Showing papers in "SoftwareX in 2019"

TL;DR: The R package RTransferEntropy is described in detail and its functionality is demonstrated by means of several simulated processes and an application to financial time series is presented.

TL;DR: Usiigaci is introduced, an all-in-one, semi-automated pipeline to segment, track, and visualize cell movement and morphological changes in PCM using a mask regional convolutional neural network (Mask R-CNN).

TL;DR: NetKet provides algorithms for several key tasks in quantum many-body physics and quantum technology, namely quantum state tomography, supervised learning from wave-function data, and ground state searches for a wide range of customizable lattice models.

TL;DR: The package provides classes to interact with different Scopus APIs to retrieve information as diverse as citation counts, author information or document abstracts to facilitate reproducibility of research projects and enhances data integrity for researchers using Scopus data.

TL;DR: This paper describes a Python-3 based tool PyTOPS for TOPSIS with the Berkeley Software Distribution (BSD)-3-Clause license, widely used in various multi-attribute decision making problems.

TL;DR: FMC computes the different earthquake parameters that can be obtained from focal mechanism data, classifies the rupture type of each focal mechanism, performs a clustering analysis of the data if required by the user, outputs the parameters in different formats and generates a classification diagram from the input data.

TL;DR: An open source toolbox dedicated to Forward Error Correction (FEC or channel coding), AFF3CT supports a broad range of codes, and emphasizes the reproducibility of state-of-the-art results by providing public references and open, modular source code.

TL;DR: In this article, the authors introduce pyphysio as a data science approach oriented to compute physiological indicators, in particular of the Autonomic Nervous System activity, which serves as a basis for machine learning modules and it implements a suite of combinable algorithms for processing of signals from either wearable or medical-grade quality devices.

TL;DR: NURBS-Python is introduced, an object-oriented, open-source, Pure Python NURBS evaluation library with no external dependencies that allows users to access, use, and extend the library without any tedious software compilation steps or licensing concerns.

TL;DR: An update to ACPYPE is reported, a Python3 tool that now properly converts AMBER to GROMACS topologies for force fields that utilize nondefault and nonuniform 1–4 electrostatic and nonbonded scaling factors or negative dihedral force constants.

TL;DR: The RxpsG is a public domain software with an easy user friendly interface oriented to X-ray Photoelectron Spectroscopy and Auger Electron spectroscopy data manipulation based on the R platform.

TL;DR: GPU Optimized Monte Carlo can be used to study vapor–liquid equilibria, adsorption in porous materials, surfactant self-assembly, and condensed phase structure for complex molecules.

TL;DR: Higra is a generic toolbox for graph analysis that can be utilized in a large variety of application fields like machine learning, data science, pattern analysis and computer vision and contains an image analysis module easing the handling of pixel grid graphs by providing efficient algorithms dedicated to this field.

TL;DR: An object-oriented approach to load-balanced adaptive mesh refinement in two and three dimensions is presented for OpenFOAM, a mature C++ library for computational fluid dynamics.

TL;DR: QXMD is a scalable, parallel program for Quantum Molecular Dynamics simulations with various eXtensions based on (time-dependent) density functional theory using pseudopotentials and a plane-wave basis set.

TL;DR: EOF-Library is a software that couples Elmer and OpenFOAM simulation packages that enables efficient internal field interpolation and communication between the finite element and the finite volume frameworks.

TL;DR: The Itinerum platform is a smartphone travel survey platform that allows researchers to customize the Itinerums app with their own questions and prompts, distribute these surveys, monitor, visualize and increasingly process collected data without a background in programming.

TL;DR: HexagDLy as discussed by the authors extends the PyTorch deep learning framework with convolution and pooling operations on hexagonal grids, aiming to ease the access to convolutional neural networks for applications that rely on hexagonally sampled data as, for example, commonly found in ground-based astroparticle physics experiments.

TL;DR: Switch 2.0 is an open-source platform for planning transitions to low-emission electric power systems, designed to satisfy 21st century grid planning requirements, and allows users to compose customized models by choosing built-in modules a la carte or writing custom modules.

TL;DR: An open source smart grid software infrastructure for co-simulation between cloud-based energy management systems and a building energy model, which provides a protocol abstraction as a decoupling mechanism between the control algorithms and the building, thereby facilitating the development and testing of intelligent controllers.

TL;DR: This work describes the ‘movecost’ package, designed for the free R statistical environment, which provides the facility to produce, in a relatively straightforward way, various accumulated slope-dependent cost surfaces and least-cost outputs from different models of movement across the terrain.

TL;DR: A novel software platform that provides rule-based spreadsheet data extraction and transformation to a structured form and demonstrates that one ruleset can be applied to process arbitrary tables having the same features of layout, style, or content.

TL;DR: The CCPi-Regularisation toolkit provides a set of variational regularisers (denoisers) which can be embedded in a plug-and-play fashion into proximal splitting methods for image reconstruction, and gives recommendations for selecting a suitable prior model.

TL;DR: DPsim is a real-time capable solver for power systems that operates in the dynamic phasor and electromagnetic transient (EMT) domain and it is closely integrated with the VILLASframework to support a wide range of interfaces for co-simulation.

TL;DR: In this paper, a new approach of flexible data structures and algorithms on them is introduced with the provided software dwr-diffusion of the DTM++ project, which contributes to the efficient embedding of space-time adaptive methods in an application free way for numerical screening tools.

TL;DR: The open source software stack of the MapX platform, its key functionalities as well as its planned features and concludes by capturing some of the key lessons learned are described.

TL;DR: TBTK provides data structures tailored for second-quantization that will encourage reusability and enable scalability for quantum mechanical calculations.

TL;DR: This paper proposed a framework DM-MCDA based on association rules mining as a preliminary task to extract relationships between variables related to a road accident, and then integrate multiple criteria analysis to help decision-makers to make their choice of the most relevant rules.

TL;DR: KipTool is a multi-platform general purpose software to process and enhance 2D and 3D imaging data implemented in C++ that allows for image file handling and conversions, threshold-based image segmentation, and stitching of registered data sets.

TL;DR: The CameraTransform software package simplifies camera matrix-based image transformations and the extraction of quantitative image information and allows the user to correct for perspective distortion, transform images to “bird’s-eye" view projections, or transform image-coordinates to real-world coordinates and vice versa.