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The reproduction and replication of reported scientific results is a hot topic within the academic community. The retraction of numerous studies from a wide range of disciplines, from climate science to bioscience, has drawn the focus of…
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…
Objective: To (1) demonstrate the implementation of a data science platform built on open-source technology within a large, academic healthcare system and (2) describe two computational healthcare applications built on such a platform.…
Development of scientific and engineering software is usually different and could be more challenging than the development of conventional enterprise software. The authors were involved in a technology-transfer project between academia and…
Modern software systems rely on dependency networks of reusable libraries, where breaking changes propagate and cause downstream consumers to fail. Despite growing research across ecosystems, no comprehensive synthesis exists. We conduct a…
This report summarises the outcomes of a systematic literature search to identify Bayesian network models used to support decision making in healthcare. After describing the search methodology, the selected research papers are briefly…
As software in industry grows in size and complexity, so does the volume of engineering data that companies generate and use. Ideally, this data could be used for many purposes, including informing decisions on engineering priorities.…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…
Software repository mining is the foundation for many empirical software engineering studies. The collection and analysis of detailed data can be challenging, especially if data shall be shared to enable replicable research and open science…
With the rise of the library ecosystem (such as NPM for JavaScript and PyPI for Python), a developer has access to a multitude of library packages that they can adopt as dependencies into their application.Prior work has found that these…
This chapter defines and presents different kinds of software ecosystems. The focus is on the development, tooling and analytics aspects of software ecosystems, i.e., communities of software developers and the interconnected software…
Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for…
Build-time configuration and environment assumptions are hampering progress and usability in scientific software. That which would be utterly unacceptable in non-scientific software somehow passes for the norm in scientific packages. The…
Dependency analysis is recognized as an important field of software engineering due to a variety of reasons. There exists a large pool of tools providing assistance to software developers and architects. Analysis of inter- and intra-project…
The proliferation of open-source scientific software for science and research presents opportunities and challenges. In this paper, we introduce the SciCat dataset -- a comprehensive collection of Free-Libre Open Source Software (FLOSS)…
Scientific software projects evolve rapidly in their initial development phase, yet at the end of a funding period, the completion of a research project, thesis, or publication, further engagement in the project may slow down or cease…
We conduct a systematic literature review on the concept of trust in the worldwide software ecosystem. We acknowledge that trust is something between two actors in the software ecosystem, and we examine what role trust plays in the…
The research landscape in science and engineering is heavily reliant on computation and data storage. The intensity of computation required for many research projects illustrates the importance of the availability of high performance…
Effective science mapping relies on high-quality representations of scientific documents. As an important task in scientometrics and information studies, science mapping is often challenged by the complex and heterogeneous nature of…
The traditional foundation of science lies on the cornerstones of theory and experiment. Theory is used to explain experiment, which in turn guides the development of theory. Since the advent of computers and the development of…