Related papers: Biomedical Open Source Software: Crucial Packages …
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
Cloud computing recently developed into a viable alternative to on-premises systems for executing high-performance computing (HPC) applications. With the emergence of new vendors and hardware options, there is now a growing need to…
Following the widespread digitalization of scholarship, software has become essential for research, but the current sociotechnical system of citation does not reflect this sufficiently. Citation provides context for research, but the…
The use of several open source scientific packages in the Schr\"odinger Materials Science Suite will be discussed. A typical workflow for materials discovery will be described, discussing how open source packages have been incorporated at…
Open source software ecosystems consist of thousands of interdependent libraries, which users can combine to great effect. Recent work has pointed out two kinds of risks in these systems: that technical problems like bugs and…
Free and open source software package ecosystems have existed for a long time and are among the most sophisticated human-made systems. One of the oldest and most popular software package ecosystems is CRAN, the repository of packages of the…
Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become…
A representation of the cause-effect mechanism is needed to enable artificial intelligence to represent how the world works. Bayesian Networks (BNs) have proven to be an effective and versatile tool for this task. BNs require constructing a…
Large language models (LLMs) have developed rapidly in recent years, revolutionizing various fields. Despite their widespread success, LLMs heavily rely on external code dependencies from package management systems, creating a complex and…
Modern science is relying on software more than ever. The behavior and outcomes of this software shape the scientific and public discourse on important topics like climate change, economic growth, or the spread of infections. Most…
High-Performance Computing (HPC) platforms enable scientific software to achieve breakthroughs in many research fields such as physics, biology, and chemistry, by employing Research Software Engineering (RSE) techniques. These include 1)…
Modern research heavily relies on software. A significant challenge researchers face is understanding the complex software used in specific research fields. We target two scenarios in this context, namely long onboarding times for newcomers…
Research software -- specialist software used to support or undertake research -- is of huge importance to researchers. It contributes to significant advances in the wider world and requires collaboration between people with diverse skills…
The rise of user-contributed Open Source Software (OSS) ecosystems demonstrate their prevalence in the software engineering discipline. Libraries work together by depending on each other across the ecosystem. From these ecosystems emerges a…
Software is an important tool for scholarly work, but software produced for research is in many cases not easily identifiable or discoverable. A potential first step in linking research and software is software identification. In this paper…
What are the landmark papers in scientific disciplines? On whose shoulders does research in these fields stand? Which papers are indispensable for scientific progress? These are typical questions which are not only of interest for…
A plethora of scientific software packages are published in repositories, e.g., Zenodo and figshare. These software packages are crucial for the reproducibility of published research. As an additional route to scholarly knowledge graph…
Complex software systems are among most sophisticated human-made systems, yet only little is known about the actual structure of 'good' software. We here study different software systems developed in Java from the perspective of network…
The proliferation of sensor technologies and advancements in data collection methods have enabled the accumulation of very large amounts of data. Increasingly, these datasets are considered for scientific research. However, the design of…
Modern research in the sciences, engineering, humanities, and other fields depends on software, and specifically, research software. Much of this research software is developed in universities, by faculty, postdocs, students, and staff. In…