Related papers: SEAMM: A Simulation Environment for Atomistic and …
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
Processing-in-Memory (PIM) has emerged as a promising computing paradigm to address the memory wall and the fundamental bottleneck of the von Neumann architecture by reducing costly data movement between memory and processing units. As with…
EnsembleSVM is a free software package containing efficient routines to perform ensemble learning with support vector machine (SVM) base models. It currently offers ensemble methods based on binary SVM models. Our implementation avoids…
The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor…
We present an application, EasyScan_HEP, for connecting programs to scan the parameter space of High Energy Physics (HEP) models using various sampling algorithms. We develop EasyScan_HEP according to the principle of flexibility and…
With the increase in scale and availability of digital text generated on the web, enterprises such as online retailers and aggregators often use text analytics to mine and analyze the data to improve their services and products alike. Text…
The interdependencies of food, energy, and water (FEW) systems create a nexus opportunity to explore the strengths and vulnerabilities of individual and cross-sector interactions within FEW systems. However, the variables quantifying nexus…
The Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of…
Nowadays interactive digital scientific environments have become an integral part of scientific computing in solving various scientific tasks in research, but also STEM education. We introduce SageMath or shortly Sage -- a free open…
A web application prototype is described, aimed at the generation of synthetic seismograms for user-defined earthquake models. The web application graphical user interface hides the complexity of the underlying computational engine, which…
Modern programming frameworks come with large libraries, with diverse applications such as for matching regular expressions, parsing XML files and sending email. Programmers often use search engines such as Google and Bing to learn about…
Quantum computing (QC) holds the potential to solve classically intractable problems. Although there has been significant progress towards the availability of quantum hardware, a software infrastructure to integrate them is still missing.…
PYSCF is a Python-based general-purpose electronic structure platform that both supports first-principles simulations of molecules and solids, as well as accelerates the development of new methodology and complex computational workflows.…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
YAMLE: Yet Another Machine Learning Environment is an open-source framework that facilitates rapid prototyping and experimentation with machine learning (ML) models and methods. The key motivation is to reduce repetitive work when…
Understanding decision-making in clinical environments is of paramount importance if we are to bring the strengths of machine learning to ultimately improve patient outcomes. Several factors including the availability of public data, the…
The recently proposed generalized epidemic modeling framework (GEMF) \cite{sahneh2013generalized} lays the groundwork for systematically constructing a broad spectrum of stochastic spreading processes over complex networks. This article…
This paper introduces a novel software visualisation and animation method, manifested in a prototype software tool - AnimArch. The introduced method is based on model fusion of static and dynamic models. The static model is represented by…
Scanning probe microscopy (SPM) is a valuable technique by which one can investigate the physical characteristics of the surfaces of materials. However, its widespread use is hampered by the time-consuming nature of running an experiment…
Xsuite is a newly developed modular simulation package combining in a single flexible and modern framework the capabilities of different tools developed at CERN in the past decades, notably Sixtrack, Sixtracklib, COMBI and PyHEADTAIL. The…