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Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years sustainable software development practices have made progress in being considered as an integral component of research.…
The Semantic Publishing Challenge series aims at investigating novel approaches for improving scholarly publishing using Linked Data technology. In 2014 we had bootstrapped this effort with a focus on extracting information from…
Small to medium-scale data science experiments often rely on research software developed ad-hoc by individual scientists or small teams. Often there is no time to make the research software fast, reusable, and open access. The consequence…
Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists' research increasingly depends on the quality and availability of software upon which their…
Software, and software source code in particular, is widely used in modern research. It must be properly archived, referenced, described and cited in order to build a stable and long lasting corpus of scientic knowledge. In this article we…
An essential part of research and scientific communication is researchers' ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to…
Scientific publishing seems to be at a turning point. Its paradigm has stayed basically the same for 300 years but is now challenged by the increasing volume of articles that makes it very hard for scientists to stay up to date in their…
Innovation is slowing greatly in the pharmaceutical sector. It is considered here how part of the problem is due to overly limiting intellectual property relations in the sector. On the other hand, computing and software in particular are…
The growing availability of open source projects has facilitated developers to reuse existing software artifacts and leverage them to develop new software. However, it is hard to understand the notion of similarity as it varies from…
The Linked Data Paradigm is one of the most promising technologies for publishing, sharing, and connecting data on the Web, and offers a new way for data integration and interoperability. However, the proliferation of distributed,…
Contemporary debates on "open science" mostly focus on the pub- lic accessibility of the products of scientific and academic work. In contrast, this paper presents arguments for "opening" the ongoing work of science. That is, this paper is…
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…
While software and algorithms have become increasingly important in astronomy, the majority of authors who publish computational astronomy research do not share the source code they develop, making it difficult to replicate and reuse the…
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…
The security of research software is essential for ensuring the integrity and reproducibility of scientific results. However, research software security is still largely unexplored. Due to its dependence on open source components and…
Datasets collecting software mentions from scholarly publications can potentially be used for research into the software that has been used in the published research, as well as into the practice of software citation. Recently, new software…
Research methods are essential parts in conducting any research project. Although they have been theorized and summarized based on best practices, every field of science requires an adaptation of the overall approaches to perform research…
Scientific publishing is in a transition between the old paper-bound, static forms and the new electronic media with its interactive, dynamic possibilities. This takes place in the context of imploding library budgets and exploding magazine…
Context: Traceability is a key quality attribute of artifacts that are used in knowledge-intensive tasks and supports software engineers in producing higher-quality software. Despite its clear benefits, traceability is often neglected in…
Over the past few years, deep learning methods have been applied for a wide range of Software Engineering (SE) tasks, including in particular for the important task of automatically predicting and localizing faults in software. With the…