• 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 reaction-diffusion 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 reaction-transport processes in complex geometries ... software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular...
  • ASA

  • Referenced in 77 articles [sw04736]
  • Adaptive Simulated Annealing (ASA) is a C-language 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 reaction-diffusion 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 general-purpose 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 tau-leaping with automatic step...
  • COMPASS

  • Referenced in 37 articles [sw03040]
  • measure is estimated via a stochastic, discrete-event simulation, and the decision variables are integer...
  • StochPy

  • Referenced in 8 articles [sw27252]
  • Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes. Single-cell and single-molecule 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...