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We present the first public release (v0.1) of the open-source GADGET Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing…
Data compression is a critical technology for large-scale plasma simulations. Storing complete particle information requires Terabyte-scale data storage, and analysis requires ad-hoc scalable post-processing tools. We propose a…
We present NeuralMag, a flexible and high-performance open-source Python library for micromagnetic simulations. NeuralMag leverages modern machine learning frameworks, such as PyTorch and JAX, to perform efficient tensor operations on…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
The simulation of high-energy physics collision events is a key element for data analysis at present and future particle accelerators. The comparison of simulation predictions to data allows looking for rare deviations that can be due to…
The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization.The PETSc design for performance…
Mathematical models implemented on a computer have become the driving force behind the acceleration of the cycle of scientific processes. This is because computer models are typically much faster and economical to run than physical…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
PyGALAX is a Python package for geospatial analysis that integrates automated machine learning (AutoML) and explainable artificial intelligence (XAI) techniques to analyze spatial heterogeneity in both regression and classification tasks.…
Electronic structure simulation (ESS) has been used for decades to provide quantitative scientific insights on an atomistic scale, enabling advances in chemistry, biology, and materials science, among other disciplines. Following standard…
AsaPy is a custom-made Python library designed to simplify and optimize the analysis of aerospace simulation data. Instead of introducing new methodologies, it excels in combining various established techniques, creating a unified,…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Vibrational spectroscopy is an indispensable analytical tool that provides structural fingerprints for molecules, solids, and interfaces thereof. This study introduces THeSeuSS (THz Spectra Simulations Software) - an automated computational…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
We present DySample, an ultra-lightweight and effective dynamic upsampler. While impressive performance gains have been witnessed from recent kernel-based dynamic upsamplers such as CARAFE, FADE, and SAPA, they introduce much workload,…
Gaussian Process (GP) emulators are widely used to approximate complex computer model behaviour across the input space. Motivated by the problem of coupling computer models, recently progress has been made in the theory of the analysis of…
Simulation offers a simple and flexible way to estimate the power of a clinical trial when analytic formulae are not available. The computational burden of using simulation has, however, restricted its application to only the simplest of…
ScopeSim is a flexible multipurpose instrument data simulation framework built in Python. It enables both raw and reduced observation data to be simulated for a wide range of telescopes and instruments quickly and efficiently on a personal…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…