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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…
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…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…
We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations Genarris employs a Harris approximation,…
I present a fast Python tool, SpectRes, for carrying out the resampling of spectral flux densities and their associated uncertainties onto different wavelength grids. The function works with any grid of wavelength values, including…
SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…
In a continued quest to monitor subsecond surface dynamics on the atomic scale and to improve imaging resolution, a FAST module to accelerate existing scanning probe microscopy setups was previously presented. Hereby, the speedup is enabled…
We propose a programming technology that bridges cross-platform compatibility and hardware acceleration in ray tracing applications. Our methodology enables developers to define algorithms while our translator manages implementation…
We present the labscript suite, an open-source experiment control system for automating shot-based experiments and their analysis. Experiments are composed as Python code, which is used to produce low-level hardware instructions. They are…
rigidPy is a Python package that provides a set of tools necessary for studying rigidity and mechanical response in spring networks. It also includes suitable modules for generating new realizations of networks with applications in glassy…
The TRAIN code, developed in 1995 as a post-processor for second-order transport maps from MAD, has been used extensively at the LEP and the LHC to study self-consistent closed orbits, tunes and chromaticities of bunch trains under the…
GMP-Featurizer is a lightweight, accurate, efficient, and scalable software package for calculating the Gaussian Multipole (GMP) features \cite{GMP} for a variety of atomic systems with elements across the periodic table. Starting from the…
In this note we present the starry_process code, which implements an interpretable Gaussian process (GP) for modeling variability in stellar light curves. As dark starspots rotate in and out of view, the total flux received from a distant…
The wavelet scattering transform is an invariant signal representation suitable for many signal processing and machine learning applications. We present the Kymatio software package, an easy-to-use, high-performance Python implementation of…
We present the GPry algorithm for fast Bayesian inference of general (non-Gaussian) posteriors with a moderate number of parameters. GPry does not need any pre-training, special hardware such as GPUs, and is intended as a drop-in…
Grounded theory (GT) is a qualitative research method for building theory grounded in data. GT uses textual and numeric data and follows various stages of coding or tagging data for sense-making, such as open coding and selective coding.…
A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without…
A primary goal of direct imaging techniques is to spectrally characterize the atmospheres of planets around other stars at extremely high contrast levels. To achieve this goal, coronagraphic instruments have favored integral field…
Libpsht (or "library for Performant Spherical Harmonic Transforms") is a collection of algorithms for efficient conversion between spatial-domain and spectral-domain representations of data defined on the sphere. The package supports…
A combined N--body/SPH code is presented which benefits from the high speed of the special purpose hardware GRAPE (GRAvity PipE). Besides gravitational forces, GRAPE also returns the list of neighbours and can, therefore, be used to speed…