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The BumpHunter algorithm is widely used in the search for new particles in High Energy Physics analysis. This algorithm offers the advantage of evaluating the local and global p-values of a localized deviation in the observed data without…
1. Natural sounds have been recorded for millions of hours over the previous decades using passive acoustic monitoring. Improvements in deep learning models have vastly accelerated the analysis of large portions of this data. While new…
Containers are an emerging technology that hold promise for improving productivity and code portability in scientific computing. We examine Linux container technology for the distribution of a non-trivial scientific computing software stack…
With ever-increasing computational capabilities, robust and automated research workflows have become essential for orchestrating large numbers of interdependent simulations. However, significant technical expertise is still required to…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
Background and Objective: Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues…
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…
PypeIt is a Python package for semi-automated reduction of astronomical, spectroscopic data. Its algorithms build on decades-long development of previous data reduction pipelines by the developers (Bernstein, Burles, & Prochaska, 2015;…
SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging…
Convex clustering is a popular clustering model without requiring the number of clusters as prior knowledge. It can generate a clustering path by continuously solving the model with a sequence of regularization parameter values. This paper…
Open-source scientific software is abundant, yet most tools remain difficult to compile, configure, and reuse, sustaining a small-workshop mode of scientific computing. This deployment bottleneck limits reproducibility, large-scale…
The purpose of this paper is to show how existing scientific software can be parallelized using a separate thin layer of Python code where all parallel communication is implemented. We provide specific examples on such layers of code, and…
Managing data and code in open scientific research is complicated by two key problems: large datasets often cannot be stored alongside code in repository platforms like GitHub, and iterative analysis can lead to unnoticed changes to data,…
Bibliometric analysis is a critical tool for understanding the structure, dynamics, and impact of scientific research. Traditional methods often fall short in capturing the intricate relationships and evolving trends within scientific…
In software development there is a constant pressure to produce code faster and faster without compromising on quality. New tools supporting developers are created in response to this demand. Currently a new generation of such solutions is…
Software is now a vital scientific instrument, providing the tools for data collection and analysis across disciplines from bioinformatics and computational physics, to the humanities. The software used in research is often home-grown and…
Be it for a malicious or legitimate purpose, packing, a transformation that consists in applying various operations like compression or encryption to a binary file, i.e. for making reverse engineering harder or obfuscating code, is widely…
This study introduces Pedophysics, an open-source Python package designed to facilitate solutions for users who work in the field of soil assessment using near-surface geophysical electromagnetic techniques. At the core of this software is…
Development of scientific software involves tradeoffs between ease of use, generality, and performance. We describe the design of a general hyperbolic PDE solver that can be operated with the convenience of MATLAB yet achieves efficiency…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…