Related papers: Biomedical Open Source Software: Crucial Packages …
Software supply chain attacks have revealed blind spots in existing SCA tools, which are often limited to a single ecosystem and assess either software artifacts or community activity in isolation. This fragmentation across tools and…
Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopic techniques. All optical, electron and scanning probe microscopy advanced with new detector technologies and integration of…
As modern software extensively uses open source packages, developers regularly pull in new upstream code through frequent updates. While a manual review of all upstream changes may not be practical, developers may rely on the authors' and…
Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…
Research software (also called scientific software) is essential for advancing scientific endeavours. Research software encapsulates complex algorithms and domain-specific knowledge and is a fundamental component of all science. A pervasive…
How should software engineering be adapted for Computational Science (CS)? If we understood that, then we could better support software sustainability, verifiability, reproducibility, comprehension, and usability for CS community. For…
One of the biggest strength of many modern programming languages is their rich open source package ecosystem. Indeed, modern language-specific package managers have made it much easier to share reusable code and depend on components written…
AI systems rest on software with low integrity mechanisms, leaving AI systems exposed across every stage from data acquisition to final inference. This paper makes the AI supply chain a first-class object of analysis, decomposing it across…
In Open Source Software, resources of any project are open for reuse by introducing dependencies or copying the resource itself. In contrast to dependency-based reuse, the infrastructure to systematically support copy-based reuse appears to…
Software ecosystems (e.g., npm, PyPI) are the backbone of modern software developments. Developers add new packages to ecosystems every day to solve new problems or provide alternative solutions, causing obsolete packages to decline in…
The real-world implementation of federated learning is complex and requires research and development actions at the crossroad between different domains ranging from data science, to software programming, networking, and security. While…
Many open source software (OSS) projects need more human resources for maintenance, improvements, and sometimes even their survival. These needs allegedly apply even to vital OSS projects that can be seen as being a part of the world's…
A key issue hindering discoverability, attribution and reusability of open research software is that its existence often remains hidden within the manuscript of research papers. For these resources to become first-class bibliographic…
Much of the success of modern software development can be attributed to code reuse. The ability to reuse existing functionality via third-party dependencies has enabled massive gains in productivity, but for a long time the dominant…
High performance computing (HPC) software ecosystems are inherently heterogeneous, comprising scientific applications that depend on hundreds of external packages, each with distinct build systems, options, and dependency constraints. Tools…
There is a growing relationship between academic libraries and cloud computing. Therefore, understanding the beginnings and the current use of cloud base services in libraries is important. This will help understand the factors that…
Different communities rely heavily on software, but use quite different software development practices. {\bf Objective}: We wanted to measure the state of the practice in the area of statistical software for psychology to understand how it…
Under the data-driven research paradigm, research software has come to play crucial roles in nearly every stage of scientific inquiry. Scholars are advocating for the formal citation of software in academic publications, treating it on par…