Related papers: Simulated single molecule microscopy with SMeagol
This paper introduces Polyphorm, an interactive visualization and model fitting tool that provides a novel approach for investigating cosmological datasets. Through a fast computational simulation method inspired by the behavior of Physarum…
Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from desktops…
Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often…
Traditionally, a simulation of a dense stellar system required choosing an initial model, running an integrator, and analyzing the output. Almost all of the effort went into writing a clever integrator that could handle binaries, triples…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
In today's world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a…
This article describes SimEngine, an open-source R package for structuring, maintaining, running, and debugging statistical simulations on both local and cluster-based computing environments. Several R packages exist for structuring…
Multiplexed immunofluorescence microscopy captures detailed measurements of spatially resolved, multiple biomarkers simultaneously, revealing tissue composition and cellular interactions in situ among single cells. The growing scale and…
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these…
Rapid, reliable, and accurate interpretation of medical time-series signals is crucial for high-stakes clinical decision-making. Deep learning methods offered unprecedented performance in medical signal processing but at a cost: they were…
Metacells are disjoint and homogeneous groups of single-cell profiles, representing discrete and highly granular cell states. Existing metacell algorithms tend to use only one modality to infer metacells, even though single-cell multi-omics…
We give an overview of the SImulation of X-ray TElescopes (SIXTE) software package, a generic, mission-independent Monte Carlo simulation toolkit for X-ray astronomical instrumentation. The package is based on a modular approach for the…
In this paper we will present SDeval, a software project that contains tools for creating and running benchmarks with a focus on problems in computer algebra. It is built on top of the Symbolic Data project, able to translate problems in…
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has…
We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment --- simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by 4 million…
Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
The field of structural bioinformatics has seen significant advances with the use of Molecular Dynamics (MD) simulations of biological systems. The MD methodology has allowed to explain and discover molecular mechanisms in a wide range of…
SALMON (Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids…
This work introduces a new software package `Sesame' for the numerical computation of classical semiconductor equations. It supports 1 and 2-dimensional systems and provides tools to easily implement extended defects such as grain…