Related papers: PyExoCross: a Python program for generating spectr…
X-ray propagation-based imaging techniques are well-established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase retrieval algorithms, have been…
Movies of human induced pluripotent stem cell (hiPSC)-derived engineered cardiac tissue (microbundles) contain abundant information about structural and functional maturity. However, extracting these data in a reproducible and…
Extensive rovibrational line lists are constructed for 12 isotopologues of carbon dioxide: $^{12}$C$^{16}$O$_2$, $^{13}$C$^{16}$O$_2$, $^{12}$C$^{17}$O$_2$, $^{13}$C$^{17}$O$_2$, $^{12}$C$^{18}$O$_2$, $^{13}$C$^{18}$O$_2$,…
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms. These chemical building blocks, or…
The study of research trends is pivotal for understanding scientific development on specific topics. Traditionally, this involves keyword analysis within scholarly literature, yet comprehensive tools for such analysis are scarce, especially…
ixpeobssim is a simulation and analysis framework, based on the Python programming language and the associated scientific ecosystem, specifically developed for the Imaging X-ray Polarimetry Explorer (IXPE). Given a source model and the…
`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…
PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…
Linear operators and optimisation are at the core of many algorithms used in signal and image processing, remote sensing, and inverse problems. For small to medium-scale problems, existing software packages (e.g., MATLAB, Python numpy and…
Polarized Resonant Soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and…
SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: 1) atomic and molecular absorption spectra,…
Despite the explosion of interest in healthcare AI research, the reproducibility and benchmarking of those research works are often limited due to the lack of standard benchmark datasets and diverse evaluation metrics. To address this…
Synchrotron processes, the radiative processes associated with the interaction of energetic charged particles with magnetic field, are of interest in many areas in astronomy, from the interstellar medium to extreme environments near compact…
SporTran is a Python utility designed to estimate generic transport coefficients in extended systems, based on the Green-Kubo theory of linear response and the recently introduced cepstral analysis of the current time series generated by…
We introduce the \texttt{pyunicorn} (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…
Transmission spectroscopy is among the most fruitful techniques to infer the main opacity sources present in the upper atmosphere of a transiting planet and to constrain the composition of the thermosphere and of the unbound exosphere. Not…
Accurate rotation-vibration line lists are calculated for silicon monoxide. Line lists are presented for the main isotopologue, $^{28}$Si$^{16}$O, and for four monosubsituted isotopologues ($^{29}$Si$^{16}$O, $^{30}$Si$^{16}$O,…
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…