Related papers: Simulated single molecule microscopy with SMeagol
Simulations of galaxy evolution aim to capture our current understanding as well as to make predictions for testing by future experiments. Simulations and observations are often compared in an indirect fashion: physical quantities are…
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources…
Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Background: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. New method: Here we describe the…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
The Imaging Computational Microscope (ICM) is a suite of computational tools for automated analysis of functional imaging data that runs under the cross-platform MATLAB environment (The Mathworks, Inc.). ICM uses a semi-supervised…
Sequential sampling models (SSMs) are a widely used framework describing decision-making as a stochastic, dynamic process of evidence accumulation. SSMs popularity across cognitive science has driven the development of various software…
Bioelectrochemistry is crucial for understanding biological functions and driving applications in synthetic biology, healthcare, and catalysis. However, current simulation methods fail to capture both the stochastic nature of molecular…
Argon molecular dynamics (MD) simulations are performed with a newly developed MD program, Easy M(1)odular M(2)olecular M(3)echanics (EM3). The program was developed in an object-oriented fashion containing classes for each critical part of…
State space models (SSMs) have recently achieved strong performance on long sequence modeling tasks while offering improved memory and computational efficiency compared to transformer based architectures. However, their evaluation has been…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Mass spectrometry (MS) based single-cell proteomics (SCP) explores cellular heterogeneity by focusing on the functional effectors of the cells - proteins. However, extracting meaningful biological information from MS data is far from…
Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
We present a web-based software tool, the Virtual Quantum Optics Laboratory (VQOL), that may be used for designing and executing realistic simulations of quantum optics experiments. A graphical user interface allows one to rapidly build and…
The aim of this paper is to present and describe SimLab 1.1 (Simulation Laboratory for Uncertainty and Sensitivity Analysis) software designed for Monte Carlo analysis that is based on performing multiple model evaluations with…
Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries,…
This paper describes the architecture and demonstrates the capabilities of a newly developed, physically-based imaging simulator environment called SISPO, developed for small solar system body fly-by and terrestrial planet surface mission…
We develop a modeling and simulation framework capable of massively parallel simulation of multicellular systems with spatially resolved stochastic kinetics in individual cells. By the use of operator-splitting we decouple the simulation of…
We present the 'simage' software suite for the simulation of artificial extragalactic images, based empirically around real observations of the Hubble Ultra Deep Field (UDF). The simulations reproduce galaxies with realistic and complex…