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Structural equation modeling (SEM) is a popular tool in the social and behavioural sciences, where it is being applied to ever more complex data types. The high-dimensional data produced by modern sensors, brain images, or (epi)genetic…
We present Decapodes, a diagrammatic tool for representing, composing, and solving partial differential equations. Decapodes provides an intuitive diagrammatic representation of the relationships between variables in a system of equations,…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
We present the version 2.0 of the program package GoSam, which is a public program package to compute one-loop QCD and/or electroweak corrections to multi-particle processes within and beyond the Standard Model. The extended version of the…
Semiconductor devices are scaled down to the level which constituent materials are no longer considered continuous. To account for atomistic randomness, surface effects and quantum mechanical effects, an atomistic modeling approach needs to…
Ordinary Differential Equations (ODE) are used throughout science where the capture of rates of change in states is sought. While both pieces of commercial and open software exist to study such systems, their efficient and accurate usage…
The urgency of the energy transition requires improving the performance and longevity of hydrogen technologies. AlphaPEM is a dynamic one-dimensional (1D) physics-based PEM fuel cell system simulator, programmed in Python and experimentally…
Simulation has become the evaluation method of choice for many areas of distributing computing research. However, most existing simulation packages have several limitations on the size and complexity of the system being modeled. Fine…
An early-stage version of simulation package ' ELSES' (Extra-Large-Scale Electronic-Structure calculation) is developed for electronic structure and dynamics of large systems, particularly, nm-scale or 10nm-scale systems (www.elses.jp).…
We present GoSam 2.0, a fully automated framework for the generation and evaluation of one loop amplitudes in multi leg processes. The new version offers numerous improvements both on generational aspects as well as on the reduction side.…
The Transfer Matrix Method (TMM) has become a prominent tool for the optical simulation of thin$-$film solar cells, particularly among researchers specializing in organic semiconductors and perovskite materials. As the commercial viability…
The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…
An online software tool for the easy preparation of ephemerides of the solar surface features is presented. It was developed as a helper tool for the preparation of observations of the Sun with the Atacama Large Millimeter/submillimeter…
We develop the Mechanic package, which is a new numerical framework for dynamical astronomy. The aim of our software is to help in massive numerical simulations by efficient task management and unified data storage. The code is built on top…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Extension of the open-source simulation package GSEIM for power electronics applications is presented. Recent developments in GSEIM, including those oriented specifically towards power electronic circuits, are described. Some examples of…
Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…
We introduce cellanneal, a python-based software for deconvolving bulk RNA sequencing data. cellanneal relies on the optimization of Spearman's rank correlation coefficient between experimental and computational mixture gene expression…
LevelScheme is a scientific figure preparation system for Mathematica. The main emphasis is upon the construction of level schemes, or level energy diagrams, as used in nuclear, atomic, molecular, and hadronic physics. LevelScheme also…
simpcomp is an extension (a so called package) to GAP, the well known system for computational discrete algebra. The package enables the user to compute numerous properties of (abstract) simplicial complexes, provides functions to construct…