Related papers: BioSimulator.jl: Stochastic simulation in Julia
We present StochasticPrograms.jl, a user-friendly and powerful open-source framework for stochastic programming written in the Julia language. The framework includes both modeling tools and structure-exploiting optimization algorithms.…
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…
Agent-based models capture heterogeneity among individuals in a population and are widely used in studies of multi-cellular systems, disease, epidemics and demography to name a few. However, existing frameworks consider discrete time-step…
The stochastic simulation algorithm commonly known as Gillespie's algorithm is now used ubiquitously in the modelling of biological processes in which stochastic effects play an important role. In well-mixed scenarios at the sub-cellular…
Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms to estimate system…
Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed,…
Motivation: Estimating model parameters from experimental observations is one of the key challenges in systems biology and can be computationally very expensive. While the Julia programming language was recently developed as a high-level…
Many physical and biological processes are stochastic in nature. Computational models and simulations of such processes are a mathematical and computational challenge. The basic stochastic simulation algorithm was published by D. Gillespie…
Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow…
Random variables and their distributions are a central part in many areas of statistical methods. The Distributions.jl package provides Julia users and developers tools for working with probability distributions, leveraging Julia features…
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie…
We introduce the Scheduling.jl Julia package, which is intended for collaboratively conducting scheduling research and for sharing implementations of algorithms. It provides the fundamental building blocks for implementing scheduling…
Many multiagent dynamics, including various collective dynamics occurring on networks, can be modeled as a stochastic process in which the agents in the system change their state over time in interaction with each other. The Gillespie…
Increasing emphasis on data and quantitative methods in the biomedical sciences is making biological research more computational. Collecting, curating, processing, and analysing large genomic and imaging data sets poses major computational…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
SpiDy.jl solves the non-Markovian stochastic dynamics of interacting classical spin vectors and harmonic oscillator networks in contact with a dissipative environment. The methods implemented allow the user to include arbitrary memory…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
Scorio.jl is a Julia package for evaluating and ranking systems from repeated responses to shared tasks. It provides a common tensor-based interface for direct score-based, pairwise, psychometric, voting, graph, and listwise methods, so the…
Stochastic dominance is a fundamental concept in decision-making under uncertainty and quantitative finance, yet its practical application is hindered by computational intractability due to infinitely many constraints. We introduce the…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…