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The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward…
In medical imaging, there is a growing interest to provide real-time images with good quality for large anatomical structures. To cope with this issue, we developed a library that allows to replace, for some specific clinical applications,…
Understanding decision-making in clinical environments is of paramount importance if we are to bring the strengths of machine learning to ultimately improve patient outcomes. Several factors including the availability of public data, the…
diffpy$.$morph addresses a need to gain scientific insights from 1D scientific spectra in model independent ways. A powerful approach for this is to take differences between pairs of spectra and look for meaningful changes that might…
Dataframes are a popular abstraction to represent, prepare, and analyze data. Despite the remarkable success of dataframe libraries in Rand Python, dataframes face performance issues even on moderately large datasets. Moreover, there is…
Eye-tracking datasets are often shared in the format used by their creators for their original analyses, usually resulting in the exclusion of data considered irrelevant to the primary purpose. In order to increase re-usability of existing…
$clustertools$ is a Python package for analyzing star cluster simulations. The package is built around the $StarCluster$ class, which stores all data read in from the snapshot of a given model star cluster. The package contains functions…
Software ecosystems are collections of projects that are developed and evolve together in the same environment. Existing literature investigates software ecosystems as isolated entities whose boundaries do not overlap and assumes they are…
In this article, we present Gammapy, an open-source Python package for the analysis of astronomical $\gamma$-ray data, and illustrate the functionalities of its first long-term-support release, version 1.0. Built on the modern Python…
`scores` is a Python package containing mathematical functions for the verification, evaluation and optimisation of forecasts, predictions or models. It supports labelled n-dimensional (multidimensional) data, which is used in many…
The reuse of research software is central to research efficiency and academic exchange. The application of software enables researchers with varied backgrounds to reproduce, validate, and expand upon study findings. Furthermore, the…
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…
Researchers in the field of materials science, chemistry, and computational physics are regularly posed with the challenge of managing large and heterogeneous data spaces. The amount of data increases in lockstep with computational…
Scientific workflows are powerful tools for management of scalable experiments, often composed of complex tasks running on distributed resources. Existing cyberinfrastructure provides components that can be utilized within repeatable…
Malicious Python packages make software supply chains vulnerable by exploiting trust in open-source repositories like Python Package Index (PyPI). Lack of real-time behavioral monitoring makes metadata inspection and static code analysis…
PYSCF is a Python-based general-purpose electronic structure platform that both supports first-principles simulations of molecules and solids, as well as accelerates the development of new methodology and complex computational workflows.…
Understanding how the brain functions is one of the biggest challenges of our time. The analysis of experimentally recorded neural firing patterns (spike trains) plays a crucial role in addressing this problem. Here, the PySpike library is…
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer…
Leadership computing facilities around the world support cutting-edge scientific research across a broad spectrum of disciplines including understanding climate change, combating opioid addiction, or simulating the decay of a neutron. While…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…