efficiency of the technology. On the one hand, medical devices hardware is more powerful and its integration with the software…
Our analysis of recent AI4H publications reveals that, despite a trend toward utilizing open datasets and sharing modeling code, 74% of AI4H papers still rely on private datasets or do not share their code. This is especially concerning in…
With the popularity of software ecosystems, the number of open source components (known as packages) has grown rapidly. Identifying high-quality and well-maintained packages from a large pool of packages to depend on is a basic and…
The communities who develop and support open source scientific software packages are crucial to the utility and success of such packages. Moreover, these communities form an important part of the human infrastructure that enables scientific…
Particle physics has an ambitious and broad global experimental programme for the coming decades. Large investments in building new facilities are already underway or under consideration. Scaling the present processing power and data…
Scientific software-defined as computer programs, scripts, or code used in scientific research, data analysis, modeling, or simulation-has become central to modern research. However, there is limited research on the readability and…
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…
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…
As software systems increase in complexity, conventional monitoring methods struggle to provide a comprehensive overview or identify performance issues, often missing unexpected problems. Observability, however, offers a holistic approach,…
The R package ecosystem is expanding fast and dependencies among packages in the ecosystem are becoming more complex. In this study, we explored the package dependencies from a new aspect. We applied a new metric named "dependency…
The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016.…
Two large, open source software systems are analyzed from the vantage point of complex adaptive systems theory. For both systems, the full dependency graphs are constructed and their properties are shown to be consistent with the assumption…
Applications integrating analysis components require a programmable interface which defines statistical operations independently of any programming language. By separating concerns of scientific computing from application and implementation…