Related papers: Simulated single molecule microscopy with SMeagol
The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the…
Medical image computing software is essential for identifying imaging biomarkers that can support diagnosis, prognosis, treatment planning, and clinical research. However, the lack of standardized, user-friendly, and reproducible software…
We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents…
We introduce Perceval, an open-source software platform for simulating and interfacing with discrete-variable photonic quantum computers, and describe its main features and components. Its Python front-end allows photonic circuits to be…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
This paper introduces EGG, the Empirical Galaxy Generator, a tool designed within the ASTRODEEP collaboration to generate mock galaxy catalogs for deep fields with realistic fluxes and simple morphologies. The simulation procedure is based…
We substantially update the capabilities of the open-source software instrument Modules for Experiments in Stellar Astrophysics (MESA). MESA can now simultaneously evolve an interacting pair of differentially rotating stars undergoing…
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
SimOmics is an R package designed to generate realistic, multivariate, and multi-omics synthetic datasets. It is intended for use in benchmarking, method development, and reproducibility in bioinformatics, particularly in the context of…
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…
The Geant4 toolkit is the leading software for the simulation of particle transport through matter, widely used in nuclear physics, high-energy physics, and medical physics. However, the initial learning curve for new developers can be…
This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic…
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…
Accurate particle simulations are essential for the next generation of experiments in astroparticle physics. The Monte Carlo simulation library PROPOSAL is a flexible tool to efficiently propagate high-energy leptons and photons through…
We present an XML-based simulation authoring environment. The proposed description language allows to describe mathematical objects such as systems of ordinary differential equations, partial differential equations in two dimensions, or…
CELES is a freely available MATLAB toolbox to simulate light scattering by many spherical particles. Aiming at high computational performance, CELES leverages block-diagonal preconditioning, a lookup-table approach to evaluate costly…
A low cost remote imaging platform for biological applications was developed. The "Picroscope" is a device that allows the user to perform longitudinal imaging studies on multi-well cell culture plates. Here we present the network…
SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: 1) atomic and molecular absorption spectra,…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…