Related papers: Biomedical Open Source Software: Crucial Packages …
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
We describe the CZ Software Mentions dataset, a new dataset of software mentions in biomedical papers. Plain-text software mentions are extracted with a trained SciBERT model from several sources: the NIH PubMed Central collection and from…
The use of third-party packages is becoming increasingly popular and has led to the emergence of large software package ecosystems with a maze of inter-dependencies. Since the reliance on these ecosystems enables developers to reduce…
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…
Software is vital for the advancement of biology and medicine. Analysis of usage and impact metrics can help developers determine user and community engagement, justify additional funding, encourage additional use, identify unanticipated…
A large number of computational scientific research projects make use of open source software packages. However, the development process of such tools frequently differs from conventional software development; partly because of the nature…
Scientific software is essential to scientific innovation and in many ways it is distinct from other types of software. Abandoned (or unmaintained), buggy, and hard to use software, a perception often associated with scientific software can…
Knowledge about software used in scientific investigations is important for several reasons, for instance, to enable an understanding of provenance and methods involved in data handling. However, software is usually not formally cited, but…
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…
As computer systems become more and more complex, software and tools lag more and more behind. This is especially true for scientific software that often demands high performance, and thus needs to take advantage of parallelisms, memory…
Research software is essential to modern science, yet many research-performing organisations lack coherent policies to support its development, sustainability, and recognition. Despite its central role in research outcomes, research…
Software is a central part of modern science, and knowledge of its use is crucial for the scientific community with respect to reproducibility and attribution of its developers. Several studies have investigated in-text mentions of software…
Science advances not only through the accumulation of facts but also through the evolution of tools. Crucially, tools are rarely used in isolation. They form tool portfolios, combinations shaped by a discipline's workflows and analytical…
Open source software development, particularly within institutions such as universities and research laboratories, is often decentralized and difficult to track. Although academic teams produce many impactful scientific tools, their…
Software is a critical part of modern research, and yet there are insufficient mechanisms in the scholarly ecosystem to acknowledge, cite, and measure the impact of research software. The majority of academic fields rely on a…
Open source software is a rapidly evolving center for distributed work, and understanding the characteristics of this work across its different contexts is vital for informing policy, economics, and the design of enabling software. The…
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…
Open-source software (OSS) supply chain security has become a topic of concern for organizations. Patching an OSS vulnerability can require updating other dependent software products in addition to the original package. However, the…
Due to their increasing complexity, today's software systems are frequently built by leveraging reusable code in the form of libraries and packages. Software ecosystems (e.g., npm) are the primary enablers of this code reuse, providing…
Software is increasingly produced in the form of ecosystems, collections of interdependent components maintained by a distributed community. These ecosystems act as network organizations, not markets, and thus often lack actionable…