Related papers: An Analytics Tool for Exploring Scientific Softwar…
Considerable scientific work involves locating, analyzing, systematizing, and synthesizing other publications. Its results end up in a paper's "background" section or in standalone articles, which include meta-analyses and systematic…
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…
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…
The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers. Since sharing materials reproducibly is challenging, several…
The value of structured scholarly knowledge for research and society at large is well understood, but producing scholarly knowledge (i.e., knowledge traditionally published in articles) in structured form remains a challenge. We propose an…
Context: Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to…
With the advent of open source software, a veritable treasure trove of previously proprietary software development data was made available. This opened the field of empirical software engineering research to anyone in academia. Data that is…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
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…
This paper proposes a software repository model together with associated tooling and consists of several complex, open-source GUI driven applications ready to be used in empirical software research. We start by providing the rationale for…
This study introduces a novel software tool leveraging large language model (LLM) prompts, designed to automate the generation of academic articles from Python code a significant advancement in the fields of biomedical informatics and…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
Large language models (LLMs) have been touted to enable increased productivity in many areas of today's work life. Scientific research as an area of work is no exception: the potential of LLM-based tools to assist in the daily work of…
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…
As software has become an integral part of scientific workflows, reproducible research practices must take it into account. In what way? Archiving source code is a necessary but insufficient condition. The ability to redeploy software…
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…
With an exponentially growing number of scientific papers published each year, advanced tools for exploring and discovering publications of interest are becoming indispensable. To empower users beyond a simple keyword search provided e.g.…
Although computer science papers are often accompanied by software artifacts, connecting research papers to their software artifacts and vice versa is not always trivial. First of all, there is a lack of well-accepted standards for how such…
Being able to duplicate published research results is an important process of conducting research whether to build upon these findings or to compare with them. This process is called "replicability" when using the original authors'…
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…