Showing papers in "SoftwareX in 2015"

TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.

TL;DR: In this paper, an updated implementation of the Monte Carlo based Glauber Model calculation is presented, which originally was used by the PHOBOS collaboration, and the main improvement w.r.t. the earlier version (v1) (Alver et al. 2008) is the inclusion of Tritium, Helium-3, and Uranium, as well as the treatment of deformed nuclei and GlauBER-Gribov fluctuations of the proton in p + A collisions.

TL;DR: Abstract COMPSs is a programming framework that aims to facilitate the parallelization of existing applications written in Java, C/C++ and Python scripts and provides scalability and elasticity features allowing the dynamic provision of resources.

TL;DR: The basic concepts underpinning SAGA, the most comprehensive community effort to date to address the heterogeneity by defining a simple, uniform access layer, are described.

TL;DR: VTK's rendering code was rewritten to take advantage of modern graphics cards, maintaining most of the toolkit’s programming interfaces, and offers the opportunity to compare the performance of old and new rendering code on the same systems/cards.

TL;DR: This code computes the largest Lyapunov exponent and tests for the presence of a chaotic dynamics, as opposed to stochastic dynamics, in a noisy scalar series.

TL;DR: AnyFish 2.0 dramatically expands anyFish’s utility by allowing users to create animations of members of several groups of fish from model systems in ecology and evolution, and serves as a model for transparency, repeatability, and collaboration.

TL;DR: The second revision of Skinware is described, discussing the differences with respect to the first version, and providing abstractions and real-time acquisition mechanisms for robot skin technologies.

TL;DR: The ‘CAinterprTools’ package, designed to be used in the free R statistical environment, aims at filling the gap in the interpretation of Correspondence Analysis results by freeing the user from the need to inspect and scrutinize tabular CA outputs, and to look up values and statistics on which further calculations are necessary.

TL;DR: A software package called MaskDensity14 is described, written in the R language, that uses a computational approach to solve the technical issues and makes the method of the sample-moment-based density approximant feasible.

TL;DR: In this paper, the authors present R functions to map PD or PE weighted by area of occupancy (AOO) or frequency to estimate the spatial range of branch-length (i.e. phylogenetic range-rarity), rather than extent of occurrence (EOO), which is known to produce different range estimates.

TL;DR: In this article, a micromagnetic simulator running on GPUs is presented, which achieves a significant performance boost as compared to previous central processing unit (CPU) simulators, up to two orders of magnitude.