
COPASI
 Referenced in 66 articles
[sw12253]
 behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events can be included...

XPPAUT
 Referenced in 430 articles
[sw05543]
 XPPAUT is software for the analysis and simulation of dynamic systems. It includes AUTO ... other useful routines. Differential equations, maps, stochastic systems, delay equations, integral equations, and other systems...

sde
 Referenced in 53 articles
[sw23230]
 package sde: Simulation and Inference for Stochastic Differential Equations. Companion package to the book Simulation...

MesoRD
 Referenced in 31 articles
[sw18202]
 Stochastic reactiondiffusion simulation with MesoRD ... Summary: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular...

DifferentialEquations.jl
 Referenced in 39 articles
[sw23910]
 covers discrete equations (function maps, discrete stochastic (Gillespie/Markov) simulations), ordinary differential equations, stochastic differential equations...

Dizzy
 Referenced in 18 articles
[sw35541]
 Dizzy is a tool for stochastic and deterministic simulation of chemical reactions. Developed ... original with implementations of faster stochastic simulation algorithms such as the optimised direct method ... compare the effectiveness of the stochastic simulators on the problems which interest them. As alternatives ... stochastic simulation, users can solve their models using both ordinary and stochastic differential equation solvers...

URDME
 Referenced in 25 articles
[sw10400]
 Urdme: a modular framework for stochastic simulation of reactiontransport processes in complex geometries ... software framework for general stochastic reactiontransport modeling and simulation. URDME uses Unstructured triangular...

ASA
 Referenced in 77 articles
[sw04736]
 Adaptive Simulated Annealing (ASA) is a Clanguage code developed to statistically find the best ... robust tuning over many classes of nonlinear stochastic systems...

gss
 Referenced in 282 articles
[sw06099]
 spline ANOVA models Nonparametric function estimation with stochastic data, otherwise known as smoothing, has been ... facilities is illustrated in the book through simulated and real data examples...

BIOCHAM
 Referenced in 43 articles
[sw09927]
 systems (compatible with SBML); several simulators (boolean, differential, stochastic), a temporal logic based language...

STEPS
 Referenced in 18 articles
[sw17866]
 simulation platform for modeling and stochastic simulation of coupled reactiondiffusion systems with complex...

SSJ
 Referenced in 13 articles
[sw08862]
 framework for stochastic simulation in Java. We introduce SSJ, an organized set of software tools ... offering generalpurpose facilities for stochastic simulation programming. It supports the event view, process view...

sbtoolbox
 Referenced in 17 articles
[sw07391]
 build applications for the analysis and simulation of biological and biochemical systems. Additionally ... analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis...

GillespieSSA
 Referenced in 10 articles
[sw21016]
 package GillespieSSA: Gillespie’s Stochastic Simulation Algorithm (SSA). GillespieSSA provides a simple to use, intuitive ... extensible interface to several stochastic simulation algorithms for generating simulated trajectories of finite population continuous ... Currently it implements Gillespie’s exact stochastic simulation algorithm (Direct method) and several approximate methods...

StochKit2
 Referenced in 10 articles
[sw14081]
 StochKit2: software for discrete stochastic simulation of biochemical systems with events. Summary: StochKit2 ... major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efficient implementations ... several variants of Gillespie’s stochastic simulation algorithm (SSA), and tauleaping with automatic step...

COMPASS
 Referenced in 37 articles
[sw03040]
 measure is estimated via a stochastic, discreteevent simulation, and the decision variables are integer...

StochPy
 Referenced in 8 articles
[sw27252]
 Comprehensive, UserFriendly Tool for Simulating Stochastic Biological Processes. Singlecell and singlemolecule measurements ... flexible software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms ... statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with ... comprehensive software package for stochastic simulation of the molecular control networks of living cells...

StochKit
 Referenced in 10 articles
[sw06978]
 StochKit is an extensible stochastic simulation framework developed in C++ that aims to make stochastic ... simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic...

STOCKS
 Referenced in 13 articles
[sw10438]
 STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm. STOCKS, software for the stochastic...

SGN Sim
 Referenced in 8 articles
[sw29325]
 stochastic genetic networks simulator. We present SGNSim, ’Stochastic Gene Networks Simulator’, a tool to model ... dynamics is driven by a stochastic simulation algorithm (SSA) able to deal with multiple time...