Related papers: Biomedical Open Source Software: Crucial Packages …
The structural identifiability and the observability of a model determine the possibility of inferring its parameters and states by observing its outputs. These properties should be analysed before attempting to calibrate a model.…
Medical imaging papers often focus on methodology, but the quality of the algorithms and the validity of the conclusions are highly dependent on the datasets used. As creating datasets requires a lot of effort, researchers often use…
The number of scientific publications continues to rise exponentially, especially in Computer Science (CS). However, current solutions to analyze those publications restrict access behind a paywall, offer no features for visual analysis,…
Developing software to undertake complex, compute-intensive scientific processes requires a challenging combination of both specialist domain knowledge and software development skills to convert this knowledge into efficient code. As…
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…
Software plays a central role in scientific discovery. Improving how we develop and use software for research can have both broad and deep impacts on a spectrum of challenges and opportunities society faces today. The emergence of Research…
The development of scientific software is often a partnership between domain scientists and scientific software engineers. It is especially important to embrace these collaborations when developing advanced scientific software, where…
The rise of software as a research object is mirrored in the increasing interests towards quantitative studies of scientific software. However, due to the inconsistent practice of citing software, most of the existing studies analyzing the…
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…
High-quality research software is a cornerstone of modern scientific progress, enabling researchers to analyze complex data, simulate phenomena, and share reproducible results. However, creating such software requires adherence to best…
In the evolving landscape of clinical informatics, the integration and utilization of software tools developed through governmental funding represent a pivotal advancement in research and application. However, the dispersion of these tools…
Developers rely on open-source packages and must review dependencies to safeguard against vulnerable or malicious upstream code. A careful review of all dependencies changes often does not occur in practice. Therefore, developers need…
User studies are paramount for advancing science. However, researchers face several barriers when performing them despite the existence of supporting tools. In this work, we study how existing tools and their features cope with previously…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Critical goals of scientific computing are to increase scientific rigor, reproducibility, and transparency while keeping up with ever-increasing computational demands. This work presents an integrated framework well-suited for data…
Broad efforts are underway to capture metadata about research software and retain it across services; notable in this regard is the CodeMeta project. What metadata are important to have about (research) software? What metadata are useful…
Sustainable software ecosystems are difficult to build, and require concerted effort, community norms and collaborations. In science it is especially important to establish communities in which faculty, staff, students and open-source…
In this chapter we first outline some of the popular computing environments used for analysing neural data, followed by a brief discussion of 'software carpentry', basic tools and skills from software engineering that can be of great use to…
We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i)…
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation…